From 8bfdad3fbf0382e657bd72e83830722dd44aa716 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 23 Jun 2022 07:00:06 -0700 Subject: [PATCH 001/553] adding easyconfigs: Regenie-3.1.1-GCC-11.2.0.eb, BGEN-enkre-1.1.7-GCC-11.2.0.eb, Boost-1.55.0-GCC-11.2.0.eb and patches: regenie-3.1.1_Makefile.patch, 3rd-party-removal.patch, BGEN-enkre_streampos.patch --- .../b/BGEN-enkre/3rd-party-removal.patch | 176 ++++++++++++++++++ .../BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb | 71 +++++++ .../b/BGEN-enkre/BGEN-enkre_streampos.patch | 12 ++ .../b/Boost/Boost-1.55.0-GCC-11.2.0.eb | 21 +++ .../r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb | 45 +++++ .../r/Regenie/regenie-3.1.1_Makefile.patch | 41 ++++ 6 files changed, 366 insertions(+) create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch diff --git a/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch new file mode 100644 index 00000000000..83f35651997 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch @@ -0,0 +1,176 @@ +Removal of sqlite3, boost and zstd from 3-party modules +Author: J. Sassmannshausen +diff --git a/bgen.tgz.orig/3rd_party/wscript b/bgen.tgz/3rd_party/wscript +index 220728a..e69de29 100644 +--- a/bgen.tgz.orig/3rd_party/wscript ++++ b/bgen.tgz/3rd_party/wscript +@@ -1,2 +0,0 @@ +-def build( bld ): +- bld.recurse( [ 'boost_1_55_0', 'sqlite3', 'zstd-1.1.0' ] ) +diff --git a/bgen.tgz.orig/Makefile b/bgen.tgz/Makefile +index a7b0ac8..c62ac16 100644 +--- a/bgen.tgz.orig/Makefile ++++ b/bgen.tgz/Makefile +@@ -1,14 +1,9 @@ + FLAGS = -g -std=c++11 -lz \ + -I genfile/include \ + -I db/include \ +--I 3rd_party/boost_1_55_0 \ +--I 3rd_party/zstd-1.1.0 \ +--I 3rd_party/zstd-1.1.0/lib \ +--I 3rd_party/zstd-1.1.0/lib/common \ +--I 3rd_party/zstd-1.1.0/lib/compress \ +--I 3rd_party/zstd-1.1.0/lib/decompress \ +--I 3rd_party/sqlite3 \ +--I include/3rd_party/sqlite3 \ ++-I ${EBBOST}/include \ ++-I ${EBDEVELZSTD}/include \ ++-I ${EBSQLITE3}/include \ + -D SQLITE_ENABLE_COLUMN_METADATA \ + -D SQLITE_ENABLE_STAT4 \ + -D SQLITE_MAX_EXPR_DEPTH=10000 \ +diff --git a/bgen.tgz.orig/db/include/db/SQLStatement.hpp b/bgen.tgz/db/include/db/SQLStatement.hpp +index e107bd2..fca5957 100644 +--- a/bgen.tgz.orig/db/include/db/SQLStatement.hpp ++++ b/bgen.tgz/db/include/db/SQLStatement.hpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp b/bgen.tgz/db/include/db/SQLite3Connection.hpp +index b4bd219..cfbbd3a 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Connection.hpp +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/Connection.hpp" + #include "db/Transaction.hpp" + #include "db/Error.hpp" +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp b/bgen.tgz/db/include/db/SQLite3Statement.hpp +index d41a710..76dbfb6 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Statement.hpp +@@ -11,7 +11,7 @@ + #include + #include + +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + +diff --git a/bgen.tgz.orig/db/src/SQLStatement.cpp b/bgen.tgz/db/src/SQLStatement.cpp +index 60168c6..32576ca 100644 +--- a/bgen.tgz.orig/db/src/SQLStatement.cpp ++++ b/bgen.tgz/db/src/SQLStatement.cpp +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLStatement.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/src/SQLite3Statement.cpp b/bgen.tgz/db/src/SQLite3Statement.cpp +index 84e0658..03b3d5e 100644 +--- a/bgen.tgz.orig/db/src/SQLite3Statement.cpp ++++ b/bgen.tgz/db/src/SQLite3Statement.cpp +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + #include "db/SQLite3Statement.hpp" +diff --git a/bgen.tgz.orig/db/wscript b/bgen.tgz/db/wscript +index 7b0b617..a3861f0 100644 +--- a/bgen.tgz.orig/db/wscript ++++ b/bgen.tgz/db/wscript +@@ -5,8 +5,8 @@ def build( bld ): + bld.stlib( + target = 'db', + source = sources, +- includes='./include', ++ includes='${EBSQLITE}/include ./include', + cxxflags = [], + use = 'boost sqlite3', +- export_includes = './include' ++ export_includes = '${EBSQLITE}/include ./include' + ) +diff --git a/bgen.tgz.orig/wscript b/bgen.tgz/wscript +index a6385d9..47b9fc9 100644 +--- a/bgen.tgz.orig/wscript ++++ b/bgen.tgz/wscript +@@ -63,7 +63,7 @@ def build( bld ): + use = 'zlib zstd sqlite3 db', + export_includes = 'genfile/include' + ) +- bld.recurse( [ '3rd_party', 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) ++ bld.recurse( [ 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) + # Copy files into rbgen package directory + for source in bgen_sources: + bld( rule = 'cp ${SRC} ${TGT}', source = source, target = 'R/rbgen/src/bgen/' + os.path.basename( source.abspath() ), always = True ) +@@ -126,12 +126,12 @@ class ReleaseBuilder: + shutil.copytree( 'R/package/', rbgen_dir ) + os.makedirs( os.path.join( rbgen_dir, "src", "include" )) + os.makedirs( os.path.join( rbgen_dir, "src", "include", "boost" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd" )) + os.makedirs( os.path.join( rbgen_dir, "src", "db" )) + os.makedirs( os.path.join( rbgen_dir, "src", "bgen" )) + os.makedirs( os.path.join( rbgen_dir, "src", "boost" )) + os.makedirs( os.path.join( rbgen_dir, "src", "sqlite3" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "zstd" )) + + # Copy source files in + from glob import glob +@@ -141,11 +141,11 @@ class ReleaseBuilder: + for filename in glob( 'db/src/*.cpp' ): + shutil.copy( filename, os.path.join( rbgen_dir, "src", "db", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) + + boostGlobs = [ + 'libs/system/src/*.cpp', +@@ -160,14 +160,14 @@ class ReleaseBuilder: + 'libs/chrono/src/*.cpp', + ] + +- for pattern in boostGlobs: +- for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) ++# for pattern in boostGlobs: ++# for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) + + include_paths = [ +- "3rd_party/boost_1_55_0/boost/", +- "3rd_party/zstd-1.1.0/", +- "3rd_party/sqlite3/", ++ "${EBBOOST}", ++ "${EBROOTZSTD}", ++ "${EBROOTSQLITE}", + "genfile/include/genfile", + "db/include/db" + ] diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..a4bb6387868 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -0,0 +1,71 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/release/'] +sources = ['%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] +checksums = [ + '8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb', # 1.1.7.tgz + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('Python', '3.9.6'), +] + +dependencies = [ + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch new file mode 100644 index 00000000000..5d7c0e471c3 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch @@ -0,0 +1,12 @@ +diff -ruN 1.1.7.tgz.orig/src/View.cpp 1.1.7.tgz/src/View.cpp +--- 1.1.7.tgz.orig/src/View.cpp 2020-06-29 01:19:43.000000000 -0700 ++++ 1.1.7.tgz/src/View.cpp 2022-06-06 18:05:10.650577000 -0700 +@@ -177,7 +177,7 @@ + + // get file size + { +- std::ios::streampos origin = m_stream->tellg() ; ++ std::streampos origin = m_stream->tellg() ; + m_stream->seekg( 0, std::ios::end ) ; + m_file_metadata.size = m_stream->tellg() - origin ; + m_stream->seekg( 0, std::ios::beg ) ; diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..1814c8648e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..7f008d0c180 --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'MakeCp' + +name = 'Regenie' +version = '3.1.1' + +homepage = 'https://rgcgithub.github.io/regenie' +description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide +association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/rgcgithub/regenie/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s_Makefile.patch'] + +checksums = [] + +dependencies = [ + ('Boost', '1.55.0'), + ('BGEN-enkre', '1.1.7'), + ('OpenBLAS', '0.3.18'), +] + +build_cmd = "make BGEN_PATH=$EBROOTBGENMINENKRE HAS_BOOST_IOSTREAM=1 " +build_cmd += "OPENBLAS_ROOT=$EBROOTOPENBLAS BOOST=$EBROOTBOOST STATIC=0" + +files_to_copy = [ + (['regenie'], 'bin'), + (['example/*'], 'example'), + (['docs/*'], 'docs'), +] + +sanity_check_commands = ['regenie --help'] + +sanity_check_paths = { + 'files': ['bin/regenie'], + 'dirs': ['bin', 'example', 'docs'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch new file mode 100644 index 00000000000..3fc4820cc4d --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch @@ -0,0 +1,41 @@ +Patch to remove 3rd party software and replace lapack(e) with openblas and boost 1.55 +base on the work of Author: J. Sassmannshausen NHS/GSTT +diff -ruN regenie-3.1.1.orig/Makefile regenie-3.1.1/Makefile +--- regenie-3.1.1.orig/Makefile 2022-05-05 10:59:29.000000000 -0700 ++++ regenie-3.1.1/Makefile 2022-06-21 13:34:54.464076000 -0700 +@@ -44,7 +44,7 @@ + # detect OS architecture and add flags + UNAME_S := $(shell uname -s) + ifeq ($(UNAME_S),Linux) +- INC = -I${BGEN_PATH}/3rd_party/boost_1_55_0 ++ INC = -I${BOOST} + CFLAGS += -fopenmp + ifeq ($(strip $(STATIC)),1) + LPATHS = -static-libgcc -static-libstdc++ +@@ -103,10 +103,10 @@ + INC += -I${OPENBLAS_ROOT}/include/ + # static linking + ifeq ($(strip $(STATIC)),1) +- SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas + # dynamic linking + else +- DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas -lgfortran + endif + endif + endif +@@ -119,11 +119,10 @@ + OBJECTS = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp)) + + PGEN_PATH = ./external_libs/pgenlib/ +-INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/ ++INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/include/ -I${BOOST}/include -I./external_libs/ + +-LPATHS += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/ + +-LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost ++LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost_system -lboost_filesystem -lboost_thread -lboost_timer + LIBS += -lz ${DLIBS} -lm -ldl -lgfortran + + From f1b3396edbfe16fba1d4f55cc65b6682a6e1e699 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 12 Jul 2022 15:08:55 -0700 Subject: [PATCH 002/553] bump version --- ...ie-3.1.1-GCC-11.2.0.eb => Regenie-3.1.2-GCC-11.2.0.eb} | 8 +++++--- ...-3.1.1_Makefile.patch => regenie-3.1.2_Makefile.patch} | 0 2 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/Regenie/{Regenie-3.1.1-GCC-11.2.0.eb => Regenie-3.1.2-GCC-11.2.0.eb} (84%) rename easybuild/easyconfigs/r/Regenie/{regenie-3.1.1_Makefile.patch => regenie-3.1.2_Makefile.patch} (100%) diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb similarity index 84% rename from easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb index 7f008d0c180..09b2ac462d6 100644 --- a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Regenie' -version = '3.1.1' +version = '3.1.2' homepage = 'https://rgcgithub.github.io/regenie' description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide @@ -17,8 +17,10 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/rgcgithub/regenie/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(namelower)s-%(version)s_Makefile.patch'] - -checksums = [] +checksums = [ + 'b2e5e98bb310d9b9071ae5c63c5207be853bb1ec7918574e1acfdd0c83e744ff', # v3.1.2.tar.gz + '8be5d4b3b237d7a1820727061227857770554970aa136da614b71c14767e655e', # regenie-3.1.2_Makefile.patch +] dependencies = [ ('Boost', '1.55.0'), diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch similarity index 100% rename from easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch rename to easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch From 3a3be3ac7cef30ab20ec5866fc61dd6c24ec1848 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Nov 2022 11:53:39 +0100 Subject: [PATCH 003/553] adding easyconfigs: NTPoly-2.7.1-foss-2022a.eb, ELSI-2.9.1-foss-2022a-PEXSI.eb, libmbd-0.12.6-foss-2022a.eb --- .../e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb | 45 ++++++++++++++ .../l/libmbd/libmbd-0.12.6-foss-2022a.eb | 59 +++++++++++++++++++ .../n/NTPoly/NTPoly-2.7.1-foss-2022a.eb | 28 +++++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb new file mode 100644 index 00000000000..d5ef7e3da14 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb @@ -0,0 +1,45 @@ +name = 'ELSI' +version = '2.9.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://wordpress.elsi-interchange.org/wp-content/uploads/2022/05'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + {'elsi_interface-v2.9.1.tar.gz': 'ad3dc163159a79f7a83f360265f2446920c151ecce9c294136e630fe424f1d29'}, + {'pexsi-1.2.0-mpi30.patch': 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb'}, + {'ELSI-2.7.1_bison_3.7_compat.patch': '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('NTPoly', '2.7.1'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb new file mode 100644 index 00000000000..e0e689460f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ELSI', '2.9.1', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb new file mode 100644 index 00000000000..e6ef7ccfb3e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.23.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From cad0d9420497ef406689035b0024059c81266f63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 23:17:56 +0100 Subject: [PATCH 004/553] {bio}foss/2022a] CellRank v2.0.2, scVelo v0.2.5, slepc4py v3.17.2, petsc4py v3.17.4 --- .../c/CellRank/CellRank-2.0.2-foss-2022a.eb | 67 +++++++++++++++++++ .../c/CellRank/pygam-0.9.0_fix-poetry.patch | 26 +++++++ .../p/petsc4py/petsc4py-3.17.4-foss-2022a.eb | 26 +++++++ .../s/scVelo/scVelo-0.2.5-foss-2022a.eb | 47 +++++++++++++ .../s/slepc4py/slepc4py-3.17.2-foss-2022a.eb | 26 +++++++ 5 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch create mode 100644 easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..1bd10280160 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('petsc4py', '3.17.4'), + ('slepc4py', '3.17.2'), + ('scikit-learn', '1.1.2'), + ('scVelo', '0.2.5'), + ('scanpy', '1.9.1'), # also provides anndata + ('numba', '0.56.4'), + ('networkx', '2.8.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +_preinstallopts_pygam = """sed -i -e 's/numpy = .*/numpy = "^1.22.3"/g' """ +_preinstallopts_pygam += """-e 's/scipy = .*/scipy = "^1.8.1"/g' pyproject.toml && """ + +exts_list = [ + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('python-utils', '3.8.1', { + 'checksums': ['ec3a672465efb6c673845a43afcfafaa23d2594c24324a40ec18a0c59478dc0b'], + }), + ('progressbar2', '4.3.2', { + 'modulename': 'progressbar', + 'checksums': ['c37e6e1b4e57ab43f95c3d0e8d90061bec140e4fed56b8343183db3aa1e19a52'], + }), + ('pygam', '0.9.0', { + 'patches': ['pygam-0.9.0_fix-poetry.patch'], + 'checksums': [ + {'pygam-0.9.0.tar.gz': 'dba62285a275cdd15a6adf764f6717b3cd077502f01cf1bcee5ce7cbda221956'}, + {'pygam-0.9.0_fix-poetry.patch': '90460a5416167f146f5bf2c55e46c23d1e7a8f864652e24665354a1b39d7e3d0'}, + ], + 'preinstallopts': _preinstallopts_pygam, + }), + ('pygpcca', '1.0.4', { + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + 'preinstallopts': "sed -i 's/jinja2==/jinja2>=/g' requirements.txt && ", + }), + ('cellrank', version, { + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + # strip away too strict version requirements for pandas + anndata + 'preinstallopts': "sed -i -e 's/pandas>=1.5.0/pandas/g' -e 's/anndata>=0.9/anndata/g' pyproject.toml && ", + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import cellrank as cr'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch new file mode 100644 index 00000000000..cc463d4ea64 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch @@ -0,0 +1,26 @@ +workaround for: + RuntimeError: The Poetry configuration is invalid: + - Additional properties are not allowed ('group' was unexpected) +author: Kenneth Hoste (HPC-UGent) +--- pygam-0.9.0/pyproject.toml.orig 2024-01-05 22:13:47.399107878 +0100 ++++ pygam-0.9.0/pyproject.toml 2024-01-05 22:13:52.323119792 +0100 +@@ -12,19 +12,6 @@ + scipy = "^1.10.1" + progressbar2 = "^4.2.0" + +-[tool.poetry.group.dev.dependencies] +-pytest = "^7.2.2" +-flake8 = "^6.0.0" +-codecov = "^2.1.12" +-pytest-cov = "^4.0.0" +-mock = "^5.0.1" +-nbsphinx = "^0.9.0" +-sphinx-rtd-theme = "^1.2.0" +-sphinxcontrib-napoleon = "^0.7" +-ipython = "^8.11.0" +-pandas = "^1.5.3" +-black = "^23.1.0" +- + [tool.black] + line-length = 88 + skip-string-normalization = true diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb new file mode 100644 index 00000000000..a944c674694 --- /dev/null +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'petsc4py' +version = '3.17.4' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['216c3da074557946615d37d0826bc89f1f2e599323e2dacbdc45326d78bd50c6'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PETSc', version), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from petsc4py import PETSc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb new file mode 100644 index 00000000000..5e7f3b40ba6 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scVelo' +version = '0.2.5' + +homepage = "https://scvelo.org" +description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), + ('PyTables', '3.8.0'), + ('statsmodels', '0.13.1'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('tqdm', '4.64.0'), + ('scanpy', '1.9.1'), # also provides anndata + ('Seaborn', '0.12.1'), + ('loompy', '3.0.7'), # also provides numpy-groupies + ('umap-learn', '0.5.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'scvelo', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['7e32d9e34245971330d69c12f4339cebe0acebb61e59a8b1aca9b369078b5207'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb new file mode 100644 index 00000000000..c34f17533e0 --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.17.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e5b235486b6901cd4ff0d94083f0e5eeacaef3a2893e1714769717ad488a3885'] + +dependencies = [ + ('Python', '3.10.4'), + ('SLEPc', version), + ('petsc4py', '3.17.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' From 7576c039389ffb7fcc18784eda4a294cc93e0606 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 15 Apr 2024 12:35:09 +0100 Subject: [PATCH 005/553] adding easyconfigs: OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb --- .../OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8cf271071e7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From bb46f2258544f2fa9dc6094a11aedecb0c5f411d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Apr 2024 21:05:19 +0200 Subject: [PATCH 006/553] adding easyconfigs: SCRIPro-1.0.18-foss-2023a.eb --- .../s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb new file mode 100644 index 00000000000..e7d07a0b329 --- /dev/null +++ b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'SCRIPro' +version = '1.0.18' +local_commit = 'e9087fd' + +homepage = 'https://github.com/xuyunfan9991/SCRIPro' +description = "SCRIPro, an extended framework of SCRIP that suits both single-cell and spatial multi-ome data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('scanpy', '1.9.8'), + ('Seaborn', '0.13.2'), + ('PyTables', '3.8.0'), + ('tqdm', '4.66.1'), + ('dill', '0.3.7'), + ('leidenalg', '0.10.2'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), # provides PyTorch-Ignite + ('tensorboardX', '2.6.2.2'), + ('pybedtools', '0.9.1'), + ('jupyter-server', '2.7.2'), # ipywidgets +] + +use_pip = True + +exts_list = [ + ('lisa2', '2.3.2', { + 'checksums': ['dc9df3495322c94f93c12372fb8d88d355447f7b8b69ea639394fc6274e9affb'], + 'modulename': 'lisa', + }), + ('parse', '1.20.1', { + 'checksums': ['09002ca350ad42e76629995f71f7b518670bcf93548bdde3684fd55d2be51975'], + }), + ('pynvml', '11.5.0', { + 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + }), + ('sparse', '0.15.1', { + 'checksums': ['973adcb88a8db8e3d8047953331e26d3f64a5657f9b46a6b859c47663c3eef99'], + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", + }), + ('scglue', '0.3.2', { + 'checksums': ['fd57ebfa400233cbb1ab4fab4ad6a9dbf4db2c5ca715ba31c71c7a36cc931241'], + }), + ('scripro', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'source_urls': ['https://github.com/xuyunfan9991/SCRIPro/archive'], + 'sources': [{'download_filename': 'e9087fd.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6636c31f3f5797d33d57a5d0266c89f80cc37389dd9c139806b4d17ecad74252'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scripro'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scripro --help"] + +moduleclass = 'bio' From 1172d644dac2263e599f152c7415699a1da6c5ef Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 23 Apr 2024 09:18:36 +0000 Subject: [PATCH 007/553] adding easyconfigs: Gubbins-3.3.5-foss-2022b.eb, rapidNJ-2.3.3-GCCcore-12.2.0.eb, FastTree-2.1.11-GCCcore-12.2.0.eb, multiprocess-0.70.15-gfbf-2022b.eb, Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb --- ...oconf-archive-2023.02.20-GCCcore-12.2.0.eb | 53 +++++++++++++++ .../FastTree-2.1.11-GCCcore-12.2.0.eb | 42 ++++++++++++ .../g/Gubbins/Gubbins-3.3.5-foss-2022b.eb | 64 +++++++++++++++++++ .../multiprocess-0.70.15-gfbf-2022b.eb | 24 +++++++ .../r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb | 41 ++++++++++++ 5 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb create mode 100644 easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..73e0608725b --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2023.02.20' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('makeinfo', '7.0.3'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..abb4f293128 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.39')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb new file mode 100644 index 00000000000..1a19d74c757 --- /dev/null +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -0,0 +1,64 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Gubbins' +version = '3.3.5' + +homepage = "https://nickjcroucher.github.io/gubbins/" +description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that + iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, + while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. + Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term + bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Autoconf-archive', '2023.02.20'), + ('pkgconf', '1.9.3'), + ('Check', '0.15.2'), + ('subunit', '1.4.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('DendroPy', '4.5.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.02'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.6'), + ('rapidNJ', '2.3.3'), + ('RAxML', '8.2.12', '-avx2'), + ('RAxML-NG', '1.2.0'), + ('SKA2', '0.3.7'), + ('dill', '0.3.7'), + ('multiprocess', '0.70.15'), +] + +preconfigopts = "autoreconf -i && " +# runtest = 'check' # runs the Python tests and this causes package to be installed into the Python install +postinstallcmds = [ + """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""", + "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . " +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [ + "gubbins --help", + "run_gubbins.py --version", + 'python -c "import gubbins"', + 'python -m pip check', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb new file mode 100644 index 00000000000..2bac0d9bfe6 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.15' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'] + +dependencies = [ + ('Python', '3.10.8'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), # if needed rebuild --from-pr 19758 +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b6fc9da5925 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.39')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' From 23345de3862df7c9eee34c06a4d44f39d1538c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2024 19:10:26 +0200 Subject: [PATCH 008/553] {bio}[foss/2023a] dorado v0.6.1, kineto v0.4.0 w/ CUDA 12.1.1 --- .../dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb | 87 +++++++++++++++++++ .../dorado/dorado-0.6.1_include-fstream.patch | 27 ++++++ .../k/kineto/kineto-0.4.0-GCC-12.3.0.eb | 35 ++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch create mode 100644 easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..22a9289b01a --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,87 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['dorado-0.6.1_include-fstream.patch'] +checksums = [ + None, + 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +# -Wno-error option is required to fix: +# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used +# -Wno-error=stringop-overflow is required to fix: +# error: writing 16 bytes into a region of size 11 +# -Wno-error=maybe-uninitialized is required to fix: +# error: ... may be used uninitialized +#toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function -Wno-error=stringop-overflow -Wno-error=maybe-uninitialized"} +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch new file mode 100644 index 00000000000..c1165f3fe5c --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4dd6b4afdf1 --- /dev/null +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'kineto' +version = '0.4.0' + +homepage = 'https://github.com/pytorch/kineto' +description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pytorch/kineto/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +start_dir = 'libkineto' + +sanity_check_paths = { + 'files': ['lib/libkineto.a'], + 'dirs': ['include/kineto'], +} + +moduleclass = 'perf' From 20c400a15d346d8ff9768b7b8cf4877e46f1f500 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2024 19:38:00 +0200 Subject: [PATCH 009/553] remove extra comments w.r.t. stripping out -Werror from dorado 0.6.1 easyconfig --- .../d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb index 22a9289b01a..e292bfcc18b 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -61,13 +61,6 @@ preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt # disable treating warnings like errors by stripping out -Werror # cfr. https://github.com/nanoporetech/dorado/issues/779 -# -Wno-error option is required to fix: -# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used -# -Wno-error=stringop-overflow is required to fix: -# error: writing 16 bytes into a region of size 11 -# -Wno-error=maybe-uninitialized is required to fix: -# error: ... may be used uninitialized -#toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function -Wno-error=stringop-overflow -Wno-error=maybe-uninitialized"} preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " From b993aeed7c5023d8c65e082c778f0551268b0bd4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 Apr 2024 19:59:21 +0200 Subject: [PATCH 010/553] adding easyconfigs: CAMPARI-4.0-foss-2023a.eb --- .../c/CAMPARI/CAMPARI-4.0-foss-2023a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb new file mode 100644 index 00000000000..af659719245 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.1'), + ('libtirpc', '1.3.3'), +] + +start_dir = 'source' + +# remove hardcoded paths in configure script +preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' +# ignore default compiler settings and use EB build environment +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags +configopts += '--enable-mpi=auto ' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' + +buildopts = 'all' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' From 31925564e48688a549911a21b25134436081f865 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 Apr 2024 20:01:18 +0200 Subject: [PATCH 011/553] sync configopts in CAMPARI v4.0 on foss/2023a and intel/2023a --- easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb index 203b4e4cd9f..743bf47a462 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb @@ -30,9 +30,10 @@ start_dir = 'source' # remove hardcoded paths in configure script preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' # ignore default compiler settings and use EB build environment -configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="$FCFLAGS" ' +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags configopts += '--enable-mpi=auto ' -configopts += 'LIBS="$LIBS $LIBFFT -ltirpc"' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' buildopts = 'all' From dad682330109923e467e0d5ebb11f90e4f7ecd44 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 10 May 2024 13:29:03 +0200 Subject: [PATCH 012/553] adding easyconfigs: R-tesseract-5.2.1-foss-2023a.eb, tesseract-5.3.4-GCCcore-12.3.0.eb, Leptonica-1.84.1-GCCcore-12.3.0.eb --- .../Leptonica-1.84.1-GCCcore-12.3.0.eb | 32 +++++++++ .../R-tesseract-5.2.1-foss-2023a.eb | 51 ++++++++++++++ .../tesseract-5.3.4-GCCcore-12.3.0.eb | 66 +++++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee92fb98c62 --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.84.1' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b3e1254b1cca381e77c819b59ca99774ff43530209b9aeb511e1d46588a64f6'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.1'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb new file mode 100644 index 00000000000..4981b999b95 --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.2.1' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('R', '4.3.2'), + ('poppler', '23.09.0'), + ('tesseract', '5.3.4'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('qpdf', '1.3.3', { + 'checksums': ['415610be6fa73f60a31872b81fea089288b07f9cb6d078088009207c5e60fe53'], + }), + ('pdftools', '3.4.0', { + 'checksums': ['0b9d7b2100a6d7959c56e144285b9638ca6ff4a7f484a31ff814a99d71482c64'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['ffaba641c5d531a2b6d4ded3608a669206b1e0690cb5e013e3fc9db8aea117fe'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['qpdf', 'pdftools'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..94cf0915ff9 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.4' +_tessdata_ver = '4.1.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '%s.tar.gz' % _tessdata_ver, + 'filename': 'tessdata_best-%s.tar.gz' % _tessdata_ver, + }, +] +checksums = [ + {'5.3.4.tar.gz': '141afc12b34a14bb691a939b4b122db0d51bd38feda7f41696822bacea7710c7'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5') +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('Leptonica', '1.84.1'), + ('libarchive', '3.6.2'), + ('ICU', '73.2'), + ('fontconfig', '2.14.2'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('Pango', '1.50.14'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-*/configs', + 'rm -rf %(builddir)s/tessdata_best-*/tessconfigs', + 'mv %(builddir)s/tessdata_best-*/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'share/tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + +moduleclass = 'vis' From e2c3ef10c8193d142a647729c93858e5345ae576 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2024 14:17:47 +0200 Subject: [PATCH 013/553] adding easyconfigs: sleuth-0.30.1-foss-2023a.eb --- .../s/sleuth/sleuth-0.30.1-foss-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb new file mode 100644 index 00000000000..f03005cda38 --- /dev/null +++ b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'sleuth' +version = '0.30.1' + +homepage = 'https://pachterlab.github.io/sleuth' +description = """Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pachterlab/sleuth/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c8efca5d726471cb71187e8db07097a50f63aadf42f6fa25c59e7eed635f982'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From a8646f52d10cf3ce89068b5545826c0c6c4cf988 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 27 May 2024 17:15:43 +0200 Subject: [PATCH 014/553] adding easyconfigs: Julia-1.10.3-linux-x86_64.eb, IJulia-1.24.2-Julia-1.10.3.eb --- .../i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb | 84 +++++++++++++++++++ .../j/Julia/Julia-1.10.3-linux-x86_64.eb | 30 +++++++ 2 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb new file mode 100644 index 00000000000..f2072785aa5 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb @@ -0,0 +1,84 @@ +easyblock = 'JuliaBundle' + +name = 'IJulia' +version = '1.24.2' +_julia_ver = '1.10.3' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_list = [ + ('Preferences', '1.4.3', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['02b995891818b91266f98bcb46eefc513dfb66b177b5a6a0d1cff97be3e4582d'], + }), + ('JLLWrappers', '1.5.0', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['6e83b81afd0c57636e80bcf52ad51f6ba43d98643cac999727b958d9ab3d4a01'], + }), + ('SnoopPrecompile', '2.10.8', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['9b3204ce72fa3d0f1a359428e9f2ae43db2ee91f7ba77407056aced39d74d9d6'], + }), + ('PrecompileTools', '1.2.1', { + 'source_urls': ['https://github.com/JuliaLang/PrecompileTools.jl/archive/'], + 'checksums': ['af58b384e08b488b2da5ad19e72817b8b0ddb026997f8cf85f2964cc2c26cd34'], + }), + ('Parsers', '2.8.1', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['6ea035be48ef5daaecdff62ac8f29c6110aaf20f3349058a4f96e2503f55b693'], + }), + ('JSON', '0.21.4', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['c6b620ad4150ec5a154367f50c9579af800e3a89a6d8f9cb5dd30215a5d3f552'], + }), + ('MbedTLS', '1.1.9', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['d421bb36f9eb7f8840bd7108c2c33a9a5532454ac9465861e2f7797f89c1f56b'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.10.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2007170cad58d6f27626500abd52bd782023b8ecb7a7d05a678d7aec3c0f9948'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['29d1f35e48c1436743a6da28518cb7aeccb32af4b439c3976df1967c6a252e87'], + }), + ('ZMQ', '1.2.4', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['a15fe752d2b049ad7521d03909ae8ad6c28e4cf46fc823f666cbc1cc6f5795ba'], + }), + (name, version, { + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['de215348c7c41e1ca15c0d21f5f9a78bedce77b02ef89d67f38702c4d57ee80d'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb new file mode 100644 index 00000000000..c93803c3f49 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, + {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 0c95b0d8221aaa7301fc9a7ddaa5078be09559ee Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 27 May 2024 20:42:03 +0200 Subject: [PATCH 015/553] adding easyconfigs: TF-COMB-1.1-foss-2022b.eb, TOBIAS-0.16.1-foss-2022b.eb, svist4get-1.3.1-foss-2022b.eb, adjustText-0.7.3-foss-2022b.eb, python-louvain-0.16-foss-2022b.eb, GOATOOLS-1.4.5-foss-2022b.eb, pydot-2.0.0-GCCcore-12.2.0.eb --- .../adjustText/adjustText-0.7.3-foss-2022b.eb | 27 +++++++ .../g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb | 73 +++++++++++++++++++ .../p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb | 25 +++++++ .../python-louvain-0.16-foss-2022b.eb | 24 ++++++ .../s/svist4get/svist4get-1.3.1-foss-2022b.eb | 62 ++++++++++++++++ .../t/TF-COMB/TF-COMB-1.1-foss-2022b.eb | 52 +++++++++++++ .../t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb | 55 ++++++++++++++ 7 files changed, 318 insertions(+) create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb new file mode 100644 index 00000000000..4c13c121047 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb new file mode 100644 index 00000000000..1f34441c1cb --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.5' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['ba92ad89f9c91b3aadd1c36ae58f77c1725e64dbf00e27910e5b00d3d7348c61'] + +builddependencies = [('cURL', '7.86.0')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XlsxWriter', '3.1.2'), + ('statsmodels', '0.14.0'), + ('pydot', '2.0.0'), + ('openpyxl', '3.1.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d39e368e0cd --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '2.0.0' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +exts_list = [ + (name, version, { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb new file mode 100644 index 00000000000..6e61e7cf51b --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.10.8'), + ('networkx', '2.8.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb new file mode 100644 index 00000000000..df059031ffe --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb @@ -0,0 +1,62 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('pybedtools', '0.9.0'), + ('Biopython', '1.81'), + ('Pillow', '9.4.0'), + ('ImageMagick', '7.1.0-53'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + (name, version, { + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb new file mode 100644 index 00000000000..0f8dab61983 --- /dev/null +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'TF-COMB' +version = '1.1' + +homepage = 'https://github.com/loosolab/TF-COMB' +description = """Transcription Factor Co-Occurrence using Market Basket analysis.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('Pysam', '0.21.0'), + ('matplotlib', '3.7.0'), + ('networkx', '2.8.8'), + ('Graphviz', '8.1.0'), + ('statsmodels', '0.14.0'), + ('dill', '0.3.7'), + ('Seaborn', '0.12.2'), + ('IPython', '8.14.0'), + ('TOBIAS', '0.16.1'), + ('python-louvain', '0.16'), + ('GOATOOLS', '1.4.5'), + ('qnorm', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +# remove graphviz from deps - the pip check failing, should be "import gv" +local_tfcomb_preinstallopts = "sed -i '70d' setup.py && " +# fix "import graphviz" to "import gv" +local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && " + +exts_list = [ + ('uropa', '4.0.3', { + 'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'], + }), + (name, version, { + 'preinstallopts': local_tfcomb_preinstallopts, + 'modulename': 'tfcomb', + 'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'], + }), +] + +sanity_check_commands = [ + "python -c 'import gv'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb new file mode 100644 index 00000000000..9150965319e --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.16.1' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Seaborn', '0.12.2'), + ('Pysam', '0.21.0'), + ('pybedtools', '0.9.0'), + ('boto3', '1.26.163'), + ('pyBigWig', '0.3.22'), + ('scikit-learn', '1.2.1'), + ('PyYAML', '6.0'), + ('XlsxWriter', '3.1.2'), + ('svist4get', '1.3.1'), + ('adjustText', '0.7.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('tobias', version, { + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '81d' setup.py && ", + 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], + }), +] + +sanity_check_commands = ["python -c 'import pyBigWig'"] + +moduleclass = 'bio' From 6212ea21536f581688c7e6ff613f1a24e32a5c06 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 27 May 2024 21:34:07 +0200 Subject: [PATCH 016/553] add qnorm dep + checksum --- .../python-louvain-0.16-foss-2022b.eb | 1 + .../q/qnorm/qnorm-0.8.1-foss-2022b.eb | 36 +++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb index 6e61e7cf51b..e69d4eb0dbe 100644 --- a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -9,6 +9,7 @@ description = "Louvain algorithm for community detection" toolchain = {'name': 'foss', 'version': '2022b'} sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] dependencies = [ ('Python', '3.10.8'), diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb new file mode 100644 index 00000000000..99c6ebe1e23 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('numba', '0.58.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 70d790457bc00847c15ae3f8cc4ac7576f47d9df Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 28 May 2024 10:57:00 +0200 Subject: [PATCH 017/553] fix svist4get - delete statistics dep --- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb index df059031ffe..72d977763e9 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb @@ -41,10 +41,9 @@ exts_list = [ ('Wand', '0.6.10', { 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], }), - ('statistics', '1.0.3.5', { - 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], - }), (name, version, { + # unpin statistics dependency - it is old package and interfering with python lib statistics + 'preinstallopts': "sed -i 's/statistics//' setup.py && ", 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], }), ] From 9adc2be4402836f927967c8b9808e2af7fa4064c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 28 May 2024 13:16:05 +0200 Subject: [PATCH 018/553] fix networkx version to pass tests --- .../p/python-louvain/python-louvain-0.16-foss-2022b.eb | 2 +- easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb index e69d4eb0dbe..5c6085a41e6 100644 --- a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -13,7 +13,7 @@ checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] dependencies = [ ('Python', '3.10.8'), - ('networkx', '2.8.8'), + ('networkx', '3.0'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb index 0f8dab61983..2dcd3a55fdf 100644 --- a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -14,7 +14,7 @@ dependencies = [ ('tqdm', '4.64.1'), ('Pysam', '0.21.0'), ('matplotlib', '3.7.0'), - ('networkx', '2.8.8'), + ('networkx', '3.0'), ('Graphviz', '8.1.0'), ('statsmodels', '0.14.0'), ('dill', '0.3.7'), From 8c87d280779fc084627639466ed170c492a686e5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 28 May 2024 13:37:33 +0200 Subject: [PATCH 019/553] Update GOATOOLS-1.4.5-foss-2022b.eb checksum --- easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb index 1f34441c1cb..46728a39e63 100644 --- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb @@ -22,7 +22,7 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = ['ba92ad89f9c91b3aadd1c36ae58f77c1725e64dbf00e27910e5b00d3d7348c61'] +checksums = [None] builddependencies = [('cURL', '7.86.0')] From 3f44e140a8440450b3e64cc80e43f044a90e9ac1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 May 2024 10:09:31 +0200 Subject: [PATCH 020/553] adding easyconfigs: CORSIKA-77550-foss-2023a.eb --- .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb new file mode 100644 index 00000000000..0a11129ccb9 --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "MakeCp" + +name = 'CORSIKA' +version = '77550' + +homepage = "https://www.iap.kit.edu/corsika" +description = """CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed +simulation of extensive air showers initiated by high energy cosmic ray +particles. Protons, light nuclei up to iron, photons, and many other particles +may be treated as primaries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_instructions = "Sources have to be requested to the developers" +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'] + +dependencies = [ + ("ROOT", "6.30.06"), +] + +# run in non-interactive mode +build_cmd = "./coconut --batch" +# coconut script does not accept "-j" +parallel = False + +files_to_copy = [ + (['run/corsika77550Linux_EPOS_urqmd'], 'bin'), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s corsika77550Linux_EPOS_urqmd corsika", +] + +sanity_check_paths = { + 'files': ['bin/corsika', 'bin/corsika77550Linux_EPOS_urqmd'], + 'dirs': [] +} + +moduleclass = "phys" From 82889a3fb821091eef03901f37e6cf9cc70e2504 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jun 2024 23:56:02 +0200 Subject: [PATCH 021/553] run custom configure in CORSIKA v77550 that enables MPI --- .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb index 0a11129ccb9..c516f698db4 100644 --- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -1,4 +1,4 @@ -easyblock = "MakeCp" +easyblock = "ConfigureMake" name = 'CORSIKA' version = '77550' @@ -10,7 +10,7 @@ particles. Protons, light nuclei up to iron, photons, and many other particles may be treated as primaries.""" toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'pic': True, 'usempi': True} +toolchainopts = {'usempi': True} download_instructions = "Sources have to be requested to the developers" sources = [SOURCELOWER_TAR_GZ] @@ -20,21 +20,23 @@ dependencies = [ ("ROOT", "6.30.06"), ] -# run in non-interactive mode -build_cmd = "./coconut --batch" -# coconut script does not accept "-j" +# custom coconut script does not recognize -j parallel = False -files_to_copy = [ - (['run/corsika77550Linux_EPOS_urqmd'], 'bin'), -] +# execute ./coconut manually with your own options and extract configure command from top of config.log +configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD " +configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS " +configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB " -postinstallcmds = [ - "cd %(installdir)s/bin && ln -s corsika77550Linux_EPOS_urqmd corsika", -] +build_cmd = "./coconut" +buildopts = "--batch" + +preinstallopts = "mkdir -p %(installdir)s/bin && " +install_cmd = "cp" +installopts = "%(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/" sanity_check_paths = { - 'files': ['bin/corsika', 'bin/corsika77550Linux_EPOS_urqmd'], + 'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel'], 'dirs': [] } From 0de008c09fc276734514fe3c2e62ef70fbd6973e Mon Sep 17 00:00:00 2001 From: yqshao Date: Sat, 13 Apr 2024 15:22:18 +0000 Subject: [PATCH 022/553] adding easyconfigs: TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 223 ++++++++++++++++++ 1 file changed, 223 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..156ab402187 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,223 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.15.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('Bazel', '6.1.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # Protobuf disabled since 2.13.0 easyconfigs: + # Compiling with system protobuf don't seem to work, see: + # https://github.com/tensorflow/tensorflow/issues/61593 + # ('protobuf', '24.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('ml_dtypes', '0.3.2'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + ('grpcio', '1.57.0'), +] + +# Dependencies created and updated using findPythonDeps, see: +# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps +# Notable changes since 2.13.0-foss-2023a +# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7) +# - portpicker for tests no longer needed (TF@e85860e838) +# - opt_einsum now comes from ml_dtypes +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('tensorflow-estimator', '2.15.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], + }), + ('Werkzeug', '3.0.2', { + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], + }), + ('tensorboard-data-server', '0.7.2', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '2.0.0', { + 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.4.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('google-auth', '2.29.0', { + 'modulename': 'google.auth', + 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('tensorboard', '2.15.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], + }), + ('keras', '2.15.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.15.1_remove-libclang-dep.patch', + 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', + 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': ( + '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_tag_filters_gpu': ( + 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ', + 'testopts_gpu': ( + '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ' + '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute ' + ), + 'with_xla': True, + 'checksums': [ + {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch': + 'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'}, + {'TensorFlow-2.15.1_remove-libclang-dep.patch': + '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, + {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': + 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, + {'TensorFlow-2.15.1_add-default-shell-env.patch': + '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': + '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, + {'TensorFlow-2.15.1_fix-pybind11-build.patch': + '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': + '9bae97c04a3d64f237e772161ac3a2854bd658fed2034295484aad197175f9ab'}, + ], + }), +] + +# Taken from tensorboard-2.15.1-gfbf-2023a.eb: +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', +] + +moduleclass = 'lib' From d2f85a3eca36a5c68ed19283b247d7a7cf4ad41b Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Fri, 12 Apr 2024 23:13:54 +0200 Subject: [PATCH 023/553] Add patches for TensorFlow-2.15.1 w/ CUDA 12.1.1 --- ...ensorFlow-2.15.1_fix-cuda_build_defs.patch | 36 ++++++++++++ ...ow-2.15.1_remove-duplicate-gpu-tests.patch | 55 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch new file mode 100644 index 00000000000..4f995b7372c --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch @@ -0,0 +1,36 @@ +diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl +index 405d1e7298b..6e2a22a950b 100644 +--- a/third_party/nccl/system.BUILD.tpl ++++ b/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@org_tensorflow//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/nccl/system.BUILD.tpl +index 13328fdeeac..6e2a22a950b 100644 +--- a/third_party/xla/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_xla//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +index b45138eaa79..6e2a22a950b 100644 +--- a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_tsl//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..7c6d72c89c9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index a1531f55cca..3b9c977dcc4 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1626,22 +1626,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, From 9b6a94984a15c1bf303b85ecaf6f3077bf43cd13 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Fri, 7 Jun 2024 10:27:46 +0200 Subject: [PATCH 024/553] Add comment for cuda_build_defs patch --- .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 2 +- .../t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 156ab402187..f140621e37f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -206,7 +206,7 @@ exts_list = [ {'TensorFlow-2.15.1_fix-pybind11-build.patch': '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': - '9bae97c04a3d64f237e772161ac3a2854bd658fed2034295484aad197175f9ab'}, + '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch index 4f995b7372c..0982df21bb9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch @@ -1,3 +1,7 @@ +Backport cuda_build_defs path fix for TF 2.15, see: + +https://github.com/tensorflow/tensorflow/commit/1536f2ca228099f0cf7793d3031d9b9bebbf03ed + diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl index 405d1e7298b..6e2a22a950b 100644 --- a/third_party/nccl/system.BUILD.tpl From 1bb28dfbf31dd8c76836a8746bbea793699afe55 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Fri, 7 Jun 2024 12:04:34 +0200 Subject: [PATCH 025/553] Include fix-cuda-build patch for TF 2.15.1 --- .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index f140621e37f..8b2595c2823 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -142,6 +142,7 @@ exts_list = [ }), (name, version, { 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', @@ -189,6 +190,8 @@ exts_list = [ 'with_xla': True, 'checksums': [ {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, {'TensorFlow-2.4.0_dont-use-var-lock.patch': 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': From 13109c393436bb81fac35c7aa01c05c18e2cbfd0 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Fri, 7 Jun 2024 14:48:00 +0200 Subject: [PATCH 026/553] Include disable-avx512-extensions patch for TF 2.15.1 --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 3 +++ .../TensorFlow-2.15.1-foss-2023a.eb | 3 +++ ...low-2.15.1_disable-avx512-extensions.patch | 19 +++++++++++++++++++ 3 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 8b2595c2823..176839679e8 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -152,6 +152,7 @@ exts_list = [ 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -210,6 +211,8 @@ exts_list = [ '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 014f3bbd7a5..61fff81cebe 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -145,6 +145,7 @@ exts_list = [ 'TensorFlow-2.15.1_add-default-shell-env.patch', 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -195,6 +196,8 @@ exts_list = [ '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, {'TensorFlow-2.15.1_fix-pybind11-build.patch': '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch new file mode 100644 index 00000000000..7778d2b4a91 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +index 5301914ad37..8923bfed7bf 100644 +--- a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h ++++ b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +@@ -20,7 +20,7 @@ limitations under the License. + #include "tsl/framework/fixedpoint_types.h" + + // Use optimized implementations whenever available +-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "tsl/framework/fixedpoint/PacketMathAVX512.h" + #include "tsl/framework/fixedpoint/TypeCastingAVX512.h" + From 0bcde971cb7af9ddbce66ed2e5f6e2ace362f4ba Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Fri, 7 Jun 2024 14:48:37 +0200 Subject: [PATCH 027/553] Include exclude-xnnpack-on-ppc patch for TF 2.15.1 --- .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 3 +++ .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 176839679e8..c42d4201898 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -145,6 +145,7 @@ exts_list = [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', @@ -197,6 +198,8 @@ exts_list = [ 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch': 'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'}, {'TensorFlow-2.15.1_remove-libclang-dep.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 61fff81cebe..6db18627261 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -140,6 +140,7 @@ exts_list = [ (name, version, { 'patches': [ 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.15.1_add-default-shell-env.patch', @@ -186,6 +187,8 @@ exts_list = [ {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, {'TensorFlow-2.15.1_remove-libclang-dep.patch': '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': From 8e6aa82ef4f44d4309efaedd0b16e0b10d7135bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 13 Jun 2024 08:58:31 +0200 Subject: [PATCH 028/553] Add patch fixing compilation on AVX512 systems > invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float' --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 3 ++ .../TensorFlow-2.15.1-foss-2023a.eb | 3 ++ ...-2.15.1_fix-AVX512-eigen-compilation.patch | 47 +++++++++++++++++++ 3 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index c42d4201898..93dcd628ac3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -150,6 +150,7 @@ exts_list = [ 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', @@ -208,6 +209,8 @@ exts_list = [ 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, {'TensorFlow-2.15.1_add-default-shell-env.patch': '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, {'TensorFlow-2.15.1_fix-pybind11-build.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 6db18627261..506cbafd52b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -144,6 +144,7 @@ exts_list = [ 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', 'TensorFlow-2.15.1_disable-avx512-extensions.patch', @@ -195,6 +196,8 @@ exts_list = [ 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, {'TensorFlow-2.15.1_add-default-shell-env.patch': '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, {'TensorFlow-2.15.1_fix-pybind11-build.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch new file mode 100644 index 00000000000..514f215cde9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch @@ -0,0 +1,47 @@ +Fix a compilation error for CPUs with AVX512 features where an issue in Eigen leads to +> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float' + +See https://gitlab.com/libeigen/eigen/-/issues/2829 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-avx512.patch b/third_party/eigen3/fix-avx512.patch +new file mode 100644 +index 00000000000..0650d52a0c9 +--- /dev/null ++++ b/third_party/eigen3/fix-avx512.patch +@@ -0,0 +1,22 @@ ++diff --git a/Eigen/src/Core/arch/AVX512/TypeCasting.h b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++index 02c56282f..e253e6b49 100644 ++--- a/Eigen/src/Core/arch/AVX512/TypeCasting.h +++++ b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++@@ -145,8 +145,6 @@ template<> EIGEN_STRONG_INLINE Packet8bf preinterpret(con ++ return _mm256_castsi256_si128(a); ++ } ++ ++-#ifndef EIGEN_VECTORIZE_AVX512FP16 ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16h& a) { ++ return half2float(a); ++ } ++@@ -155,8 +153,6 @@ template<> EIGEN_STRONG_INLINE Packet16h pcast(const Packe ++ return float2half(a); ++ } ++ ++-#endif ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16bf& a) { ++ return Bf16ToF32(a); ++ } +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index d1d8d4ac486..da549e37432 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,6 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", ++ patch_file = ["//third_party/eigen3:fix-avx512.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), From 18289aa7c7bf24d2fc3eac7f565b2772ffa0b88f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 19 Jun 2024 10:33:58 +0200 Subject: [PATCH 029/553] adding easyconfigs: OpenForceField-Toolkit-0.16.0-foss-2023a.eb --- ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..3ef84650f5e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'OpenForceField-Toolkit' +version = '0.16.0' + +homepage = 'https://github.com/openforcefield/openff-toolkit' +description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, +parameterization engine, and other tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('typing-extensions', '4.9.0'), + ('pydantic', '2.5.3'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('PyYAML', '6.0'), + ('RDKit', '2024.03.3'), + ('MDTraj', '1.9.9'), + ('JupyterNotebook', '7.0.2'), + ('AmberTools', '23.6'), + ('Pint', '0.23'), + ('nglview', '3.1.2'), +] + +use_pip = True + +exts_list = [ + ('qcelemental', '0.26.0', { + 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('apsw', '3.46.0.0', { + 'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'], + }), + ('zstandard', '0.18.0', { + 'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'], + }), + ('qcportal', '0.55', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('bson', '0.5.10', { + 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('intermol', '0.1.2', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], + }), + ('SMIRNOFF99Frosst', '1.1.0', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], + }), + ('SMIRNOFF-Plugins', '2024.01.0', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], + }), + ('OpenForceField-ForceFields', '2024.04.0', { + 'modulename': 'openforcefields', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], + }), + ('OpenForceField-Amber-FF-Ports', '0.0.4', { + 'modulename': 'openff.amber_ff_ports', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], + }), + ('OpenForceField-Utilities', '0.1.12', { + 'modulename': 'openff.utilities', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], + }), + ('OpenForceField-Units', '0.2.2', { + 'modulename': 'openff.units', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], + }), + ('OpenForceField-NAGL-Models', '0.2.0', { + 'modulename': 'openff.nagl_models', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], + 'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'], + }), + ('OpenForceField-Models', '0.1.2', { + 'modulename': 'openff.models', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], + }), + ('OpenForceField-Interchange', '0.3.27', { + 'modulename': 'openff.interchange', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], + }), + (name, version, { + 'modulename': 'openff.toolkit', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'], + }), +] + +sanity_check_commands = [ + "python -c 'from openff.toolkit import Molecule, Topology, ForceField'", + "python -c 'from openff.interchange import Interchange'", + "python -c 'from openff.units import unit'", + "python -c 'from openff.interchange.components.mdconfig import MDConfig'", + "python -c 'from openff.interchange.models import TopologyKey'", + "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", +] + +sanity_pip_check = True + +moduleclass = 'bio' From a1cb8f07918ca3334f7a02ccc4404fb624281ea2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jun 2024 18:37:03 +0200 Subject: [PATCH 030/553] adding easyconfigs: CESM-deps-2-foss-2023a.eb --- .../c/CESM-deps/CESM-deps-2-foss-2023a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb new file mode 100644 index 00000000000..1144c2b34cc --- /dev/null +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'CESM-deps' +version = '2' + +homepage = 'https://www.cesm.ucar.edu/models/cesm2/' +description = """CESM is a fully-coupled, community, global climate model that +provides state-of-the-art computer simulations of the Earth's past, present, +and future climate states.""" + +# The following environment is suitable for CESM >= 2.2.2 and CTSM >= 5.2.0 +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('Perl', '5.36.1'), + ('XML-LibXML', '2.0209'), + ('ESMF', '8.6.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('PnetCDF', '1.12.3'), + ('git', '2.41.0', '-nodocs'), + ('git-lfs', '3.5.1', '', SYSTEM), +] + +components = [ + # install extra configuration tools and files for VSC clusters + ('cesm-config', '1.7.0', { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['c5aeb50595ca4d342a5024d593c2549acf16e72dadc5f39d9a7915d3dc8f3c13'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'], + 'dirs': ['machines', 'irods'], +} + +usage = """Environment to build and run CESM v2 simulations + 1. Download a release of CESM v2: `git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2` + 2. Add external programs for CESM: `cd cesm-2.2.2; ./manage_externals/checkout_externals` + 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/` + 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`""" + +moduleclass = 'geo' From ff04eb945b65680edc8967faaa04bf912a31755d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 25 Jun 2024 11:08:02 +0100 Subject: [PATCH 031/553] adding easyconfigs: R-4.4.1-gfbf-2023b.eb, R-bundle-CRAN-2024.06-foss-2023b.eb --- .../R-bundle-CRAN-2024.06-foss-2023b.eb | 3430 +++++++++++++++++ .../easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb | 371 ++ 2 files changed, 3801 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb new file mode 100644 index 00000000000..f2bea4e2d62 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -0,0 +1,3430 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2024.06' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Xvfb', '21.1.9'), + ('Autotools', '20220317'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('R', '4.4.1'), + ('libxml2', '2.11.5'), # for XML + ('GMP', '6.3.0'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '74.1'), # for rJava & gdsfmt + ('HDF5', '1.14.3'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-34'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '20.9.0'), # for V8 (required by rstan) + ('GDAL', '3.9.0'), # for sf + ('MPFR', '4.2.1'), # for Rmpfr + ('PostgreSQL', '16.1'), # for RPostgreSQL +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.20', { + 'checksums': ['3ffe06a0685123c36cd306b874f89a59a70c864c8f78c5569f82a86abedc21db'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.12', { + 'checksums': ['08af355a9a10fe29d48d085abc7cf1f975e1a4a670668a4f8d9632d087fb41bf'], + }), + ('bnlearn', '4.9.4', { + 'checksums': ['ce3d8d89451fed9277f879c03bb02bc17acab13f1f35587aab8175b80246eeea'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.5', { + 'checksums': ['dee9b6c1152db1a5dc427d074b32bbbb738708683f17a95e0e95e4d79fdf174b'], + }), + ('gdata', '3.0.0', { + 'checksums': ['a456b9921765a705fe8e51780dfbbc6ca005abc948b2f80effeccd468601b17f'], + }), + ('GSA', '1.03.3', { + 'checksums': ['5459786190f40339addc45e7bb58c6a983548aa8feac7277ea7ec0662c5a282c'], + }), + ('infotheo', '1.2.0.1', { + 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], + }), + ('lars', '1.3', { + 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], + }), + ('lazy', '1.2-18', { + 'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'], + }), + ('kernlab', '0.9-32', { + 'checksums': ['654ef34e343deb4d2c4c139a44e5397d6e38876088ce1c53c7deb087935d6fdc'], + }), + ('markdown', '1.13', { + 'checksums': ['385421c674cf5bf2ba04d1df7c16bb5d857bec03755a36321999ac37f5b3cfd9'], + }), + ('mlbench', '2.1-5', { + 'checksums': ['4dbfd652adda7c0caf544d3a6cd23a2ee97c22faefe4d15b8a6782061cc9e76f'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '6.1.1', { + 'checksums': ['ddd7018e5e6ea7f92c7fc9872b391491b7e91c2cd89ef1dcaf4408afb5116775'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-61', { + 'checksums': ['3144c8bf579dd7b7c47c259728c27f53f53e294e7ed307da434dfd144e800a90'], + }), + ('lattice', '0.22-6', { + 'checksums': ['4b377211e472ece7872b9d6759f9b9c660b09594500462eb6146312a1d4d00f7'], + }), + ('nlme', '3.1-165', { + 'checksums': ['fc37bba493c2138be2f38fcfd2a67327d81ab91a37bad6f698226bb400ec9499'], + }), + ('segmented', '2.1-0', { + 'checksums': ['6d7ba0248cb5aa23dfdfc3fc53b6aab2f564323c671420fc73c5274e03640cf2'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.7', { + 'checksums': ['6b5527e2635c0ff762eb7af8154704c85e66d7f79a9524089a5c98dfa94dab08'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3.1', { + 'checksums': ['8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c'], + }), + ('pspline', '1.0-20', { + 'checksums': ['eaa7cd9b870d5d10cf457c435ebcbe698ba0d463e3a996fbe758a4b57b93eb8a'], + }), + ('timeDate', '4032.109', { + 'checksums': ['402841bda47e8c31f49773de2ff5447e9780bc7c8af5fb18be9287b546fcb958'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('pixmap', '0.4-13', { + 'checksums': ['e3dbc641a0497575b45a4140dadc6bf43cdf39b02393f93f1b0ee4f4d026e711'], + }), + ('sp', '2.1-4', { + 'checksums': ['e185e7fb61d2d7dbc50fd765a93e170fa778083a653588db1f5e99d019479f0a'], + }), + ('hms', '1.1.3', { + 'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'], + }), + ('progress', '1.2.3', { + 'checksums': ['ea2b079b894de85c3ab12088c9c52aec06432245047a961d5b4b8aa6889f9276'], + }), + ('RcppArmadillo', '0.12.8.4.0', { + 'checksums': ['cabf6865073204c184ddad4dec1f30aae1b8020b4c9d6e74d1a6b0baaef03046'], + }), + ('ade4', '1.7-22', { + 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], + }), + ('AlgDesign', '1.2.1', { + 'checksums': ['5989626c526bd7c3d9bdda326c962056879be03392065a0b7ddb9b8cf9309d05'], + }), + ('BH', '1.84.0-0', { + 'checksums': ['6fb660755f572cd975073d7052075654acf8db12d208954ca223b8e4f77ef1ac'], + }), + ('Matrix', '1.7-0', { + 'checksums': ['fb97bba0df370222eb4f7e2da2e94dd01053b5e054b1c51829ff9a6efc08ad37'], + }), + ('Brobdingnag', '1.2-9', { + 'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'], + }), + ('corpcor', '1.6.10', { + 'checksums': ['71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09'], + }), + ('longitudinal', '1.1.13', { + 'checksums': ['57f04a0f387c1cc30d2feb945dc3ed35d2a304d94d21d3bc2cac8c92571fdc10'], + }), + ('backports', '1.5.0', { + 'checksums': ['0d3ed9db8f1505e88967f48d669b2a257e0c6b7e6320ea64b946c1bd40897ca2'], + }), + ('checkmate', '2.3.1', { + 'checksums': ['e7e6ba0cca400137f352a599ea29cf35a83f40a5ad26e7c4f06e6c35471884f6'], + }), + ('cubature', '2.1.0', { + 'checksums': ['5d82785609611200d5bea069b93b0bf75bafec808f7eeef7b052eb516f273665'], + }), + ('DEoptimR', '1.1-3', { + 'checksums': ['8dd8a61b07b02022493d7021dc62ef2c4dc2d596cff897846713c5f8dd784694'], + }), + ('fastmatch', '1.1-4', { + 'checksums': 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['d06bcaa1ccb52ef775f7c8b2d6d4676408dbc2813dfc128da34ffa4c7740f3e4'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.38.0', { + 'checksums': ['cb2f313e2351a3cde03be55561b592318ec5376fba3b10e371eeff1986deca8d'], + }), + ('umap', '0.2.10.0', { + 'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'], + }), + ('KODAMA', '2.4', { + 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-3', { + 'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'], + }), + ('dtw', '1.23-1', { + 'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.6', { + 'checksums': ['efccaa309a150d11c6b402b912e618ea041f25cca3101f32cd821a6f41684e35'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-11', { + 'checksums': ['26274f2b710b2417a8bca314d400abf320d4ccf0387ad082743056699501b53d'], + }), + ('hdf5r', '1.3.10', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['92496e0693a27c0a1c8caba671c51fcecc3a120f8ef7eb0cb3cd686a3e49124e'], + }), + ('DTRreg', '2.2', { + 'checksums': ['9c8954d5c342af85611d13dab5be64c4a7a5904644a6e04ff21d5494559e2fc7'], + }), + ('pulsar', '0.3.11', { + 'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'], + }), + ('bayesm', '3.1-6', { + 'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'], + }), + ('gsl', '2.1-8', { + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], + }), + ('energy', '1.7-11', { + 'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'], + }), + ('compositions', '2.0-8', { + 'checksums': ['c5063488f456992b5821458b3237322addffd3451ae91f9474707886971ef290'], + }), + ('clustree', '0.5.1', { + 'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.11', { + 'checksums': ['b08d6cae4fc17575adf5df0113ea5f4f819bb2c7f87987e0d66c8eabfc933fa4'], + }), + ('ergm', '4.6.0', { + 'checksums': ['b471a60c39eb5b478e06dd0caf1d085f4b0927f1c260de699f1c8d4fe831a7f7'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.4', { + 'checksums': ['6bf3e216a444f183ff925e29560fae4c2362cc2a9fed19b3e116a9d9f1184a46'], + }), + ('ergm.multi', '0.2.1', { + 'checksums': ['e09dd0d7207a8214746ea251a50c93f6f5de255175309dc8757206f419a01902'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.2', { + 'checksums': ['9bce70b64a2f60b242603b771370b40d7f7aeed37ed426670131fd966c13b020'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.7-0', { + 'checksums': ['846073d710017ec1dc9a2b4616cb6aeb60ce04e3500a37214522818d34045def'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.44.0.3', { + 'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.14', { + 'checksums': ['66e455bb0e66d3c04af84d9dddc9b89f40b4cf9fe9ad1cf0714bcf30aa1b6837'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-8', { + 'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.1.1', { + 'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-7', { + 'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.2', { + 'checksums': ['6051b07019003c698ae016d79f13945bfe2edec26f8a688126b978cb90adcfff'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': 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('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2.1', { + 'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'], + }), + ('ISOcodes', '2024.02.12', { + 'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': 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['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-28', { + 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('minty', '0.0.1', { + 'checksums': ['cfbdc6603c8fb54ea4d43091e2aee4c99212e6e20a335ed89576156d86237acd'], + }), + ('readODS', '2.3.0', { + 'checksums': ['1e120ff8fdb34c7e00f07726b4843cfaeee9c680bfdc2982e83422c24e4c0491'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-4', { + 'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.2', { + 'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'], + }), + ('lmom', '3.0', { + 'checksums': ['4b0ae8638a63b45ddedfd65c15e3206d34e947a2b5d31e9aa8c55446d69a0291'], + }), + ('gld', '2.6.6', { + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], + }), + ('DescTools', '0.99.54', { + 'checksums': ['470a16405d52d7e8595ac025a0d2bf50b78edaebe83af358903e201168a80b9b'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8-1', { + 'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.2.6', { + 'checksums': ['b759553446892a4b8697be0c696f5d2c5aafdb64cff1ca1b22557687ea7218bd'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-7', { + 'checksums': ['e440c2464b3bd3b452e02583bb280eecba6acecf0f2c04b6b9fe4dcdd128db3e'], + }), + ('blavaan', '0.5-5', { + 'checksums': ['a8d3bc5e9d15a2e8496950e87ed3c6bc6d769e761ec068e1f063f2d255330b6d'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.6-0', { + 'checksums': ['07344cc3bd87b8bd25ef998e9a6ce322ae8e448ef5af06ec3e79631724e18666'], + }), + ('RNifti', '1.7.0', { + 'checksums': ['e58cf73a0f5fbf5d6a2c845bfdeea193eb5262c73d0f329beae17d68f40e18e8'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), + ('fmri', '1.9.12', { + 'checksums': ['d8b55f8867bb0487d1a8241b340099c41d990ae5aa49768b2dc0f9db58af65b3'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.6', { + 'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2024.2-1', { + 'checksums': ['e3b21b08b7db3c2c06543a21718e1c18a2b2d2ddf4c92f0e44841d10f55d5c40'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2022-4.30', { + 'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '3.5.4', { + 'checksums': ['2c2ab38ed5ae140e1d5d045a1d4b95ef9d286b13467301be37477258de87804f'], + }), + ('miceadds', '3.17-44', { + 'checksums': ['6ef69dd1ac3b547a1450ca54c719c5d1f983a585207cb09ae3ad6b42a8cc2165'], + }), + ('visdat', '0.6.0', { + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-11.1', { + 'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'], + }), + ('naniar', '1.1.0', { + 'checksums': ['a94c46c3a78893bd935a0a51adb6a523915afb35427a56ce650b1e1ab28c6f44'], + }), + ('stringdist', '0.9.12', { + 'checksums': ['e1843452ff4184b8d3bc5168732c0c65d3fce11f0df9fcf92173a22ef92e66c4'], + }), + ('image.binarization', '0.1.3', { + 'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.11', { + 'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'], + }), + ('truncnorm', '1.0-9', { + 'checksums': ['5156acc4d63243bf95326d6285b0ba3cdf710697d67c233a12ae56f3d87ec708'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.9.5', { + 'checksums': ['7392bd644efe82f96da0df470a962de398f1d0162273cba1ff31c2ecd7f17a53'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('admisc', '0.35', { + 'checksums': ['cf4b5b3f09f0fd0ad085d97bd589be0cfe6652e5a365f7b09c0e93515b5aed3f'], + }), + ('polycor', '0.8-1', { + 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], + }), + ('multipol', '1.0-9', { + 'checksums': ['4ec305565c214872705f7d5ea4928c8761750663d664a77f1676d81a1ca0c632'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('rngWELL', '0.10-9', { + 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], + }), + ('randtoolbox', '2.0.4', { + 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], + }), + ('TruncatedNormal', '2.2.2', { + 'checksums': ['aef567e8962a64d1afbdfd98ab8f385f32966c3c42acb54ee20f02dceab18e15'], + }), + ('cSEM', '0.5.0', { + 'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'], + }), + ('cubelyr', '1.0.2', { + 'checksums': ['18b10f1fe561305a1e115a438460264b88b301b3e8c086b931500a798be39b94'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('broom.mixed', '0.2.9.5', { + 'checksums': ['959fa6cd26135ad408d3ee447d4423919c9cdaa9a6ecc4396f858c90d30b5ab3'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': 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['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 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('withr', '3.0.0', { + 'checksums': ['8c78eede6d0e648c23d38a6695f642aed2819ef708239d00b36cbc15eabbe0e7'], + }), + ('glue', '1.7.0', { + 'checksums': ['1af51b51f52c1aeb3bfe9349f55896dd78b5542ffdd5654e432e4d646e4a86dc'], + }), + ('rstudioapi', '0.16.0', { + 'checksums': ['74ffa867199e87a54386fbd26919233371f314f73d7338dd4e4695708fed4fe6'], + }), + ('pkgload', '1.3.4', { + 'checksums': ['60b04b948cda4dc56257b1e89f9b0a4b1273cacecdb2bd995d66dd76e89926ce'], + }), + ('fastmap', '1.2.0', { + 'checksums': ['b1da04a2915d1d057f3c2525e295ef15016a64e6667eac83a14641bbd83b9246'], + }), + ('htmltools', '0.5.8.1', { + 'checksums': ['f9f62293ec06c353c4584db6ccedb06a2da12e485208bd26b856f17dd013f176'], + }), + ('yaml', '2.3.8', { + 'checksums': ['9ed079e2159cae214f3fefcbc4c8eb3b888ceabe902350adbdb1d181eda23fd8'], + }), + ('knitr', '1.47', { + 'checksums': ['fadd849bf94a4e02520088a6626577c3c636227fe11c5cd7e8fcc5d51a7aa6cf'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.5', { + 'checksums': ['a9f22335ea39039de25bb27bccd5ff1ffb2b743579b31d150b6b91c9ea81d0b8'], + }), + ('jsonlite', '1.8.8', { + 'checksums': ['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'], + }), + ('lifecycle', '1.0.4', { + 'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'], + }), + ('vctrs', '0.6.5', { + 'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'], + }), + ('stringr', '1.5.1', { + 'checksums': ['a4adec51bb3f04214b1d8ef40d3a58949f21b1497cbeaf2ba552e0891eef45de'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], + }), + ('testthat', '3.2.1.1', { + 'checksums': ['d785ce3975939e28b61048b0e28d881c80904534ff21e5b1a79a0a934124e9f7'], + }), + ('xml2', '1.3.6', { + 'checksums': ['e81991ff99bff3616dde8683c1327194e3ea64fa3b8062f52d8ce32673dd308f'], + }), + ('curl', '5.2.1', { + 'checksums': ['4a7a4d8c08aa1bca2fcd9c58ade7b4b0ea2ed9076d0521071be29baac8adfa90'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], + }), + ('openssl', '2.2.0', { + 'checksums': ['18b8b46ae8db4bd57c7bcc8e10d0bb549ae63e383502051cef86102ab617ddb3'], + }), + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.9', { + 'checksums': ['e133049aad7964e0f6150257e1470b3748f36029322265ee797b8caf7517d4d2'], + }), + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], + }), + ('cachem', '1.1.0', { + 'checksums': ['550839fc2ae5d865db475ba2c1714144f07fa0c052c72135b0e4a70287492e21'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.7.0', { + 'checksums': ['2135d9841af382673b815a14454abff2f2ce0f5dc97484d1499298b85b752ca0'], + }), + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], + }), + ('tinytex', '0.51', { + 'checksums': ['bb113b51b4b58e78902a0220d709650c1458a8c6d3fa03f58ba007f0eb74c8ea'], + }), + ('rmarkdown', '2.27', { + 'checksums': ['61e9cb3eab4f8587fea98d3358652695b7e77eda858caa4c8985241ba6502b9f'], + }), + ('downlit', '0.4.4', { + 'checksums': ['55c377dcee4adc48c1060e14079f3d1832453d066a2cf070530caa210c48f828'], + }), + ('cpp11', '0.4.7', { + 'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'], + }), + ('systemfonts', '1.1.0', { + 'checksums': ['1941069bd20320284ec026a38c53cb736be60bda431303ceaf8fd27ae13fb644'], + }), + ('textshaping', '0.4.0', { + 'checksums': ['35e940786bb278560de61bb55d4f46f8c86c878d0461613ceb8c98ba9b239d7a'], + }), + ('ragg', '1.3.2', { + 'checksums': ['8037a45209fdd50acf101208af8e832b840a11ad4201cf7fb480de432e6b6931'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.9', { + 'checksums': ['6e542216c03b5286cb9901175d1a7937a664db2572bc28bb51e9000269fcdda0'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.3.0', { + 'checksums': ['f8209df3bab33340c1bc8c0d26caee2890fafb93129ff1423302abae5931fad3'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.15', { + 'checksums': ['5e6ded3623a39df3e1db6cb7e7292b4c03c80b3c6c5faaac3b78b711cb205ed0'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.1.1', { + 'checksums': ['a38d5fb5d750e2c2091ce9101f138c1f9bc7009bbb195227a3519c5d97e36753'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.1', { + 'checksums': ['e3b278b8c324a1aa2650141dd89d01253eea5c2555007422c797915689b29aec'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.5.0', { + 'checksums': ['4d663f1426cd88d42f4070f23d969305c575e0499ed1397be6607b0770d2850c'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.1', { + 'checksums': ['33e92d830981b33cd5e55068b500c57dbfb72329c2fce54be3163c63b217f1b2'], + }), + ('gh', '1.4.1', { + 'checksums': ['76bd3f2a31eeaf76a633362899a20b0f7e8fb6159d4777baf3da2a47854292af'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From d21815d15033a209f1260c5180bfb185086eff44 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 27 Jun 2024 09:28:37 +0100 Subject: [PATCH 032/553] alt checksums for signal --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index f2bea4e2d62..db0c3c07b28 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -1592,7 +1592,10 @@ exts_list = [ 'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'], }), ('signal', '1.8-0', { - 'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'], + 'checksums': [ + ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684', + '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'), + ], }), ('tuneR', '1.4.7', { 'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'], From c7df21c3568bd5283cea8fe6e677d639f36bd031 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Thu, 27 Jun 2024 09:04:20 +0200 Subject: [PATCH 033/553] Disable TF32 in fused matmul tests --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 3 ++ ...1_disable-tf32-in-fused-matmul-tests.patch | 46 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 93dcd628ac3..1d1c871f3d5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -155,6 +155,7 @@ exts_list = [ 'TensorFlow-2.15.1_fix-pybind11-build.patch', 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', 'TensorFlow-2.15.1_disable-avx512-extensions.patch', + 'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch' ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -219,6 +220,8 @@ exts_list = [ '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, {'TensorFlow-2.15.1_disable-avx512-extensions.patch': '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, + {'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch': + 'f78aa0e8f814a57e8d2e6b24ff095df49e8654aadb797393fa95a9378d0aa662'}, ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch new file mode 100644 index 00000000000..9cc742e53d0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch @@ -0,0 +1,46 @@ +Fixes failing FusedMatMul test on certain GPU models + +diff --git a/tensorflow/core/kernels/matmul_op_test.cc b/tensorflow/core/kernels/matmul_op_test.cc +index 8d81d4c796e..2de0365f067 100644 +--- a/tensorflow/core/kernels/matmul_op_test.cc ++++ b/tensorflow/core/kernels/matmul_op_test.cc +@@ -21,6 +21,7 @@ limitations under the License. + #include "tensorflow/core/framework/tensor.h" + #include "tensorflow/core/kernels/ops_testutil.h" + #include "tensorflow/core/lib/core/status_test_util.h" ++#include "tensorflow/core/platform/tensor_float_32_utils.h" + #include "tensorflow/core/platform/test.h" + #include "tensorflow/core/platform/test_benchmark.h" + #include "tensorflow/core/protobuf/rewriter_config.pb.h" +@@ -287,6 +288,7 @@ TYPED_TEST_SUITE_P(FusedMatMulWithBiasOpTest); + // -------------------------------------------------------------------------- // + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 128, 64, false, false); + this->VerifyMatMulWithBias(256, 128, 64, true, false); + this->VerifyMatMulWithBias(256, 128, 64, false, true); +@@ -294,6 +296,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(1, 256, 256, false, false); + this->VerifyMatMulWithBias(4, 128, 256, false, false); + this->VerifyMatMulWithBias(1, 256, 256, true, false); +@@ -302,6 +305,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x256x1) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 256, 1, false, false); + this->VerifyMatMulWithBias(256, 128, 4, false, false); + this->VerifyMatMulWithBias(256, 256, 1, true, false); +@@ -314,6 +318,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x1) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64WithActivation) { ++ tensorflow::enable_tensor_float_32_execution(false); + for (const string& activation : {"Relu", "Relu6", "Elu", "LeakyRelu"}) { + this->VerifyConv2DWithBiasAndActivation(256, 128, 64, false, false, + activation); From 37e673217efbecc359d6008dcf19f8dbf72e777c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 28 Jun 2024 12:40:54 +0100 Subject: [PATCH 034/553] alt checksums for pan --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index db0c3c07b28..c042ee83af9 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -580,7 +580,10 @@ exts_list = [ 'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'], }), ('pan', '1.9', { - 'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'], + 'checksums': [ + ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52', + 'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'), + ], }), ('mitml', '0.4-5', { 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], From b425e87a652e3ff3b12df500274889131ab68b56 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sat, 29 Jun 2024 11:29:54 +0200 Subject: [PATCH 035/553] fixes bug that resulted in test failure on zen4 --- .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb | 8 +++- ...ighway-1.0.4-zen4-fix-TruncateTo-bug.patch | 44 +++++++++++++++++++ 2 files changed, 51 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb index a05239847d3..824460d1be2 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -12,7 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] +patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch'] + +checksums = [ + {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'}, + {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch': + '7eb68cfa702648f8f82fe3b7bdc5f0f0ab171840f966040f6d8ec470e3eed712'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch new file mode 100644 index 00000000000..b4e71737d22 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch @@ -0,0 +1,44 @@ +diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h +index 4e2e83e8..2fbf99c7 100644 +--- a/hwy/ops/x86_256-inl.h ++++ b/hwy/ops/x86_256-inl.h +@@ -4185,7 +4185,7 @@ HWY_INLINE Vec128 LookupAndConcatHalves(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = { + LO, HI, 0x10101010 + LO, 0x10101010 + HI, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + #else + alignas(32) static constexpr uint32_t kMap[8] = {LO, HI, ~0u, ~0u, + ~0u, ~0u, LO, HI}; +@@ -4208,7 +4208,7 @@ HWY_INLINE Vec128 LookupAndConcatQuarters(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint16_t kMap[16] = { + LO, HI, 0x1010 + LO, 0x1010 + HI, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d16, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d16, kMap).raw, v.raw); + return LowerHalf(Vec128{_mm256_castsi256_si128(result)}); + #else + constexpr uint16_t ff = static_cast(~0u); +@@ -4229,7 +4229,7 @@ HWY_API Vec32 TruncateTo(D /* tag */, Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = {0x18100800u, 0, 0, 0, + 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + return LowerHalf(LowerHalf(LowerHalf(Vec256{result}))); + #else + alignas(32) static constexpr uint32_t kMap[8] = {0xFFFF0800u, ~0u, ~0u, ~0u, +diff --git a/hwy/ops/x86_512-inl.h b/hwy/ops/x86_512-inl.h +index 167922d8..83f2ee67 100644 +--- a/hwy/ops/x86_512-inl.h ++++ b/hwy/ops/x86_512-inl.h +@@ -3497,7 +3497,7 @@ HWY_API Vec128 TruncateTo(D /* tag */, const Vec512 v) { + alignas(16) static constexpr uint8_t k8From32[16] = { + 0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60}; + const Vec512 bytes{ +- _mm512_permutexvar_epi32(LoadDup128(d8, k8From32).raw, v.raw)}; ++ _mm512_permutexvar_epi8(LoadDup128(d8, k8From32).raw, v.raw)}; + #else + const Full512 d32; + // In each 128 bit block, gather the lower byte of 4 uint32_t lanes into the From e650d171f888bfb7bc5556f9afce6846d5d08ea7 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Tue, 2 Jul 2024 23:00:11 +0200 Subject: [PATCH 036/553] Add pkgconf to builddependencies --- .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 1d1c871f3d5..60b44928e03 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -14,6 +14,7 @@ use_pip = True sanity_pip_check = True builddependencies = [ + ('pkgconf', '1.9.5'), ('Bazel', '6.1.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.41.0', '-nodocs'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 506cbafd52b..57b010cb652 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -13,6 +13,7 @@ use_pip = True sanity_pip_check = True builddependencies = [ + ('pkgconf', '1.9.5'), ('Bazel', '6.1.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.41.0', '-nodocs'), From 22620e9ada1f2624a8bcbe775d8040377ffd7704 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 3 Jul 2024 01:19:25 +0200 Subject: [PATCH 037/553] fix checksum of julia.wrapper in Julia-1.10.3-linux-x86_64.eb --- easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb index c93803c3f49..599edfd33ea 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] patches = [('julia.wrapper', 'bin/')] checksums = [ {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, - {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, ] # install wrapper with linking safeguards for Julia libraries From 79abc87410ab0baa0a7284efa908a056a6f042bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jul 2024 12:02:48 +0200 Subject: [PATCH 038/553] copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command --- .../easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index c1457cc041c..63246fc43ac 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -45,16 +45,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make runtest = 'test' -files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] +files_to_copy = [ + (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', - 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', - 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref', + 'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', 'rsem-synthesis-reference-transcripts']], 'dirs': [], } +sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"] + moduleclass = 'bio' From 1e66580a610f4b795642c58a9a7a9bdf41691991 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Wed, 3 Jul 2024 21:16:09 +0200 Subject: [PATCH 039/553] Revert "Add pkgconf to builddependencies" This reverts commit e650d171f888bfb7bc5556f9afce6846d5d08ea7. --- .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 1 - .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 60b44928e03..1d1c871f3d5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -14,7 +14,6 @@ use_pip = True sanity_pip_check = True builddependencies = [ - ('pkgconf', '1.9.5'), ('Bazel', '6.1.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.41.0', '-nodocs'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 57b010cb652..506cbafd52b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -13,7 +13,6 @@ use_pip = True sanity_pip_check = True builddependencies = [ - ('pkgconf', '1.9.5'), ('Bazel', '6.1.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.41.0', '-nodocs'), From 03ec2eb4a0a0b87fd282df9f5869b77c065c28b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 4 Jul 2024 14:16:06 +0200 Subject: [PATCH 040/553] adding easyconfigs: Transrate-1.0.3-GCC-12.3.0.eb, crb-blast-0.6.9-GCC-12.3.0.eb, colorize-0.7.7-GCC-12.3.0.eb, yell-2.2.2-GCC-12.3.0.eb --- .../c/colorize/colorize-0.7.7-GCC-12.3.0.eb | 31 ++++++++++ .../c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb | 62 +++++++++++++++++++ .../t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 37 +++++++++++ .../y/yell/yell-2.2.2-GCC-12.3.0.eb | 30 +++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..526fcb3a820 --- /dev/null +++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'RubyGem' + +name = 'colorize' +version = '0.7.7' + +homepage = 'https://github.com/fazibear/colorize' +description = """Ruby gem for colorizing text using ANSI escape sequences. +Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'] + +gem_file = '%(name)s-%(version)s.gem' + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..57d50e1b02b --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Ruby', '3.3.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('bio', '1.6.0.pre.20181210', { + 'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..ac272dff125 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'RubyGem' + +name = 'Transrate' +version = '1.0.3' + +homepage = 'https://hibberdlab.com/transrate' +description = """Transrate is software for de-novo transcriptome assembly quality analysis. + It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, + reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, + filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/blahah/transrate/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Ruby', '3.3.0'), + ('crb-blast', '0.6.9'), + ('colorize', '0.7.7'), + ('yell', '2.2.2'), +] + +preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..c42c506c4f3 --- /dev/null +++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RubyGem' + +name = 'yell' +version = '2.2.2' + +homepage = 'https://github.com/rudionrails/yell' +description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'] + +gem_file = '%(name)s-%(version)s.gem' + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' From 7fad6a1c1a9d40499b7be77fd85cb21411b82587 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jul 2024 15:56:56 +0200 Subject: [PATCH 041/553] disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index a8881dbe118..0dd0b641ceb 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -61,6 +61,10 @@ fix_perl_shebang_for = [ 'bashtime2csh.pl_lapw', ] +# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz +# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken... +runtest = False + tests = [ # test case 1: NaCl ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), From d280af8d8bc19a9f0bf010a6f3336e10bba37e2b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 9 Jul 2024 13:56:11 +0200 Subject: [PATCH 042/553] add visit and update vtk-9.3.0 --- .../q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb | 39 ++++++++ .../easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb | 98 +++++++++++++++++++ .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 8 +- .../v/Visit/Visit-3.4.1-foss-2023a.eb | 75 ++++++++++++++ 4 files changed, 219 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f208a034542 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.3.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + {'qwt-6.3.0.tar.bz2': 'dcb085896c28aaec5518cbc08c0ee2b4e60ada7ac929d82639f6189851a6129a'}, + {'Qwt-6.2.0_fix-install-prefix.patch': 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Qt5', '5.15.10'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb new file mode 100644 index 00000000000..5c6c6f7a122 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb @@ -0,0 +1,98 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +# Update: Pavel Tománek (Inuits) +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.2.6' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'}, + {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XZ', '5.4.2'), + ('libGLU', '9.0.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " +configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb index 9278837da13..740fd888dfb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -2,6 +2,7 @@ # Authors:: # * Fotis Georgatos # * Robert Mijakovic +# Update: Pavel Tománek (Inuits) ## easyblock = 'CMakeNinja' @@ -42,6 +43,7 @@ dependencies = [ ('XZ', '5.4.2'), ('libGLU', '9.0.3'), ('X11', '20230603'), + ('Qt5', '5.15.10'), ] separate_build_dir = True @@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb new file mode 100644 index 00000000000..a049601ec0e --- /dev/null +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -0,0 +1,75 @@ +easyblock = 'CMakeMake' + +name = 'Visit' +version = '3.4.1' + +homepage = 'https://github.com/visit-dav/visit' +description = """ +VisIt is an Open Source, interactive, scalable, visualization, animation +and analysis tool. From Unix, Windows or Mac workstations, users can +interactively visualize and analyze data ranging in scale from small +(<101 core) desktop-sized projects to large (>105 core) leadership-class +computing facility simulation campaigns. Users can quickly generate +visualizations, animate them through time, manipulate them with a +variety of operators and mathematical expressions, and save the +resulting images and animations for presentations. VisIt contains a rich +set of visualization features to enable users to view a wide variety of +data including scalar and vector fields defined on two- and +three-dimensional (2D and 3D) structured, adaptive and unstructured +meshes. Owing to its customizeable plugin design, VisIt is capabable of +visualizing data from over 120 different scientific data formats. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/visit-dav', + 'repo_name': 'visit', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [('CMake', '3.26.3')] +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libglvnd', '1.6.0'), + ('Qt5', '5.15.10'), + ('Qwt', '6.3.0'), + ('VTK', '9.2.6'), + ('FFmpeg', '6.0'), +] + +srcdir = "src" + +configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB " +configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK " +configopts += "-DVISIT_QWT_DIR=$EBROOTQWT " +configopts += "-DVISIT_QT_VERSION=$EBVERSIONQT5 -DVISIT_QT_DIR=$EBROOTQT5 " +configopts += "-DVISIT_OSMESA_DIR=$EBROOTMESA " +configopts += "-DVISIT_MESAGL_DIR=$EBROOTLIBGLVND " +configopts += "-DPYTHON_DIR=$EBROOTPYTHON " +configopts += "-DVISIT_PYTHON_SKIP_INSTALL=ON " +configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPILER_CXX=$MPICXX " +configopts += "-DOpenGL_GL_PREFERENCE=GLVND " + +# add missing include to fix make step +prebuildopts = "sed -i '23 a #include ' %(builddir)s/visit/src/gui/QvisStripChart.C && " + +test_cmd = 'cd %(builddir)s/easybuild_obj/test && ./run_visit_test_suite.sh -n %(parallel)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']], + 'dirs': ['%(version)s/bin'], +} + +moduleclass = 'vis' From e76990d73b1878c07dd2b54ea788561fc1af95dd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jul 2024 15:11:18 +0200 Subject: [PATCH 043/553] adding easyconfigs: SIRIUS-7.5.2-foss-2023a.eb, Umpire-2024.02.1-foss-2023a.eb, COSTA-2.2.2-foss-2023a.eb, spla-1.6.1-foss-2023a.eb, SpFFT-1.1.0-foss-2023a.eb, spglib-2.5.0-GCCcore-12.3.0.eb --- .../c/COSTA/COSTA-2.2.2-foss-2023a.eb | 27 +++++++++++++ .../s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb | 40 +++++++++++++++++++ .../s/SpFFT/SpFFT-1.1.0-foss-2023a.eb | 30 ++++++++++++++ .../s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb | 34 ++++++++++++++++ .../s/spla/spla-1.6.1-foss-2023a.eb | 31 ++++++++++++++ .../u/Umpire/Umpire-2024.02.1-foss-2023a.eb | 28 +++++++++++++ 6 files changed, 190 insertions(+) create mode 100644 easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb new file mode 100644 index 00000000000..0f347ce481e --- /dev/null +++ b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'COSTA' +version = '2.2.2' + +homepage = 'https://github.com/eth-cscs/COSTA' +description = """OSTA is a communication-optimal, highly-optimised algorithm for data redistribution +accross multiple processors, using MPI and OpenMP and offering the possibility +to transpose and scale some or all data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/COSTA/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcosta.a'], + 'dirs': ['include/costa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb new file mode 100644 index 00000000000..3189ace9091 --- /dev/null +++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'SIRIUS' +version = '7.5.2' + +homepage = 'https://github.com/electronic-structure/SIRIUS' +description = """SIRIUS is a domain specific library for electronic structure calculations. +It implements pseudopotential plane wave (PP-PW) and +full potential linearized augmented plane wave (FP-LAPW) methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/electronic-structure/SIRIUS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9ae01935578532c84f1d0d673dbbcdd490e26be22efa6c4acf7129f9dc1a0c60'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxc', '6.2.2'), + ('HDF5', '1.14.0'), + ('spglib','2.5.0'), + ('SpFFT', '1.1.0'), + ('spla', '1.6.1'), + ('COSTA', '2.2.2'), + ('Umpire', '2024.02.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/sirius.scf', + 'lib/libsirius.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include/sirius'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..608918e373c --- /dev/null +++ b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SpFFT' +version = '1.1.0' + +homepage = 'https://github.com/eth-cscs/SpFFT/' +description = """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/SpFFT/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4673b3135aebfa1c440723226fe976d518ff881285b3d4787f1aa8210eac81e'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = "-DSPFFT_OMP=ON -DSPFFT_MPI=ON " + +sanity_check_paths = { + 'files': [ + 'include/spfft/spfft.h', + 'lib/libspfft.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5a00e03ac05 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# with thanks to akesandgren for the easyconfig for 2022a +# updated for 2022b by BEAR Software team at University of Birmingham +# update to v2.5.0 for GCC/12.3.0 by Pavel Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.5.0' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['80c060b1a606a76b15f2cc708e9fdd4a83479924ebff9ac16ed26a87a0eac1a9'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb new file mode 100644 index 00000000000..98308699678 --- /dev/null +++ b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spla' +version = '1.6.1' + +homepage = 'https://github.com/eth-cscs/spla/' +description = """SPLA provides specialized functions for linear algebra computations with a C++ and C interface, +which are inspired by requirements in computational material science codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/spla/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62b51e6ce05c41cfc1c6f6600410f9549a209c50f0331e1db41047f94493e02f'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = '-DBLA_VENDOR=FlexiBLAS' + +sanity_check_paths = { + 'files': [ + 'include/spla/spla.h', + 'lib/libspla.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb new file mode 100644 index 00000000000..c3c16eb26c8 --- /dev/null +++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Umpire' +version = '2024.02.1' + +homepage = 'https://github.com/LLNL/Umpire' +description = """Umpire is a resource management library that allows the discovery, provision, +and management of memory on machines with multiple memory devices like NUMA and GPUs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/LLNL', + 'repo_name': 'Umpire', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +moduleclass = 'lib' From 357360c12d023abadbe5b7e23c4434e7c98a540c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 10 Jul 2024 15:45:03 +0200 Subject: [PATCH 044/553] Update SIRIUS-7.5.2-foss-2023a.eb fix whitespace --- easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb index 3189ace9091..5c7da32ecff 100644 --- a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb @@ -22,7 +22,7 @@ dependencies = [ ('GSL', '2.7'), ('libxc', '6.2.2'), ('HDF5', '1.14.0'), - ('spglib','2.5.0'), + ('spglib', '2.5.0'), ('SpFFT', '1.1.0'), ('spla', '1.6.1'), ('COSTA', '2.2.2'), From 6b4eaa094b98af683d900074148da77ecc070e68 Mon Sep 17 00:00:00 2001 From: Yunqi Shao Date: Thu, 11 Jul 2024 00:00:10 +0200 Subject: [PATCH 045/553] Backport cudaMemcpyAsync bugfix for NCCL 2.18.3 --- .../NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 6 +- .../NCCL-2.18.3_fix-cudaMemcpyAsync.patch | 174 ++++++++++++++++++ 2 files changed, 179 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index c85b7a97e48..569d09f9859 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,11 +11,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.16.2_fix-cpuid.patch'] +patches = [ + 'NCCL-2.16.2_fix-cpuid.patch', + 'NCCL-2.18.3_fix-cudaMemcpyAsync.patch', +] checksums = [ ('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'), {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, + {'NCCL-2.18.3_fix-cudaMemcpyAsync.patch': '7dc8d0d1b78e4f8acefbc400860f47432ef67c225b50d73c732999c23483de90'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch new file mode 100644 index 00000000000..68542656733 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch @@ -0,0 +1,174 @@ +Backported from (original message attached below): +https://github.com/NVIDIA/nccl/commit/4365458757e4107ecbf629b2fd6e0e19a5d237c2 + +From: Kaiming Ouyang +Date: Wed, 20 Sep 2023 05:51:14 -0700 +Subject: [PATCH] Fix cudaMemcpyAsync bug + +We are trying to use the copy result of first cudaMemcpyAsync in the +second cudaMemcpyAsync without sync in between. This patch fixes it +by allocating a CPU side array to cache device side addr so that we +can avoid this consecutive cuda mem copy. + +Fixes #957 +--- + src/channel.cc | 12 ++++++++++++ + src/include/comm.h | 2 ++ + src/init.cc | 2 +- + src/transport.cc | 8 ++------ + src/transport/nvls.cc | 10 ++++------ + 5 files changed, 21 insertions(+), 13 deletions(-) + +diff --git a/src/channel.cc b/src/channel.cc +index 3edcc2f..245dfd5 100644 +--- a/src/channel.cc ++++ b/src/channel.cc +@@ -42,9 +42,11 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + /* channel->devPeers is not shared, so just free it when calling commFree() */ + NCCLCHECK(ncclCudaCallocAsync(&channel->devPeers, nPeers, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devPeers); ++ NCCLCHECK(ncclCalloc(&channel->devPeersHostPtr, nPeers)); + for (int r = 0; r < nRanks; r++) { + uintptr_t addr = (uintptr_t)(comm->sharedRes->devPeers[channelId] + comm->topParentRanks[r]); + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[r] = (struct ncclDevChannelPeer*)addr; + } + } + +@@ -52,6 +54,8 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + NCCLCHECK(ncclCudaCallocAsync(&channel->devRingUserRanks, nRanks, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devRingUserRanks); + ++ /* guarantee addr has been copied into channel->devPeers */ ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -77,6 +81,7 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(parent->channels[channelId].nvlsDevPeers + tr); + channel->peers[comm->nRanks + 1 + r] = parent->channels[channelId].nvlsPeers + tr; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].nvlsPeers[tr].refCount); + } + } else { +@@ -86,10 +91,12 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(channel->nvlsDevPeers + r); + channel->peers[comm->nRanks + 1 + r] = channel->nvlsPeers + r; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->nvlsPeers[r].refCount); + } + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -114,6 +121,7 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)parent->channels[channelId].collnetDevPeers; + channel->peers[comm->nRanks] = parent->channels[channelId].collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].collnetPeers->refCount); + } else { + NCCLCHECK(ncclCalloc(&channel->collnetPeers, 1)); +@@ -121,9 +129,11 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)channel->collnetDevPeers; + channel->peers[comm->nRanks] = channel->collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->collnetPeers->refCount); + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -156,5 +166,7 @@ ncclResult_t freeChannel(struct ncclChannel* channel, int nRanks, int collnetNRa + } + } + } ++ ++ free(channel->devPeersHostPtr); + return ncclSuccess; + } +diff --git a/src/include/comm.h b/src/include/comm.h +index e79bf54..8986f93 100644 +--- a/src/include/comm.h ++++ b/src/include/comm.h +@@ -124,6 +124,8 @@ struct ncclSharedResources { + struct ncclChannel { + struct ncclChannelPeer** peers; + struct ncclDevChannelPeer** devPeers; ++ /* devPeer pointer array used for host side access */ ++ struct ncclDevChannelPeer** devPeersHostPtr; + struct ncclRing ring; + int* devRingUserRanks; + struct ncclTree tree; +diff --git a/src/init.cc b/src/init.cc +index 1ea1d7e..309ce10 100644 +--- a/src/init.cc ++++ b/src/init.cc +@@ -437,7 +437,7 @@ static ncclResult_t devCommSetup(ncclComm_t comm) { + + NCCLCHECKGOTO(ncclCudaMemcpyAsync(devCommAndChans, &tmpCommAndChans, 1, comm->sharedRes->deviceStream.cudaStream), ret, fail); + exit: +- CUDACHECK(cudaStreamSynchronize(comm->sharedRes->deviceStream.cudaStream)); ++ NCCLCHECK(ncclStrongStreamSynchronize(&comm->sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &comm->sharedRes->deviceStream)); + return ret; + fail: +diff --git a/src/transport.cc b/src/transport.cc +index f4b8a2a..9817beb 100644 +--- a/src/transport.cc ++++ b/src/transport.cc +@@ -147,11 +147,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, sendData[i] + sendDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[sendPeer]->send[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[sendPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[sendPeer]->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +@@ -167,11 +165,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, recvData[i] + recvDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[recvPeer]->recv[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[recvPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[recvPeer]->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +diff --git a/src/transport/nvls.cc b/src/transport/nvls.cc +index 633cb04..07be99d 100644 +--- a/src/transport/nvls.cc ++++ b/src/transport/nvls.cc +@@ -359,12 +359,10 @@ ncclResult_t ncclNvlsSetup(struct ncclComm* comm, struct ncclComm* parent) { + peer->send[0].conn.tail = (uint64_t*)(mem + buffSize + memSize / 2); + peer->send[0].conn.flags |= NCCL_NVLS_MIN_POLL; + +- struct ncclDevChannelPeer* addr; +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, comm->channels[c].devPeers + nvlsPeer, sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); + + /*INFO(NCCL_INIT|NCCL_NVLS, "Peer %d Channel %d MC buff %p/%p UC Buff %p/%p", + nvlsPeer, c, +-- +2.45.2 From 369de49e4d12555ad23072a357835ef265b676e6 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Thu, 11 Jul 2024 11:03:23 +0000 Subject: [PATCH 046/553] Add checksum --- easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb index 1a19d74c757..57a08aeb182 100644 --- a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2022b'} source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774'] builddependencies = [ ('Autotools', '20220317'), From f652ed0644aff2e0e02a6ba23dae180a7c160b3a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 11 Jul 2024 13:45:11 +0200 Subject: [PATCH 047/553] update umpire.eb --- .../easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb index c3c16eb26c8..fddfdf851cf 100644 --- a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb +++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb @@ -25,4 +25,9 @@ builddependencies = [ ('CMake', '3.26.3'), ] +sanity_check_paths = { + 'files': ['lib/libcamp.a', 'include/umpire/Umpire.hpp'], + 'dirs': ['bin', 'include'], +} + moduleclass = 'lib' From d4e1b178a5a9eafd272b871cab7d64334e52b0d6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 12 Jul 2024 10:12:55 +0200 Subject: [PATCH 048/553] adding easyconfigs: ParaView-5.12.0-foss-2023b-Qt5.eb --- .../ParaView-5.12.0-foss-2023b-Qt5.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb new file mode 100644 index 00000000000..91d1f93661e --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -0,0 +1,74 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.12.0' +versionsuffix = '-Qt5' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), + ('XZ', '5.4.4'), + ('HDF5', '1.14.3'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('Qt5', '5.15.13'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + # Embedded docs not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742 + '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF', + '-DCMAKE_AUTOMOC=OFF', # err Qt6? + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From d8300153dc3bf4fd08a30d6576fe38f8fef90c5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 12 Jul 2024 11:30:23 +0200 Subject: [PATCH 049/553] Fix qt6 issues, e.g. representation selection --- .../p/ParaView/ParaView-5.12.0-foss-2023b.eb | 10 +- .../ParaView/ParaView-5.12.0-qt6_fixes.patch | 126 ++++++++++++++++++ 2 files changed, 134 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb index 018edd70431..ed8408c9301 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -12,11 +12,15 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +patches = [ + 'ParaView-5.11.1-remove_glew_init_warning.patch', + 'ParaView-5.12.0-qt6_fixes.patch', +] checksums = [ {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, + {'ParaView-5.12.0-qt6_fixes.patch': '015d07ac6b74c7355b56ed7f67166f0d5b765f9d6ac135b7246a675a317063df'}, ] builddependencies = [('CMake', '3.27.6')] @@ -58,7 +62,9 @@ _copts = [ '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', - '-DVTK_OPENGL_HAS_OSMESA=OFF'] + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] + configopts = ' '.join(_copts) sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch new file mode 100644 index 00000000000..838d6fe5d32 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch @@ -0,0 +1,126 @@ +This patch solves qt6 compatibility issues. For details see +https://gitlab.kitware.com/paraview/paraview/-/merge_requests/6836 + +diff --git a/Plugins/CAVEInteraction/pqVRDockPanel.cxx b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +index 7a3d352b993f2930716b47dd98512ca88697374c..448ac4d3833ec1582d99139b3f3fea6bbdf7d3ce 100644 +--- a/Plugins/CAVEInteraction/pqVRDockPanel.cxx ++++ b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +@@ -159,8 +159,8 @@ void pqVRDockPanel::initStyles() + this->Internals->stylesCombo->addItem(QString::fromStdString(styleDescs[i])); + } + +- connect(this->Internals->stylesCombo, SIGNAL(currentIndexChanged(QString)), this, +- SLOT(styleComboChanged(QString)), Qt::UniqueConnection); ++ QObject::connect(this->Internals->stylesCombo, &QComboBox::currentTextChanged, this, ++ &pqVRDockPanel::styleComboChanged, Qt::UniqueConnection); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqCustomFilterDefinitionWizard.cxx b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +index 9c140a37abca11b19f0c04bf7c41645b756457d6..acd7bd99e19017a5557a41c4585586b39e5ffc58 100644 +--- a/Qt/Components/pqCustomFilterDefinitionWizard.cxx ++++ b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +@@ -134,8 +134,8 @@ pqCustomFilterDefinitionWizard::pqCustomFilterDefinitionWizard( + SLOT(clearNameOverwrite(const QString&))); + + // When combo selection changes, update new label to be same as old. +- QObject::connect(this->Form->PropertyCombo, SIGNAL(currentIndexChanged(const QString&)), +- this->Form->PropertyName, SLOT(setText(const QString&))); ++ QObject::connect(this->Form->PropertyCombo, &QComboBox::currentTextChanged, ++ this->Form->PropertyName, &QLineEdit::setText); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqDataInformationWidget.cxx b/Qt/Components/pqDataInformationWidget.cxx +index f151d584fc8b683b5666c11c7dfad85219c1e94f..7079507a14bad98dd10bff7ddf65af896cf5e919 100644 +--- a/Qt/Components/pqDataInformationWidget.cxx ++++ b/Qt/Components/pqDataInformationWidget.cxx +@@ -103,8 +103,8 @@ pqDataInformationWidget::pqDataInformationWidget(QWidget* _parent /*=0*/) + this->Model->setActiveView(pqActiveObjects::instance().activeView()); + + // Clicking on the header should sort the column. +- QObject::connect(this->View->horizontalHeader(), SIGNAL(sectionClicked(int)), this->View, +- SLOT(sortByColumn(int))); ++ QObject::connect(this->View->horizontalHeader(), &QHeaderView::sectionClicked, this->View, ++ [=](int col) { this->View->sortByColumn(col, Qt::AscendingOrder); }); + + // Set the context menu policy for the header. + this->View->horizontalHeader()->setContextMenuPolicy(Qt::CustomContextMenu); +diff --git a/Qt/Components/pqDisplayRepresentationWidget.cxx b/Qt/Components/pqDisplayRepresentationWidget.cxx +index 3e08e05e560618457e628afc9bf1fdbf3167b9f0..4d9bc9958a0034e3e2b1e7920a333a5d7f794db6 100644 +--- a/Qt/Components/pqDisplayRepresentationWidget.cxx ++++ b/Qt/Components/pqDisplayRepresentationWidget.cxx +@@ -111,8 +111,8 @@ pqDisplayRepresentationWidget::pqDisplayRepresentationWidget(QWidget* _p) + { + this->Internal = new pqDisplayRepresentationWidget::pqInternals(); + this->Internal->setupUi(this); +- this->connect(this->Internal->comboBox, SIGNAL(currentIndexChanged(const QString&)), +- SLOT(comboBoxChanged(const QString&))); ++ QObject::connect(this->Internal->comboBox, &QComboBox::currentTextChanged, this, ++ &pqDisplayRepresentationWidget::comboBoxChanged); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqLinksEditor.cxx b/Qt/Components/pqLinksEditor.cxx +index 6f02d16d44b82f616a236557f16174d3ffa96425..ae66b1c97c3d82425c2f8b849c6d656deecc64a8 100644 +--- a/Qt/Components/pqLinksEditor.cxx ++++ b/Qt/Components/pqLinksEditor.cxx +@@ -452,8 +452,8 @@ pqLinksEditor::pqLinksEditor(vtkSMLink* link, QWidget* p) + QObject::connect(this->Ui->lineEdit, SIGNAL(textChanged(const QString&)), this, + SLOT(updateEnabledState()), Qt::QueuedConnection); + +- QObject::connect(this->Ui->comboBox, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(updateSelectedProxies()), Qt::QueuedConnection); ++ QObject::connect(this->Ui->comboBox, &QComboBox::currentTextChanged, this, ++ &pqLinksEditor::updateSelectedProxies, Qt::QueuedConnection); + + QObject::connect( + this->Ui->interactiveViewLinkCheckBox, &QCheckBox::stateChanged, this, +diff --git a/Qt/Core/pqFileDialog.cxx b/Qt/Core/pqFileDialog.cxx +index 2a87c723a5ef4af856c71e3589ce9a5efa95b65b..6f369d1163a32e5ae3c7e3bcc00a22081e81e2a2 100644 +--- a/Qt/Core/pqFileDialog.cxx ++++ b/Qt/Core/pqFileDialog.cxx +@@ -322,7 +322,7 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.NavigateForward, SIGNAL(clicked(bool)), this, SLOT(onNavigateForward())); + impl.Ui.NavigateUp->setIcon(style()->standardPixmap(QStyle::SP_FileDialogToParent)); +- impl.Ui.NavigateUp->setShortcut(Qt::ALT + Qt::Key_Up); ++ impl.Ui.NavigateUp->setShortcut(Qt::ALT | Qt::Key_Up); + impl.Ui.NavigateUp->setToolTip( + tr("Navigate Up (%1)").arg(impl.Ui.NavigateUp->shortcut().toString())); + impl.Ui.CreateFolder->setIcon(style()->standardPixmap(QStyle::SP_FileDialogNewFolder)); +@@ -378,8 +378,8 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.Parents, SIGNAL(activated(const QString&)), this, SLOT(onNavigate(const QString&))); + +- QObject::connect(impl.Ui.EntityType, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(onFilterChange(const QString&))); ++ QObject::connect( ++ impl.Ui.EntityType, &QComboBox::currentTextChanged, this, &pqFileDialog::onFilterChange); + + QObject::connect(impl.Ui.Favorites, SIGNAL(clicked(const QModelIndex&)), this, + SLOT(onClickedFavorite(const QModelIndex&))); +diff --git a/Qt/Widgets/pqSignalAdaptors.cxx b/Qt/Widgets/pqSignalAdaptors.cxx +index 0015c9148b80eddd926ba37c17b7d777250c1a78..8e218b945c5f7a8962ffaced17d4a011c00db153 100644 +--- a/Qt/Widgets/pqSignalAdaptors.cxx ++++ b/Qt/Widgets/pqSignalAdaptors.cxx +@@ -16,10 +16,15 @@ + pqSignalAdaptorComboBox::pqSignalAdaptorComboBox(QComboBox* p) + : QObject(p) + { +- QObject::connect(p, SIGNAL(currentIndexChanged(const QString&)), this, +- SIGNAL(currentTextChanged(const QString&))); +- +- QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SIGNAL(currentIndexChanged(int))); ++ QObject::connect( ++ p, &QComboBox::currentTextChanged, this, &pqSignalAdaptorComboBox::currentTextChanged); ++ ++#if QT_VERSION > QT_VERSION_CHECK(6, 0, 0) ++ QObject::connect( ++ p, &QComboBox::currentIndexChanged, this, &pqSignalAdaptorComboBox::currentIndexChanged); ++#else ++ QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SLOT(currentIndexChanged(int))); ++#endif + } + + //---------------------------------------------------------------------------- From 672c0eb3491e46d30d3314fa6960de778304234c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 12 Jul 2024 13:33:01 +0200 Subject: [PATCH 050/553] adding easyconfigs: ilastik-napari-0.2.4-foss-2023a.eb, fastfilters-0.3-foss-2023a.eb --- .../fastfilters/fastfilters-0.3-foss-2023a.eb | 46 +++++++++++++++++++ .../ilastik-napari-0.2.4-foss-2023a.eb | 37 +++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb new file mode 100644 index 00000000000..a9d67a03798 --- /dev/null +++ b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'fastfilters' +version = '0.3' + +homepage = 'https://github.com/ilastik/fastfilters/' +description = """Fast gaussian and derivative convolutional filters.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'optarch': False} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ilastik', + 'repo_name': 'fastfilters', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('pybind11', '2.11.1'), +] + +configopts = '-DFF_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages/" ' +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'], +} + +sanity_check_commands = ["python -c 'import fastfilters'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb new file mode 100644 index 00000000000..64e20f93f38 --- /dev/null +++ b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ilastik-napari' +version = '0.2.4' + +homepage = 'https://github.com/ilastik/ilastik-napari/' +description = "Napari plugin for interactive pixel classification." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('QtPy', '2.4.1'), + ('scikit-learn', '1.3.1'), + ('numba', '0.58.1'), + ('fastfilters', '0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.15.4', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['76ec76fee2aee82a84eb97155dd530a9644e3b1fdea2406bc4b454698b36d938'], + }), + (name, version, { + 'source_tmpl': 'ilastik_napari-%(version)s.tar.gz', + 'modulename': 'ilastik', + 'checksums': ['8e971a70389f9257eaca7561637301f996f316fdff2cb223c5828d162970bec4'], + }), +] + +moduleclass = 'vis' From 5b56aeb89410b6ed13921fe3330a6d4993bca27c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 12 Jul 2024 15:20:23 +0200 Subject: [PATCH 051/553] Update ParaView-5.12.0-foss-2023b-Qt5.eb for OpenFOAM in-situ visualization with Catalyst --- .../p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb index 91d1f93661e..1642881e802 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -39,9 +39,6 @@ dependencies = [ _copts = [ # Basic configuration - # Embedded docs not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742 - '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF', - '-DCMAKE_AUTOMOC=OFF', # err Qt6? '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', @@ -59,7 +56,8 @@ _copts = [ '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', - '-DVTK_OPENGL_HAS_OSMESA=OFF'] + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFFVTK_PYTHON_=OFF'] configopts = ' '.join(_copts) sanity_check_paths = { From 6948f3e57054f5b3ccefa317f7f4287dcbfb389a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Jul 2024 15:32:38 +0200 Subject: [PATCH 052/553] make pytest v7.4.2 independent of Python-bundle-PyPI --- .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb index 9d0b6f0c25d..45ab5fae484 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -13,11 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), + ('flit', '3.9.0'), ] dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), + ('hypothesis', '6.82.0'), ] use_pip = True @@ -39,15 +40,14 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('setuptools-scm', '8.0.4', { - 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], }), - ('flit-core', '3.9.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + ('exceptiongroup', '1.1.1', { + 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], }), - ('hypothesis', '6.88.1', { - 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], }), ('elementpath', '4.1.5', { 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], From 92b55ac0b7cc568449374e2f98586d353f25cea3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 12 Jul 2024 16:25:11 +0200 Subject: [PATCH 053/553] fix spglib checksum --- easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb index 5a00e03ac05..a7e62a33f21 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/spglib/spglib/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['80c060b1a606a76b15f2cc708e9fdd4a83479924ebff9ac16ed26a87a0eac1a9'] +checksums = ['b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914'] builddependencies = [ ('binutils', '2.40'), From 2d06f3a69d111bf2e14e08b8bb88e3cf7fc9b4fd Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 12 Jul 2024 14:41:19 -0700 Subject: [PATCH 054/553] multi checksum --- .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb index a4bb6387868..f64038e8dfe 100644 --- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -26,13 +26,16 @@ patches = [ '3rd-party-removal.patch', 'BGEN-enkre_streampos.patch', ] + checksums = [ - '8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb', # 1.1.7.tgz + ('8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb', + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), # 1.1.7.tgz '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch ] builddependencies = [ + ('binutils', '2.37'), ('Python', '3.9.6'), ] From 08fa65756d160d2b9b3bf0e5e0f0cb34aa40616e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 15 Jul 2024 01:30:40 +0200 Subject: [PATCH 055/553] adding easyconfigs: GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb --- ...MC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4cd71cb5340 --- /dev/null +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'GOMC' +version = '2.76-20230613' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '9fc85fb' + +homepage = 'https://gomc-wsu.org/' +description = """GPU Optimized Monte Carlo (GOMC) is a parallel molecular +simulation code designed for high-performance simulation of large systems.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/GOMC-WSU/GOMC/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['14725836707e4525cc7daea219a6eb47a8aeb675d01ef6d16ad60a9986dd3c1e'] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['6.0', '7.0', '7.5', '8.0', '8.6'] +configopts = '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' + +preinstallopts = 'mkdir %(installdir)s/bin &&' +install_cmd = 'cp' +installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' + +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _gomc_exe], + 'dirs': [], +} + +moduleclass = 'chem' From 22a31b9b535b87a997d376c997f5d0de47022450 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 15 Jul 2024 11:15:56 +0200 Subject: [PATCH 056/553] fix too long line in GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb --- .../g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb index 4cd71cb5340..7b3db4cc18b 100644 --- a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -36,7 +36,9 @@ preinstallopts = 'mkdir %(installdir)s/bin &&' install_cmd = 'cp' installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' -_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', + 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in _gomc_exe], 'dirs': [], From 40ea6f1a3116b9f6ad6b3a019b9af51db8305757 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 16 Jul 2024 10:52:38 +0200 Subject: [PATCH 057/553] Update easyconfigs.py exception for VTK-9.2.6 --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f0273368053..069bf5314db 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -662,6 +662,10 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15 'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])], + 'VTK': [ + # Visit-3.4.1 requires VTK 9.2.x + (r'9\.2\.0-20180606', [r'Visit-3\.4\.1']), + ], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 From 3e83e3b487600ed49663aa0ed975a66185004081 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jul 2024 17:22:22 +0200 Subject: [PATCH 058/553] adding easyconfigs: TELEMAC-MASCARET-8p5r0-foss-2023a.eb --- .../TELEMAC-MASCARET-8p5r0-foss-2023a.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb new file mode 100644 index 00000000000..7ab63c49433 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb @@ -0,0 +1,88 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p5r0' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['2beb9793fb83d17de31b17f001f985fc30702c151e2ced614f5e0117e8e34aa0'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # provides numpy, scipy + ('matplotlib', '3.7.2'), + ('HDF5', '1.14.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S10.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild.dyn", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) + +sanity_check_paths = { + 'files': ['builds/easybuild.dyn/bin/telemac2d', 'builds/easybuild.dyn/bin/telemac3d', + 'builds/easybuild.dyn/lib/libtelemac2d.%s' % SHLIB_EXT, + 'builds/easybuild.dyn/lib/libtelemac3d.%s' % SHLIB_EXT], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild.dyn/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild.dyn', +} + +moduleclass = 'geo' From f0f877f193b24dbadbcf9683dea004cd432da977 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 17 Jul 2024 10:57:16 +0200 Subject: [PATCH 059/553] Update easyconfigs.py - VTK exception update --- test/easyconfigs/easyconfigs.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 41a2f9e624c..4d7b85dac79 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -663,10 +663,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15 'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])], - 'VTK': [ - # Visit-3.4.1 requires VTK 9.2.x - (r'9\.2\.0-20180606', [r'Visit-3\.4\.1']), - ], + # Visit-3.4.1 requires VTK 9.2.x + 'VTK': [('9.2.6;', ['Visit-3.4.1-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 From c3b95c8ac0256531e5225e3000ccba86d6800e61 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 17 Jul 2024 10:31:35 -0700 Subject: [PATCH 060/553] change source file v1.1.7 --- .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb index f64038e8dfe..b6850c17621 100644 --- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -21,15 +21,15 @@ bioArxiv 308296; doi: https://doi.org/10.1101/308296 toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://code.enkre.net/bgen/tarball/release/'] -sources = ['%(version)s.tgz'] +sources = ['v%(version)s.tgz'] patches = [ '3rd-party-removal.patch', 'BGEN-enkre_streampos.patch', ] checksums = [ - ('8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb', - 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), # 1.1.7.tgz + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch ] From 8a57f451e38fa56f0ada909280eba1c25b61c745 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 18 Jul 2024 10:24:23 +0200 Subject: [PATCH 061/553] adding easyconfigs: SingleM-0.16.0-foss-2023a.eb, smafa-0.8.0-GCC-12.3.0.eb, psycopg-3.2.1-GCCcore-12.3.0.eb, CD-HIT-4.8.1-GCC-12.3.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb | 38 +++ .../p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb | 26 ++ .../s/SingleM/SingleM-0.16.0-foss-2023a.eb | 107 ++++++++ .../s/smafa/smafa-0.8.0-GCC-12.3.0.eb | 235 ++++++++++++++++++ 4 files changed, 406 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..c4cacfb04bf --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c0aab8a54e --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psycopg' +version = '3.2.1' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..25fc18b7c63 --- /dev/null +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb @@ -0,0 +1,107 @@ +easyblock = 'PythonBundle' + +name = 'SingleM' +version = '0.16.0' + +homepage = 'https://github.com/wwood/singlem' +description = """SingleM is a tool for profiling shotgun metagenomes. +It has a particular strength in detecting microbial lineages which are not in reference databases. +The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, +finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('DIAMOND', '2.1.8'), + ('HMMER', '3.4'), + ('MAFFT', '7.520', '-with-extensions'), + ('OrfM', '0.7.1'), + ('mfqe', '0.5.0'), + ('KronaTools', '2.8.1'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('SRA-Toolkit', '3.0.10'), + ('Seqmagick', '0.8.6'), + ('ExpressBetaDiversity', '1.0.10'), + ('FastTree', '2.1.11'), + ('SQLAlchemy', '2.0.25'), + ('CD-HIT', '4.8.1'), + ('smafa', '0.8.0'), + ('prodigal', '2.6.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), + ('zenodo_backpack', '0.3.1', { + 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], + }), + ('bird_tool_utils', '0.4.1', { + 'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'], + }), + ('fastalite', '0.4.1', { + 'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + ('extern', '0.4.1', { + 'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'], + }), + ('graftm', '0.15.1', { + 'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'], + }), + ('singlem', version, { + 'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/graftM', 'bin/singlem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "graftM --help", + "singlem --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..342d27e7548 --- /dev/null +++ b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb @@ -0,0 +1,235 @@ +easyblock = 'Cargo' + +name = 'smafa' +version = '0.8.0' + +homepage = 'https://github.com/wwood/smafa' +description = 'Biological sequence aligner for pre-aligned sequences.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wwood/smafa/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.8.0.tar.gz': '6f103ecd5cdf36fb61572a757732eeb07e905c61b497fa247c1a8397ee775c2d'}, + {'addr2line-0.22.0.tar.gz': '6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.14.tar.gz': '418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b'}, + {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'}, + {'anstyle-parse-0.2.4.tar.gz': 'c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4'}, + {'anstyle-query-1.1.0.tar.gz': 'ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391'}, + {'anstyle-wincon-3.0.3.tar.gz': '61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19'}, + {'assert_cli-0.6.3.tar.gz': 'a29ab7c0ed62970beb0534d637a8688842506d0ff9157de83286dacd065c8149'}, + {'atomic-polyfill-1.0.3.tar.gz': '8cf2bce30dfe09ef0bfaef228b9d414faaf7e563035494d7fe092dba54b300f4'}, + {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'}, + {'backtrace-0.3.73.tar.gz': '5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a'}, + {'bird_tool_utils-0.4.1.tar.gz': '6f5f475a22ef913421b64a8d09fad619d9a3a828a5a7450e9b32ab177aa3df56'}, + {'bird_tool_utils-man-0.4.0.tar.gz': 'a263d1717fd146db3c9bfc0668f9bf19d9078a79fa2c1ba54f00b6d8702d4e0b'}, + {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'}, + {'buffer-redux-1.0.1.tar.gz': '4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5'}, + {'bytecount-0.6.8.tar.gz': '5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce'}, + {'byteorder-1.5.0.tar.gz': 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'0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, +] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +crates = [ + ('addr2line', '0.22.0'), + ('adler', '1.0.2'), + ('aho-corasick', '1.1.3'), + ('anstream', '0.6.14'), + ('anstyle', '1.0.7'), + ('anstyle-parse', '0.2.4'), + ('anstyle-query', '1.1.0'), + ('anstyle-wincon', '3.0.3'), + ('assert_cli', '0.6.3'), + ('atomic-polyfill', '1.0.3'), + ('autocfg', '1.3.0'), + ('backtrace', '0.3.73'), + ('bird_tool_utils', '0.4.1'), + ('bird_tool_utils-man', '0.4.0'), + ('bitflags', '2.6.0'), + ('buffer-redux', '1.0.1'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cargo-husky', '1.5.0'), + ('cc', '1.1.5'), + ('cfg-if', '1.0.0'), + ('clap', '4.5.9'), + ('clap_builder', '4.5.9'), + ('clap_lex', '0.7.1'), + ('cobs', '0.2.3'), + ('colorchoice', '1.0.1'), + ('colored', '1.9.4'), + ('crc32fast', '1.4.2'), + ('critical-section', '1.1.2'), + ('difference', '2.0.0'), + ('embedded-io', '0.4.0'), + ('env_logger', '0.10.2'), + ('environment', '0.1.1'), + ('errno', '0.3.9'), + ('failure', '0.1.8'), + ('failure_derive', '0.1.8'), + ('fastrand', '2.1.0'), + ('flate2', '1.0.30'), + ('gimli', '0.29.0'), + ('hash32', '0.2.1'), + ('heapless', '0.7.17'), + ('hermit-abi', '0.3.9'), + ('humantime', '2.1.0'), + ('is-terminal', '0.4.12'), + ('is_terminal_polyfill', '1.70.0'), + ('itoa', '1.0.11'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.7.4'), + ('needletail', '0.5.1'), + ('object', '0.36.1'), + ('pkg-config', '0.3.30'), + ('postcard', '1.0.8'), + ('proc-macro2', '1.0.86'), + ('quote', '1.0.36'), + ('regex', '1.10.5'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('roff', '0.1.0'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.4.0'), + ('rustix', '0.38.34'), + ('ryu', '1.0.18'), + ('scopeguard', '1.2.0'), + ('semver', '1.0.23'), + ('serde', '1.0.204'), + ('serde_derive', '1.0.204'), + ('serde_json', '1.0.120'), + ('spin', '0.9.8'), + ('stable_deref_trait', '1.2.0'), + ('strsim', '0.11.1'), + ('syn', '1.0.109'), + ('syn', '2.0.71'), + ('synstructure', '0.12.6'), + ('tempfile', '3.10.1'), + ('termcolor', '1.4.1'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.2.4'), + ('utf8parse', '0.2.2'), + ('version-compare', '0.1.1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.8'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), +] + +moduleclass = 'bio' From f3d65d25392fe06b1b61e404747111869e8d495a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 19 Jul 2024 12:51:00 +0200 Subject: [PATCH 062/553] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index 3ef84650f5e..effa0f88656 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -28,8 +28,6 @@ dependencies = [ ('nglview', '3.1.2'), ] -use_pip = True - exts_list = [ ('qcelemental', '0.26.0', { 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], @@ -139,6 +137,7 @@ sanity_check_commands = [ "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", ] +use_pip = True sanity_pip_check = True moduleclass = 'bio' From b94bb4c5b8df22f68a6b0cdbb75b09b4806520e5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 19 Jul 2024 12:56:25 +0200 Subject: [PATCH 063/553] fix checksum of toolkit --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index effa0f88656..a656f10d6ab 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -28,6 +28,8 @@ dependencies = [ ('nglview', '3.1.2'), ] +use_pip = True + exts_list = [ ('qcelemental', '0.26.0', { 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], @@ -124,7 +126,7 @@ exts_list = [ 'modulename': 'openff.toolkit', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], - 'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'], + 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], }), ] @@ -137,7 +139,6 @@ sanity_check_commands = [ "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", ] -use_pip = True sanity_pip_check = True moduleclass = 'bio' From 48d40dcb19b97cda7ef44f0fb5685c19068a91e7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 19 Jul 2024 14:40:22 +0200 Subject: [PATCH 064/553] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb fix whitespace --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index a656f10d6ab..06e5075f674 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -8,7 +8,7 @@ description = """The Open Force Field Toolkit provides implementations of the SM parameterization engine, and other tools.""" toolchain = {'name': 'foss', 'version': '2023a'} - + builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), From c62afab0f964a42584a3951f9a7f0a6b520f9608 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 20 Jul 2024 12:29:37 +0200 Subject: [PATCH 065/553] adding easyconfigs: Biotite-0.41.0-gfbf-2023a.eb, ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb, ESM3-3.0.0.post2-foss-2023a.eb --- .../b/Biotite/Biotite-0.41.0-gfbf-2023a.eb | 32 ++++++++++++ ...ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++ .../e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb | 47 ++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8d4385e45f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Biotite' +version = '0.41.0' + +homepage = 'https://www.biotite-python.org/' +description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to +identify homologous sequence regions in a protein family or you would like to +find disulfide bonds in a protein structure: Biotite has the right tool for +you. This package bundles popular tasks in computational molecular biology into +a uniform Python library.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), +] + +use_pip = True + +exts_list = [ + ('biotite', version, { + 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b316a1a4441 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb new file mode 100644 index 00000000000..0470d9c4ec6 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 6f4dda3324c8024f4d1547a6655fd26cf990fef2 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Sun, 21 Jul 2024 15:51:17 +0000 Subject: [PATCH 066/553] adding easyconfigs: PyAEDT-0.9.9-gfbf-2023b.eb --- .../p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb new file mode 100644 index 00000000000..f3047e4bc6d --- /dev/null +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'PyAEDT' +version = '0.9.9' + +homepage = 'https://aedt.docs.pyansys.com/version/stable' +description = """PyAEDT is a Python library that interacts directly with the +Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient +automation in your workflow.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('dotNET-Core', '8.0', '', SYSTEM), + ('libspatialindex', '1.9.3'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Pillow', '10.2.0'), + ('pydantic', '2.7.4'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('dotnetcore2', '3.1.23', { + 'sources': ['dotnetcore2-3.1.23-py3-none-manylinux1_x86_64.whl'], + 'checksums': ['5f076ddc39da0c685e7de20ecb91ee81185928918ec86fbeb3bffc55dd867ab5'], + }), + ('clr_loader', '0.2.6', { + 'checksums': ['019348ae6b6a83c7a406d14537c277cecf7a3a53b263ec342c81ded5845a67ee'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('ansys-pythonnet', '3.1.0rc3', { + 'modulename': 'pythonnet', + 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', + }), + ('pytomlpp', '1.0.13', { + 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], + }), + ('fpdf2', '2.7.9', { + 'modulename': 'fpdf', + 'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('rpyc', '6.0.0', { + 'checksums': ['a7e12b31f40978cbd6b74e0b713da389d4b2565cef612adcb0f4b41aeb188230'], + }), + ('rtree', '1.3.0', { + 'modulename': 'rtree', + 'checksums': ['b36e9dd2dc60ffe3d02e367242d2c26f7281b00e1aaf0c39590442edaaadd916'], + }), + ('pyedb', '0.21.0', { + 'checksums': ['3c91cb8a72a080864d3582ae7ec1de2f04d90aee477dadc096a7144f7823258d'], + }), + ('pyaedt', version, { + 'checksums': ['714728230ab3ede4744a30a7c0d45aaa104cdc1887bfbfe8feb928a8f10cc72f'], + }), +] + +modloadmsg = "NOTE: You also need load a AEDT module before you start using PyAEDT." + +moduleclass = "phys" From ed5b120d8ab5f6b18833123eb3cee0c37701aa0e Mon Sep 17 00:00:00 2001 From: c3-builder Date: Sun, 21 Jul 2024 16:05:48 +0000 Subject: [PATCH 067/553] Add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` --- easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb index aee9ba9ea19..894b488cd3e 100644 --- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb @@ -43,6 +43,7 @@ exts_list = [ ('ansys-pythonnet', '3.1.0rc3', { 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], 'modulename': 'pythonnet', + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', }), ('pytomlpp', '1.0.13', { 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], From 12ef0f174250928ca9a5ccf47e4f7ca0ce56811f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 22 Jul 2024 11:09:33 +0100 Subject: [PATCH 068/553] dbarts ARM fix --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index c042ee83af9..ce8233bc4a5 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -60,6 +60,14 @@ local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver ! local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + # !! order of packages is important !! # packages updated on 24 June 2024 exts_list = [ @@ -2585,6 +2593,7 @@ exts_list = [ }), ('dbarts', '0.9-28', { 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], From db8fcd6c993be1d290a1f962a11eb86e73dc6a40 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 22 Jul 2024 17:19:36 +0200 Subject: [PATCH 069/553] adding easyconfigs: CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb, CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb --- ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 55 +++++++++++++++++ ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 59 +++++++++++++++++++ 2 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..27df4a0986e --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '11.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb new file mode 100644 index 00000000000..c69748cec08 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '12.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '12.2.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' From bc7fbb5213ccb355b57efb8ea89d3c32bc1872a6 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 22 Jul 2024 17:24:15 +0200 Subject: [PATCH 070/553] Pass cuda compute capabilities through buildopts --- .../c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 2 +- .../c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 2 +- .../c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index b71d2bfad4d..31d65369f80 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -32,7 +32,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index d4240930bd1..8e3cbc72ee2 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 3e7ffe79da0..3444ef46f27 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -58,7 +58,7 @@ if ARCH == 'aarch64': local_filters += "Samples/3_CUDA_Features/cdpQuadtree/Makefile " local_filters += "Samples/3_CUDA_Features/cdpAdvancedQuicksort/Makefile " -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters # Remove libraries in the bin dir after a successful 'make' buildopts += " && rm bin/*/linux/release/lib*.so.*" From 9616f27ad1c0e04c515fb27903887e5cd12f4a94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 23 Jul 2024 14:26:23 +0200 Subject: [PATCH 071/553] avoid the `winsize` error --- .../easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb index ac272dff125..341875e7575 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -25,8 +25,12 @@ dependencies = [ ('yell', '2.2.2'), ] +# requirement is too strict preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ +# to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error +preinstallopts += "sed -i '/terminal_columns > 70/d' lib/transrate/cmdline.rb && " + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['gems/%(namelower)s-%(version)s'], From 3452e8244cebda0858b9035680facacf591b18b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 23 Jul 2024 14:59:03 +0200 Subject: [PATCH 072/553] add missing checksum --- easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb index 341875e7575..6ad1e622a9a 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/blahah/transrate/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'] builddependencies = [ ('binutils', '2.40'), From 2c66b3d9c2101b784812f0bca6a95c4350a7bdce Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 23 Jul 2024 17:34:56 +0200 Subject: [PATCH 073/553] adding easyconfigs: OpenFOAM-v2406-foss-2023a.eb and patches: OpenFOAM-v2406-cleanup.patch --- .../o/OpenFOAM/OpenFOAM-v2406-cleanup.patch | 180 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 48 +++++ 2 files changed, 228 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch new file mode 100644 index 00000000000..6e719c21dae --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch @@ -0,0 +1,180 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# +# ChangeLog: +# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup +# author: Jiri Furst +# +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,8 @@ ++##Easybuild## settings -*- sh -*- ++ ++export MPFR_ARCH_PATH="$EBROOTMPFR" ++export GMP_ARCH_PATH="$EBROOTGMP" ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ +--- OpenFOAM-v2312/etc/config.sh/setup.orig 2024-01-11 09:49:24.823571481 +0100 ++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100 +@@ -207,7 +207,9 @@ + _foamEtc -config CGAL + _foamEtc -config scotch + _foamEtc -config FFTW +- ++_foamEtc -config metis ++_foamEtc -config kahip ++_foamEtc -config readline + + # Finalize library paths + # ~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb new file mode 100644 index 00000000000..185cfead980 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -0,0 +1,48 @@ +name = 'OpenFOAM' +version = 'v2406' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++14', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2406-cleanup.patch', 1), + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), +] +checksums = [ + {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, + {'OpenFOAM-v2406-cleanup.patch': '3ed44da40e9872d1cf096bb0bfd9d5c79ca984d7bc01e4ae30c14b3e7223d749'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.16'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' From 2f6431bdf5f39ef21b713068a7ad8fbf1d8d8415 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:11:07 +0200 Subject: [PATCH 074/553] reorganize Flax/JAX stack in 2023a: scvi-tools, Flax, Optax, jax, absl-py --- .../a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 26 ++++++ .../f/Flax/Flax-0.8.4-gfbf-2023a.eb | 42 +++++++++ ...foss-2023a.eb => jax-0.4.25-gfbf-2023a.eb} | 86 +++++++++---------- .../o/Optax/Optax-0.2.2-gfbf-2023a.eb | 35 ++++++++ .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb | 15 +--- 5 files changed, 145 insertions(+), 59 deletions(-) create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb rename easybuild/easyconfigs/j/jax/{jax-0.4.25-foss-2023a.eb => jax-0.4.25-gfbf-2023a.eb} (52%) create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8b2c928998b --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb new file mode 100644 index 00000000000..dedc08531c3 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), + ('Optax', '0.2.2'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb similarity index 52% rename from easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb rename to easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb index 64a723ffe37..26fb967339f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -1,25 +1,23 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS) -# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119 - +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) easyblock = 'PythonBundle' name = 'jax' version = '0.4.25' -homepage = 'https://jax.readthedocs.io/' +homepage = 'https://pypi.python.org/pypi/jax' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('Bazel', '6.3.1'), ('pytest-xdist', '3.3.1'), - # git 2.x required to fetch repository 'io_bazel_rules_docker' - ('git', '2.41.0', '-nodocs'), - ('matplotlib', '3.7.2'), + ('git', '2.41.0', '-nodocs'), # bazel used git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py ('poetry', '1.5.1'), ('pybind11', '2.11.1'), ] @@ -27,86 +25,84 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('zlib', '1.2.13'), + ('absl-py', '2.1.0'), ('flatbuffers-python', '23.5.26'), ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), ] -use_pip = True - +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' -local_extract_cmd = 'cp %s %(builddir)s/archives' - -local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" ' -local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' -local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' - -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, -} +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' components = [ - ('absl-py', '2.1.0', { - 'options': {'modulename': 'absl'}, - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), ('jaxlib', version, { 'sources': [ - '%(name)s-v%(version)s.tar.gz', { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], 'download_filename': '%s.tar.gz' % local_xla_commit, - 'filename': 'xla-%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], 'extract_cmd': local_extract_cmd, }, { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], 'download_filename': '%s.tar.gz' % local_tfrt_commit, - 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], 'extract_cmd': local_extract_cmd, }, ], - 'source_urls': [ - 'https://github.com/google/jax/archive/', - 'https://github.com/tensorflow/runtime/archive', - 'https://github.com/openxla/xla/archive' - ], 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], 'checksums': [ {'jaxlib-v0.4.25.tar.gz': 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, - {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz': + {'xla-4ccfe33c.tar.gz': '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, - {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz': + {'tf_runtime-0aeefb16.tar.gz': 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, {'jax-0.4.25_fix-pybind11-systemlib.patch': 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, ], 'start_dir': 'jax-jaxlib-v%(version)s', - # Avoid warning (treated as error) in upb/table.c - 'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"' + 'buildopts': _jaxlib_buildopts }), ] +use_pip = True + exts_list = [ (name, version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + ], 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], - 'source_tmpl': '%(name)s-v%(version)s.tar.gz', - 'source_urls': ['https://github.com/google/jax/archive/'], 'checksums': [ {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, {'jax-0.4.25_fix_env_test_no_log_spam.patch': 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, ], + 'runtest': "pytest -n %(parallel)s tests", }), ] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d447a77bbd2 --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb index f79f5895f45..be427d2af9e 100644 --- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb @@ -22,7 +22,7 @@ dependencies = [ ('PyTorch-Lightning', '2.2.1'), ('pyro-ppl', '1.9.0'), ('ml-collections', '0.1.1'), - ('Optax', '0.2.2'), + ('Flax', '0.8.4'), ] use_pip = True @@ -37,19 +37,6 @@ exts_list = [ ('numpyro', '0.15.0', { 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], }), - ('nest_asyncio', '1.6.0', { - 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], - }), - ('orbax_checkpoint', '0.5.15', { - 'modulename': 'orbax.checkpoint', - 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], - }), - ('tensorstore', '0.1.60', { - 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], - }), - ('flax', '0.8.4', { - 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], - }), ('docrep', '0.3.2', { 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], }), From a0ebc51ee9412cc8fc924f60d5b595a02d723de7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:13:43 +0200 Subject: [PATCH 075/553] downgrade Optax v0.2.2 from foss/2023a to gfbf/2023a --- .../o/Optax/Optax-0.2.2-foss-2023a.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb deleted file mode 100644 index be05f009e9e..00000000000 --- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Optax' -version = '0.2.2' - -homepage = 'https://github.com/deepmind/optax' -description = """Optax is a gradient processing and optimization library for JAX.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25'), -] - -use_pip = True - -exts_list = [ - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('flit_core', '3.9.0', { - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('chex', '0.1.86', { - 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], - }), - ('optax', version, { - 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], - }), -] - -sanity_pip_check = True - -sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] - -moduleclass = 'lib' From 17f7abeca74a18c792b6b32caf6af2751fe9e70c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:16:19 +0200 Subject: [PATCH 076/553] reinstate all authorship on jax-0.4.25-gfbf-2023a.eb --- easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb index 26fb967339f..f78da6a06e4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -1,6 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak # Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) # Updated by: Thomas Hoffmann (EMBL Heidelberg) easyblock = 'PythonBundle' From 496f749f46446c8fb1c8da0000e72babe9b33dad Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:22:34 +0200 Subject: [PATCH 077/553] use readtehdocs URL as homepage of jax-0.4.25-gfbf-2023a.eb --- easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb index f78da6a06e4..f913cfe9e97 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -8,7 +8,7 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.4.25' -homepage = 'https://pypi.python.org/pypi/jax' +homepage = 'https://jax.readthedocs.io/' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" From b3c2dcd3a28130caa607474cd1e016768cab069e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:31:59 +0200 Subject: [PATCH 078/553] fix typo in comment of jax-0.4.25-gfbf-2023a.eb --- easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb index f913cfe9e97..a4a86382ad6 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('Bazel', '6.3.1'), ('pytest-xdist', '3.3.1'), - ('git', '2.41.0', '-nodocs'), # bazel used git to fetch repositories + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py ('poetry', '1.5.1'), ('pybind11', '2.11.1'), From ac92bb78c36ab8bb172b103110ec904a3ee65155 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 12:43:40 +0200 Subject: [PATCH 079/553] Flax/JAX stack in 2023a w/ CUDA 12.1.1: scvi-tools, Flax, Optax, jax, absl-py --- .../a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 26 ++++ .../Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb | 44 +++++++ .../jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb | 117 ++++++++---------- .../Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb | 37 ++++++ ...scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb | 57 +++++++++ 5 files changed, 218 insertions(+), 63 deletions(-) create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8b2c928998b --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..4aeb0c7d815 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), + ('Optax', '0.2.2', versionsuffix), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb index c193b35c83b..75355c6c842 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb @@ -1,6 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak # Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) # Updated by: Thomas Hoffmann (EMBL Heidelberg) easyblock = 'PythonBundle' @@ -8,7 +9,7 @@ name = 'jax' version = '0.4.25' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://pypi.python.org/pypi/jax' +homepage = 'https://jax.readthedocs.io/' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" @@ -18,8 +19,7 @@ cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9 builddependencies = [ ('Bazel', '6.3.1'), ('pytest-xdist', '3.3.1'), - # git 2.x required to fetch repository 'io_bazel_rules_docker' - ('git', '2.41.0', '-nodocs'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py ('poetry', '1.5.1'), ('pybind11', '2.11.1'), @@ -29,23 +29,65 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), ('NCCL', '2.18.3', versionsuffix), - ('zlib', '1.2.13'), ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), ('flatbuffers-python', '23.5.26'), ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), ] # downloading xla and other tarballs to avoid that Bazel downloads it during the build -# note: this *must* be the exact same commit as used in third_party/{xla,"other"}/workspace.bzl +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' -local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' -local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" ' -local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' -local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] # Some tests require an isolated run: local_isolated_tests = [ @@ -74,71 +116,20 @@ local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests]) use_pip = True -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, -} - -components = [ - ('absl-py', '2.1.0', { - 'options': {'modulename': 'absl'}, - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('jaxlib', version, { - 'sources': [ - '%(name)s-v%(version)s.tar.gz', - { - 'download_filename': '%s.tar.gz' % local_xla_commit, - 'filename': 'xla-%s.tar.gz' % local_xla_commit, - 'extract_cmd': local_extract_cmd, - }, - { - 'download_filename': '%s.tar.gz' % local_tfrt_commit, - 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit, - 'extract_cmd': local_extract_cmd, - }, - ], - 'source_urls': [ - 'https://github.com/google/jax/archive/', - 'https://github.com/tensorflow/runtime/archive', - 'https://github.com/openxla/xla/archive' - ], - 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], - 'checksums': [ - {'jaxlib-v0.4.25.tar.gz': - 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, - {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz': - '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, - {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz': - 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, - {'jax-0.4.25_fix-pybind11-systemlib.patch': - 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, - ], - 'start_dir': 'jax-jaxlib-v%(version)s', - # Avoid warning (treated as error) in upb/table.c - 'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"' - }), -] - exts_list = [ (name, version, { - 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], - 'runtest': local_test, 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], 'checksums': [ {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, {'jax-0.4.25_fix_env_test_no_log_spam.patch': 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, ], + 'runtest': local_test, }), ] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..61000b1388c --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..ce1e90cec46 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('h5py', '3.9.0'), + ('jax', '0.4.25', versionsuffix), + ('Flax', '0.8.4', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0'), + ('ml-collections', '0.1.1'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From ce2dc5e7a30246e258f2cfd25df771353aea8a3c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 14:04:07 +0200 Subject: [PATCH 080/553] fix partial installation of ESM3 by swicthing to wheel sources --- .../ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb | 12 ++++++++---- .../e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb index b316a1a4441..1382c12efc6 100644 --- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -38,12 +38,16 @@ exts_list = [ 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], }), ('esm', version, { - 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], }), ] sanity_pip_check = True -moduleclass = 'lib' +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb index 0470d9c4ec6..60125c1af46 100644 --- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -36,12 +36,16 @@ exts_list = [ 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], }), ('esm', version, { - 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], }), ] sanity_pip_check = True -moduleclass = 'lib' +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' From a01ab8635d54ad1c4d55041072d64372e67eb865 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 24 Jul 2024 15:05:44 +0200 Subject: [PATCH 081/553] avoid the `winsize` error --- easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb index 6ad1e622a9a..cef48298a80 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ # to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error -preinstallopts += "sed -i '/terminal_columns > 70/d' lib/transrate/cmdline.rb && " +preinstallopts += "sed -i '/terminal_columns > 70/d;/def terminal_columns/,+3d' lib/transrate/cmdline.rb && " sanity_check_paths = { 'files': ['bin/%(namelower)s'], From d666e08e90510f8d108fe83c7a4b61721729440b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 15:11:15 +0200 Subject: [PATCH 082/553] add build dependency on binutils to absl-py-2.1.0-GCCcore-12.3.0.eb --- easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb index 8b2c928998b..faadde2a51d 100644 --- a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -10,6 +10,8 @@ been extensively tested and used in production.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] + dependencies = [('Python', '3.11.3')] use_pip = True From d8d15c50a152bfe202bcf3b01262394b5a64459d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 15:11:50 +0200 Subject: [PATCH 083/553] add build dependency on binutils to absl-py-2.1.0-GCCcore-12.3.0.eb --- easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb index 8b2c928998b..faadde2a51d 100644 --- a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -10,6 +10,8 @@ been extensively tested and used in production.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] + dependencies = [('Python', '3.11.3')] use_pip = True From 85d4f022684e479164f705fd6570515ef95a0346 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 16:41:17 +0200 Subject: [PATCH 084/553] fix dependency on pyro-ppl of scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb --- .../s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb index ce1e90cec46..c434f381cfd 100644 --- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -23,7 +23,7 @@ dependencies = [ ('jax', '0.4.25', versionsuffix), ('Flax', '0.8.4', versionsuffix), ('PyTorch-Lightning', '2.2.1', versionsuffix), - ('pyro-ppl', '1.9.0'), + ('pyro-ppl', '1.9.0', versionsuffix), ('ml-collections', '0.1.1'), ] From 26dd8451a48d2b1f559885d85016fe8d1849c316 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 24 Jul 2024 16:20:29 -0700 Subject: [PATCH 085/553] change source file v1.1.7 --- .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb index b6850c17621..b0c0bc1be02 100644 --- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -20,7 +20,7 @@ bioArxiv 308296; doi: https://doi.org/10.1101/308296 toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://code.enkre.net/bgen/tarball/release/'] +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] sources = ['v%(version)s.tgz'] patches = [ '3rd-party-removal.patch', From 831ecc2d0db6350a1080b7bbdf3ea68274d534ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 25 Jul 2024 11:29:45 +0200 Subject: [PATCH 086/553] add a patch to fix the `winsize` error --- .../t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 9 ++-- ...Transrate-1.0.3_undefined_method_fix.patch | 42 +++++++++++++++++++ 2 files changed, 47 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb index cef48298a80..297dd9260b3 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -13,7 +13,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/blahah/transrate/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'] +patches = ['Transrate-1.0.3_undefined_method_fix.patch'] +checksums = [ + {'v1.0.3.tar.gz': '2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'}, + {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'}, +] builddependencies = [ ('binutils', '2.40'), @@ -29,9 +33,6 @@ dependencies = [ # requirement is too strict preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ -# to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error -preinstallopts += "sed -i '/terminal_columns > 70/d;/def terminal_columns/,+3d' lib/transrate/cmdline.rb && " - sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['gems/%(namelower)s-%(version)s'], diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch new file mode 100644 index 00000000000..47526bd2242 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch @@ -0,0 +1,42 @@ +to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error +Author: Petr Král (INUITS) +--- lib/transrate/cmdline.rb.orig 2016-06-06 15:10:26.000000000 +0200 ++++ lib/transrate/cmdline.rb 2024-07-25 11:23:20.250369056 +0200 +@@ -87,11 +87,6 @@ + end + end + +- def terminal_columns +- require 'io/console' +- IO.console.winsize.last +- end +- + def help_message + <<-EOS + +@@ -117,19 +112,17 @@ + end + + def transrate_banner +- if terminal_columns > 70 +- txp = '░▓▓▓^▓▓▓░' +- toptxp = txp.green +- midtxp = txp.yellow +- bottxp = txp.red +- puts <<-EOS ++ txp = '░▓▓▓^▓▓▓░' ++ toptxp = txp.green ++ midtxp = txp.yellow ++ bottxp = txp.red ++ puts <<-EOS + _ _ + | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___ + #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp} + #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp} + #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp} +- EOS +- end ++ EOS + "" + end + From b846d62500f9df5f50e39d9f232b3f5e4044b257 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 25 Jul 2024 15:21:51 +0100 Subject: [PATCH 087/553] adding easyconfigs: snpEff-5.2c-GCCcore-12.2.0-Java-11.eb --- .../snpEff-5.2c-GCCcore-12.2.0-Java-11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb new file mode 100644 index 00000000000..3b25c1e949f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 9f68ebec38eba01f34825e4c624f8f100cb498bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 25 Jul 2024 15:22:25 +0100 Subject: [PATCH 088/553] adding easyconfigs: Platypus-Opt-1.2.0-foss-2022b.eb --- .../Platypus-Opt-1.2.0-foss-2022b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb new file mode 100644 index 00000000000..b1c5a4f74ea --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Platypus-Opt' +version = '1.2.0' + +homepage = 'https://github.com/Project-Platypus/Platypus' +description = """Platypus is a framework for evolutionary computing in Python with a focus on + multiobjective evolutionary algorithms (MOEAs).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'platypus'} + +moduleclass = 'math' From da7746aeed4c7841a988343ffee89e78c7e72f56 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 25 Jul 2024 16:50:23 +0200 Subject: [PATCH 089/553] enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 --- easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb | 9 +++++---- easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb index 85715fef495..0c588b9f16b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb index 87862215507..5219bd9c54f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' From ee9078ee0686f4a3f5d39e2782bd198d655f2997 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 25 Jul 2024 11:41:16 -0700 Subject: [PATCH 090/553] [GCC-12.3.0] beagle-lib v4.0.1 --- ...beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..12802801834 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.1' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('CUDA', '12.1.1', '', SYSTEM), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_CUDA=ON ' + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' From 6ecf2744a327b910c703966ec9f08a8e597b4dd3 Mon Sep 17 00:00:00 2001 From: Alexander Salois Date: Thu, 25 Jul 2024 14:53:38 -0600 Subject: [PATCH 091/553] Added a newer BayesTraits --- .../b/BayesTraits/BayesTraits-4.1.2-Linux.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb new file mode 100644 index 00000000000..0ae8355e6e1 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -0,0 +1,29 @@ +easyblock = "Tarball" + +name = 'BayesTraits' +version = '4.1.2' +versionsuffix = '-Linux' + +homepage = 'https://www.evolution.reading.ac.uk/SoftwareMain.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = SYSTEM + +source_urls = ['https://www.evolution.reading.ac.uk/BayesTraitsV%(version)s/Files/'] +sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0'] + +sanity_check_paths = { + 'files': ['BayesTraitsV4','Artiodactyl.trees','Bird.trees','Mammal.trees','Marsupials.trees','NortheastBantu.trees','Primates.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 4ad0b74e5c7be07f9cf5b48cf0d47d453c1c5b2c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 26 Jul 2024 09:58:01 +0100 Subject: [PATCH 092/553] add mpi4py dep --- .../easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb index b1c5a4f74ea..a0e995d4f45 100644 --- a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb @@ -15,6 +15,7 @@ checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a'] dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), ] download_dep_fail = True From 0682e03a9771363a0655c976c04f1a44b1910540 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jul 2024 15:07:39 +0200 Subject: [PATCH 093/553] adding easyconfigs: chewBBACA-3.3.9-foss-2022b.eb --- .../c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb new file mode 100644 index 00000000000..b9964db690a --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '3.3.9' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome +MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm". +BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and +could be thought of as "Comprehensive and Highly Efficient Workflow".""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40 + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('Cython', '3.0.8'), + ('Biopython', '1.81'), + ('plotly.py', '5.13.1'), + ('BLAST+', '2.14.0'), + ('prodigal', '2.6.3'), + ('MAFFT', '7.505', '-with-extensions'), + ('FastTree', '2.1.11'), + ('archspec', '0.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyrodigal', '3.5.1', { + 'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '7.0.0', { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), + ('SPARQLWrapper', '2.0.0', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + # relax numpy version requirement + 'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ", + 'runtest': "python setup.py test", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chewBBACA.py', 'bin/chewie'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', + 'chewie --help', +] + +moduleclass = 'bio' From 1c47eb36cf85e5a0f0f0ba4dc16cf01832f9609e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 26 Jul 2024 15:36:08 +0200 Subject: [PATCH 094/553] adding easyconfigs: ORCA-6.0.0-gompi-2023a.eb --- .../o/ORCA/ORCA-6.0.0-gompi-2023a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb new file mode 100644 index 00000000000..8bf88fa8129 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +moduleclass = 'chem' From b9fd6b88fdb5d641b5aa501bf0e6dd97596008ff Mon Sep 17 00:00:00 2001 From: Alexander Salois Date: Fri, 26 Jul 2024 09:11:16 -0600 Subject: [PATCH 095/553] Ran --check-contrib Found some code style issues. They have now been fixed and `--check-contrib` passes --- easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb index 0ae8355e6e1..b07ea0bb7a1 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -20,7 +20,8 @@ sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0'] sanity_check_paths = { - 'files': ['BayesTraitsV4','Artiodactyl.trees','Bird.trees','Mammal.trees','Marsupials.trees','NortheastBantu.trees','Primates.trees'], + 'files': ['BayesTraitsV4', 'Artiodactyl.trees', 'Bird.trees', 'Mammal.trees', + 'Marsupials.trees', 'NortheastBantu.trees', 'Primates.trees'], 'dirs': [], } From 324edb1a6927674324754a6fa4386ee51ae027e1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 26 Jul 2024 19:15:29 +0200 Subject: [PATCH 096/553] adding easyconfigs: PCAngsd-1.2-gfbf-2023a.eb --- .../p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d534bfa0f78 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PCAngsd' +version = '1.2' + +homepage = "https://www.popgen.dk/software/index.php/PCAngsd" +description = "Framework for analyzing low depth NGS data in heterogeneous populations using PCA." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cython', '3.0.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Rosemeis/pcangsd/archive/refs/tags/'], + 'checksums': ['286f09851c37e380c9abf5859595e7cd0ad8cb49f1d48b1b0ae409aab0eae62e'], + }), +] + +sanity_check_commands = [ + 'pcangsd --help', +] + +moduleclass = 'bio' From 02f083f5306edfa2e2476a6e917dc55ee24393b2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 28 Jul 2024 09:27:27 +0200 Subject: [PATCH 097/553] adding easyconfigs: elfutils-0.191-GCCcore-13.3.0.eb, libdwarf-0.10.1-GCCcore-13.3.0.eb --- .../elfutils/elfutils-0.191-GCCcore-13.3.0.eb | 41 +++++++++++++++++++ .../libdwarf-0.10.1-GCCcore-13.3.0.eb | 33 +++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e5eb4ef3c7d --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.191' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['df76db71366d1d708365fc7a6c60ca48398f14367eb2b8954efc8897147ad871'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.4'), + ('XZ', '5.4.5'), + ('zstd', '1.5.6'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95a46c43114 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.10.1' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['b511a2dc78b98786064889deaa2c1bc48a0c70115c187900dd838474ded1cc19'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('elfutils', '0.191'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' From 6ecba6a0c33d1398671b9702b7b0180df5083a5a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 28 Jul 2024 09:38:25 +0200 Subject: [PATCH 098/553] adding easyconfigs: gc-8.2.6-GCCcore-13.3.0.eb, libunistring-1.2-GCCcore-13.3.0.eb, Guile-3.0.10-GCCcore-13.3.0.eb --- .../g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb | 46 +++++++++++++++++++ .../g/gc/gc-8.2.6-GCCcore-13.3.0.eb | 42 +++++++++++++++++ .../libunistring-1.2-GCCcore-13.3.0.eb | 35 ++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..46917679856 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.10' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dbdbc97598b2faf31013564efb48e4fed44131d28e996c26abe8a5b23b56c2a'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3a120e6a4e9 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.6' +local_libatomic_version = '7.8.2' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.6.tar.gz': 'b9183fe49d4c44c7327992f626f8eaa1d8b14de140f243edb1c9dcff7719a7fc'}, + {'libatomic_ops-7.8.2.tar.gz': 'd305207fe207f2b3fb5cb4c019da12b44ce3fcbc593dfd5080d867b1a2419b51'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7fa2f46eb1f --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.2' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['632bd65ed74a881ca8a0309a1001c428bd1cbd5cd7ddbf8cedcd2e65f4dcdc44'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From db2c50c022387ca7dbe9ffd8b685b372b6811ae4 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 28 Jul 2024 09:48:24 +0200 Subject: [PATCH 099/553] adding easyconfigs: BeautifulSoup-4.12.3-GCCcore-13.3.0.eb --- .../BeautifulSoup-4.12.3-GCCcore-13.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95cb6cf3228 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.12.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.5', { + 'checksums': ['5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051'], + }), +] + +moduleclass = 'data' From 272df972c32870f1c1861bfbbe792fd2dc76cdcd Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Mon, 29 Jul 2024 10:55:37 +0100 Subject: [PATCH 100/553] adding easyconfigs: spglib-python-2.5.0-gfbf-2023b.eb --- .../spglib-python-2.5.0-gfbf-2023b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb new file mode 100644 index 00000000000..5893038d9fd --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3') +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + (name, version, { + 'modulename': 'spglib', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'], + 'sources': ['spglib-%(version)s.tar.gz'], + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' From 6fbdc20fb5b80b97e37081171b72b29a3503a938 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 12:24:45 +0200 Subject: [PATCH 101/553] adding easyconfigs: flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb --- ...-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..0ef79545ba0 --- /dev/null +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'flash-attention' +version = '2.6.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/Dao-AILab/flash-attention' +description = """Fast and memory-efficient exact attention.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('Ninja', '1.11.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('einops', '0.7.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'flash_attn', + 'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'], + }), +] + +sanity_check_commands = [ + "python -c 'from flash_attn import flash_attn_qkvpacked_func, flash_attn_func'", +] + +moduleclass = 'lib' From 685f34d47e1e3f051879830e549db7f63eb142c0 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Mon, 29 Jul 2024 13:02:08 +0200 Subject: [PATCH 102/553] Describe patch to fix failing test on Zen4 --- .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb | 2 +- .../Highway-1.0.4-zen4-fix-TruncateTo-bug.patch | 15 +++++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb index 824460d1be2..993087b828c 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -17,7 +17,7 @@ patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch'] checksums = [ {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'}, {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch': - '7eb68cfa702648f8f82fe3b7bdc5f0f0ab171840f966040f6d8ec470e3eed712'}, + 'e571413c290076a729dbb1df105a4bfa106099238d1b438e74a9dfc9557eb4a2'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch index b4e71737d22..f489a6bd15f 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch @@ -1,3 +1,18 @@ +A single test failed when building on AMD Genoa a.k.a Zen4 with the error message +reported in https://github.com/google/highway/issues/1913 + +Building v1.0.5 passed all tests. Hence, this patch uses some of the changes made +in v1.0.5 to let the single failing test succeed. + +Looking at the PRs added by v1.0.5 a promising candidate was identified +(https://github.com/google/highway/pull/1276) and all changed files in the PR +were "studied in detail" (assessed if the changes could be related to the failing +test on Zen4). Luckily, the four changes provided in the patch below were +found to resolve the issue. It was also tested if a subset of these four changes +would resolve the issue, but this did not succeed. + +Author: Thomas Roeblitz (University of Bergen) + diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h index 4e2e83e8..2fbf99c7 100644 --- a/hwy/ops/x86_256-inl.h From 988d69ad55c8496712729680d0226a1b2add844d Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 29 Jul 2024 13:30:56 +0200 Subject: [PATCH 103/553] Include patch to make things work for multiple cuda compute capabilities --- ...UDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 1 + ...UDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 1 + ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 1 + ...UDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 1 + ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 1 + .../cuda-samples-11.X_multiple-sms.patch | 31 ++++++++++ .../cuda-samples-12.X_multiple-sms.patch | 56 +++++++++++++++++++ 7 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index 31d65369f80..31db9bd5579 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.X_multiple-sms.patch'] checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index 8e3cbc72ee2..1cb33c8ed72 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.X_multiple-sms.patch'] checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb index 27df4a0986e..4dc6f0f47d1 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.X_multiple-sms.patch'] checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 3444ef46f27..1f2d76136f1 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-12.X_multiple-sms.patch'] checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb index c69748cec08..1f3f081ad15 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-12.X_multiple-sms.patch'] checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466'] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch new file mode 100644 index 00000000000..b6613f6a3c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch @@ -0,0 +1,31 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile +--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 ++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 +@@ -321,6 +321,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -401,7 +407,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch new file mode 100644 index 00000000000..8c4e36f7e74 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch @@ -0,0 +1,56 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 +@@ -313,6 +313,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -394,7 +400,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 +@@ -307,6 +307,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -390,7 +396,7 @@ + endif + + $(PTX_FILE): ptxjit_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) From 238ce2cf062cbd9d63a3f4566f79ab5de9380541 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 29 Jul 2024 14:33:52 +0200 Subject: [PATCH 104/553] Fix which patch to apply where... the filestructure was restructured in the CUDA sources starting at 11.6 --- ...UDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 2 +- ...UDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 2 +- ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 2 +- ...UDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 2 +- ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 2 +- .../cuda-samples-11.3_multiple-sms.patch | 31 ++++++++++ .../cuda-samples-11.6_multiple-sms.patch | 56 +++++++++++++++++++ 7 files changed, 92 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index 31db9bd5579..7c19b967f55 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['cuda-samples-11.X_multiple-sms.patch'] +patches = ['cuda-samples-11.3_multiple-sms.patch'] checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index 1cb33c8ed72..1411d458852 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['cuda-samples-11.X_multiple-sms.patch'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb index 4dc6f0f47d1..db2b3fe617c 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['cuda-samples-11.X_multiple-sms.patch'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 1f2d76136f1..d18522518c8 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['cuda-samples-12.X_multiple-sms.patch'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] dependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb index 1f3f081ad15..092528fda97 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['cuda-samples-12.X_multiple-sms.patch'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466'] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch new file mode 100644 index 00000000000..b6613f6a3c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch @@ -0,0 +1,31 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile +--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 ++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 +@@ -321,6 +321,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -401,7 +407,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch new file mode 100644 index 00000000000..8c4e36f7e74 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch @@ -0,0 +1,56 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 +@@ -313,6 +313,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -394,7 +400,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 +@@ -307,6 +307,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -390,7 +396,7 @@ + endif + + $(PTX_FILE): ptxjit_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) From cb3952a4bf2120cd12be7720b7b0349e9d23a637 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 14:42:07 +0200 Subject: [PATCH 105/553] adding easyconfigs: scenicplus-1.0a1-18072024-foss-2023a.eb, gensim-4.3.2-foss-2023a.eb, pyfasta-0.5.2-foss-2023a.eb, Kaleido-0.2.1-GCCcore-12.3.0.eb, numexpr-2.9.0-foss-2023a.eb, scrublet-0.2.3-foss-2023a.eb, Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb and patches: scenicplus-1.0a1-18072024_requirements.txt.patch --- .../g/gensim/gensim-4.3.2-foss-2023a.eb | 31 + .../k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb | 32 + .../n/numexpr/numexpr-2.9.0-foss-2023a.eb | 21 + .../p/pyfasta/pyfasta-0.5.2-foss-2023a.eb | 44 + .../Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb | 33 + .../scenicplus-1.0a1-18072024-foss-2023a.eb | 274 +++++ ...plus-1.0a1-18072024_requirements.txt.patch | 998 ++++++++++++++++++ .../s/scrublet/scrublet-0.2.3-foss-2023a.eb | 35 + 8 files changed, 1468 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch create mode 100644 easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb new file mode 100644 index 00000000000..cb315af1a31 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.3.2' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +exts_list = [ + ('smart_open', '7.0.4', { + 'checksums': ['62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524'], + }), + (name, version, { + 'checksums': ['99ac6af6ffd40682e70155ed9f92ecbf4384d59fb50af120d343ea5ee1b308ab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..231466bb169 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +if ARCH == 'x86_64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl' +elif ARCH == 'aarch64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux2014_%(arch)s.whl' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'checksums': ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb new file mode 100644 index 00000000000..74e99150d4b --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.9.0' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4df4163fcab20030137e8f2aa23e88e1e42e6fe702387cfd95d7675e1d84645e'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb new file mode 100644 index 00000000000..127a798d38a --- /dev/null +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +local_preinstallopts = ( + "sed -i" + " -e 's/from fasta/from pyfasta.fasta/'" + " -e 's/from records/from pyfasta.records/'" + " -e 's/from split_fasta/from pyfasta.split_fasta/'" + " %(name)s/__init__.py && " +) +local_preinstallopts += "sed -i 's/from collections/from collections.abc/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/from records/from pyfasta.records/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/import cPickle/import _pickle as cPickle/' pyfasta/records.py && " +local_preinstallopts += "sed -i 's/from cStringIO import StringIO/from io import StringIO/' pyfasta/split_fasta.py && " + +exts_list = [ + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['pyfasta extract --help'] +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c41639bc3ad --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb new file mode 100644 index 00000000000..c536bd85bc5 --- /dev/null +++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb @@ -0,0 +1,274 @@ +easyblock = 'PythonBundle' + +name = 'scenicplus' +version = '1.0a1-18072024' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1'), + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), + ('Sphinx-RTD-Theme', '2.0.0'), + ('scrublet', '0.2.3'), + ('numexpr', '2.9.0'), + ('Kaleido', '0.2.1'), + ('pyfasta', '0.5.2'), + ('gensim', '4.3.2'), +] + +# unpin version restriction and delete typing requirement +local_pycistopic_preinstallopts = ( + "sed -i" + " -e 's/pyscenic>=0.12.0/pyscenic/'" + " -e 's/pandas==1.5/pandas/'" + " -e 's/python-Levenshtein/Levenshtein/'" + " -e 's/python-igraph/igraph/'" + " -e '/typing/d'" + # delete pyscenic and loomxpy req from commit - have versions now + " -e '60,61d'" + " requirements.txt && " + "sed -i" + " -e 's/pandas == 1.5/pandas/'" + " -e 's/matplotlib < 3.7/matplotlib/'" + " pyproject.toml && " +) +# delete typing from requirements +local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " +# unpin version restriction and delete poetry.lock +local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " +local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " +local_loomxpy_preinstallopts += "rm poetry.lock && " + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bs4', '0.0.2', { + 'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'], + }), + ('attr', '0.3.2', { + 'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'], + }), + ('attrs', '23.2.0', { + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('lda', '3.0.0', { + 'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'], + }), + ('zope.interface', '6.2', { + 'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'], + }), + ('zope.event', '5.0', { + 'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'], + }), + ('gevent', '24.2.1', { + 'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('suds-community', '1.1.2', { + 'modulename': 'suds', + 'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'], + }), + ('grequests', '0.7.0', { + 'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('easydev', '0.12.1', { + 'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'], + }), + ('bioservices', '1.11.2', { + 'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'], + }), + ('gseapy', '0.10.8', { + 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pybigtools', '0.1.2', { + 'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], + }), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('pyranges', '0.0.111', { + 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], + }), + ('pyrle', '0.0.39', { + 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], + }), + ('pyvis', '0.3.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests_cache', '1.2.0', { + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('scanorama', '1.7.4', { + 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + ('scatac_fragment_tools', '0.1.0', { + 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], + }), + ('snakemake_interface_common', '1.17.1', { + 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], + }), + ('snakemake_interface_report_plugins', '1.0.0', { + 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('globre', '0.1.5', { + 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], + }), + ('bidict', '0.23.1', { + 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], + }), + ('tmtoolkit', '0.12.0', { + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4', { + 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], + }), + ('nbsphinx-link', '1.3.0', { + 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], + }), + ('numpydoc', '1.7.0', { + 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('ansicolors', '1.1.8', { + 'modulename': 'colors', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], + }), + ('papermill', '2.6.0', { + 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('marshmallow', '3.21.1', { + 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], + }), + ('dataclasses_json', '0.6.4', { + 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], + }), + ('loomxpy', '0.4.2', { + 'preinstallopts': local_loomxpy_preinstallopts, + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '2.0a-dca4bb6', { + 'modulename': 'pycisTopic', + 'preinstallopts': local_pycistopic_preinstallopts, + # download commit dca4bb6 to be compatible with pycistarget + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], + 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], + }), + ('pycistarget', '1.0a1-16d14b9', { + 'preinstallopts': local_pycistarget_preinstallopts, + # download commit 16d14b9 to make '$ scenicplus' work + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], + 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], + }), + (name, version, { + 'patches': [ + 'scenicplus-1.0a1-18072024_requirements.txt.patch', + ], + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}], + 'checksums': [ + {'scenicplus-1.0a1-18072024-fa55dae.tar.gz': + '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'}, + {'scenicplus-1.0a1-18072024_requirements.txt.patch': + 'fdfba5d9413f6088d657e315ce7aa28cd645154521e9173a7325bd6c4fdd7e7a'}, + ], + }), +] + +# copy files to let 'scenicplus init_snakemake' works +postinstallcmds = [ + 'cp -r %(builddir)s/scenicplus/scenicplus-fa55dae55203951c0c42e359b65a28010cd544f6/src/scenicplus/snakemake ' + '%(installdir)s/lib/python%(pyshortver)s/site-packages/scenicplus' +] + +sanity_check_commands = ['scenicplus init_snakemake --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch new file mode 100644 index 00000000000..ecfeed15e29 --- /dev/null +++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch @@ -0,0 +1,998 @@ +--- requirements.txt.orig 2024-07-24 10:54:46.267978000 +0200 ++++ requirements.txt 2024-07-24 12:06:31.676022842 +0200 +@@ -1,918 +1,77 @@ +-# +-# This file is autogenerated by pip-compile with Python 3.11 +-# by the following command: +-# +-# pip-compile --output-file=requirements.txt pyproject.toml +-# +-adjusttext==1.0.4 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-aiohttp==3.9.3 +- # via pyscenic +-aiosignal==1.3.1 +- # via +- # aiohttp +- # ray +-anndata==0.10.5.post1 +- # via +- # mudata +- # scanpy +- # scenicplus (pyproject.toml) +-annoy==1.17.3 +- # via +- # bbknn +- # scanorama +- # scenicplus (pyproject.toml) +- # scrublet +-appdirs==1.4.4 +- # via +- # bioservices +- # snakemake +-arboreto==0.1.6 +- # via +- # pyscenic +- # scenicplus (pyproject.toml) +-argparse-dataclass==2.0.0 +- # via +- # snakemake-interface-common +- # snakemake-interface-executor-plugins +-array-api-compat==1.5.1 +- # via anndata +-asttokens==2.4.1 +- # via stack-data +-attr==0.3.2 +- # via scenicplus (pyproject.toml) +-attrs==23.2.0 +- # via +- # aiohttp +- # cattrs +- # jsonschema +- # pyscenic +- # referencing +- # requests-cache +- # scenicplus (pyproject.toml) +-bbknn==1.6.0 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-beautifulsoup4==4.12.3 +- # via +- # bioservices +- # bs4 +- # scenicplus (pyproject.toml) +-bidict==0.23.1 +- # via tmtoolkit +-bioservices==1.11.2 +- # via gseapy +-blosc2==2.5.1 +- # via tables +-bokeh==3.4.0 +- # via dask +-boltons==23.1.1 +- # via pyscenic +-bs4==0.0.2 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-cattrs==23.2.3 +- # via requests-cache +-certifi==2024.2.2 +- # via requests +-charset-normalizer==3.3.2 +- # via requests +-click==8.1.7 +- # via +- # dask +- # distributed +- # loompy +- # loomxpy +- # ray +-cloudpickle==3.0.0 +- # via +- # dask +- # distributed +- # pyscenic +-colorama==0.4.6 +- # via easydev +-colorlog==6.8.2 +- # via +- # bioservices +- # easydev +-conda-inject==1.3.1 +- # via snakemake +-configargparse==1.7 +- # via +- # snakemake +- # snakemake-interface-common +-connection-pool==0.0.3 +- # via snakemake +-contourpy==1.2.0 +- # via +- # bokeh +- # matplotlib +-ctxcore==0.2.0 +- # via +- # pycistarget +- # pyscenic +- # scenicplus (pyproject.toml) +-cycler==0.12.1 +- # via matplotlib +-cython==0.29.37 +- # via +- # bbknn +- # macs2 +- # pyranges +- # scenicplus (pyproject.toml) +- # scrublet +-cytoolz==0.12.3 +- # via +- # ctxcore +- # pyscenic +- # scenicplus (pyproject.toml) +-dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1 +- # via +- # arboreto +- # distributed +- # pyscenic +- # scenicplus (pyproject.toml) +-dataclasses-json==0.6.4 +- # via loomxpy +-datrie==0.8.2 +- # via snakemake +-decorator==5.1.1 +- # via ipython +-dill==0.3.8 +- # via +- # multiprocessing-on-dill +- # scenicplus (pyproject.toml) +-distributed==2024.2.1 +- # via +- # arboreto +- # dask +- # pyscenic +-docutils==0.20.1 +- # via +- # snakemake +- # statistics +-dpath==2.1.6 +- # via +- # snakemake +- # yte +-easydev==0.13.1 +- # via bioservices +-et-xmlfile==1.1.0 +- # via openpyxl +-executing==2.0.1 +- # via stack-data +-fastjsonschema==2.19.1 +- # via nbformat +-fbpca==1.0 +- # via +- # geosketch +- # scanorama +-filelock==3.13.1 +- # via ray +-fonttools==4.50.0 +- # via matplotlib +-frozendict==2.4.0 +- # via +- # ctxcore +- # pyscenic +-frozenlist==1.4.1 +- # via +- # aiohttp +- # aiosignal +- # ray +-fsspec==2024.3.1 +- # via +- # dask +- # pyscenic +-future==1.0.0 +- # via pybiomart +-gensim==4.3.2 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-geosketch==1.2 +- # via scanorama +-gevent==24.2.1 +- # via grequests +-gitdb==4.0.11 +- # via gitpython +-gitpython==3.1.42 +- # via snakemake +-globre==0.1.5 +- # via tmtoolkit +-greenlet==3.0.3 +- # via gevent +-grequests==0.7.0 +- # via bioservices +-gseapy==0.10.8 +- # via scenicplus (pyproject.toml) +-h5py==3.10.0 +- # via +- # anndata +- # loompy +- # mudata +- # pycistarget +- # scanpy +- # scenicplus (pyproject.toml) +-harmonypy==0.0.9 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-humanfriendly==10.0 +- # via snakemake +-idna==3.6 +- # via +- # requests +- # yarl +-igraph==0.11.4 +- # via +- # leidenalg +- # pycistopic +- # scenicplus (pyproject.toml) +-imageio==2.34.0 +- # via +- # scenicplus (pyproject.toml) +- # scikit-image +-immutables==0.20 +- # via snakemake +-importlib-metadata==7.0.1 +- # via +- # dask +- # scenicplus (pyproject.toml) +-importlib-resources==6.1.2 +- # via scenicplus (pyproject.toml) +-interlap==0.2.7 +- # via pyscenic +-intervaltree==3.1.0 +- # via +- # scanorama +- # scenicplus (pyproject.toml) +-ipython==8.22.2 +- # via +- # pycistarget +- # pyvis +-jedi==0.19.1 +- # via ipython +-jinja2==3.1.3 +- # via +- # bokeh +- # dask +- # distributed +- # pyvis +- # snakemake +-joblib==1.3.2 +- # via +- # gseapy +- # pynndescent +- # scanpy +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +- # scikit-learn +-jsonpickle==3.0.3 +- # via pyvis +-jsonschema==4.21.1 +- # via +- # nbformat +- # ray +- # snakemake +-jsonschema-specifications==2023.12.1 +- # via jsonschema +-jupyter-core==5.7.2 +- # via nbformat +-kaleido==0.2.1 +- # via scenicplus (pyproject.toml) +-kiwisolver==1.4.5 +- # via matplotlib +-lazy-loader==0.3 +- # via scikit-image +-lda==3.0.0 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-leidenalg==0.10.2 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-line-profiler==4.1.2 +- # via easydev +-llvmlite==0.42.0 +- # via +- # numba +- # pynndescent +- # pyscenic +-locket==1.0.0 +- # via +- # distributed +- # partd +-loompy==3.0.7 +- # via +- # loomxpy +- # pyscenic +-loomxpy @ git+https://github.com/aertslab/LoomXpy@main +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-lxml==5.1.0 +- # via +- # bioservices +- # pycistopic +- # scenicplus (pyproject.toml) +-lz4==4.3.3 +- # via dask +-macs2==2.2.9.1 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-markdown-it-py==3.0.0 +- # via rich +-markupsafe==2.1.5 +- # via jinja2 +-marshmallow==3.21.1 +- # via dataclasses-json +-matplotlib==3.6.3 +- # via +- # adjusttext +- # bioservices +- # gseapy +- # mizani +- # plotnine +- # pycistopic +- # scanorama +- # scanpy +- # scenicplus (pyproject.toml) +- # scrublet +- # seaborn +- # tmtoolkit +- # tspex +-matplotlib-inline==0.1.6 +- # via ipython +-mdurl==0.1.2 +- # via markdown-it-py +-mizani==0.9.3 +- # via plotnine +-msgpack==1.0.8 +- # via +- # blosc2 +- # distributed +- # ray +-mudata==0.2.3 +- # via scenicplus (pyproject.toml) +-multidict==6.0.5 +- # via +- # aiohttp +- # yarl +-multiprocessing-on-dill==3.5.0a4 +- # via pyscenic +-mypy-extensions==1.0.0 +- # via typing-inspect +-natsort==8.4.0 +- # via +- # anndata +- # pyranges +- # pyrle +- # scanpy +-nbformat==5.10.3 +- # via snakemake +-ncls==0.0.68 +- # via +- # pyranges +- # scenicplus (pyproject.toml) +-ndindex==1.8 +- # via blosc2 +-networkx==3.2.1 +- # via +- # pyscenic +- # pyvis +- # scanpy +- # scenicplus (pyproject.toml) +- # scikit-image +-numba==0.59.0 +- # via +- # ctxcore +- # loompy +- # pynndescent +- # pyscenic +- # scanpy +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +- # scrublet +- # umap-learn +-numexpr==2.9.0 +- # via +- # pyscenic +- # scenicplus (pyproject.toml) +- # tables +-numpy==1.26.4 +- # via +- # adjusttext +- # anndata +- # arboreto +- # bbknn +- # blosc2 +- # bokeh +- # contourpy +- # ctxcore +- # dask +- # gensim +- # geosketch +- # gseapy +- # h5py +- # harmonypy +- # imageio +- # lda +- # loompy +- # loomxpy +- # macs2 +- # matplotlib +- # mizani +- # mudata +- # ncls +- # numba +- # numexpr +- # numpy-groupies +- # pandas +- # patsy +- # plotnine +- # pyarrow +- # pybedtools +- # pybigtools +- # pycistarget +- # pycistopic +- # pygam +- # pyrle +- # pyscenic +- # scanorama +- # scanpy +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +- # scikit-image +- # scikit-learn +- # scipy +- # scrublet +- # seaborn +- # sorted-nearest +- # statsmodels +- # tables +- # tifffile +- # tmtoolkit +- # tspex +- # umap-learn +-numpy-groupies==0.10.2 +- # via +- # loompy +- # scenicplus (pyproject.toml) +-openpyxl==3.1.2 +- # via tmtoolkit +-packaging==24.0 +- # via +- # anndata +- # bokeh +- # dask +- # distributed +- # marshmallow +- # matplotlib +- # plotly +- # ray +- # scanpy +- # scikit-image +- # snakemake +- # statsmodels +- # tables +-pandas==1.5.0 +- # via +- # anndata +- # arboreto +- # bbknn +- # bioservices +- # bokeh +- # ctxcore +- # dask +- # gseapy +- # harmonypy +- # loomxpy +- # mizani +- # mudata +- # plotnine +- # pybiomart +- # pycistarget +- # pycistopic +- # pyranges +- # pyrle +- # pyscenic +- # scanpy +- # scenicplus (pyproject.toml) +- # scrublet +- # seaborn +- # statsmodels +- # tmtoolkit +- # tspex +-parso==0.8.3 +- # via jedi +-partd==1.4.1 +- # via dask +-patsy==0.5.6 +- # via +- # plotnine +- # scanpy +- # statsmodels +-pexpect==4.9.0 +- # via +- # easydev +- # ipython +-pillow==10.2.0 +- # via +- # bokeh +- # imageio +- # matplotlib +- # scikit-image +-plac==1.4.3 +- # via yte +-platformdirs==4.2.0 +- # via +- # easydev +- # jupyter-core +- # requests-cache +-plotly==5.19.0 +- # via scenicplus (pyproject.toml) +-plotnine==0.12.4 +- # via scenicplus (pyproject.toml) +-polars==0.20.13 +- # via +- # pycistopic +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +-progressbar2==4.4.2 +- # via pygam +-prompt-toolkit==3.0.43 +- # via ipython +-protobuf==5.26.0 +- # via ray +-psutil==5.9.8 +- # via +- # distributed +- # snakemake +-ptyprocess==0.7.0 +- # via pexpect +-pulp==2.8.0 +- # via snakemake +-pure-eval==0.2.2 +- # via stack-data +-py-cpuinfo==9.0.0 +- # via +- # blosc2 +- # tables +-pyarrow==15.0.0 +- # via +- # ctxcore +- # dask +- # pycistopic +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +-pyarrow-hotfix==0.6 +- # via +- # dask +- # scenicplus (pyproject.toml) +-pybedtools==0.9.1 +- # via scenicplus (pyproject.toml) +-pybigtools==0.1.2 +- # via +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +-pybigwig==0.3.22 +- # via +- # scatac-fragment-tools +- # scenicplus (pyproject.toml) +-pybiomart==0.2.0 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-pycistarget @ git+https://github.com/aertslab/pycistarget +- # via scenicplus (pyproject.toml) +-pycistopic @ git+https://github.com/aertslab/pycisTopic +- # via scenicplus (pyproject.toml) +-pyfasta==0.5.2 +- # via scenicplus (pyproject.toml) +-pygam==0.9.0 +- # via scenicplus (pyproject.toml) +-pygments==2.17.2 +- # via +- # ipython +- # rich +-pynndescent==0.5.11 +- # via +- # bbknn +- # umap-learn +-pyparsing==3.1.2 +- # via matplotlib +-pyranges==0.0.111 +- # via +- # pycistarget +- # pycistopic +- # scenicplus (pyproject.toml) +-pyrle==0.0.39 +- # via +- # pyranges +- # scenicplus (pyproject.toml) +-pysam==0.22.0 +- # via +- # pybedtools +- # scenicplus (pyproject.toml) +-pyscenic @ git+https://github.com/aertslab/pySCENIC@master +- # via +- # loomxpy +- # pycistopic +- # scenicplus (pyproject.toml) +-python-dateutil==2.9.0.post0 +- # via +- # matplotlib +- # pandas +-python-utils==3.8.2 +- # via progressbar2 +-pytz==2024.1 +- # via pandas +-pyvis==0.3.2 +- # via scenicplus (pyproject.toml) +-pyyaml==6.0.1 +- # via +- # bokeh +- # conda-inject +- # ctxcore +- # dask +- # distributed +- # pyscenic +- # ray +- # snakemake +- # yte +-ray==2.9.3 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-referencing==0.34.0 +- # via +- # jsonschema +- # jsonschema-specifications +-requests==2.31.0 +- # via +- # bioservices +- # grequests +- # gseapy +- # pybiomart +- # pyscenic +- # ray +- # requests-cache +- # scenicplus (pyproject.toml) +- # snakemake +-requests-cache==1.2.0 +- # via +- # bioservices +- # pybiomart +- # scenicplus (pyproject.toml) +-reretry==0.11.8 +- # via +- # snakemake +- # snakemake-interface-storage-plugins +-rich==13.7.1 +- # via rich-argparse +-rich-argparse==1.4.0 +- # via scatac-fragment-tools +-rpds-py==0.18.0 +- # via +- # jsonschema +- # referencing +-scanorama==1.7.4 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-scanpy==1.8.2 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-scatac-fragment-tools==0.1.0 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-scikit-image==0.22.0 +- # via +- # scenicplus (pyproject.toml) +- # scrublet +-scikit-learn==1.3.2 +- # via +- # arboreto +- # bbknn +- # geosketch +- # harmonypy +- # loomxpy +- # pycistarget +- # pycistopic +- # pynndescent +- # pyscenic +- # scanorama +- # scanpy +- # scenicplus (pyproject.toml) +- # scrublet +- # umap-learn +-scipy==1.12.0 +- # via +- # adjusttext +- # anndata +- # arboreto +- # bbknn +- # gensim +- # gseapy +- # harmonypy +- # loompy +- # mizani +- # plotnine +- # pygam +- # pynndescent +- # pyscenic +- # scanorama +- # scanpy +- # scenicplus (pyproject.toml) +- # scikit-image +- # scikit-learn +- # scrublet +- # statsmodels +- # tmtoolkit +- # umap-learn +-scrublet==0.2.3 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-seaborn==0.13.2 +- # via +- # pycistopic +- # scanpy +- # scenicplus (pyproject.toml) +-sinfo==0.3.4 +- # via scanpy +-six==1.16.0 +- # via +- # asttokens +- # patsy +- # pybedtools +- # python-dateutil +- # url-normalize +-smart-open==6.4.0 +- # via +- # gensim +- # snakemake +-smmap==5.0.1 +- # via gitdb +-snakemake==8.5.5 +- # via scenicplus (pyproject.toml) +-snakemake-interface-common==1.17.1 +- # via +- # scenicplus (pyproject.toml) +- # snakemake +- # snakemake-interface-executor-plugins +- # snakemake-interface-report-plugins +- # snakemake-interface-storage-plugins +-snakemake-interface-executor-plugins==8.2.0 +- # via +- # scenicplus (pyproject.toml) +- # snakemake +-snakemake-interface-report-plugins==1.0.0 +- # via +- # scenicplus (pyproject.toml) +- # snakemake +-snakemake-interface-storage-plugins==3.1.1 +- # via +- # scenicplus (pyproject.toml) +- # snakemake +-sorted-nearest==0.0.39 +- # via pyranges +-sortedcontainers==2.4.0 +- # via +- # distributed +- # intervaltree +-soupsieve==2.5 +- # via beautifulsoup4 +-stack-data==0.6.3 +- # via ipython +-statistics==1.0.3.5 +- # via scenicplus (pyproject.toml) +-statsmodels==0.14.1 +- # via +- # plotnine +- # pycistopic +- # scanpy +- # scenicplus (pyproject.toml) +-stdlib-list==0.10.0 +- # via sinfo +-stopit==1.1.2 +- # via snakemake +-suds-community==1.1.2 +- # via bioservices +-tables==3.9.2 +- # via scanpy +-tabulate==0.9.0 +- # via +- # pyranges +- # pyrle +- # snakemake +-tblib==3.0.0 +- # via distributed +-tenacity==8.2.3 +- # via plotly +-texttable==1.7.0 +- # via igraph +-threadpoolctl==3.4.0 +- # via scikit-learn +-throttler==1.2.2 +- # via +- # snakemake +- # snakemake-interface-executor-plugins +- # snakemake-interface-storage-plugins +-tifffile==2024.2.12 +- # via scikit-image +-tmtoolkit==0.12.0 +- # via +- # pycistopic +- # scenicplus (pyproject.toml) +-toolz==0.12.1 +- # via +- # cytoolz +- # dask +- # distributed +- # partd +-toposort==1.10 +- # via snakemake +-tornado==6.4 +- # via +- # bokeh +- # distributed +-tqdm==4.66.2 +- # via +- # bioservices +- # ctxcore +- # pyscenic +- # scanpy +- # scenicplus (pyproject.toml) +- # umap-learn +-traitlets==5.14.2 +- # via +- # ipython +- # jupyter-core +- # matplotlib-inline +- # nbformat +-tspex==0.6.3 +- # via scenicplus (pyproject.toml) +-typing==3.7.4.3 +- # via scenicplus (pyproject.toml) +-typing-extensions==4.10.0 +- # via +- # python-utils +- # typing-inspect +-typing-inspect==0.9.0 +- # via dataclasses-json +-umap-learn==0.5.5 +- # via +- # bbknn +- # pyscenic +- # scanpy +- # scenicplus (pyproject.toml) +- # scrublet +-url-normalize==1.4.3 +- # via requests-cache +-urllib3==2.2.1 +- # via +- # distributed +- # requests +- # requests-cache +-wcwidth==0.2.13 +- # via prompt-toolkit +-wheel==0.43.0 +- # via tmtoolkit +-wrapt==1.16.0 +- # via +- # bioservices +- # snakemake +- # snakemake-interface-storage-plugins +-xlrd==2.0.1 +- # via +- # tmtoolkit +- # tspex +-xmltodict==0.13.0 +- # via bioservices +-xyzservices==2023.10.1 +- # via bokeh +-yarl==1.9.4 +- # via aiohttp +-yte==1.5.4 +- # via snakemake +-zict==3.0.0 +- # via distributed +-zipp==3.18.1 +- # via importlib-metadata +-zope-event==5.0 +- # via gevent +-zope-interface==6.2 +- # via gevent +- +-# The following packages are considered to be unsafe in a requirements file: +-# setuptools ++adjusttext ++anndata ++annoy ++arboreto ++attr ++attrs ++bbknn ++beautifulsoup4 ++bs4 ++ctxcore ++cytoolz ++dask ++dill ++gensim ++gseapy ++h5py ++harmonypy ++igraph ++imageio ++importlib-metadata ++importlib-resources ++intervaltree ++joblib ++kaleido ++lda ++leidenalg ++loomxpy ++lxml ++macs2 ++matplotlib ++mudata ++ncls ++networkx ++numba ++numexpr ++numpy ++numpy-groupies ++pandas ++plotly ++plotnine ++polars ++pyarrow ++pybedtools ++pybigtools ++pybigwig ++pybiomart ++pycistarget ++pycistopic ++pyfasta ++pygam ++pyranges ++pyrle ++pysam ++pyscenic ++pyvis ++ray ++requests ++requests-cache ++scanorama ++scanpy ++scatac-fragment-tools ++scikit-image ++scikit-learn ++scipy ++scrublet ++seaborn ++snakemake ++snakemake-interface-common ++snakemake-interface-executor-plugins ++snakemake-interface-report-plugins ++snakemake-interface-storage-plugins ++statistics ++statsmodels ++tmtoolkit ++tqdm ++tspex ++umap-learn diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb new file mode 100644 index 00000000000..5b6d65b6bb4 --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'scrublet' +version = '0.2.3' + +homepage = 'https://github.com/swolock/scrublet' +description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 7978e63207611c999dfe391a1aaaaf2b3a376975 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 29 Jul 2024 14:48:04 +0200 Subject: [PATCH 106/553] Delete easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch --- .../cuda-samples-11.X_multiple-sms.patch | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch deleted file mode 100644 index b6613f6a3c4..00000000000 --- a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch +++ /dev/null @@ -1,31 +0,0 @@ -# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" -# fatal compilation issue when building for multiple SM architectures -# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 - -# Author: Caspar van Leeuwen - -diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile ---- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 -+++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 -@@ -321,6 +321,12 @@ - ifneq ($(HIGHEST_SM),) - GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) - endif -+ -+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there -+LOWEST_SM := $(firstword $(sort $(SMS))) -+ifneq ($(LOWEST_SM),) -+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) -+endif - endif - - ifeq ($(TARGET_OS),darwin) -@@ -401,7 +407,7 @@ - endif - - $(PTX_FILE): memMapIpc_kernel.cu -- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< -+ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< - $(EXEC) mkdir -p data - $(EXEC) cp -f $@ ./data - $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) From faf3cc66560d16cf312022ce3be0afbc27fdfdcc Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 29 Jul 2024 14:48:14 +0200 Subject: [PATCH 107/553] Delete easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch --- .../cuda-samples-12.X_multiple-sms.patch | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch deleted file mode 100644 index 8c4e36f7e74..00000000000 --- a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch +++ /dev/null @@ -1,56 +0,0 @@ -# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" -# fatal compilation issue when building for multiple SM architectures -# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 - -# Author: Caspar van Leeuwen - -diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile ---- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 -+++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 -@@ -313,6 +313,12 @@ - ifneq ($(HIGHEST_SM),) - GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) - endif -+ -+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there -+LOWEST_SM := $(firstword $(sort $(SMS))) -+ifneq ($(LOWEST_SM),) -+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) -+endif - endif - - ifeq ($(TARGET_OS),darwin) -@@ -394,7 +400,7 @@ - endif - - $(PTX_FILE): memMapIpc_kernel.cu -- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< -+ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< - $(EXEC) mkdir -p data - $(EXEC) cp -f $@ ./data - $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) -diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile ---- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 -+++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 -@@ -307,6 +307,12 @@ - ifneq ($(HIGHEST_SM),) - GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) - endif -+ -+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there -+LOWEST_SM := $(firstword $(sort $(SMS))) -+ifneq ($(LOWEST_SM),) -+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) -+endif - endif - - ifeq ($(TARGET_OS),darwin) -@@ -390,7 +396,7 @@ - endif - - $(PTX_FILE): ptxjit_kernel.cu -- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< -+ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< - $(EXEC) mkdir -p data - $(EXEC) cp -f $@ ./data - $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) From d1a7b5e14e79bdedaf6da84fe3ff9fbef1ca8aeb Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 29 Jul 2024 15:08:48 +0200 Subject: [PATCH 108/553] Fix checksum --- .../CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb index 092528fda97..89e1c6fc87b 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['cuda-samples-11.6_multiple-sms.patch'] -checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466'] +checksums = [ + {'v12.2.tar.gz': '1823cfe28e97a9230107aa72b231f78952c0f178b71a920f036d360518480bdc'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] builddependencies = [ ('CMake', '3.24.3'), From 4691ffca1960536051e69bb74e71f22b218caa3e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 15:11:00 +0200 Subject: [PATCH 109/553] add patch description --- .../s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb | 2 +- .../scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb index c536bd85bc5..9b94d6619f9 100644 --- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb @@ -258,7 +258,7 @@ exts_list = [ {'scenicplus-1.0a1-18072024-fa55dae.tar.gz': '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'}, {'scenicplus-1.0a1-18072024_requirements.txt.patch': - 'fdfba5d9413f6088d657e315ce7aa28cd645154521e9173a7325bd6c4fdd7e7a'}, + 'e39f643872263bcfa305c6483d125bde9ebf9ef3bd146247aa9b924c2ac76c56'}, ], }), ] diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch index ecfeed15e29..3a565b2a10d 100644 --- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch +++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch @@ -1,3 +1,4 @@ +Fix requirements.txt and unpin exact versions --- requirements.txt.orig 2024-07-24 10:54:46.267978000 +0200 +++ requirements.txt 2024-07-24 12:06:31.676022842 +0200 @@ -1,918 +1,77 @@ From e99bfd0d4c27bac671a57371e804961b37985b9b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 29 Jul 2024 15:41:01 +0200 Subject: [PATCH 110/553] Fix checksum --- .../CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 5 ++++- .../CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 5 ++++- .../CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 5 ++++- .../CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 5 ++++- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index 7c19b967f55..ad7b6aba80b 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['cuda-samples-11.3_multiple-sms.patch'] -checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] +checksums = [ + {'v11.3.tar.gz': '2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'}, + {'cuda-samples-11.3_multiple-sms.patch': 'b31613f4160456f0d0abf82999c7fb7eee781f0efadc8b9bbb5a02ef0f37e21d'}, +] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index 1411d458852..ea78eae4061 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['cuda-samples-11.6_multiple-sms.patch'] -checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] +checksums = [ + {'v11.6.tar.gz': '75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb index db2b3fe617c..be16c76f3be 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['cuda-samples-11.6_multiple-sms.patch'] -checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'] +checksums = [ + {'v11.8.tar.gz': '1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index d18522518c8..5a886ca74d4 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['cuda-samples-11.6_multiple-sms.patch'] -checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] +checksums = [ + {'v12.1.tar.gz': 'f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), From b57330039d2066726c3d4a026108d26577c92eec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Jul 2024 14:54:28 +0100 Subject: [PATCH 111/553] Fix section spacing --- .../b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb index 12802801834..2c2bbf6705b 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -3,6 +3,7 @@ easyblock = 'CMakeMake' name = 'beagle-lib' version = '4.0.1' versionsuffix = '-CUDA-%(cudaver)s' + homepage = 'https://github.com/beagle-dev/beagle-lib' description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.""" From bf491029d92dbe570bb839c09525c2e30a35e521 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 16:12:02 +0200 Subject: [PATCH 112/553] adding easyconfigs: RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb, SOCI-4.0.3-GCC-12.3.0.eb --- ...023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 120 ++++++++++++++++++ .../s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb | 52 ++++++++ 2 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb new file mode 100644 index 00000000000..54037456dd8 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb @@ -0,0 +1,120 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = "2023.09.1+494" +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = 'cd7011dce393115d3a7c3db799dda4b1c7e88711' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['38526a5816e980b12aeaef7debd2151f08ef2e54fed83af2622eb7cdeeb479a2'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.3.2'), + ('SOCI', '4.0.3'), # CREATED OK + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-packages", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +modloadmsg = """ +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +moduleclass = 'lang' + +# ERROR1: + # -> use version 2023.09.1+494 commit: cd7011dce393115d3a7c3db799dda4b1c7e88711 -> req boost 1.78.0 + # https://github.com/rstudio/rstudio/blob/v2023.09.1%2B494/dependencies/common/install-boost + # CMake Error at /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message): + # Could NOT find Boost: Found unsuitable version "1.82.0", but required is at + # least "1.83.0" (found + # /apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include, ) + # Call Stack (most recent call first): + # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:598 (_FPHSA_FAILURE_MESSAGE) + # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindBoost.cmake:2377 (find_package_handle_standard_args) + # src/cpp/CMakeLists.txt:296 (find_package) diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..e100da22edb --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('SQLite', '3.42.0'), + ('PostgreSQL', '16.1'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' From 1b4c1915919fc8b75ed79d0458387c369c327537 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 16:52:02 +0200 Subject: [PATCH 113/553] clean ec from comments --- ...erver-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb index 54037456dd8..c4c3d741b5e 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb @@ -106,15 +106,3 @@ and then used with: """ moduleclass = 'lang' - -# ERROR1: - # -> use version 2023.09.1+494 commit: cd7011dce393115d3a7c3db799dda4b1c7e88711 -> req boost 1.78.0 - # https://github.com/rstudio/rstudio/blob/v2023.09.1%2B494/dependencies/common/install-boost - # CMake Error at /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message): - # Could NOT find Boost: Found unsuitable version "1.82.0", but required is at - # least "1.83.0" (found - # /apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include, ) - # Call Stack (most recent call first): - # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:598 (_FPHSA_FAILURE_MESSAGE) - # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindBoost.cmake:2377 (find_package_handle_standard_args) - # src/cpp/CMakeLists.txt:296 (find_package) From b2ae8a6ba2cbfff86c088abd7f8e6b868af440b8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 29 Jul 2024 16:54:15 +0200 Subject: [PATCH 114/553] Update RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb delete comments --- .../RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb index c4c3d741b5e..020dde50a43 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb @@ -36,7 +36,7 @@ dependencies = [ ('Boost', '1.82.0'), ('Java', '11', '', SYSTEM), ('R', '4.3.2'), - ('SOCI', '4.0.3'), # CREATED OK + ('SOCI', '4.0.3'), ('yaml-cpp', '0.7.0'), ] From 434a5ab03dc9f4367f686edfc6e66c30fbe5f965 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jul 2024 17:02:27 +0200 Subject: [PATCH 115/553] adding easyconfigs: nanopolish-0.14.0-foss-2023a.eb, VBZ-Compression-1.0.3-gompi-2023a.eb --- .../nanopolish-0.14.0-foss-2023a.eb | 61 +++++++++++++++++++ .../VBZ-Compression-1.0.3-gompi-2023a.eb | 43 +++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb new file mode 100644 index 00000000000..d32ee79a46a --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.14.0' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + { + 'source_urls': ['https://github.com/jts/nanopolish/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'], + 'download_filename': 'v1.1.0.tar.gz', + 'filename': 'slow5lib-v1.1.0.tar.gz', + }, +] +checksums = [ + {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'}, + {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'}, +] + +builddependencies = [('Eigen', '3.4.0')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('HDF5', '1.14.0'), + ('HTSlib', '1.18'), + ('minimap2', '2.26'), + ('VBZ-Compression', '1.0.3'), +] + +prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb new file mode 100644 index 00000000000..3a3c79f3875 --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.3' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'}, + {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' From 661d543e08e36b2be5063e6196d091f6fff681fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 29 Jul 2024 20:06:39 +0200 Subject: [PATCH 116/553] adding easyconfigs: GLib-2.80.4-GCCcore-13.3.0.eb --- .../g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f95eacd4a7b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.80.4' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['24e029c5dfc9b44e4573697adf33078a9827c48938555004b3b9096fa4ea034f'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('gettext', '0.22.5'), + ('libxml2', '2.12.7'), + ('PCRE2', '10.43'), + ('util-linux', '2.40'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' From f2c5b9e3873f959b022e10c5978bd7ce4e92d66a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 29 Jul 2024 20:13:39 +0200 Subject: [PATCH 117/553] adding easyconfigs: parallel-20240722-GCCcore-13.3.0.eb --- .../parallel-20240722-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..92658cc24b7 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20240722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Perl', '5.38.2')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' From e13a2b443c46d1a3d3eddcf6a2119ad870693cbf Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 29 Jul 2024 20:32:35 +0200 Subject: [PATCH 118/553] adding easyconfigs: cairo-1.18.0-GCCcore-13.3.0.eb, pixman-0.43.4-GCCcore-13.3.0.eb --- .../c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb | 51 +++++++++++++++++++ .../p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb | 30 +++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2622f010126 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.18.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('pixman', '0.43.4'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('X11', '20240607'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b15cf9f2ef6 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'pixman' +version = '0.43.4' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0624db90180c7ddb79fc7a9151093dc37c646d8c38d3f232f767cf64b85a226'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From a0a182de1ef88dfc06a346e4a8b55c4155f949b8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 30 Jul 2024 15:41:57 +0200 Subject: [PATCH 119/553] adding easyconfigs: wradlib-2.0.3-foss-2023a.eb --- .../w/wradlib/wradlib-2.0.3-foss-2023a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb new file mode 100644 index 00000000000..c347e7280c7 --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('xarray', '2023.9.0'), + ('Cartopy', '0.22.0'), + ('dask', '2023.9.2'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.14.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'checksums': ['b71021164b005f3270afd2079b8ed831a01ed43accbb7fc42c79e31a342546c5'], + }), + (name, version, { + 'checksums': ['0d5448a1dd0e030bdd36f7bbc69fa50aee7fb74dbc7b6407d2dc52d18ea40c49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 8de3b0c38f0edcd1b043b6741402129887cd0aa2 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Wed, 31 Jul 2024 07:08:39 +0100 Subject: [PATCH 120/553] Update easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb Co-authored-by: Sam Moors --- .../s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb index 5893038d9fd..9f26cade5d3 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb @@ -29,10 +29,7 @@ exts_list = [ ('pyproject_metadata', '0.8.0', { 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], }), - (name, version, { - 'modulename': 'spglib', - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'], - 'sources': ['spglib-%(version)s.tar.gz'], + ('spglib', version, { 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], }), ] From fa3863f056f8364298c9d080bb6bbbc6e624c25c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 31 Jul 2024 17:31:03 +0200 Subject: [PATCH 121/553] adding easyconfigs: timm-1.0.8-foss-2023a-CUDA-12.1.1.eb --- .../timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 137 ++++++++++++++++++ 1 file changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7c284c62cfe --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,137 @@ +easyblock = 'CargoPythonBundle' + +name = 'timm' +version = '1.0.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0', versionsuffix), + +] + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0'), # for safetensors + ('PDM', '2.12.4'), +] + +crates = [ + ('autocfg', '1.2.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('heck', '0.4.1'), + ('indoc', '2.0.5'), + ('itoa', '1.0.11'), + ('libc', '0.2.153'), + ('lock_api', '0.4.11'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.80'), + ('pyo3', '0.21.1'), + ('pyo3-build-config', '0.21.1'), + ('pyo3-ffi', '0.21.1'), + ('pyo3-macros', '0.21.1'), + ('pyo3-macros-backend', '0.21.1'), + ('quote', '1.0.36'), + ('redox_syscall', '0.4.1'), + ('ryu', '1.0.17'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.115'), + ('smallvec', '1.13.2'), + ('syn', '2.0.59'), + ('target-lexicon', '0.12.14'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] + + +sources = [SOURCE_TAR_GZ] +checksums = [ + {'timm-1.0.8.tar.gz': 'f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'}, + {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, + {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'}, + {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'}, + {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'}, + {'memmap2-0.9.4.tar.gz': 'fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322'}, + {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, + {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.80.tar.gz': 'a56dea16b0a29e94408b9aa5e2940a4eedbd128a1ba20e8f7ae60fd3d465af0e'}, + {'pyo3-0.21.1.tar.gz': 'a7a8b1990bd018761768d5e608a13df8bd1ac5f678456e0f301bb93e5f3ea16b'}, + {'pyo3-build-config-0.21.1.tar.gz': '650dca34d463b6cdbdb02b1d71bfd6eb6b6816afc708faebb3bac1380ff4aef7'}, + {'pyo3-ffi-0.21.1.tar.gz': '09a7da8fc04a8a2084909b59f29e1b8474decac98b951d77b80b26dc45f046ad'}, + {'pyo3-macros-0.21.1.tar.gz': '4b8a199fce11ebb28e3569387228836ea98110e43a804a530a9fd83ade36d513'}, + {'pyo3-macros-backend-0.21.1.tar.gz': '93fbbfd7eb553d10036513cb122b888dcd362a945a00b06c165f2ab480d4cc3b'}, + {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, + {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'}, + {'serde_json-1.0.115.tar.gz': '12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'syn-2.0.59.tar.gz': '4a6531ffc7b071655e4ce2e04bd464c4830bb585a61cabb96cf808f05172615a'}, + {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + ('safetensors', '0.4.3', { + 'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From ccbd3bd18cb3bf1a8ebd0ec05dadc4afb2134dfd Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 31 Jul 2024 18:05:11 +0200 Subject: [PATCH 122/553] remove whitespace --- .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index 7c284c62cfe..998631b3eed 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -20,8 +20,7 @@ dependencies = [ ('PyTorch', '2.1.2', versionsuffix), ('PyYAML', '6.0'), ('tqdm', '4.66.1'), - ('torchvision', '0.16.0', versionsuffix), - + ('torchvision', '0.16.0', versionsuffix), ] builddependencies = [ From 5d139de05e2534935a8973c35d844988e97929aa Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 31 Jul 2024 18:28:55 +0200 Subject: [PATCH 123/553] adding easyconfigs: Tinker-8.11.3-foss-2023a.eb --- .../t/Tinker/Tinker-8.11.3-foss-2023a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb new file mode 100644 index 00000000000..32aa981f2ac --- /dev/null +++ b/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Tinker' +version = '8.11.3' + +homepage = 'https://dasher.wustl.edu/tinker' +description = """The Tinker molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +srcdir = 'cmake' + +# copy executables into bin directory +test_cmd = 'find -maxdepth 1 -mindepth 1 -type f -executable |xargs -I % cp % ../tinker/bin/ && ' +test_cmd += 'cd ../tinker/test/ && ' +# run all .run scripts in the /tinker/test directory +test_cmd += 'EC=0; for x in *.run; do echo "START TEST: $x"; ./$x || (EC=$? echo "FAILED TEST: $x"); done; exit $EC' + +# sanity_check_commands is not possible since all the programs require multiple other inputs + +moduleclass = 'chem' From f8b201473ce2dd6d2220b6b8d1e870b11953e690 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Wed, 31 Jul 2024 19:03:33 +0200 Subject: [PATCH 124/553] Update easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb --- .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index 998631b3eed..93f0d02792f 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('PyTorch', '2.1.2', versionsuffix), ('PyYAML', '6.0'), ('tqdm', '4.66.1'), - ('torchvision', '0.16.0', versionsuffix), + ('torchvision', '0.16.0', versionsuffix), ] builddependencies = [ From 55838830b9ec28356a7f106e55d4ecc94fe93688 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 31 Jul 2024 19:22:30 +0200 Subject: [PATCH 125/553] adding easyconfigs: CLANS-2.0.8-foss-2023a.eb --- .../c/CLANS/CLANS-2.0.8-foss-2023a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb new file mode 100644 index 00000000000..4d2d1d0eafe --- /dev/null +++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'CLANS' +version = '2.0.8' + +homepage = 'https://github.com/inbalpaz/CLANS' +description = """ +CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on +their sequence similarities. CLANS visualizes the dynamic clustering process and enables the +user to interactively control it and explore the cluster map in various ways. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('VisPy', '0.14.1'), + ('Biopython', '1.83'), + ('Pillow', '10.0.0'), + ('PyQt5', '5.15.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/inbalpaz/CLANS/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7b856ec3b13c420dbe30169e8cdd7d6899acb79042ca66920eafd05adf4d2815'], + }), +] + +sanity_check_commands = ['python -m clans -h'] + +moduleclass = 'vis' From 2159744f0d49f9748b839a9c15400ebeb17f8a01 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 31 Jul 2024 18:54:20 +0000 Subject: [PATCH 126/553] adding easyconfigs: HPL-2.3-foss-2024a.eb, gfbf-2024a.eb, gompi-2024a.eb, OSU-Micro-Benchmarks-7.4-gompi-2024a.eb, FFTW.MPI-3.3.10-gompi-2024a.eb, foss-2024a.eb, SciPy-bundle-2024.05-gfbf-2024a.eb, ScaLAPACK-2.2.0-gompi-2024a-fb.eb --- .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb | 19 ++++ easybuild/easyconfigs/f/foss/foss-2024a.eb | 28 ++++++ easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb | 20 ++++ easybuild/easyconfigs/g/gompi/gompi-2024a.eb | 20 ++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb | 21 ++++ .../OSU-Micro-Benchmarks-7.4-gompi-2024a.eb | 26 +++++ .../ScaLAPACK-2.2.0-gompi-2024a-fb.eb | 40 ++++++++ .../SciPy-bundle-2024.05-gfbf-2024a.eb | 97 +++++++++++++++++++ 8 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2024a.eb create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2024a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb new file mode 100644 index 00000000000..2ed420c412f --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2024a.eb b/easybuild/easyconfigs/f/foss/foss-2024a.eb new file mode 100644 index 00000000000..7e9a4ba5112 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb new file mode 100644 index 00000000000..51b74722cb5 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024a.eb b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb new file mode 100644 index 00000000000..c49f4050ff8 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb new file mode 100644 index 00000000000..8a70a42bb41 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb new file mode 100644 index 00000000000..0d9573028dd --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb new file mode 100644 index 00000000000..1bccc16f38b --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.4.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb new file mode 100644 index 00000000000..c140938671c --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 7a153d214bfca0dc62ff38ca785a17efc342d055 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 31 Jul 2024 19:04:39 +0000 Subject: [PATCH 127/553] {toolchain}[iimpi/2024a,system/system] Rename intel-2024.06 toolchain to 2024a --- .../h/HPL/{HPL-2.3-intel-2024.06.eb => HPL-2.3-intel-2024a.eb} | 2 +- .../easyconfigs/i/iimpi/{iimpi-2024.06.eb => iimpi-2024a.eb} | 2 +- ...4.2.0-iimpi-2024.06.eb => imkl-FFTW-2024.2.0-iimpi-2024a.eb} | 2 +- .../easyconfigs/i/intel/{intel-2024.06.eb => intel-2024a.eb} | 2 +- ...iimpi-2024.06.eb => OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb} | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.3-intel-2024.06.eb => HPL-2.3-intel-2024a.eb} (94%) rename easybuild/easyconfigs/i/iimpi/{iimpi-2024.06.eb => iimpi-2024a.eb} (95%) rename easybuild/easyconfigs/i/imkl-FFTW/{imkl-FFTW-2024.2.0-iimpi-2024.06.eb => imkl-FFTW-2024.2.0-iimpi-2024a.eb} (84%) rename easybuild/easyconfigs/i/intel/{intel-2024.06.eb => intel-2024a.eb} (97%) rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb => OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb} (92%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb similarity index 94% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb index ca7fc54ce2f..5544839d177 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2024.06'} +toolchain = {'name': 'intel', 'version': '2024a'} toolchainopts = {'usempi': True} source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb similarity index 95% rename from easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb index 82db31cd099..d6150133621 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb @@ -2,7 +2,7 @@ easyblock = 'Toolchain' name = 'iimpi' -version = '2024.06' +version = '2024a' homepage = 'https://software.intel.com/parallel-studio-xe' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb similarity index 84% rename from easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb rename to easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb index 7984030b590..b26ab65f452 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb @@ -4,7 +4,7 @@ version = '2024.2.0' homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' description = "FFTW interfaces using Intel oneAPI Math Kernel Library" -toolchain = {'name': 'iimpi', 'version': '2024.06'} +toolchain = {'name': 'iimpi', 'version': '2024a'} dependencies = [('imkl', version, '', SYSTEM)] diff --git a/easybuild/easyconfigs/i/intel/intel-2024.06.eb b/easybuild/easyconfigs/i/intel/intel-2024a.eb similarity index 97% rename from easybuild/easyconfigs/i/intel/intel-2024.06.eb rename to easybuild/easyconfigs/i/intel/intel-2024a.eb index 43a052dc1ea..7b08707e0fc 100644 --- a/easybuild/easyconfigs/i/intel/intel-2024.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2024a.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'intel' -version = '2024.06' +version = '2024a' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb index 6f36b886477..3122923be15 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb @@ -6,7 +6,7 @@ version = '7.4' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'iimpi', 'version': '2024.06'} +toolchain = {'name': 'iimpi', 'version': '2024a'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] From 230e702e1a3915600e98e1f021b0f7ef4a4501fb Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 1 Aug 2024 10:24:54 +0200 Subject: [PATCH 128/553] Use same 'VisPy' as other dependencies in '2023a' toolchain generation --- easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb index 4d2d1d0eafe..e1ce2f2a9e1 100644 --- a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('numba', '0.58.1'), - ('VisPy', '0.14.1'), + ('VisPy', '0.12.2'), ('Biopython', '1.83'), ('Pillow', '10.0.0'), ('PyQt5', '5.15.10'), From c404a40ced18408c5bc4d261cd86078f1e2ef029 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 1 Aug 2024 11:20:06 +0200 Subject: [PATCH 129/553] adding easyconfigs: submitit-1.2.0-foss-2023a.eb --- .../s/submitit/submitit-1.2.0-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb new file mode 100644 index 00000000000..0ce1edf2766 --- /dev/null +++ b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'submitit' +version = '1.2.0' + +homepage = 'https://github.com/facebookincubator/submitit' +description = """ +Submitit is a lightweight tool for submitting Python functions +for computation within a Slurm cluster. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('typing_extensions', '4.12.2', { + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + (name, version, { + 'checksums': ['16c099ed80943fbf942a7a37c6356a598b1f2b9d7ce40dd5fe058a6c7827e600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 500b7af459e843ca517e979e5bb8fb1ce5ddc33f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 1 Aug 2024 12:50:01 +0100 Subject: [PATCH 130/553] Description typo fix --- easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb index c347e7280c7..d53e56422bc 100644 --- a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb @@ -5,7 +5,7 @@ version = '2.0.3' homepage = 'https://docs.wradlib.org/' description = """ -The wradlib project has been initiated in order facilitate the use of weather +The wradlib project has been initiated in order to facilitate the use of weather radar data as well as to provide a common platform for research on new algorithms.""" From febcfade1effac79b1e24948a5fa79a5a95f7296 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 1 Aug 2024 14:07:52 +0200 Subject: [PATCH 131/553] fix issues --- .../t/Tinker/Tinker-8.11.3-foss-2023a.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb index 32aa981f2ac..ab73f098789 100644 --- a/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb @@ -22,9 +22,17 @@ srcdir = 'cmake' # copy executables into bin directory test_cmd = 'find -maxdepth 1 -mindepth 1 -type f -executable |xargs -I % cp % ../tinker/bin/ && ' test_cmd += 'cd ../tinker/test/ && ' -# run all .run scripts in the /tinker/test directory -test_cmd += 'EC=0; for x in *.run; do echo "START TEST: $x"; ./$x || (EC=$? echo "FAILED TEST: $x"); done; exit $EC' +# run all .run scripts in the test directory +# (ifabp succeeds but exits with a memory error) +test_cmd += 'for x in *.run; do echo "START TEST: $x" && ./$x; done' -# sanity_check_commands is not possible since all the programs require multiple other inputs +postinstallcmds = ['cd %(start_dir)s && cp -a params perl python %(installdir)s'] + +sanity_check_paths = { + 'files': ['lib/libtinker.a'], + 'dirs': ['bin', 'params', 'perl', 'python'], +} + +# (no sanity_check_commands since all programs require multiple other inputs) moduleclass = 'chem' From bbdf9cff5a7eda681987b3c96219d0afa39a3435 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 1 Aug 2024 16:56:16 +0200 Subject: [PATCH 132/553] use safetensors module --- .../timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 93 +------------------ 1 file changed, 1 insertion(+), 92 deletions(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index 93f0d02792f..d46060d9a6b 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -21,6 +21,7 @@ dependencies = [ ('PyYAML', '6.0'), ('tqdm', '4.66.1'), ('torchvision', '0.16.0', versionsuffix), + ('Safetensors', '1.4.3'), ] builddependencies = [ @@ -28,104 +29,12 @@ builddependencies = [ ('PDM', '2.12.4'), ] -crates = [ - ('autocfg', '1.2.0'), - ('bitflags', '1.3.2'), - ('cfg-if', '1.0.0'), - ('heck', '0.4.1'), - ('indoc', '2.0.5'), - ('itoa', '1.0.11'), - ('libc', '0.2.153'), - ('lock_api', '0.4.11'), - ('memmap2', '0.9.4'), - ('memoffset', '0.9.1'), - ('once_cell', '1.19.0'), - ('parking_lot', '0.12.1'), - ('parking_lot_core', '0.9.9'), - ('portable-atomic', '1.6.0'), - ('proc-macro2', '1.0.80'), - ('pyo3', '0.21.1'), - ('pyo3-build-config', '0.21.1'), - ('pyo3-ffi', '0.21.1'), - ('pyo3-macros', '0.21.1'), - ('pyo3-macros-backend', '0.21.1'), - ('quote', '1.0.36'), - ('redox_syscall', '0.4.1'), - ('ryu', '1.0.17'), - ('scopeguard', '1.2.0'), - ('serde', '1.0.197'), - ('serde_derive', '1.0.197'), - ('serde_json', '1.0.115'), - ('smallvec', '1.13.2'), - ('syn', '2.0.59'), - ('target-lexicon', '0.12.14'), - ('unicode-ident', '1.0.12'), - ('unindent', '0.2.3'), - ('windows-targets', '0.48.5'), - ('windows_aarch64_gnullvm', '0.48.5'), - ('windows_aarch64_msvc', '0.48.5'), - ('windows_i686_gnu', '0.48.5'), - ('windows_i686_msvc', '0.48.5'), - ('windows_x86_64_gnu', '0.48.5'), - ('windows_x86_64_gnullvm', '0.48.5'), - ('windows_x86_64_msvc', '0.48.5'), -] - - -sources = [SOURCE_TAR_GZ] -checksums = [ - {'timm-1.0.8.tar.gz': 'f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'}, - {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, - {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, - {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, - {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, - {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, - {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'}, - {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'}, - {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'}, - {'memmap2-0.9.4.tar.gz': 'fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322'}, - {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, - {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, - {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, - {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, - {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, - {'proc-macro2-1.0.80.tar.gz': 'a56dea16b0a29e94408b9aa5e2940a4eedbd128a1ba20e8f7ae60fd3d465af0e'}, - {'pyo3-0.21.1.tar.gz': 'a7a8b1990bd018761768d5e608a13df8bd1ac5f678456e0f301bb93e5f3ea16b'}, - {'pyo3-build-config-0.21.1.tar.gz': '650dca34d463b6cdbdb02b1d71bfd6eb6b6816afc708faebb3bac1380ff4aef7'}, - {'pyo3-ffi-0.21.1.tar.gz': '09a7da8fc04a8a2084909b59f29e1b8474decac98b951d77b80b26dc45f046ad'}, - {'pyo3-macros-0.21.1.tar.gz': '4b8a199fce11ebb28e3569387228836ea98110e43a804a530a9fd83ade36d513'}, - {'pyo3-macros-backend-0.21.1.tar.gz': '93fbbfd7eb553d10036513cb122b888dcd362a945a00b06c165f2ab480d4cc3b'}, - {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, - {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, - {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'}, - {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, - {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, - {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'}, - {'serde_json-1.0.115.tar.gz': '12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd'}, - {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, - {'syn-2.0.59.tar.gz': '4a6531ffc7b071655e4ce2e04bd464c4830bb585a61cabb96cf808f05172615a'}, - {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, - {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, - {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, - {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, - {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, - {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, - {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, - {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, - {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, - {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, - {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, -] - use_pip = True exts_list = [ ('huggingface_hub', '0.24.5', { 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], }), - ('safetensors', '0.4.3', { - 'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'], - }), (name, version, { 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], }), From 51e18c92424c8ece63c43ec5bd9f4014ea465324 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 1 Aug 2024 17:02:24 +0200 Subject: [PATCH 133/553] use safetensors module --- .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index d46060d9a6b..f0b67fec7c0 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -1,4 +1,4 @@ -easyblock = 'CargoPythonBundle' +easyblock = 'PythonBundle' name = 'timm' version = '1.0.8' From bf59190ce7f467186548c67005a24d378698b074 Mon Sep 17 00:00:00 2001 From: Alexander Salois Date: Thu, 1 Aug 2024 09:34:55 -0600 Subject: [PATCH 134/553] Restored attribution and added my own --- .../b/BayesTraits/BayesTraits-4.1.2-Linux.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb index b07ea0bb7a1..541dedf129e 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# Updated by +# Author: Alex Salois +# Research Cyberinfrastructure +# Montana State University + easyblock = "Tarball" name = 'BayesTraits' From 94a2311f410b10cf6f29c0ba56f50f519ff31fc2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 1 Aug 2024 18:39:21 +0200 Subject: [PATCH 135/553] adding easyconfigs: EvidentialGene-2023.07.15-gompi-2023a.eb, Exonerate-2.4.0-GCC-12.3.0.eb --- .../EvidentialGene-2023.07.15-gompi-2023a.eb | 40 ++++++++++++++++ .../e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb | 47 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb new file mode 100644 index 00000000000..c4ae0c4e12d --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2023.07.15' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4e57e85a280 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GLib', '2.77.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['share'], +} + +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + +moduleclass = 'bio' From dc345946f8e6cb42c8c0d059ce542443af488369 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 1 Aug 2024 18:59:39 +0200 Subject: [PATCH 136/553] adding easyconfigs: accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb --- ...ccelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7f6d595a7c5 --- /dev/null +++ b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'accelerate' +version = '0.33.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/huggingface/accelerate' +description = """A simple way to launch, train, and use PyTorch models on almost any device and +distributed configuration, automatic mixed precision (including fp8), +and easy-to-configure FSDP and DeepSpeed support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('Safetensors', '0.4.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.24.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'], + }), +] + +sanity_check_commands = ['accelerate test'] + +moduleclass = 'ai' From 50b0d544337de78be983633a502bed8a0f7503a4 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 1 Aug 2024 21:36:15 +0000 Subject: [PATCH 137/553] Fix download URLs for old Intel software (2018-23) Intel changed "irc_nas" to "IRC_NAS". Newer packages (2023.1+) already use that, but older ones need changing. Mirrors https://github.com/spack/spack/pull/43286 Fixes #21104 --- easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb | 2 +- .../i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb | 2 +- .../i/IntelPython/IntelPython-2.7.15-2019.2.066.eb | 2 +- .../easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb | 2 +- .../easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb | 2 +- .../easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb | 2 +- .../easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb | 2 +- ...kl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb | 2 +- .../i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb | 2 +- .../impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb | 2 +- .../impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 2 +- .../impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb | 2 +- .../impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb | 2 +- .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb | 2 +- .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb | 2 +- .../easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb | 2 +- .../impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 2 +- .../impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../i/impi/impi-2019.12.320-iccifort-2020.4.304.eb | 2 +- .../impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 2 +- .../impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb | 2 +- .../i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb | 2 +- .../easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb | 2 +- .../easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb | 2 +- .../easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb | 2 +- .../easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb | 2 +- .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb | 2 +- .../i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb | 2 +- .../i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb | 2 +- .../i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb | 2 +- .../i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb | 2 +- .../i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb | 2 +- .../i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb | 2 +- .../i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb | 2 +- .../i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb | 2 +- .../easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb | 4 ++-- .../easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb | 4 ++-- easybuild/easyconfigs/i/itac/itac-2021.2.0.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2021.5.0.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2021.6.0.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb | 2 +- 130 files changed, 140 insertions(+), 140 deletions(-) diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 24ce3fe1c31..2e121781a46 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index a9f9a888154..7b025287362 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb index 6a0d2fa4ece..cbcdab88d6e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15825/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15825/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb index 2a7de357e47..144362e2eb7 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17730/'] sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh'] checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb index 55354cc6e25..ec07e00e07e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18220/'] sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh'] checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb index 58235ccff90..34a2115a37c 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18730/'] sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh'] checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb index 187fcafa180..e6d811a03a0 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb @@ -11,7 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM source_urls = [ - 'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/'] + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19094/'] sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh'] checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb index b27635916ca..179e26005de 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15827/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15827/'] sources = ['inspector_%(version)s.tar.gz'] checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb index 11b56c0bc1c..494b031a5e1 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18239/'] sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh'] checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb index 430cc62b2d4..22f082dd1f4 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18363/'] sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb index a7772259cc8..33515e7a8e5 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18712/'] sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh'] checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e'] diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb index 55107c33e8a..c0357dea2d0 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -13,7 +13,7 @@ can be identified and practical resolutions provided. toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18359/'] sources = ['l_clck_p_%(version)s.560_offline.sh'] checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index c46f42bb81b..48ab0a8f836 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index fd51e3b2082..d0c2dc13c67 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index ca49a084587..f6eb99cebdc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index 9b3a071f005..c04b1a09909 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 3918ba3f3f1..f2d6c096878 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz'] checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index b78d2e8e11c..5cf05e6a559 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 7b37d3169dc..f2341a844c3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index f192fd17472..9f9b71a21df 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 65821a417db..2d194db100a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index 5cefbfc2dee..85453f37251 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15537/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index c080762f21d..b4eb6588ec7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15813/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb index a8f9c94588f..a21e15527d5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 70593480c69..4ad42c13a31 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb index 89d42319787..98e64dff918 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb index fbd8bc1719b..056539c7f76 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 66cf55bd0c0..2ce7d5ee7f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 8572f079dca..3bdc51210af 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 7668ec76749..3f9f1de0c45 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 3457239087d..453cf476095 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index c47117b085b..c6c03d9340f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 924762c6de2..5a043c03822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index b8eb911adc2..b996c679995 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb index 65486c1a522..1af220dba70 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 770acb76d87..a90fc9aaaac 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index f340d755ee2..c873144967b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 6ead35efc9a..89a3f33d184 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index 7f53145d6a3..450dc0082e2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index aeabee4d300..0fcf2f60e8e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index 02dba60737e..7d2dc1809af 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018.04'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13725/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index a382ae20ac7..d222e9cd3b3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13575/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb index aa6a03a6929..ae7e676174e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index e63cc1a2695..15e03750772 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 782473ec9fa..dcd07853ae8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb index b8fb1ebef4c..af64b61bfd7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 3a5e6baedc4..e7a42454f04 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index 645ffaf31a7..8cd693cc5ec 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.02'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15095/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index 2c06461ab97..8685b03cc91 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.03'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15275/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb index 3c2759d1539..940151b46dc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb index 3421505968c..91ca97f6bc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index d95d740ea28..61489356fe3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb index 62cf27a5251..b1e88a55dd3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb index 906ad9525cd..8e7d6fa5ec2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index 610ba004009..d27b6e67346 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16232/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb index dcb4894a2a4..d662fdae171 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb index 89aac0e1547..a683875dd81 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb index 3111a3509b0..aef431b9b6d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb index 3475dab254a..dbfbc356455 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb index 3eca90fc0a2..1f80ac1e253 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index 75ac380269e..71a9f0f37b9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'NVHPC', 'version': '21.2'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 541c3c12aea..1526523c788 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb index e07323d8ee3..570499af77d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index e1f7dd0c3fd..15ccb6b8c77 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index a350ab4a6ed..73aac3a85e7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 89d0c991d88..68e2a157d3d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb index 737f7462d7d..363e95f7dc9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2020.12'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/'] sources = ['l_onemkl_p_%(version)s.52_offline.sh'] checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb index ff7c13049ea..77a41fb58ed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb index aa8f14f2250..741b626f55c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb index 60282631f05..2bb82fd3380 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb index 07a876f213e..a4746816d23 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17901'] sources = ['l_onemkl_p_%(version)s.520_offline.sh'] checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb index a6e0651ef64..4f45be5badc 100755 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021b'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb index f3e3040b1ee..bacd9ba4607 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb index 67a5563ac0b..c348328e0e4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18444/'] sources = ['l_onemkl_p_%(version)s.117_offline.sh'] checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb index 2eb923c837e..955038d0fc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2022a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb index c34d533cf35..b0653443859 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb index 82776023871..a3c46807fc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18898/'] sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb index 3daf55958a3..f2a7a15068e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19038/'] sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb index 4e6e5afb344..f29032bc3dd 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19138/'] sources = ['l_onemkl_p_%(version)s.25398_offline.sh'] checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb index 5e4f3cb8b1d..5c8f63a0644 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2023a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 21ad001e53c..a0341a987d6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12405/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index e39879ac218..60f2eed4dd9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index f4e9e1a638f..0fc63f042f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 060befc0a5a..75004db76a8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e6c3602e1e3..d4574181af9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb index 137bf491a27..c28ff1e7e55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index 8f89b212fa4..4cb68a33fc8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb index 4c7b3a6b0df..e27d2ec5b55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb index 02e2ace8251..2f959f48e46 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 2f60b422703..77755c77620 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13584/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8e2ed0b3980..6a222b3ed18 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14879/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb index a5ba5409ff0..2bf8b19fb29 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 7cdc6aca429..5f75ad2ec68 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15040/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index c0b1f565c0a..cb1ec1f179c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15260/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb index e19a15d6e33..49f0fa7a8d7 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.0.166-GCC-9.2.0'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16120/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb index d0ad0188c0d..07f8323810c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb index 557e0a8eab1..8a5646c25c1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb index d4a9ef76ae4..d723d12dc1c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb index 3305cf60a8d..7082d103ec8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 1a0fbe3b035..d8a92d6db7e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/'] sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb index 345fd82fc3d..ecd3c9521f1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17729/'] sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh'] checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index 8a736821926..1507acd5413 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17947'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb index a0c8a98edd8..24180258119 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18186/'] sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb index bee00810199..ea941c35ab2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18370/'] sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb index b1d328caa62..288c103cd03 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18714/'] sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh'] checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb index 8f400fabac4..2df8a69062f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18926/'] sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb index 68aeb9beb63..aa2976fafaf 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19010/'] sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb index 86153bb28f5..89dce35e1f2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19131/'] sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh'] checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7'] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 820a237e44d..67a5c1f5701 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'], 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb index 4fe1af0da99..e4986d623f0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17749/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17756/'], 'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb index efcc5a7498b..cececeebef0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb @@ -12,11 +12,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17928/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17959/'], 'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb index b12d0b8bb3c..977bf5ced0e 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18209/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18210/'], 'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb index 56c8e9b5da4..967197cdfd7 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18435/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18436/'], 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb index b54023cfe84..011509935b0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18478/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18481/'], 'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb index f25617230ac..92ac06db492 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18717/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18703/'], 'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb index 17262278b13..8c1390dae95 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18849/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18909/'], 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb index a6ae8170105..e67292301d5 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19030/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998/'], 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb index 8d97d1ec3e5..f1e9b21f009 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19123/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19105/'], 'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index 3deaaa9e711..ea2cfcb2650 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17686/'] sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb index f9d10379c85..ea05e25db95 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18367/'] sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb index 22e6230e15b..0f35b870046 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18694/'] sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh'] checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index 0938ca5f98f..8f1db4ac725 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index bd9fed83da9..50053de3925 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15214/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb index 09f9e6b6120..1390fece377 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15703/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15703/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['7b2124123347bbb593d1b8f8cf858d88829a05605769cba5c39444b0aa545473'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb index b4c024b03be..ab1cb7c1ebc 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17095/'] sources = [{'download_filename': 'vtune_profiler_2020.tar.gz', 'filename': 'vtune_profiler_%(version)s.tar.gz'}] checksums = ['b22dd61d3931ca6ab7d96df2cf8648e5e1061ab2db13b8d42e3c87586b07c974'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb index 9b6582a6610..d33e54a7818 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18012/'] sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb index cd2356a18bb..b0f65557f62 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18302/'] sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh'] checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb index e205471e1e5..16f445c0f64 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18406/'] sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb index 773718fc442..458b8143c02 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18602/'] sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh'] checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb index b8a718b77b0..e2fea76fc3a 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18656/'] sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh'] checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6'] From 95f997a46634e0c5556aabd6f6afe7ab58ab6ff9 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 1 Aug 2024 23:13:13 +0000 Subject: [PATCH 138/553] Reset executable bit on imkl-2021.4.0-iompi-2021b.eb --- easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb old mode 100755 new mode 100644 From e3d07cb66c63d92fe6a4bfa3c4b81869d4bb9270 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Fri, 2 Aug 2024 08:22:06 +0200 Subject: [PATCH 139/553] Update easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb Co-authored-by: Kenneth Hoste --- .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index f0b67fec7c0..89d1e41675c 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -21,7 +21,7 @@ dependencies = [ ('PyYAML', '6.0'), ('tqdm', '4.66.1'), ('torchvision', '0.16.0', versionsuffix), - ('Safetensors', '1.4.3'), + ('Safetensors', '0.4.3'), ] builddependencies = [ From a3c654de099ba59750b7d5b149356af445438e19 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 2 Aug 2024 09:44:40 +0200 Subject: [PATCH 140/553] remove maturin as dependency --- .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb index 89d1e41675c..aadc225d0fa 100644 --- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -25,7 +25,6 @@ dependencies = [ ] builddependencies = [ - ('maturin', '1.4.0', '-Rust-1.75.0'), # for safetensors ('PDM', '2.12.4'), ] From 3175081ed25799d70d005ec8d288c832d69ca6f9 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Aug 2024 13:45:01 +0200 Subject: [PATCH 141/553] adding easyconfigs: Flye-2.9.4-GCC-13.2.0.eb --- .../f/Flye/Flye-2.9.4-GCC-13.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..c11373f69a1 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.4' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696'] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From e6a4d5c2ae6f73e90a8df2b396b9b8be05c86377 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 2 Aug 2024 13:58:18 +0200 Subject: [PATCH 142/553] adding easyconfigs: wradlib-2.0.3-foss-2022a.eb --- .../w/wradlib/wradlib-2.0.3-foss-2022a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb new file mode 100644 index 00000000000..9bec30a5545 --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.6.0'), + ('Cartopy', '0.20.3'), + ('dask', '2022.10.0'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.12.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0337b4a0798ded019b26e0746b7b7baeb6f21344a2a2e3704965049972ccbf51'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e2b625d10bc9b3ea2f33356fe467683b474c0a5410ff10ea6a708238d9172a10'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 66c6529e64dc49318f36f04df39d092a8ffcf403 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Fri, 2 Aug 2024 16:11:25 +0200 Subject: [PATCH 143/553] adding easyconfigs: Bandage-0.9.0-GCCcore-12.3.0.eb, GetOrganelle-1.7.7.1-foss-2023a.eb --- .../b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb | 30 +++++++++++++ .../GetOrganelle-1.7.7.1-foss-2023a.eb | 43 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..acdc093c96d --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Qt5', '5.15.10')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb new file mode 100644 index 00000000000..4c6746689d9 --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.7.1' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44'] + +dependencies = [ + ('Python', '3.11.3'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2023.07'), + ('sympy', '1.12'), + ('SPAdes', '3.15.4'), + ('Bowtie2', '2.5.1'), + ('BLAST+', '2.14.1'), + ('Perl', '5.36.1'), + ('matplotlib', '3.7.2') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 2778f5c2589460252f5400c61bbec8656dc53a6a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Aug 2024 16:31:57 +0200 Subject: [PATCH 144/553] replace patch by sed in scenic+ --- .../scenicplus-1.0a1-18072024-foss-2023a.eb | 17 +- ...plus-1.0a1-18072024_requirements.txt.patch | 999 ------------------ 2 files changed, 12 insertions(+), 1004 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb index 9b94d6619f9..37f4c7d76b3 100644 --- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb @@ -53,6 +53,17 @@ dependencies = [ ('gensim', '4.3.2'), ] +# fix requirements.txt of scenicplus +local_preinstallopts = ( + "sed -i" + " -e '/typing==3.7.4.3/d'" + " -e 's/==.*//g'" + " -e '/pyarrow-hotfix/d'" + " -e '/line-profiler/d'" + " -e '/ndindex/d'" + " -e '/sinfo/d'" + " requirements.txt && " +) # unpin version restriction and delete typing requirement local_pycistopic_preinstallopts = ( "sed -i" @@ -249,16 +260,12 @@ exts_list = [ 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], }), (name, version, { - 'patches': [ - 'scenicplus-1.0a1-18072024_requirements.txt.patch', - ], + 'preinstallopts': local_preinstallopts, 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], 'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}], 'checksums': [ {'scenicplus-1.0a1-18072024-fa55dae.tar.gz': '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'}, - {'scenicplus-1.0a1-18072024_requirements.txt.patch': - 'e39f643872263bcfa305c6483d125bde9ebf9ef3bd146247aa9b924c2ac76c56'}, ], }), ] diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch deleted file mode 100644 index 3a565b2a10d..00000000000 --- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch +++ /dev/null @@ -1,999 +0,0 @@ -Fix requirements.txt and unpin exact versions ---- requirements.txt.orig 2024-07-24 10:54:46.267978000 +0200 -+++ requirements.txt 2024-07-24 12:06:31.676022842 +0200 -@@ -1,918 +1,77 @@ --# --# This file is autogenerated by pip-compile with Python 3.11 --# by the following command: --# --# pip-compile --output-file=requirements.txt pyproject.toml --# --adjusttext==1.0.4 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --aiohttp==3.9.3 -- # via pyscenic --aiosignal==1.3.1 -- # via -- # aiohttp -- # ray --anndata==0.10.5.post1 -- # via -- # mudata -- # scanpy -- # scenicplus (pyproject.toml) --annoy==1.17.3 -- # via -- # bbknn -- # scanorama -- # scenicplus (pyproject.toml) -- # scrublet --appdirs==1.4.4 -- # via -- # bioservices -- # snakemake --arboreto==0.1.6 -- # via -- # pyscenic -- # scenicplus (pyproject.toml) --argparse-dataclass==2.0.0 -- # via -- # snakemake-interface-common -- # snakemake-interface-executor-plugins --array-api-compat==1.5.1 -- # via anndata --asttokens==2.4.1 -- # via stack-data --attr==0.3.2 -- # via scenicplus (pyproject.toml) --attrs==23.2.0 -- # via -- # aiohttp -- # cattrs -- # jsonschema -- # pyscenic -- # referencing -- # requests-cache -- # scenicplus (pyproject.toml) --bbknn==1.6.0 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --beautifulsoup4==4.12.3 -- # via -- # bioservices -- # bs4 -- # scenicplus (pyproject.toml) --bidict==0.23.1 -- # via tmtoolkit --bioservices==1.11.2 -- # via gseapy --blosc2==2.5.1 -- # via tables --bokeh==3.4.0 -- # via dask --boltons==23.1.1 -- # via pyscenic --bs4==0.0.2 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --cattrs==23.2.3 -- # via requests-cache --certifi==2024.2.2 -- # via requests --charset-normalizer==3.3.2 -- # via requests --click==8.1.7 -- # via -- # dask -- # distributed -- # loompy -- # loomxpy -- # ray --cloudpickle==3.0.0 -- # via -- # dask -- # distributed -- # pyscenic --colorama==0.4.6 -- # via easydev --colorlog==6.8.2 -- # via -- # bioservices -- # easydev --conda-inject==1.3.1 -- # via snakemake --configargparse==1.7 -- # via -- # snakemake -- # snakemake-interface-common --connection-pool==0.0.3 -- # via snakemake --contourpy==1.2.0 -- # via -- # bokeh -- # matplotlib --ctxcore==0.2.0 -- # via -- # pycistarget -- # pyscenic -- # scenicplus (pyproject.toml) --cycler==0.12.1 -- # via matplotlib --cython==0.29.37 -- # via -- # bbknn -- # macs2 -- # pyranges -- # scenicplus (pyproject.toml) -- # scrublet --cytoolz==0.12.3 -- # via -- # ctxcore -- # pyscenic -- # scenicplus (pyproject.toml) --dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1 -- # via -- # arboreto -- # distributed -- # pyscenic -- # scenicplus (pyproject.toml) --dataclasses-json==0.6.4 -- # via loomxpy --datrie==0.8.2 -- # via snakemake --decorator==5.1.1 -- # via ipython --dill==0.3.8 -- # via -- # multiprocessing-on-dill -- # scenicplus (pyproject.toml) --distributed==2024.2.1 -- # via -- # arboreto -- # dask -- # pyscenic --docutils==0.20.1 -- # via -- # snakemake -- # statistics --dpath==2.1.6 -- # via -- # snakemake -- # yte --easydev==0.13.1 -- # via bioservices --et-xmlfile==1.1.0 -- # via openpyxl --executing==2.0.1 -- # via stack-data --fastjsonschema==2.19.1 -- # via nbformat --fbpca==1.0 -- # via -- # geosketch -- # scanorama --filelock==3.13.1 -- # via ray --fonttools==4.50.0 -- # via matplotlib --frozendict==2.4.0 -- # via -- # ctxcore -- # pyscenic --frozenlist==1.4.1 -- # via -- # aiohttp -- # aiosignal -- # ray --fsspec==2024.3.1 -- # via -- # dask -- # pyscenic --future==1.0.0 -- # via pybiomart --gensim==4.3.2 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --geosketch==1.2 -- # via scanorama --gevent==24.2.1 -- # via grequests --gitdb==4.0.11 -- # via gitpython --gitpython==3.1.42 -- # via snakemake --globre==0.1.5 -- # via tmtoolkit --greenlet==3.0.3 -- # via gevent --grequests==0.7.0 -- # via bioservices --gseapy==0.10.8 -- # via scenicplus (pyproject.toml) --h5py==3.10.0 -- # via -- # anndata -- # loompy -- # mudata -- # pycistarget -- # scanpy -- # scenicplus (pyproject.toml) --harmonypy==0.0.9 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --humanfriendly==10.0 -- # via snakemake --idna==3.6 -- # via -- # requests -- # yarl --igraph==0.11.4 -- # via -- # leidenalg -- # pycistopic -- # scenicplus (pyproject.toml) --imageio==2.34.0 -- # via -- # scenicplus (pyproject.toml) -- # scikit-image --immutables==0.20 -- # via snakemake --importlib-metadata==7.0.1 -- # via -- # dask -- # scenicplus (pyproject.toml) --importlib-resources==6.1.2 -- # via scenicplus (pyproject.toml) --interlap==0.2.7 -- # via pyscenic --intervaltree==3.1.0 -- # via -- # scanorama -- # scenicplus (pyproject.toml) --ipython==8.22.2 -- # via -- # pycistarget -- # pyvis --jedi==0.19.1 -- # via ipython --jinja2==3.1.3 -- # via -- # bokeh -- # dask -- # distributed -- # pyvis -- # snakemake --joblib==1.3.2 -- # via -- # gseapy -- # pynndescent -- # scanpy -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) -- # scikit-learn --jsonpickle==3.0.3 -- # via pyvis --jsonschema==4.21.1 -- # via -- # nbformat -- # ray -- # snakemake --jsonschema-specifications==2023.12.1 -- # via jsonschema --jupyter-core==5.7.2 -- # via nbformat --kaleido==0.2.1 -- # via scenicplus (pyproject.toml) --kiwisolver==1.4.5 -- # via matplotlib --lazy-loader==0.3 -- # via scikit-image --lda==3.0.0 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --leidenalg==0.10.2 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --line-profiler==4.1.2 -- # via easydev --llvmlite==0.42.0 -- # via -- # numba -- # pynndescent -- # pyscenic --locket==1.0.0 -- # via -- # distributed -- # partd --loompy==3.0.7 -- # via -- # loomxpy -- # pyscenic --loomxpy @ git+https://github.com/aertslab/LoomXpy@main -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --lxml==5.1.0 -- # via -- # bioservices -- # pycistopic -- # scenicplus (pyproject.toml) --lz4==4.3.3 -- # via dask --macs2==2.2.9.1 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --markdown-it-py==3.0.0 -- # via rich --markupsafe==2.1.5 -- # via jinja2 --marshmallow==3.21.1 -- # via dataclasses-json --matplotlib==3.6.3 -- # via -- # adjusttext -- # bioservices -- # gseapy -- # mizani -- # plotnine -- # pycistopic -- # scanorama -- # scanpy -- # scenicplus (pyproject.toml) -- # scrublet -- # seaborn -- # tmtoolkit -- # tspex --matplotlib-inline==0.1.6 -- # via ipython --mdurl==0.1.2 -- # via markdown-it-py --mizani==0.9.3 -- # via plotnine --msgpack==1.0.8 -- # via -- # blosc2 -- # distributed -- # ray --mudata==0.2.3 -- # via scenicplus (pyproject.toml) --multidict==6.0.5 -- # via -- # aiohttp -- # yarl --multiprocessing-on-dill==3.5.0a4 -- # via pyscenic --mypy-extensions==1.0.0 -- # via typing-inspect --natsort==8.4.0 -- # via -- # anndata -- # pyranges -- # pyrle -- # scanpy --nbformat==5.10.3 -- # via snakemake --ncls==0.0.68 -- # via -- # pyranges -- # scenicplus (pyproject.toml) --ndindex==1.8 -- # via blosc2 --networkx==3.2.1 -- # via -- # pyscenic -- # pyvis -- # scanpy -- # scenicplus (pyproject.toml) -- # scikit-image --numba==0.59.0 -- # via -- # ctxcore -- # loompy -- # pynndescent -- # pyscenic -- # scanpy -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) -- # scrublet -- # umap-learn --numexpr==2.9.0 -- # via -- # pyscenic -- # scenicplus (pyproject.toml) -- # tables --numpy==1.26.4 -- # via -- # adjusttext -- # anndata -- # arboreto -- # bbknn -- # blosc2 -- # bokeh -- # contourpy -- # ctxcore -- # dask -- # gensim -- # geosketch -- # gseapy -- # h5py -- # harmonypy -- # imageio -- # lda -- # loompy -- # loomxpy -- # macs2 -- # matplotlib -- # mizani -- # mudata -- # ncls -- # numba -- # numexpr -- # numpy-groupies -- # pandas -- # patsy -- # plotnine -- # pyarrow -- # pybedtools -- # pybigtools -- # pycistarget -- # pycistopic -- # pygam -- # pyrle -- # pyscenic -- # scanorama -- # scanpy -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) -- # scikit-image -- # scikit-learn -- # scipy -- # scrublet -- # seaborn -- # sorted-nearest -- # statsmodels -- # tables -- # tifffile -- # tmtoolkit -- # tspex -- # umap-learn --numpy-groupies==0.10.2 -- # via -- # loompy -- # scenicplus (pyproject.toml) --openpyxl==3.1.2 -- # via tmtoolkit --packaging==24.0 -- # via -- # anndata -- # bokeh -- # dask -- # distributed -- # marshmallow -- # matplotlib -- # plotly -- # ray -- # scanpy -- # scikit-image -- # snakemake -- # statsmodels -- # tables --pandas==1.5.0 -- # via -- # anndata -- # arboreto -- # bbknn -- # bioservices -- # bokeh -- # ctxcore -- # dask -- # gseapy -- # harmonypy -- # loomxpy -- # mizani -- # mudata -- # plotnine -- # pybiomart -- # pycistarget -- # pycistopic -- # pyranges -- # pyrle -- # pyscenic -- # scanpy -- # scenicplus (pyproject.toml) -- # scrublet -- # seaborn -- # statsmodels -- # tmtoolkit -- # tspex --parso==0.8.3 -- # via jedi --partd==1.4.1 -- # via dask --patsy==0.5.6 -- # via -- # plotnine -- # scanpy -- # statsmodels --pexpect==4.9.0 -- # via -- # easydev -- # ipython --pillow==10.2.0 -- # via -- # bokeh -- # imageio -- # matplotlib -- # scikit-image --plac==1.4.3 -- # via yte --platformdirs==4.2.0 -- # via -- # easydev -- # jupyter-core -- # requests-cache --plotly==5.19.0 -- # via scenicplus (pyproject.toml) --plotnine==0.12.4 -- # via scenicplus (pyproject.toml) --polars==0.20.13 -- # via -- # pycistopic -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) --progressbar2==4.4.2 -- # via pygam --prompt-toolkit==3.0.43 -- # via ipython --protobuf==5.26.0 -- # via ray --psutil==5.9.8 -- # via -- # distributed -- # snakemake --ptyprocess==0.7.0 -- # via pexpect --pulp==2.8.0 -- # via snakemake --pure-eval==0.2.2 -- # via stack-data --py-cpuinfo==9.0.0 -- # via -- # blosc2 -- # tables --pyarrow==15.0.0 -- # via -- # ctxcore -- # dask -- # pycistopic -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) --pyarrow-hotfix==0.6 -- # via -- # dask -- # scenicplus (pyproject.toml) --pybedtools==0.9.1 -- # via scenicplus (pyproject.toml) --pybigtools==0.1.2 -- # via -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) --pybigwig==0.3.22 -- # via -- # scatac-fragment-tools -- # scenicplus (pyproject.toml) --pybiomart==0.2.0 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --pycistarget @ git+https://github.com/aertslab/pycistarget -- # via scenicplus (pyproject.toml) --pycistopic @ git+https://github.com/aertslab/pycisTopic -- # via scenicplus (pyproject.toml) --pyfasta==0.5.2 -- # via scenicplus (pyproject.toml) --pygam==0.9.0 -- # via scenicplus (pyproject.toml) --pygments==2.17.2 -- # via -- # ipython -- # rich --pynndescent==0.5.11 -- # via -- # bbknn -- # umap-learn --pyparsing==3.1.2 -- # via matplotlib --pyranges==0.0.111 -- # via -- # pycistarget -- # pycistopic -- # scenicplus (pyproject.toml) --pyrle==0.0.39 -- # via -- # pyranges -- # scenicplus (pyproject.toml) --pysam==0.22.0 -- # via -- # pybedtools -- # scenicplus (pyproject.toml) --pyscenic @ git+https://github.com/aertslab/pySCENIC@master -- # via -- # loomxpy -- # pycistopic -- # scenicplus (pyproject.toml) --python-dateutil==2.9.0.post0 -- # via -- # matplotlib -- # pandas --python-utils==3.8.2 -- # via progressbar2 --pytz==2024.1 -- # via pandas --pyvis==0.3.2 -- # via scenicplus (pyproject.toml) --pyyaml==6.0.1 -- # via -- # bokeh -- # conda-inject -- # ctxcore -- # dask -- # distributed -- # pyscenic -- # ray -- # snakemake -- # yte --ray==2.9.3 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --referencing==0.34.0 -- # via -- # jsonschema -- # jsonschema-specifications --requests==2.31.0 -- # via -- # bioservices -- # grequests -- # gseapy -- # pybiomart -- # pyscenic -- # ray -- # requests-cache -- # scenicplus (pyproject.toml) -- # snakemake --requests-cache==1.2.0 -- # via -- # bioservices -- # pybiomart -- # scenicplus (pyproject.toml) --reretry==0.11.8 -- # via -- # snakemake -- # snakemake-interface-storage-plugins --rich==13.7.1 -- # via rich-argparse --rich-argparse==1.4.0 -- # via scatac-fragment-tools --rpds-py==0.18.0 -- # via -- # jsonschema -- # referencing --scanorama==1.7.4 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --scanpy==1.8.2 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --scatac-fragment-tools==0.1.0 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --scikit-image==0.22.0 -- # via -- # scenicplus (pyproject.toml) -- # scrublet --scikit-learn==1.3.2 -- # via -- # arboreto -- # bbknn -- # geosketch -- # harmonypy -- # loomxpy -- # pycistarget -- # pycistopic -- # pynndescent -- # pyscenic -- # scanorama -- # scanpy -- # scenicplus (pyproject.toml) -- # scrublet -- # umap-learn --scipy==1.12.0 -- # via -- # adjusttext -- # anndata -- # arboreto -- # bbknn -- # gensim -- # gseapy -- # harmonypy -- # loompy -- # mizani -- # plotnine -- # pygam -- # pynndescent -- # pyscenic -- # scanorama -- # scanpy -- # scenicplus (pyproject.toml) -- # scikit-image -- # scikit-learn -- # scrublet -- # statsmodels -- # tmtoolkit -- # umap-learn --scrublet==0.2.3 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --seaborn==0.13.2 -- # via -- # pycistopic -- # scanpy -- # scenicplus (pyproject.toml) --sinfo==0.3.4 -- # via scanpy --six==1.16.0 -- # via -- # asttokens -- # patsy -- # pybedtools -- # python-dateutil -- # url-normalize --smart-open==6.4.0 -- # via -- # gensim -- # snakemake --smmap==5.0.1 -- # via gitdb --snakemake==8.5.5 -- # via scenicplus (pyproject.toml) --snakemake-interface-common==1.17.1 -- # via -- # scenicplus (pyproject.toml) -- # snakemake -- # snakemake-interface-executor-plugins -- # snakemake-interface-report-plugins -- # snakemake-interface-storage-plugins --snakemake-interface-executor-plugins==8.2.0 -- # via -- # scenicplus (pyproject.toml) -- # snakemake --snakemake-interface-report-plugins==1.0.0 -- # via -- # scenicplus (pyproject.toml) -- # snakemake --snakemake-interface-storage-plugins==3.1.1 -- # via -- # scenicplus (pyproject.toml) -- # snakemake --sorted-nearest==0.0.39 -- # via pyranges --sortedcontainers==2.4.0 -- # via -- # distributed -- # intervaltree --soupsieve==2.5 -- # via beautifulsoup4 --stack-data==0.6.3 -- # via ipython --statistics==1.0.3.5 -- # via scenicplus (pyproject.toml) --statsmodels==0.14.1 -- # via -- # plotnine -- # pycistopic -- # scanpy -- # scenicplus (pyproject.toml) --stdlib-list==0.10.0 -- # via sinfo --stopit==1.1.2 -- # via snakemake --suds-community==1.1.2 -- # via bioservices --tables==3.9.2 -- # via scanpy --tabulate==0.9.0 -- # via -- # pyranges -- # pyrle -- # snakemake --tblib==3.0.0 -- # via distributed --tenacity==8.2.3 -- # via plotly --texttable==1.7.0 -- # via igraph --threadpoolctl==3.4.0 -- # via scikit-learn --throttler==1.2.2 -- # via -- # snakemake -- # snakemake-interface-executor-plugins -- # snakemake-interface-storage-plugins --tifffile==2024.2.12 -- # via scikit-image --tmtoolkit==0.12.0 -- # via -- # pycistopic -- # scenicplus (pyproject.toml) --toolz==0.12.1 -- # via -- # cytoolz -- # dask -- # distributed -- # partd --toposort==1.10 -- # via snakemake --tornado==6.4 -- # via -- # bokeh -- # distributed --tqdm==4.66.2 -- # via -- # bioservices -- # ctxcore -- # pyscenic -- # scanpy -- # scenicplus (pyproject.toml) -- # umap-learn --traitlets==5.14.2 -- # via -- # ipython -- # jupyter-core -- # matplotlib-inline -- # nbformat --tspex==0.6.3 -- # via scenicplus (pyproject.toml) --typing==3.7.4.3 -- # via scenicplus (pyproject.toml) --typing-extensions==4.10.0 -- # via -- # python-utils -- # typing-inspect --typing-inspect==0.9.0 -- # via dataclasses-json --umap-learn==0.5.5 -- # via -- # bbknn -- # pyscenic -- # scanpy -- # scenicplus (pyproject.toml) -- # scrublet --url-normalize==1.4.3 -- # via requests-cache --urllib3==2.2.1 -- # via -- # distributed -- # requests -- # requests-cache --wcwidth==0.2.13 -- # via prompt-toolkit --wheel==0.43.0 -- # via tmtoolkit --wrapt==1.16.0 -- # via -- # bioservices -- # snakemake -- # snakemake-interface-storage-plugins --xlrd==2.0.1 -- # via -- # tmtoolkit -- # tspex --xmltodict==0.13.0 -- # via bioservices --xyzservices==2023.10.1 -- # via bokeh --yarl==1.9.4 -- # via aiohttp --yte==1.5.4 -- # via snakemake --zict==3.0.0 -- # via distributed --zipp==3.18.1 -- # via importlib-metadata --zope-event==5.0 -- # via gevent --zope-interface==6.2 -- # via gevent -- --# The following packages are considered to be unsafe in a requirements file: --# setuptools -+adjusttext -+anndata -+annoy -+arboreto -+attr -+attrs -+bbknn -+beautifulsoup4 -+bs4 -+ctxcore -+cytoolz -+dask -+dill -+gensim -+gseapy -+h5py -+harmonypy -+igraph -+imageio -+importlib-metadata -+importlib-resources -+intervaltree -+joblib -+kaleido -+lda -+leidenalg -+loomxpy -+lxml -+macs2 -+matplotlib -+mudata -+ncls -+networkx -+numba -+numexpr -+numpy -+numpy-groupies -+pandas -+plotly -+plotnine -+polars -+pyarrow -+pybedtools -+pybigtools -+pybigwig -+pybiomart -+pycistarget -+pycistopic -+pyfasta -+pygam -+pyranges -+pyrle -+pysam -+pyscenic -+pyvis -+ray -+requests -+requests-cache -+scanorama -+scanpy -+scatac-fragment-tools -+scikit-image -+scikit-learn -+scipy -+scrublet -+seaborn -+snakemake -+snakemake-interface-common -+snakemake-interface-executor-plugins -+snakemake-interface-report-plugins -+snakemake-interface-storage-plugins -+statistics -+statsmodels -+tmtoolkit -+tqdm -+tspex -+umap-learn From 3e0d6ef516b9b14f68bb2994734075ae48e7fe68 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 2 Aug 2024 15:27:46 +0000 Subject: [PATCH 145/553] adding easyconfigs: Rust-1.79.0-GCCcore-13.3.0.eb --- .../r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..88962930f30 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.79.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.79.0-src.tar.gz': '172ecf3c7d1f9d9fb16cd2a628869782670416ded0129e524a86751f961448c0'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' From 3e708c9acca0a45a6085b1f78db879d8ffec7028 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 2 Aug 2024 17:34:46 +0200 Subject: [PATCH 146/553] adding easyconfigs: cfgrib-0.9.14.0-foss-2023a.eb --- .../c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb new file mode 100644 index 00000000000..b6b2b66159c --- /dev/null +++ b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'cfgrib' +version = '0.9.14.0' + +homepage = 'https://github.com/ecmwf/cfgrib/' +description = """ +A Python interface to map GRIB files to the NetCDF Common Data Model following the CF +Convention using ecCodes. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ecCodes', '2.31.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('findlibs', '0.0.5', { + 'checksums': ['7a801571e999d0ee83f9b92cbb598c21f861ee26ca9dba74cea8958ba4335e7e'], + }), + ('eccodes', '1.7.1', { + 'checksums': ['d3c7e9bab779d35b624cfd7b3331de111602cba6a6f6368efcc12407f30b2697'], + }), + (name, version, { + 'checksums': ['2b9a1e6bd47397e585f878ffd8aaac5969f6c9a448da767c700917b89c275bb2'], + }), +] + +sanity_check_commands = ['python -m cfgrib selfcheck'] + +moduleclass = 'tools' From 63994bddf6d2cdc04c30f7a21437f98b8700e1c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Aug 2024 17:57:45 +0200 Subject: [PATCH 147/553] {compiler} GCC v14.2.0 --- .../b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb | 28 +++++++++ .../binutils/binutils-2.42-GCCcore-14.2.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-14.2.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-14.2.0.eb | 63 +++++++++++++++++++ .../help2man-1.49.3-GCCcore-14.2.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-14.2.0.eb | 29 +++++++++ .../z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb | 27 ++++++++ 8 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..427ebbbe2b7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.42', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..94b762d7803 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.42' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.3.1'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..d91f13aa5d0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb new file mode 100644 index 00000000000..7126db6c52d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.42', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb new file mode 100644 index 00000000000..438a848145f --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.3.0.tar.bz2', + 'mpfr-4.2.1.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.4.0.20231231.tar.gz', + {'download_filename': '3136cf9.tar.gz', 'filename': 'nvptx-tools-20240801.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-14.2.0.tar.gz': '7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293'}, + {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'}, + {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'}, + {'nvptx-tools-20240801.tar.gz': 'a1106bf11b66d12e67194d8aa37196bb96996b614f44b3d3bc1b5854eefec03c'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.42'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..2161ee0b1af --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..c5c3ad83f3a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..187f8da34f7 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3.1' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From e9e089ddeee20f1d1d3661afca1268d18acc18f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Aug 2024 17:25:24 +0000 Subject: [PATCH 148/553] adding easyconfigs: Z3-4.13.0-GCCcore-13.3.0.eb --- .../z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a925168f147 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.0' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From e3443a43a1c581a8e14c1c8aa907124aa82deee0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Aug 2024 17:55:31 +0000 Subject: [PATCH 149/553] adding easyconfigs: Clang-18.1.0-GCCcore-13.3.0.eb --- .../c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..72c8aa9e801 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '18.1.0' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['758a048046ac5024f86c868bb17c631500eed8f8d2677ae6a72ab7ad01602277'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), + # Including Python bindings would require this as a runtime dep + # and SWIG as an additional build dep + ('Python', '3.12.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.42'), + ('hwloc', '2.10.0'), + ('libxml2', '2.12.7'), + ('ncurses', '6.5'), + ('GMP', '6.3.0'), + ('Z3', '4.13.0'), +] + +# If True, Flang does not currently support building with LLVM exceptions enabled. +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' From 3fb21c960cb62a987992a7420c280baf6c86d1d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Aug 2024 18:45:04 +0000 Subject: [PATCH 150/553] Update version --- ...8.1.0-GCCcore-13.3.0.eb => Clang-18.1.8-GCCcore-13.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Clang/{Clang-18.1.0-GCCcore-13.3.0.eb => Clang-18.1.8-GCCcore-13.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb similarity index 94% rename from easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb rename to easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb index 72c8aa9e801..8b096078c89 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb @@ -9,7 +9,7 @@ ## name = 'Clang' -version = '18.1.0' +version = '18.1.8' homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not @@ -23,7 +23,7 @@ source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-% sources = [ 'llvm-project-%(version)s.src.tar.xz', ] -checksums = ['758a048046ac5024f86c868bb17c631500eed8f8d2677ae6a72ab7ad01602277'] +checksums = ['0b58557a6d32ceee97c8d533a59b9212d87e0fc4d2833924eb6c611247db2f2a'] builddependencies = [ ('CMake', '3.29.3'), From 0eecd65cbbcfc8ad1e8ca93acfdd9b5cf3bc7b91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Aug 2024 14:07:12 +0000 Subject: [PATCH 151/553] adding easyconfigs: alsa-lib-1.2.11-GCCcore-13.2.0.eb, alsa-lib-1.2.11-GCCcore-13.3.0.eb --- .../alsa-lib-1.2.11-GCCcore-13.2.0.eb | 26 +++++++++++++++++++ .../alsa-lib-1.2.11-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fd05a43146f --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.40')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4333348a741 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.42')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' From 213a49b799aa3211b9262148a530ad31e8589e0e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:26:15 +0200 Subject: [PATCH 152/553] adding easyconfigs: BioPerl-1.7.8-GCCcore-13.3.0.eb, DB-18.1.40-GCCcore-13.3.0.eb, DB_File-1.859-GCCcore-13.3.0.eb, XML-LibXML-2.0210-GCCcore-13.3.0.eb, attr-2.5.2-GCCcore-13.3.0.eb --- .../a/attr/attr-2.5.2-GCCcore-13.3.0.eb | 28 ++++++++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb | 58 +++++++++++++++++ .../d/DB/DB-18.1.40-GCCcore-13.3.0.eb | 33 ++++++++++ .../d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb | 31 +++++++++ .../XML-LibXML-2.0210-GCCcore-13.3.0.eb | 65 +++++++++++++++++++ 5 files changed, 215 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fcd6d723f16 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.2' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +sanity_check_commands = ["getfattr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c6e760f5105 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64022827805 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('OpenSSL', '3', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7120c9c13e --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1d4cbe24543 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('libxml2', '2.12.7'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 5b6894fecaf6aec24ce80dcd7d49ebc3af771326 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:37:25 +0200 Subject: [PATCH 153/553] adding easyconfigs: archspec-0.2.4-GCCcore-13.3.0.eb --- .../archspec/archspec-0.2.4-GCCcore-13.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a4f3a288e9 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['eabbae22f315d24cc2ce786a092478ec8e245208c9877fb213c2172a6ecb9302'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' From 4b1ebfb6f72c80a753311f20f22f90504670945b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:39:01 +0200 Subject: [PATCH 154/553] adding easyconfigs: Brunsli-0.1-GCCcore-13.3.0.eb, Highway-1.2.0-GCCcore-13.3.0.eb, googletest-1.15.2-GCCcore-13.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb | 54 +++++++++++++++++++ .../googletest-1.15.2-GCCcore-13.3.0.eb | 28 ++++++++++ .../h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb | 32 +++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d374a07304a --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('Brotli', '1.1.0'), + ('Highway', '1.2.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..16b74bdae1b --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.15.2' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..27739befe52 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.2.0' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7e0be78b8318e8bdbf6fa545d2ecb4c90f947df03f7aadc42c1967f019e63343'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' From 6c32cbbfcdd2a63cd20b4ff7b461a709a2a2e35f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:40:39 +0200 Subject: [PATCH 155/553] adding easyconfigs: CFITSIO-4.4.1-GCCcore-13.3.0.eb, CGAL-5.6.1-GCCcore-13.3.0.eb, Coreutils-9.5-GCCcore-13.3.0.eb, cppy-1.2.1-GCCcore-13.3.0.eb --- .../c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ .../c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb | 26 +++++++++++ .../Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb | 28 ++++++++++++ .../c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb | 32 ++++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..eaa1b0866ac --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.4.1' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.4.1.tar.gz': '66a1dc3f21800f9eeabd9eac577b91fcdd9aabba678fbba3b8527319110d1d25'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] +# curl for HTTPs support +dependencies = [ + ('cURL', '8.7.1'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = "&& make shared && make testprog" + + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['cd %(installdir)s/share && testprog'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..01aa21c6311 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' +name = 'CGAL' +version = '5.6.1' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['cdb15e7ee31e0663589d3107a79988a37b7b1719df3d24f2058545d1bcdd5837'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..60e5009dc91 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.5" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +checksums = ['cd328edeac92f6a665de9f323c93b712af1858bc2e0d88f3f7100469470a1b8a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3043857d925 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 16ca0ddc6fce2b37c11d740470ee462c8c319f2e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:43:47 +0200 Subject: [PATCH 156/553] adding easyconfigs: ZeroMQ-4.3.5-GCCcore-13.3.0.eb, OpenPGM-5.2.122-GCCcore-13.3.0.eb, libsodium-1.0.20-GCCcore-13.3.0.eb --- .../libsodium-1.0.20-GCCcore-13.3.0.eb | 33 ++++++++++++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb | 44 +++++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb | 40 +++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e98d28304a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.20' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['ebb65ef6ca439333c2bb41a0c1990587288da07f6c7fd07cb3a18cc18d30ce19'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cbf6bca94d7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..98db227b9aa --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.5' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.20'), + ('util-linux', '2.40'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 70039b53fe68cd50ae1ba6d5b78e496d2e2bb949 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 4 Aug 2024 17:50:09 +0200 Subject: [PATCH 157/553] adding easyconfigs: APR-1.7.4-GCCcore-13.3.0.eb, APR-util-1.6.3-GCCcore-13.3.0.eb --- .../APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb | 32 +++++++++++++++++++ .../a/APR/APR-1.7.4-GCCcore-13.3.0.eb | 22 +++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc5f92c2b70 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.3' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('APR', '1.7.4'), + ('SQLite', '3.45.3'), + ('expat', '2.6.2'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ac5ed02a98 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.4' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' From df6c4698a143d25f1b33a335e22bfd3e745ae10f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 5 Aug 2024 11:34:25 +0200 Subject: [PATCH 158/553] adding easyconfigs: yelp-tools-42.1-GCCcore-12.3.0.eb, yelp-xsl-42.1-GCCcore-12.3.0.eb, mallard-ducktype-1.0.2-GCCcore-12.3.0.eb --- .../mallard-ducktype-1.0.2-GCCcore-12.3.0.eb | 24 +++++++++++ .../yelp-tools-42.1-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ .../yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb | 36 ++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2daef2a4ffd --- /dev/null +++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'mallard-ducktype' +version = '1.0.2' + +homepage = 'https://github.com/projectmallard/mallard-ducktype' +description = """Parser for the lightweight Ducktype syntax for Mallard""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['mallard_ducktype-%(version)s-py3-none-any.whl'] +checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918'] + +dependencies = [ + ('Python', '3.11.3'), +] + +options = {'modulename': 'mallard.ducktype'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b6b4f25ccf5 --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'yelp-tools' +version = '42.1' + +homepage = 'https://gitlab.gnome.org/GNOME/yelp-tools' +description = """yelp-tools is a collection of scripts and build utilities to help create, +manage, and publish documentation for Yelp and the web. Most of the heavy +lifting is done by packages like yelp-xsl and itstool. This package just +wraps things up in a developer-friendly way.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-tools/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4776766816aaa4fff5a9be7229d03e2444fca2f60a11f645c6171abe8bb73925'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('yelp-xsl', '42.1'), + ('ITSTool', '2.0.7'), + ('libxml2', '2.11.4'), + # docbook-xsl ? + ('mallard-ducktype', '1.0.2'), + ('lxml', '4.9.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/yelp-build', + 'bin/yelp-check', + 'bin/yelp-new', + ], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..60f61b5262d --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'yelp-xsl' +version = '42.1' + +homepage = "https://gitlab.gnome.org/GNOME/yelp-xslg" +description = """yelp-xsl is a collection of programs and data files to help you build, maintain, + and distribute documentation. It provides XSLT stylesheets that can be built upon for help + viewers and publishing systems. These stylesheets output JavaScript and CSS content, + and reference images provided by yelp-xsl. This package also redistributes copies + of the jQuery and jQuery.Syntax JavaScript libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-xsl/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00f3ee8d9fa048d80063cc09477d24a09349e35c58ffdf9ecea253a4ca882068'] + +builddependencies = [ + ('binutils', '2.40'), + ('ITSTool', '2.0.7'), + ('gettext', '0.21.1'), +] + +preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && ' + +sanity_check_paths = { + 'files': [], + 'dirs': [ + 'share/pkgconfig', + 'share/%(name)s', + ] +} + +moduleclass = 'data' From 5de3b4f6be02fcf6f142202ddd461ae8c7ed5527 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 5 Aug 2024 11:36:06 +0200 Subject: [PATCH 159/553] adding easyconfigs: MariaDB-11.6.0-GCC-12.3.0.eb, Judy-1.0.5-GCCcore-12.3.0.eb --- .../j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb | 34 ++++++++++ .../m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb | 65 +++++++++++++++++++ 2 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..183e8e08ea4 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..35743343440 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.6.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.6.0.tar.gz': '8fd5b593aee3920eb434c37ec44779d565fe96ef7dfd6b35a646fe7221103e11'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.2'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.11.4'), # needed by Connect XML + ('Boost', '1.82.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.42'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 680924ef2da4ff2bdb2d1cfccbd993cc590353a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 5 Aug 2024 12:20:59 +0200 Subject: [PATCH 160/553] add missing build dependency --- .../mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb index 2daef2a4ffd..65102800699 100644 --- a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = ['mallard_ducktype-%(version)s-py3-none-any.whl'] checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918'] +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ] From 22b46bc91267cfbc15dc26fb44f37b9fc90ee75e Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Mon, 5 Aug 2024 13:42:42 +0200 Subject: [PATCH 161/553] Szip: Update source and homepage URLs --- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb | 4 ++-- 13 files changed, 26 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb index 88e067c36e8..576e48c80b4 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb index 10b926a9b61..5cc6a339682 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb index b2d223898c7..70a9918dc8e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb index 3dc0b200849..6d34fd7a476 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb index 6f536c566dd..e58b9c3ffef 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb index e0a01221b9d..ee9fd884627 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb index 8eb12670652..5fcc21050e5 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb index f614a665648..5cebe3f7c68 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb index 924f439ed4e..8edba3b1aa2 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb index 4b9a4923df9..a9926ab81d1 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb index 7f564c5a0fa..0d07710e238 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb index 69db79f2d43..e522a3ac747 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb index 242c281b919..822080c60fe 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] From 9dde73982cb32136f32ce141e3999ef58c60c24c Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Mon, 5 Aug 2024 14:01:20 +0200 Subject: [PATCH 162/553] HDF v4.2.16-2: Rename source URL * based on issue #21105 --- easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index 453ca292d42..a6094f7f816 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb index 6f54f50d488..5b868a7fe58 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index d24dbfac77e..630c4aa2dc2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167'] From 244b56690ad0ddc7165974676c8c52ee2846516c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 5 Aug 2024 14:36:15 +0200 Subject: [PATCH 163/553] add missing build dependency --- .../easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb | 1 + easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb index b6b4f25ccf5..0ba5cdef596 100644 --- a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('CMake', '3.26.3'), + ('Autotools', '20220317'), ] dependencies = [ diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb index 60f61b5262d..ad7d8eddb4e 100644 --- a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.40'), ('ITSTool', '2.0.7'), ('gettext', '0.21.1'), + ('Autotools', '20220317'), ] preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && ' From 200191648280a8d0581ee8f7d443e6875f2fb133 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 5 Aug 2024 17:16:29 +0100 Subject: [PATCH 164/553] restore RISCV patch --- .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb index c140938671c..cdb7536e15a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -30,11 +30,16 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.26.4', { - 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], 'checksums': [ {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, ], }), ('ply', '3.11', { From ade2f9fe9f9b800a1951ca290d4655cd68790ad8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Aug 2024 19:52:55 +0200 Subject: [PATCH 165/553] change back to all-uppercase --- .../TINKER-8.11.3-foss-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/t/{Tinker/Tinker-8.11.3-foss-2023a.eb => TINKER/TINKER-8.11.3-foss-2023a.eb} (98%) diff --git a/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb similarity index 98% rename from easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb rename to easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb index ab73f098789..5a8538a55cb 100644 --- a/easybuild/easyconfigs/t/Tinker/Tinker-8.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' -name = 'Tinker' +name = 'TINKER' version = '8.11.3' homepage = 'https://dasher.wustl.edu/tinker' From ebe07a1bef0a0ef4e42ec0f47a18111510f0ebcb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 5 Aug 2024 20:28:45 -0400 Subject: [PATCH 166/553] Update easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb URL change suggested by @branfosj Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb index 5c8f63a0644..17ed1c0a2aa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2023a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] From b7e090219d352b7e83e62ed5809adad98ce416af Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 6 Aug 2024 10:52:09 +0200 Subject: [PATCH 167/553] adding easyconfigs: APOST3D-20240527-intel-compilers-2023.1.0.eb --- ...OST3D-20240527-intel-compilers-2023.1.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..0048a900d1c --- /dev/null +++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CmdCp' + +name = 'APOST3D' +version = '20240527' +local_commit = 'e06c8b0' + +description = """ +Open-source APOST-3D software features a large number of wavefunction analysis tools developed +over the past 20 years, aiming at connecting classical chemical concepts with the electronic +structure of molecules. APOST-3D relies on the identification of the atom in the molecule +(AIM), and several analysis tools are implemented in the most general way so that they can be +used in combination with any chosen AIM. +A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators. +""" +homepage = 'https://github.com/mgimferrer/APOST3D' + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +builddependencies = [ + ('make', '4.4.1'), +] + +source_urls = ['https://github.com/mgimferrer/APOST3D/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] + +local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' +# Compile local Libxc version 4.2.3 +# (needs provided Libxc, it is not possible to couple APOST-3D with newer Libxc libraries): +local_cmds += 'bash compile_libxc.sh && ' +# Compile +local_cmds += 'make -f Makefile_profgen && ' +# Run test calculations on single-processor: +local_cmds += 'bash compiler-runtest && ' +# Recompile using info geneated in previous step +local_cmds += 'make -f Makefile_profuse && ' +# Run test calculations in parallel: +local_cmds += 'bash compiler-runtest2' + +cmds_map = [('.*', local_cmds)] + +local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom'] + +files_to_copy = [(local_bin_files, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': [''], +} + +moduleclass = 'chem' From 13a988b8b0abbb9a4c125f1a3fe65dc91779764b Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Tue, 6 Aug 2024 10:55:02 +0200 Subject: [PATCH 168/553] modify comment --- .../a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb index 0048a900d1c..c5c4c40ac5b 100644 --- a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb @@ -25,8 +25,8 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' -# Compile local Libxc version 4.2.3 -# (needs provided Libxc, it is not possible to couple APOST-3D with newer Libxc libraries): +# Compile provided Libxc version 4.2.3 +# (it is not possible to couple APOST-3D with newer Libxc libraries): local_cmds += 'bash compile_libxc.sh && ' # Compile local_cmds += 'make -f Makefile_profgen && ' From e6a490dc5dcfcffc3242b508866a8eac238ec1b2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Aug 2024 11:26:50 +0200 Subject: [PATCH 169/553] update sources, skip tests --- .../v/Visit/Visit-3.4.1-foss-2023a.eb | 20 ++++--------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb index a049601ec0e..7e5eaa8b270 100644 --- a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -22,17 +22,9 @@ visualizing data from over 120 different scientific data formats. toolchain = {'name': 'foss', 'version': '2023a'} -sources = [{ - 'filename': 'v%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/visit-dav', - 'repo_name': 'visit', - 'tag': 'v%(version)s', - 'recursive': True, - 'keep_git_dir': True, - } -}] -checksums = [None] +source_urls = ['https://github.com/visit-dav/visit/releases/download/v%(version)s/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['942108cb294f4c9584a1628225b0be39c114c7e9e01805fb335d9c0b507689f5'] builddependencies = [('CMake', '3.26.3')] dependencies = [ @@ -49,8 +41,6 @@ dependencies = [ ('FFmpeg', '6.0'), ] -srcdir = "src" - configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB " configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK " configopts += "-DVISIT_QWT_DIR=$EBROOTQWT " @@ -63,9 +53,7 @@ configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPI configopts += "-DOpenGL_GL_PREFERENCE=GLVND " # add missing include to fix make step -prebuildopts = "sed -i '23 a #include ' %(builddir)s/visit/src/gui/QvisStripChart.C && " - -test_cmd = 'cd %(builddir)s/easybuild_obj/test && ./run_visit_test_suite.sh -n %(parallel)s' +prebuildopts = "sed -i '23 a #include ' %(builddir)s/%(namelower)s%(version)s/src/gui/QvisStripChart.C && " sanity_check_paths = { 'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']], From 501f4eb1d987bb001ff27ee9c3d6638bf18785fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Aug 2024 14:14:57 +0200 Subject: [PATCH 170/553] remove binutils build dependency, not needed when using GCC toolchain --- easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb | 4 ---- .../easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb | 4 ---- .../easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 4 ---- easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb | 4 ---- 4 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb index 526fcb3a820..35921013c3e 100644 --- a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb @@ -15,10 +15,6 @@ checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'] gem_file = '%(name)s-%(version)s.gem' -builddependencies = [ - ('binutils', '2.40'), -] - dependencies = [ ('Ruby', '3.3.0'), ] diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb index 57d50e1b02b..c9e4de852a5 100644 --- a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb @@ -8,10 +8,6 @@ description = """Conditional Reciprocal Best BLAST - high confidence ortholog as toolchain = {'name': 'GCC', 'version': '12.3.0'} -builddependencies = [ - ('binutils', '2.40'), -] - dependencies = [ ('Ruby', '3.3.0'), ] diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb index 297dd9260b3..a70ecf2a901 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -19,10 +19,6 @@ checksums = [ {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'}, ] -builddependencies = [ - ('binutils', '2.40'), -] - dependencies = [ ('Ruby', '3.3.0'), ('crb-blast', '0.6.9'), diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb index c42c506c4f3..48cc38e0d7c 100644 --- a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb @@ -14,10 +14,6 @@ checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'] gem_file = '%(name)s-%(version)s.gem' -builddependencies = [ - ('binutils', '2.40'), -] - dependencies = [ ('Ruby', '3.3.0'), ] From d8076ebaf8cb915762adebf88d385cc672b350dc Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 6 Aug 2024 15:57:28 +0200 Subject: [PATCH 171/553] Ensure BioPerl easyconfigs use `Bundle` easyblock --- easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 8caddd5df22..e8e52099b07 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb index b47216124f8..4212570abb1 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb index c6e760f5105..ba3029a6a41 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' From 31713d5c7756cfa95c339420a64b2c2111d8b369 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Aug 2024 16:38:41 +0200 Subject: [PATCH 172/553] update checksum openff-nagl + change to sources --- ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index 06e5075f674..f323c61f065 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -66,66 +66,66 @@ exts_list = [ 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], }), ('intermol', '0.1.2', { - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], }), ('SMIRNOFF99Frosst', '1.1.0', { - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], }), ('SMIRNOFF-Plugins', '2024.01.0', { - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], }), ('OpenForceField-ForceFields', '2024.04.0', { 'modulename': 'openforcefields', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], }), ('OpenForceField-Amber-FF-Ports', '0.0.4', { 'modulename': 'openff.amber_ff_ports', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], }), ('OpenForceField-Utilities', '0.1.12', { 'modulename': 'openff.utilities', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], }), ('OpenForceField-Units', '0.2.2', { 'modulename': 'openff.units', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], }), ('OpenForceField-NAGL-Models', '0.2.0', { 'modulename': 'openff.nagl_models', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], - 'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'], }), ('OpenForceField-Models', '0.1.2', { 'modulename': 'openff.models', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], }), ('OpenForceField-Interchange', '0.3.27', { 'modulename': 'openff.interchange', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], }), (name, version, { 'modulename': 'openff.toolkit', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], }), ] From 3cec9e4b0f2a954e37af2606305274fb287e7a53 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 6 Aug 2024 22:28:21 +0200 Subject: [PATCH 173/553] adding easyconfigs: CUDA-12.6.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb | 22 +++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb new file mode 100644 index 00000000000..24c7b5f5c90 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb @@ -0,0 +1,22 @@ +name = 'CUDA' +version = '12.6.0' +local_nv_version = '560.28.03' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c' +}] + +moduleclass = 'system' From 68bcf35dc9e71d897fb58e6b905a8af5c78e2b6b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 7 Aug 2024 09:55:36 +0100 Subject: [PATCH 174/553] Description typo fix for wradlib --- easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb index 9bec30a5545..010b73f371b 100644 --- a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb @@ -5,7 +5,7 @@ version = '2.0.3' homepage = 'https://docs.wradlib.org/' description = """ -The wradlib project has been initiated in order facilitate the use of weather +The wradlib project has been initiated in order to facilitate the use of weather radar data as well as to provide a common platform for research on new algorithms.""" From 743089f74ded750046c46ac6a50be80a0924c464 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 11:51:14 +0200 Subject: [PATCH 175/553] adding easyconfigs: MONAI-1.3.0-foss-2022b.eb, einops-0.7.0-GCCcore-12.2.0.eb, ITK-5.3.0-foss-2022b.eb, NiBabel-5.2.0-gfbf-2022b.eb, pydicom-2.4.4-GCCcore-12.2.0.eb, tensorboard-2.15.1-gfbf-2022b.eb, grpcio-1.57.0-GCCcore-12.2.0.eb, openslide-python-1.3.1-GCCcore-12.2.0.eb, OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb --- .../e/einops/einops-0.7.0-GCCcore-12.2.0.eb | 29 ++++++ .../g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb | 54 +++++++++++ .../easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb | 78 +++++++++++++++ .../m/MONAI/MONAI-1.3.0-foss-2022b.eb | 97 +++++++++++++++++++ .../n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb | 46 +++++++++ ...enSlide-3.4.1-GCCcore-12.2.0-largefiles.eb | 56 +++++++++++ .../openslide-python-1.3.1-GCCcore-12.2.0.eb | 29 ++++++ .../p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb | 26 +++++ .../tensorboard-2.15.1-gfbf-2022b.eb | 90 +++++++++++++++++ 9 files changed, 505 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7af581e455f --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.7.0' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..27e974c5de0 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-03-01'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf-python', '4.23.0'), + ('Abseil', '20230125.2'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.57.0_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.57.0.tar.gz': + '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'}, + {'grpcio-1.57.0_use-ebroot.patch': + '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb new file mode 100644 index 00000000000..2f64dbf8f87 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb @@ -0,0 +1,78 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak, Pavel Tománek (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.3.0' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ITK-5.3.0_vtk-include.patch', + 'ITK-5.3.0_fix-compatibility-swig-4-1.patch', +] +checksums = [ + {'v5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, + {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'}, + {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), + ('SWIG', '4.1.1'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('Python', '3.10.8'), + ('double-conversion', '3.2.1'), + ('expat', '2.4.9'), + ('HDF5', '1.14.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('VTK', '9.2.6'), + ('zlib', '1.2.12'), +] + +# Features +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +# Enable Python bindings +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG ' +configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +# Dependencies from EB +local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb new file mode 100644 index 00000000000..ab27a322fb6 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'Project-MONAI' + +builddependencies = [ + # ('hatchling', '1.18.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch', '1.13.1'), + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.21.0'), + ('tensorboard', '2.15.1'), + ('torchvision', '0.14.1'), + ('tqdm', '4.64.1'), + ('Pillow', '9.4.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.11.1'), +] + +use_pip = True + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel," +local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy," +local_pip_extras += "skimage,tensorboard,torchvision,tqdm" + +# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'}, + ], + }), + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'use_pip_extras': local_pip_extras, + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], + }), +] + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +local_extra_mod_check = {x: x for x in local_pip_extras.split(",")} +# Some special cases with different module name than extra name +local_extra_mod_check['pillow'] = 'PIL' +local_extra_mod_check['pyyaml'] = 'yaml' + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb new file mode 100644 index 00000000000..a930785f65b --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '5.2.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pillow', '9.4.0'), + ('pydicom', '2.4.4'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb new file mode 100644 index 00000000000..a8bdbafa429 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.10.3'), + ('SQLite', '3.39.4'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.10'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bbbaa753b40 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.3.1' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a1071f66e07 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.4.4' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb new file mode 100644 index 00000000000..304e56b390f --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), + ('grpcio', '1.57.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + ('Werkzeug', '3.0.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', +] + +moduleclass = 'lib' From 1335f8605cf78afef4924879715d8d278cbece92 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 11:55:28 +0200 Subject: [PATCH 176/553] Update MONAI-1.3.0-foss-2022b.eb delete comments --- easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb index ab27a322fb6..29dbbe424ba 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2022b'} github_account = 'Project-MONAI' builddependencies = [ - # ('hatchling', '1.18.0'), ('Ninja', '1.11.1'), ] From 88a6d55612b0ecf5eb1a1e415a8d235ffe97d19a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 7 Aug 2024 12:37:19 +0200 Subject: [PATCH 177/553] also copy data to installdir --- .../easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb index c516f698db4..dc008b79e18 100644 --- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -31,12 +31,14 @@ configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB " build_cmd = "./coconut" buildopts = "--batch" -preinstallopts = "mkdir -p %(installdir)s/bin && " -install_cmd = "cp" -installopts = "%(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/" +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/{bin,data}', + 'mv %(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/', + 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/data/', +]) sanity_check_paths = { - 'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel'], + 'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel', 'data/NUCNUCCS'], 'dirs': [] } From 965f7d460059f228a0eaac9c4afa769d19c65fa5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Aug 2024 13:05:06 +0200 Subject: [PATCH 178/553] add patch for ITK --- .../easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch new file mode 100644 index 00000000000..f77306c9f8e --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch @@ -0,0 +1,13 @@ +Manually add the include directory of VTK +dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375 +author: Alex Domingo (Vrije Universiteit Brussel) +--- Wrapping/CMakeLists.txt.orig 2023-12-21 13:41:44.845008000 +0100 ++++ Wrapping/CMakeLists.txt 2023-12-21 13:42:14.794328946 +0100 +@@ -112,6 +112,7 @@ + ############################################################################### + # Configure specific wrapper modules + ############################################################################### ++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/") + + unset(WRAP_ITK_MODULES CACHE) + \ No newline at end of file From 3dc038f64c146dc3c3caca60e8cb46aa41689d05 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 7 Aug 2024 15:17:13 +0200 Subject: [PATCH 179/553] Update ITK-5.3.0-foss-2022b.eb update checksum --- easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb index 2f64dbf8f87..9ba65978898 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb @@ -24,7 +24,7 @@ patches = [ 'ITK-5.3.0_fix-compatibility-swig-4-1.patch', ] checksums = [ - {'v5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, + {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'}, {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'}, ] From 39e7406baf1c4a71dfcee7657340c73b69b59736 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Aug 2024 18:29:39 +0200 Subject: [PATCH 180/553] Fix checksum checks for bundles Some bundle easyconfigs have a checksums parameter. The current test code clears that unconditionally which makes the test fail when it should not. As we know the easyconfig dict will be modified we can just make a copy here. --- test/easyconfigs/easyconfigs.py | 30 ++++++++++++------------------ 1 file changed, 12 insertions(+), 18 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d228333cca6..b4111d97a3b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1045,25 +1045,19 @@ def test_pr_sha256_checksums(self): 'R-bundle-Bioconductor-3.[2-5]', ] - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - bundle_easyblocks = ['Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] - for ec in self.changed_ecs: - if ec['easyblock'] in bundle_easyblocks or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + retained_changed_ecs = [ec for ec in self.changed_ecs if not ec['deprecated']] + + # The check_sha256_checksums function creates an EasyBlock instance. + # For easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__. + # Therefore, we need to a operate on a copy of those easyconfigs. + bundle_easyblocks = {'Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'} + + def is_bundle(ec): + return ec['easyblock'] in bundle_easyblocks or ec['name'] == 'Clang-AOMP' + ecs = [ec.copy() if is_bundle(ec) else ec for ec in retained_changed_ecs] + checksum_issues = check_sha256_checksums(ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() From fabca65ac85660898903540f5c79d3184f8ad62f Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 7 Aug 2024 15:44:56 -0700 Subject: [PATCH 181/553] add pkconf --- .../easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb index e355180eb49..dda0a838bf3 100644 --- a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = "Miscellaneous tools for data analysis and scientific computing" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pkgconf', '1.9.5'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From 60ff433938da75ab1ce05b0c73bb6db9cdc59f87 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 8 Aug 2024 10:04:11 +0200 Subject: [PATCH 182/553] adding easyconfigs: RHEIA-1.1.11-foss-2023a.eb --- .../r/RHEIA/RHEIA-1.1.11-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb new file mode 100644 index 00000000000..d218a83dc02 --- /dev/null +++ b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'RHEIA' +version = '1.1.11' + +homepage = 'https://github.com/rheia-framework/RHEIA' +description = "Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # deap, numpy, pandas, scipy + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('pvlib', '0.11.0', { + 'checksums': ['88b31c44dc07f0435af1e2d5ddcac067e6ce15917251a9f270366f61e9bd015b'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('SobolSequence', '0.2.1', { + 'modulename': 'sobol', + 'checksums': ['b2b4b57451b8d2e79ddb07efa23bc471dfdd436ea357d6368666bdc364df3eb1'], + }), + ('rheia', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['d6b1ea991f6338cca136b59e8e413bae2167c5ebd631163ec68fafe0040aa143'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 719a54206dd2ddefb166e415e81d13e8adbd19a4 Mon Sep 17 00:00:00 2001 From: Jessie Hernandez Date: Thu, 8 Aug 2024 10:47:57 +0200 Subject: [PATCH 183/553] adding easyconfigs: libedit-20240517-GCCcore-13.2.0.eb --- .../libedit-20240517-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..098fd8b7bde --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20240517' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['3a489097bb4115495f3bd85ae782852b7097c556d9500088d74b6fa38dbd12ff'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 42d28fe6a8e21f3945d59351c2a1cdd7bab21f4e Mon Sep 17 00:00:00 2001 From: Jessie Hernandez Date: Thu, 8 Aug 2024 10:49:33 +0200 Subject: [PATCH 184/553] adding easyconfigs: fmt-10.2.1-GCCcore-13.2.0.eb --- .../f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..45cfe72e73f --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.2.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['312151a2d13c8327f5c9c586ac6cf7cddc1658e8f53edae0ec56509c8fa516c9'] + + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 8097c1293a719ed0116d06a0724708867ae18f7d Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 8 Aug 2024 13:42:27 +0200 Subject: [PATCH 185/553] adding easyconfigs: PyRosetta-4.release-384-gompi-2022a.eb --- .../PyRosetta-4.release-384-gompi-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb new file mode 100644 index 00000000000..5769add932d --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-384' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From d7f2247920cd6a3ec8da634167ec75774204b38e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 8 Aug 2024 15:41:58 +0200 Subject: [PATCH 186/553] adding easyconfigs: MBX-1.1.0-foss-2023a.eb --- .../easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..e0ad4d59124 --- /dev/null +++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'MBX' +version = '1.1.0' + +homepage = 'https://github.com/paesanilab/MBX' +description = "MBX is an energy and force calculator for data-driven many-body simulations" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/paesanilab/MBX/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['0f55f4950226defb46fd0814ad97f906ce4ffd6403af6817bd98cb3c68996692'] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GSL', '2.7'), +] + +buildininstalldir = True + +preconfigopts = 'echo HEEERE && echo %(installdir)s && export MBX_HOME=%(installdir)s && autoreconf -fi && ' + +configopts = '--enable-shared --enable-verbose CXX="$CXX"' + +prebuildopts = 'export MBX_HOME=%(installdir)s && ' + +preinstallopts = 'export MBX_HOME=%(installdir)s && ' + +maxparallel = 3 + +runtest = 'check' + +modextrapaths = {'PYTHONPATH': '%(name)s-%(version)s/plugins/python'} + +modextravars = {'MBX_HOME': '%(installdir)s'} + +sanity_check_paths = { + 'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point', + 'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT], + 'dirs': ['include', '%(name)s-%(version)s/plugins/python/mbx'], +} + +sanity_check_commands = [ + "optimize", + "python -c 'import mbx'", +] + +moduleclass = 'chem' From 53585cf98a9d7484bcfd252535674ac035d9ac48 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 8 Aug 2024 17:14:26 +0100 Subject: [PATCH 187/553] disable use of MySQL in GDAL --- easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 2 ++ easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index a527795dfc3..831b5465ec1 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -61,8 +61,10 @@ dependencies = [ # common configopts for static, shared library builds _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', + '-DArrow_DIR=$EBROOTARROW', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', '-DPython_ROOT=$EBROOTPYTHON', + '-DGDAL_USE_MYSQL=OFF', ]) # iterative build for both static and shared libraries diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index df1c21eb72a..ad4ea255ed2 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,7 +61,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb index ba67862143a..21299457516 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb @@ -60,7 +60,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ From 06bcdf1fa9f8f722b9dddf61dd9458e0f1202def Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 8 Aug 2024 17:16:41 +0100 Subject: [PATCH 188/553] remove accidental change, as based this on EB5 --- easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 - easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index 831b5465ec1..576d90e74d6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -61,7 +61,6 @@ dependencies = [ # common configopts for static, shared library builds _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', - '-DArrow_DIR=$EBROOTARROW', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', '-DPython_ROOT=$EBROOTPYTHON', '-DGDAL_USE_MYSQL=OFF', diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index ad4ea255ed2..88e35cd4db4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,7 +61,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW -DGDAL_USE_MYSQL=OFF " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ From d4707a4d6e7b55bdb1f6bdd5f65f251a1fea2f1c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 8 Aug 2024 18:39:58 +0200 Subject: [PATCH 189/553] adding easyconfigs: miniprot-0.13-GCCcore-12.3.0.eb --- .../miniprot/miniprot-0.13-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aa598c6869b --- /dev/null +++ b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = "MakeCp" + +name = 'miniprot' +version = '0.13' + +homepage = 'https://github.com/lh3/miniprot' +description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. +It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. +Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much +faster at the residue alignment step.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/miniprot/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('zlib', '1.2.13')] + +files_to_copy = [ + (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'), + (['miniprot'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/miniprot'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' From 25ee0adf01fc5e93c5d15408cb13a0d9b717a3f0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 9 Aug 2024 14:58:14 +0200 Subject: [PATCH 190/553] get rid of buildininstalldir --- .../easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb index e0ad4d59124..3f6da986d62 100644 --- a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb @@ -20,28 +20,24 @@ dependencies = [ ('GSL', '2.7'), ] -buildininstalldir = True - -preconfigopts = 'echo HEEERE && echo %(installdir)s && export MBX_HOME=%(installdir)s && autoreconf -fi && ' +preconfigopts = 'export MBX_HOME=$PWD && autoreconf -fi && ' configopts = '--enable-shared --enable-verbose CXX="$CXX"' -prebuildopts = 'export MBX_HOME=%(installdir)s && ' - -preinstallopts = 'export MBX_HOME=%(installdir)s && ' +postinstallcmds = ["cp -a plugins %(installdir)s"] -maxparallel = 3 +maxparallel = 2 runtest = 'check' -modextrapaths = {'PYTHONPATH': '%(name)s-%(version)s/plugins/python'} +modextrapaths = {'PYTHONPATH': 'plugins/python'} modextravars = {'MBX_HOME': '%(installdir)s'} sanity_check_paths = { 'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point', 'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT], - 'dirs': ['include', '%(name)s-%(version)s/plugins/python/mbx'], + 'dirs': ['include', 'plugins/python/mbx', 'plugins/lammps/USER-MBX'], } sanity_check_commands = [ From c1e7866a009bceb9b76296a1ef49d6834572e813 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 9 Aug 2024 15:33:51 +0200 Subject: [PATCH 191/553] adding easyconfigs: Salmon-1.10.3-GCC-12.3.0.eb --- .../s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..20bd7fd9540 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb @@ -0,0 +1,59 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +# # +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.10.3' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimate from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/COMBINE-lab/salmon/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('jemalloc', '5.3.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] +dependencies = [ + ('Boost', '1.82.0'), + ('tbb', '2021.11.0'), + ('cURL', '8.0.1'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From adffacad851fccdc5ebdcfd2b8c71218da406550 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 9 Aug 2024 16:31:35 +0200 Subject: [PATCH 192/553] Update Salmon-1.10.3-GCC-12.3.0.eb fix whitespace --- easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb index 20bd7fd9540..9b52051eed3 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb @@ -28,7 +28,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/COMBINE-lab/salmon/archive'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871'] - + builddependencies = [ ('CMake', '3.26.3'), ('pkgconf', '1.9.5'), From 2e65e2d4c0fb44b6923aef29cd4c86fd13d67741 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 9 Aug 2024 17:05:46 +0200 Subject: [PATCH 193/553] adding easyconfigs: CDO-2.3.0-iimpi-2022a.eb --- .../c/CDO/CDO-2.3.0-iimpi-2022a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb new file mode 100644 index 00000000000..58cf406d164 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb @@ -0,0 +1,58 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.3.0' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29019/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10c878227baf718a6917837527d4426c2d0022cfac4457c65155b9c57f091f6b'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' From cf5afe3cecba4f61a718676687dee0e90cf8a34d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 9 Aug 2024 17:37:11 +0200 Subject: [PATCH 194/553] add ec for dep ecCodes --- .../e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb new file mode 100644 index 00000000000..b93565bb610 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 4166d5b8caa04f1097761acadaa111813f60cb23 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 9 Aug 2024 18:38:08 +0200 Subject: [PATCH 195/553] adding easyconfigs: PyCharm-2024.1.6.eb --- .../easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb new file mode 100644 index 00000000000..37d00512c27 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2024.1.6" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['539961408de4217a68b84d666d5c10ddb8d7bcf919e3a569f2489438a3237f1a'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' From 78e994dc672538f7e25eaef61133540049d97ad5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Sat, 10 Aug 2024 14:12:46 +0200 Subject: [PATCH 196/553] adding easyconfigs: dictys-1.1.0-foss-2023a.eb, dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb --- .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 102 ++++++++++++++++++ .../d/dictys/dictys-1.1.0-foss-2023a.eb | 100 +++++++++++++++++ 2 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..e5988e75d30 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,102 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0', versionsuffix), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('junos-eznc', '2.7.1', { + 'modulename': 'jnpr.junos', + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..ad4ba02e66d --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -0,0 +1,100 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0'), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('junos-eznc', '2.7.1', { + 'modulename': 'jnpr.junos', + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' From 8f3466efeb0af98784fbcd1db69657f2f3c51f84 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Sat, 10 Aug 2024 16:08:26 +0200 Subject: [PATCH 197/553] update junos-eznc version to fix tests failing --- .../d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 4 ++-- easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb index e5988e75d30..de99e242d09 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -70,9 +70,9 @@ exts_list = [ ('ncclient', '0.6.15', { 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], }), - ('junos-eznc', '2.7.1', { + ('junos-eznc', '2.7.0', { 'modulename': 'jnpr.junos', - 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], }), ('absl-py', '1.4.0', { 'modulename': 'absl', diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb index ad4ba02e66d..e0fa2174545 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -68,9 +68,9 @@ exts_list = [ ('ncclient', '0.6.15', { 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], }), - ('junos-eznc', '2.7.1', { + ('junos-eznc', '2.7.0', { 'modulename': 'jnpr.junos', - 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], }), ('absl-py', '1.4.0', { 'modulename': 'absl', From 31ec9dbe7a84e5561a70fb690c3ba3790c7d13bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Aug 2024 10:19:40 +0200 Subject: [PATCH 198/553] add sanity check commands for ecCodes 2.27.0 --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb index b93565bb610..33fddc6886a 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = ['%s -V' % x for x in local_exes if not x.startswith('codes_')] + moduleclass = 'tools' From 4f33e78baf8d98fd7229ad1d1375745c09841182 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 12 Aug 2024 12:56:03 +0200 Subject: [PATCH 199/553] add avx2 variant --- .../o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..cdc92c16f64 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +moduleclass = 'chem' From 2e1fe4fdb4897dd6ff90c2db0bd9b31c3a2589db Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 12 Aug 2024 14:52:24 +0200 Subject: [PATCH 200/553] Update R-bundle-CRAN-2023.12-foss-2023a.eb add missMDA --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index bbc343accac..90c7f3f7665 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -3424,6 +3424,9 @@ exts_list = [ ('rhandsontable', '0.3.8', { 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f6d167d010e611b3cc555a9569d5ff81f65fafd7 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Mon, 12 Aug 2024 16:28:47 +0200 Subject: [PATCH 201/553] adding easyconfigs: GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb --- .../GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb | 101 ++++++++++++++++++ 1 file changed, 101 insertions(+) create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb new file mode 100755 index 00000000000..38166a92912 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb @@ -0,0 +1,101 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +_plumedver = '2.9.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + '%(name)s-%(version)s_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': + '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), + ('PLUMED', _plumedver), +] + + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' + +# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' + From 5e1e9636e123842d013e0b7ab1ca2af1babf8e2d Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 13 Aug 2024 06:48:24 +0200 Subject: [PATCH 202/553] Added GLM and GTS --- .../g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb | 27 +++++++++++++++++ .../g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e57a89d030a --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '1.0.1' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dd36868a20d --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] +dependencies = [ + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' From 29e3dddcd0e0a394ae0a0bbb0a3434d8606b284e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 13 Aug 2024 09:05:47 +0200 Subject: [PATCH 203/553] Added gflags, gmpy2, graphite2 and Imath --- .../g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb | 35 +++++++++++++++++++ .../g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb | 25 +++++++++++++ .../graphite2-1.3.14-GCCcore-13.3.0.eb | 27 ++++++++++++++ .../i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb | 28 +++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de0ad50b22c --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d919e2ca8e3 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.2.0' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70'] + +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('MPC', '1.3.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e199ecf26b --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..05efb6d6c62 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.11' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057849585e49b8b85abe7cc1e76e22963b01bfdc3b6d83eac90c499cd760063'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' From 1e6377fb82e6ffd5c584ab0b5c35ea871c46c11c Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 13 Aug 2024 09:24:24 +0200 Subject: [PATCH 204/553] Added JsonCpp, jemalloc and json-c --- .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb | 29 +++++++++++++++ .../jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb | 37 +++++++++++++++++++ .../j/json-c/json-c-0.17-GCCcore-13.3.0.eb | 32 ++++++++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b1d3f620566 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..023c3001dd3 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..87642888aa1 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.17' +local_suff = '-20230812' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' From fa3c247ff15e3d8101171bc7b680d5a2883567b2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 13 Aug 2024 15:29:24 +0200 Subject: [PATCH 205/553] adding easyconfigs: GDMA-2.3.3_20230603-GCC-12.3.0.eb --- .../g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb new file mode 100644 index 00000000000..d22b6d74689 --- /dev/null +++ b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GDMA' +version = '2.3.3_20230603' +_commit = '6b8e81ec' + +homepage = 'https://gitlab.com/anthonyjs/gdma' +description = """ +The GDMA program carries out Distributed Multipole Analysis of wavefunctions +calculated by the Gaussian system of programs or the Psi4 package, using the +formatted checkpoint files that they can produce. The result is a set of +multipole moments at sites defined by the user (usually at the positions of the +atomic nuclei) which, given an accurate wavefunction, provide an accurate +description of the electrostatic field of the molecule.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ['https://gitlab.com/anthonyjs/gdma/-/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['cc008932ae8768e6cbd444337a998e02b2100c123492c260d6020590e76bec1e'] + +parallel = 1 + +skipsteps = ['configure'] + +# avoid using git to obtain the commit: not a cloned repo +prebuildopts = """sed -i "/^log =/,/^commit =/c commit = '%s'" src/version.py && """ % _commit + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/gdma'], + 'dirs': [], +} + +sanity_check_commands = ['echo|gdma'] + +moduleclass = 'chem' From 9bbe3338d0303e80359a2b41e8f3cac30170b0c6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 13 Aug 2024 16:14:24 +0200 Subject: [PATCH 206/553] separate econfig for junos-eznc with forked paramiko --- .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 21 +------ .../d/dictys/dictys-1.1.0-foss-2023a.eb | 21 +------ .../junos-eznc-2.7.1-GCCcore-12.3.0.eb | 56 +++++++++++++++++++ 3 files changed, 58 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb index de99e242d09..f04774b1b55 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -29,6 +29,7 @@ dependencies = [ ('paramiko', '3.2.0'), ('Jupyter-bundle', '20230823'), ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), ] # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version @@ -54,26 +55,6 @@ exts_list = [ ('pynetbox', '7.4.0', { 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], }), - ('yamlordereddictloader', '0.4.2', { - 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], - }), - ('transitions', '0.9.2', { - 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], - }), - ('scp', '0.15.0', { - 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], - }), - ('pyserial', '3.5', { - 'modulename': 'serial', - 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], - }), - ('ncclient', '0.6.15', { - 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], - }), - ('junos-eznc', '2.7.0', { - 'modulename': 'jnpr.junos', - 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], - }), ('absl-py', '1.4.0', { 'modulename': 'absl', 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb index e0fa2174545..0b97a82cfde 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -27,6 +27,7 @@ dependencies = [ ('paramiko', '3.2.0'), ('Jupyter-bundle', '20230823'), ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), ] # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version @@ -52,26 +53,6 @@ exts_list = [ ('pynetbox', '7.4.0', { 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], }), - ('yamlordereddictloader', '0.4.2', { - 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], - }), - ('transitions', '0.9.2', { - 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], - }), - ('scp', '0.15.0', { - 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], - }), - ('pyserial', '3.5', { - 'modulename': 'serial', - 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], - }), - ('ncclient', '0.6.15', { - 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], - }), - ('junos-eznc', '2.7.0', { - 'modulename': 'jnpr.junos', - 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], - }), ('absl-py', '1.4.0', { 'modulename': 'absl', 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2799845eb24 --- /dev/null +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'junos-eznc' +version = '2.7.1' + +homepage = 'https://github.com/Juniper/py-junos-eznc' +description = "Python library for Junos automation." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('PyYAML', '6.0'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py +local_preinstallopts = "sed -i '6d' setup.py && " + +exts_list = [ + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('paramiko', '3.4.0', { + # Juniper fork of paramiko - compatible with junos-eznc + 'source_urls': ['https://github.com/Juniper/paramiko/archive/'], + 'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}], + 'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'], + }), + (name, version, { + 'modulename': 'jnpr.junos', + 'preinstallopts': "sed -i '6d' setup.py && ", + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 1fb2752bda16545a6ec4df91f4a3353545e3f42d Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 13 Aug 2024 16:45:07 +0200 Subject: [PATCH 207/553] Add GPflow v2.9.2 and fix tensorflow-probability to pass pip check --- .../g/GPflow/GPflow-2.9.2-foss-2023a.eb | 51 +++++++++++++++++++ ...ensorflow-probability-0.20.0-foss-2023a.eb | 8 +++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb new file mode 100644 index 00000000000..a2a0f0a5adc --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('tensorflow-probability', '0.20.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index c86b16b035f..97a3f88a99f 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True +# avoid pip check fail when tensorflow-probability is a dependency +local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && " +local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && " +local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/'" +local_postinstallcmds += " tensorflow_probability-%(version)s.dist-info/METADATA" + exts_list = [ ('cloudpickle', '3.0.0', { 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], @@ -37,6 +43,8 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], + 'postinstallcmds': [local_postinstallcmds], + # 'installopts': local_installopts, }), ] From a0ccd08eee61bd7543fa9db173f524387a4dc3fe Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:47:07 +0200 Subject: [PATCH 208/553] remove comment --- .../tensorflow-probability-0.20.0-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index 97a3f88a99f..e18a2bc7414 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -44,7 +44,6 @@ exts_list = [ 'source_urls': ['https://github.com/tensorflow/probability/archive/'], 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], 'postinstallcmds': [local_postinstallcmds], - # 'installopts': local_installopts, }), ] From f72250be364f2c9b499330f01a2dcdd4260a0bdb Mon Sep 17 00:00:00 2001 From: software Date: Tue, 13 Aug 2024 15:08:03 +0000 Subject: [PATCH 209/553] adding easyconfigs: Kent_tools-468-GCC-12.3.0.eb --- .../k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb new file mode 100644 index 00000000000..e4fd527e908 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '468' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8'] + +dependencies = [ + ('MariaDB', '11.6.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('util-linux', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.13.0'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' From 777b5cfcb8ba74e58d2733ce8a87dac697b694b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Aug 2024 17:17:34 +0200 Subject: [PATCH 210/553] adding easyconfigs: EMMAX-20100310-foss-2023a.eb and patches: EMMAX-20100310_fix-build.patch --- .../e/EMMAX/EMMAX-20100310-foss-2023a.eb | 40 +++++++++ .../e/EMMAX/EMMAX-20100310_fix-build.patch | 88 +++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb create mode 100644 easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb new file mode 100644 index 00000000000..c68628823fb --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'EMMAX' +# version is based on datestamp of files in emmax-beta-src.tar.gz +# (last checked on 13 Aug 2024) +version = '20100310' + +homepage = 'https://csg.sph.umich.edu//kang/emmax' +description = """EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/'] +sources = [{'download_filename': 'emmax-beta-src.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['EMMAX-20100310_fix-build.patch'] +checksums = [ + {'EMMAX-20100310.tar.gz': '79670917a0ac74ff1899fb27361e2e07b0f3a7911a9d9c6e0c18cf066b8987ea'}, + {'EMMAX-20100310_fix-build.patch': 'fae62d1f9f7bd4b94c81cdeb01d5134cc2825bcab050ddbfa89ce232eca8497e'}, +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"' + +files_to_copy = [(['emmax', 'emmax-kin'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/emmax', 'bin/emmax-kin'], + 'dirs': [], +} + +sanity_check_commands = [ + "emmax 2>&1 | grep '^Usage: emmax'", + "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch new file mode 100644 index 00000000000..c2827ab10a9 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch @@ -0,0 +1,88 @@ +fix build with recent compiler & BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) + +--- emmax-beta-src/emmax.c.orig 2024-08-13 16:28:41.536119000 +0200 ++++ emmax-beta-src/emmax.c 2024-08-13 16:54:06.856501202 +0200 +@@ -7,7 +7,8 @@ + #include + #include + #include +-#include ++#include ++#include + #include + //#include "lapack_wrapper.h" + +@@ -1621,15 +1622,13 @@ + double *W, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevd_ (char *JOBZp, char *UPLOp, int *Np, +- double *A, int *LDAp, +- double *W, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevd_ (&JOBZ, &UPLO, &N, A, &LDA, ++ int32_t N32 = N; ++ int32_t LDA32 = LDA; ++ int32_t LWORK32 = LWORK; ++ dsyevd_ (&JOBZ, &UPLO, &N32, A, &LDA32, + W, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ WORK, &LWORK32, IWORK, &LIWORK, &INFO, 1, 1); + + return INFO; + } +@@ -1640,16 +1639,11 @@ + double *W, double *Z, int LDZ, int *ISUPPZ, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevr_ (char *JOBZp, char *RANGEp, char *UPLOp, int *Np, +- double *A, int *LDAp, double *VLp, double *VUp, +- int *ILp, int *IUp, double *ABSTOLp, int *Mp, +- double *W, double *Z, int *LDZp, int *ISUPPZ, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevr_ (&JOBZ, &RANGE, &UPLO, &N, A, &LDA, &VL, &VU, +- &IL, &IU, &ABSTOL, M, W, Z, &LDZ, ISUPPZ, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ int32_t N32 = N, LDA32 = LDA, IL32 = IL, IU32 = IU, LDZ32 = LDZ, LWORK32 = LWORK, LIWORK32 = LIWORK; ++ dsyevr_ (&JOBZ, &RANGE, &UPLO, &N32, A, &LDA32, &VL, &VU, ++ &IL32, &IU32, &ABSTOL, M, W, Z, &LDZ32, ISUPPZ, ++ WORK, &LWORK32, IWORK, &LIWORK32, &INFO, 1, 1, 1); + + return INFO; + } +@@ -1739,16 +1733,27 @@ + } + + /* Turn Y into its LU form, store pivot matrix */ +- info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv); ++ dgetrf_(&n, &n, Y, &n, ipiv, &info); + + /* Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs */ +- if (info!=0) return info; ++ if (info != 0) { ++ free(ipiv); ++ return info; ++ } + + /* Feed this to the lapack inversion routine. */ +- info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv); ++ int lwork = n * n; ++ double *work = malloc(lwork * sizeof(double)); ++ if (work == NULL) { ++ printf("malloc failed for work array in matrix_invert\n"); ++ free(ipiv); ++ return 2; ++ } ++ dgetri_(&n, Y, &n, ipiv, work, &lwork, &info); + + /* Cleanup and exit */ + free(ipiv); ++ free(work); + return info; + } + From 3f86fa26e8ccb794adc198fd4aa6abf19c1f8f1c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:39:23 +0100 Subject: [PATCH 211/553] stop RStudio-Server installing R packages --- .../RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb index 020dde50a43..f95b26d2a6a 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb @@ -36,6 +36,7 @@ dependencies = [ ('Boost', '1.82.0'), ('Java', '11', '', SYSTEM), ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), ('SOCI', '4.0.3'), ('yaml-cpp', '0.7.0'), ] @@ -52,7 +53,6 @@ preconfigopts = " && ".join([ "./install-dictionaries", "./install-mathjax", "./install-pandoc", - "./install-packages", "./install-panmirror", "./install-npm-dependencies)", "" From 271a36fcc22d0c56d856716a3ffe30f481f9b2d4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 13 Aug 2024 18:09:21 +0100 Subject: [PATCH 212/553] requires change in toolchain --- ... RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/r/RStudio-Server/{RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb => RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb} (98%) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb similarity index 98% rename from easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb rename to easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb index f95b26d2a6a..56585dad1c0 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb @@ -18,7 +18,7 @@ and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" """ -toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/rstudio/rstudio/archive'] sources = ['v%(version)s.tar.gz'] From 631f6a1d3b69d86783db82edde4c8d81a2ca022a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Aug 2024 10:02:04 +0200 Subject: [PATCH 213/553] update junos-eznc.eb - pre- preinstallopts --- .../j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb index 2799845eb24..ceaec648de3 100644 --- a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -17,9 +17,6 @@ dependencies = [ ('bcrypt', '4.0.1'), ] -# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py -local_preinstallopts = "sed -i '6d' setup.py && " - exts_list = [ ('yamlordereddictloader', '0.4.2', { 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], @@ -45,7 +42,8 @@ exts_list = [ }), (name, version, { 'modulename': 'jnpr.junos', - 'preinstallopts': "sed -i '6d' setup.py && ", + # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py + 'preinstallopts': "sed -i '/pip install/d' setup.py && ", 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], }), ] From 6f40b2fa172471e85e8c0e3174b537d8ea9899c8 Mon Sep 17 00:00:00 2001 From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com> Date: Wed, 14 Aug 2024 10:43:37 +0200 Subject: [PATCH 214/553] Fix style --- .../g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb index 38166a92912..943aa4ac839 100755 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb @@ -98,4 +98,3 @@ modextrapaths = { } moduleclass = 'bio' - From 344d2f82335e4576769756b1f33798ec54ade307 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 14 Aug 2024 10:47:20 +0200 Subject: [PATCH 215/553] tiny change to make spacing more consistent --- .../tensorflow-probability-0.20.0-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index e18a2bc7414..efede874267 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -31,8 +31,8 @@ use_pip = True # avoid pip check fail when tensorflow-probability is a dependency local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && " local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && " -local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/'" -local_postinstallcmds += " tensorflow_probability-%(version)s.dist-info/METADATA" +local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/' " +local_postinstallcmds += "tensorflow_probability-%(version)s.dist-info/METADATA" exts_list = [ ('cloudpickle', '3.0.0', { From b1691e04e45b28f3a7f3ef59d5236e5ab041f417 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Aug 2024 11:02:49 +0200 Subject: [PATCH 216/553] add preinstallopts to fix Invalid cross-device link error --- .../flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb index 0ef79545ba0..8f3d41e17ad 100644 --- a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -24,6 +24,9 @@ use_pip = True exts_list = [ (name, version, { 'modulename': 'flash_attn', + # solves Invalid cross-device link error + # https://github.com/Dao-AILab/flash-attention/issues/875 + 'preinstallopts': "sed -i 's/os.rename/shutil.move/' setup.py && ", 'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'], 'sources': ['v%(version)s.tar.gz'], 'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'], From e43066d8654edd9d0e1524cdc73ed2e768d8ae77 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Aug 2024 11:44:37 +0200 Subject: [PATCH 217/553] adding easyconfigs: Julia-1.10.4-linux-x86_64.eb --- .../j/Julia/Julia-1.10.4-linux-x86_64.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb new file mode 100644 index 00000000000..dccc9cb700e --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.4' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.4-linux-x86_64.tar.gz': '079f61757c3b5b40d2ade052b3cc4816f50f7ef6df668825772562b3746adff1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' \ No newline at end of file From bb6e8770ae10d4b41be762a9f16a7de63da9fbb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Aug 2024 13:40:00 +0200 Subject: [PATCH 218/553] {bio}[foss/2022a] AlphaPulldown v2.0.0b4, Uni-Core v0.0.3 --- ....0b2_fix-import-protein_letters_3to1.patch | 13 +++ .../AlphaPulldown-2.0.0b4-foss-2022a.eb | 95 +++++++++++++++++++ .../u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb | 56 +++++++++++ 3 files changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch new file mode 100644 index 00000000000..34994664f80 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch @@ -0,0 +1,13 @@ +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.SCOPData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb new file mode 100644 index 00000000000..f41935fe51d --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -0,0 +1,95 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25'), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3'), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb new file mode 100644 index 00000000000..d82f94349bc --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': local_preinstallopts, + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 9ede928c195f6d122f558ade9554cb38af831b9b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:08:52 +0200 Subject: [PATCH 219/553] Update Julia-1.10.4-linux-x86_64.eb - blank line in the end --- easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb index dccc9cb700e..767a23c33a4 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb @@ -34,4 +34,4 @@ sanity_check_paths = { } sanity_check_commands = ['julia --help'] -moduleclass = 'lang' \ No newline at end of file +moduleclass = 'lang' From 451e98e35f2ca212926ab7c7db38654266aaf064 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 14 Aug 2024 14:43:36 +0200 Subject: [PATCH 220/553] Fix file permissions --- .../g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb old mode 100755 new mode 100644 From 3738c95403e97fff3d26fb45219e53c5915821d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Aug 2024 15:07:01 +0200 Subject: [PATCH 221/553] {bio}[foss/2022a] AlphaPulldown v2.0.0b4, Uni-Core v0.0.3 w/ CUDA 11.7.0 --- ...Pulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb | 97 +++++++++++++++++++ .../Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb | 55 +++++++++++ 2 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..72746293174 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,97 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25', versionsuffix), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..2ca769764aa --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('jax', '0.3.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': "sed -i 's/torch>=[0-9.]*/torch/g' setup.py && ", + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 2280e31879494ecf5764b12fc7b580d7dac849de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Aug 2024 15:12:23 +0200 Subject: [PATCH 222/553] add missMDA extension to R-bundle-CRAN 2024.06 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index ce8233bc4a5..c8376489c57 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3433,6 +3433,9 @@ exts_list = [ ('rhandsontable', '0.3.8', { 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 747a2f3ba3d096bb9e18fc4104bd8ab8f28122ff Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 14 Aug 2024 12:41:03 -0700 Subject: [PATCH 223/553] update CUTLASS --- .../CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3322e6b4b56 --- /dev/null +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CUTLASS' +version = '3.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cutlass' +description = """CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['49f4b854acc2a520126ceefe4f701cfe8c2b039045873e311b1f10a8ca5d5de1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), +] + +_copts = [ + '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"', + '-DCUTLASS_ENABLE_CUBLAS=1', + '-DCUTLASS_ENABLE_CUDNN=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' From 6a7547282ba63a5402ad052607ae1da75dcc7023 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 15 Aug 2024 10:27:14 +0200 Subject: [PATCH 224/553] add dep CUTLASS from PR 21184 --- .../flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb index 8f3d41e17ad..754eef2c70e 100644 --- a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -16,6 +16,7 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('PyTorch-bundle', '2.1.2', versionsuffix), ('einops', '0.7.0'), + ('CUTLASS', '3.4.0', versionsuffix), ] sanity_pip_check = True From 7a1e6e91ad284dcb74058ab2093992eaa76ac9a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 15 Aug 2024 12:47:28 +0200 Subject: [PATCH 225/553] fix shebang and sanity check commands --- .../y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb index 0ba5cdef596..bbf260ff417 100644 --- a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -27,11 +27,12 @@ dependencies = [ ('yelp-xsl', '42.1'), ('ITSTool', '2.0.7'), ('libxml2', '2.11.4'), - # docbook-xsl ? ('mallard-ducktype', '1.0.2'), ('lxml', '4.9.2'), ] +fix_python_shebang_for = ['bin/*'] + sanity_check_paths = { 'files': [ 'bin/yelp-build', @@ -41,4 +42,9 @@ sanity_check_paths = { 'dirs': ['share/%(name)s'], } +sanity_check_commands = [ + 'yelp-build cache -h', + 'yelp-check hrefs -h', +] + moduleclass = 'tools' From 2335c2ed629398fe0772e1eb46f264c0ad7056e4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 16 Aug 2024 10:39:02 +0200 Subject: [PATCH 226/553] adding easyconfigs: gffread-0.12.7-GCCcore-12.3.0.eb --- .../gffread/gffread-0.12.7-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eba4233b57f --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +builddependencies = [('binutils', '2.40')] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' From 779b0bea7e2af6792cdf4c76180787964d73053f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 16 Aug 2024 15:55:46 +0100 Subject: [PATCH 227/553] remove `Time::HiRes` from `Perl-bundle-CPAN` --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 6 ------ .../Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 5 ----- .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb | 5 ----- 3 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 3921d7fefac..7e166bd251f 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1767,12 +1767,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'runtest': False, # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.45', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 9754ce8b0ae..154ff6fee8f 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1770,11 +1770,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb index 39679dc0366..7ea28abbcbb 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb @@ -1776,11 +1776,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', From cd8b1ce595195f132125d9b25a98a9efe702c72a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Fri, 16 Aug 2024 22:39:45 +0200 Subject: [PATCH 228/553] update STAR to make it build on non-x86_64 architectures --- easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index a86f215d8dd..b6fbedeec11 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -24,6 +24,9 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +#by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + builddependencies = [ ('xxd', '9.1.0307'), ] From e503cd5ccde2803bdfa7597d1d99b713b68f203f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jure=20Pe=C4=8Dar?= Date: Fri, 16 Aug 2024 23:36:31 +0200 Subject: [PATCH 229/553] Update STAR-2.7.11b-GCC-13.2.0.eb space --- easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index b6fbedeec11..099b3c1127d 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -24,7 +24,7 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] -#by default this is set to -mavx2 which makes it fail on non x86 systems +# by default this is set to -mavx2 which makes it fail on non x86 systems prebuildopts = 'CXXFLAGS_SIMD= ' builddependencies = [ From 81b3932d5fb11b01d37566c25a6e2112652c35bb Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Tue, 6 Aug 2024 13:54:52 +0200 Subject: [PATCH 230/553] HDF URLs (Issue #21131) Squash of: * Change URLs * revert archive changes * Adding missing checksums * h4toh5/2.2.2: Revert changes (no longer available upstream) --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb | 5 +++-- easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb | 4 ++-- .../easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb | 4 ++-- easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb | 4 ++-- easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb | 2 +- 21 files changed, 40 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index e115932f8ee..3e25fa94133 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.11' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb index 36b03f18536..5fade2d2248 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.12' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb index f1b4395af48..39dc5507935 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.13' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb index 84bff2749e9..74e44dbfc26 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb @@ -4,7 +4,7 @@ name = 'HDF' version = '4.2.13' versionsuffix = '-no-netcdf' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. This version suppresses the netcdf api, that gives issues with some applications""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb index 1f31e675f7a..56e705f36a2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 204d917a179..51b65acec93 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index bf3fff366f2..a78efd6cee2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index ff08dc71e80..fdee3ff0383 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index bdb2cb878ee..91e084fc238 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb index 869a6a796a2..7fff3f348bb 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb index fc36bb04673..7acaaafc09d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb index 682e5e20b6c..4af8d274164 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb index f0286cd30bd..abab2d962f5 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index fd6e6693977..7e6b5eefbe8 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index a6094f7f816..175aaba4731 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb index 5b868a7fe58..f2c20e888b9 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index 630c4aa2dc2..fd9d8d3d4ea 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb index 0b79b7cfc94..605d20f196f 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb index 81636ad6de3..079d5eb7de1 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb index 8e8e8c7f705..50fe19e455a 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb index 1a825bc8ed8..28d67776a1b 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.5' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" From e784334ae72af7eb166ce85c2e9af2f890ce57ed Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 19 Aug 2024 14:04:41 +0200 Subject: [PATCH 231/553] Add comment to ChangeLog in patch --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch index 6e719c21dae..ac5229788c5 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch @@ -6,7 +6,9 @@ # # ChangeLog: # - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup -# author: Jiri Furst +# author: Jiri Furst +# - v2406 - set MPFR_ARCH_PATH and GMP_ARCH_PATH to CGAL config +# author: Jiri Furst # # ------------------------------------------------------------------------- --- /dev/null 2020-12-14 09:05:45.272769166 +0100 From 13513c987d3df236f91a50713f88a97938a0c5a8 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 19 Aug 2024 14:32:16 +0200 Subject: [PATCH 232/553] Update patch checksum --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb index 185cfead980..cfdb5e08252 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, - {'OpenFOAM-v2406-cleanup.patch': '3ed44da40e9872d1cf096bb0bfd9d5c79ca984d7bc01e4ae30c14b3e7223d749'}, + {'OpenFOAM-v2406-cleanup.patch': '7f1a068b4f4e16735efb2878a7ee115c6fdbd470709d93e211178f8090c6d0ae'}, {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, ] From e9294735bad09f1a56189ccad578857a2c1f85f0 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 19 Aug 2024 14:57:12 +0200 Subject: [PATCH 233/553] fix patch checksum --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb index cfdb5e08252..ba59d215581 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, - {'OpenFOAM-v2406-cleanup.patch': '7f1a068b4f4e16735efb2878a7ee115c6fdbd470709d93e211178f8090c6d0ae'}, + {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'}, {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, ] From 86fb783de058d84724a157bca4f34b265ea88b8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Aug 2024 09:49:50 +0200 Subject: [PATCH 234/553] consisently set $CXXFLAGS_SIMD to empty in easyconfigs for STAR 2.7.11a + 2.7.11b --- easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 3 +++ easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb | 3 +++ easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb index 42f094bb67b..b98510247d3 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -31,6 +31,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb index 1943af96d5e..37285b73829 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -31,6 +31,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb index cf16b5c2979..4d85b037ea2 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -24,6 +24,9 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), From 765ba900daf5953e306c4dad896febe52fdd6c00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Aug 2024 10:22:41 +0200 Subject: [PATCH 235/553] add missing xxd build dependency for STAR 2.7.11* --- easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 4 ++++ easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb | 4 ++++ easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb | 8 ++++++-- easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 6 +++--- 4 files changed, 17 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb index b98510247d3..a61fe5e85bb 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.1696'), +] + dependencies = [ ('HTSlib', '1.17'), ('zlib', '1.2.12'), diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb index 37285b73829..a017a2ba109 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb index 4d85b037ea2..67cac5d0f47 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -24,8 +24,9 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] -# by default this is set to -mavx2 which makes it fail on non x86 systems -prebuildopts = 'CXXFLAGS_SIMD= ' +builddependencies = [ + ('xxd', '9.0.2112'), +] dependencies = [ ('HTSlib', '1.18'), @@ -34,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index 099b3c1127d..886aa0a24c5 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -24,9 +24,6 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] -# by default this is set to -mavx2 which makes it fail on non x86 systems -prebuildopts = 'CXXFLAGS_SIMD= ' - builddependencies = [ ('xxd', '9.1.0307'), ] @@ -38,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ From a2c2f2f1447e3d13b6d102c1c61f5cd05c4a26b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 11:24:00 +0200 Subject: [PATCH 236/553] adding easyconfigs: bliss-0.77-GCC-13.2.0.eb and patches: bliss-0.77_install_fix.patch --- .../b/bliss/bliss-0.77-GCC-13.2.0.eb | 37 +++++++++++++++++++ .../b/bliss/bliss-0.77_install_fix.patch | 31 ++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb new file mode 100644 index 00000000000..3831e26c62d --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'bliss' +version = '0.77' + +homepage = 'https://users.aalto.fi/~tjunttil/bliss/' +description = """Bliss is an open-source tool for computing canonical labelings and automorphism groups of graphs.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://users.aalto.fi/~tjunttil/bliss/downloads/'] +sources = [SOURCE_ZIP] +patches = ['bliss-0.77_install_fix.patch'] +checksums = [ + {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'}, + {'bliss-0.77_install_fix.patch': '01a0824c5b121bd6ab0df324ee9c9dd4d4f0bfd8bb2800157cf270e8a1b194ea'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +configopts = "-DUSE_GMP=OFF " + +sanity_check_paths = { + 'files': [ + 'bin/bliss', + 'lib/libbliss.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + ], +} + +sanity_check_commands = ["bliss -help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch new file mode 100644 index 00000000000..a5fcbd85018 --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch @@ -0,0 +1,31 @@ +diff -u CMakeLists.txt.orig CMakeLists.txt +--- CMakeLists.txt.orig 2021-02-18 11:59:34.000000000 +0100 ++++ CMakeLists.txt 2024-08-15 15:04:21.293765655 +0200 +@@ -62,3 +62,27 @@ + target_link_libraries(bliss-executable ${GMP_LIBRARIES}) + endif(USE_GMP) + set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss) ++ ++include(GNUInstallDirs) ++ ++set( ++ BLISS_HEADERS ++ src/bliss_C.h ++ src/uintseqhash.hh ++ src/abstractgraph.hh ++ src/stats.hh ++ src/digraph.hh ++ src/defs.hh ++ src/heap.hh ++ src/graph.hh ++ src/partition.hh ++ src/kqueue.hh ++ src/utils.hh ++ src/orbit.hh ++ src/timer.hh ++ src/bignum.hh ++) ++ ++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss) From b121b9ee706be3291051b5ddbb3852e1abc05237 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 11:33:05 +0200 Subject: [PATCH 237/553] adding easyconfigs: Rasqal-0.9.33-GCCcore-12.3.0.eb, gtk-doc-1.34.0-GCCcore-12.3.0.eb, Pygments-2.18.0-GCCcore-12.3.0.eb, dblatex-0.3.12-foss-2023a.eb --- .../d/dblatex/dblatex-0.3.12-foss-2023a.eb | 33 ++++++++++++ .../gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ .../Pygments-2.18.0-GCCcore-12.3.0.eb | 30 +++++++++++ .../r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb | 38 ++++++++++++++ 4 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb new file mode 100644 index 00000000000..db41d0c240f --- /dev/null +++ b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'dblatex' +version = '0.3.12' + +homepage = 'https://dblatex.sourceforge.net/' +description = """dblatex is a program that transforms your SGML/XML DocBook documents to DVI, + PostScript or PDF by translating them into pure LaTeX as a first process. + MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://master.dl.sourceforge.net/project/dblatex/dblatex/dblatex-%(version)s/'] +sources = ['%(name)s3-%(version)s.tar.bz2'] +checksums = ['16e82786272ed1806a079d37914d7ba7a594db792dc4cc34c1c3737dbd4da079'] + +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), + ('texlive', '20230313'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'dbtexmf.dblatex'} + +postinstallcmds = ["cp -r %(builddir)s/%(name)s3-%(version)s/scripts %(installdir)s/bin"] + +sanity_check_commands = ['dblatex --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c77d925c3a0 --- /dev/null +++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'gtk-doc' +version = '1.34.0' + +homepage = 'https://gitlab.gnome.org/GNOME/gtk-doc' +description = """Documentation tool for public library API""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/gtk-doc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1d544fa70ae60014a241b674c9d989f4ad6a96554652ebf73bbe94b4da1aa35'] + +builddependencies = [ + ('binutils', '2.40'), + ('yelp-tools', '42.1'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pygments', '2.18.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/gtkdoc-depscan', + 'bin/gtkdoc-fixxref', + 'bin/gtkdoc-check', + 'bin/gtkdocize', + 'bin/gtkdoc-mkdb', + 'bin/gtkdoc-mkhtml', + 'bin/gtkdoc-mkhtml2', + 'bin/gtkdoc-mkman', + 'bin/gtkdoc-mkpdf', + 'bin/gtkdoc-rebase', + 'bin/gtkdoc-scan', + 'bin/gtkdoc-scangobj', + ], + 'dirs': [ + 'lib/cmake/GtkDoc', + 'share/%(name)s', + ], +} + +sanity_check_commands = ['gtkdoc-depscan'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2f441283024 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.18.0' + +homepage = 'https://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_PY3_WHL] +checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a'] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': [], +} + +sanity_check_commands = ['pygmentize --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3d5e0ad9d83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Rasqal' +version = '0.9.33' +homepage = 'hhttps://librdf.org/rasqal' +description = """A library handling RDF query syntaxes, construction and execution""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6924c9ac6570bd241a9669f83b467c728a322470bf34f4b2da4f69492ccfd97c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Raptor', '2.0.16'), +] + +dependencies = [ + ('libgcrypt', '1.10.3'), + ('MPFR', '4.2.0'), + ('PCRE', '8.45'), + ('gtk-doc', '1.34.0'), + ('ICU', '73.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-static --enable-release" + +sanity_check_paths = { + 'files': ['bin/roqet', 'lib/librasqal.%s' % SHLIB_EXT], + 'dirs': ['include/rasqal/'] +} + +sanity_check_commands = ["roqet --help"] + +moduleclass = 'lib' From bbf439c07ef1487f59ade00ace40b454ba4ef075 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 11:34:44 +0200 Subject: [PATCH 238/553] adding easyconfigs: rjags-4-15-foss-2023a-R-4.3.2.eb --- .../r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..f793f925da6 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['35cd4c1faaaa8523b87ac053b881dccf29798f073f438459589e786b95ef18a1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('JAGS', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From 8e945ba48499d3865e07e7015fdf790df739abf5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 12:09:15 +0200 Subject: [PATCH 239/553] use GMP, describe patch file --- easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb | 8 ++++++-- .../easyconfigs/b/bliss/bliss-0.77_install_fix.patch | 2 ++ 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb index 3831e26c62d..ec9a99bc306 100644 --- a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb @@ -13,14 +13,18 @@ sources = [SOURCE_ZIP] patches = ['bliss-0.77_install_fix.patch'] checksums = [ {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'}, - {'bliss-0.77_install_fix.patch': '01a0824c5b121bd6ab0df324ee9c9dd4d4f0bfd8bb2800157cf270e8a1b194ea'}, + {'bliss-0.77_install_fix.patch': '1550b6c7f8208f56093c0b6bf0d2e3df42afab81cd69eb70303515c9923e9513'}, ] builddependencies = [ ('CMake', '3.27.6'), ] -configopts = "-DUSE_GMP=OFF " +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = "-DUSE_GMP=ON " sanity_check_paths = { 'files': [ diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch index a5fcbd85018..faea2ad4daf 100644 --- a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch @@ -1,3 +1,5 @@ +Adds install commands to CMakeLists.txt +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/bliss/-/blob/0.77-3/make-install.patch diff -u CMakeLists.txt.orig CMakeLists.txt --- CMakeLists.txt.orig 2021-02-18 11:59:34.000000000 +0100 +++ CMakeLists.txt 2024-08-15 15:04:21.293765655 +0200 From 69bd18a3eee3da59d3ff59f90b1da5482696a6b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 12:17:53 +0200 Subject: [PATCH 240/553] add missing build dependency --- .../easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb index 2f441283024..54edd0b830e 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCELOWER_PY3_WHL] checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a'] +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ] From 9a1b9fe0912997fc63755b129abddc076b5aee9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 13:01:07 +0200 Subject: [PATCH 241/553] add missing easyconfig --- .../r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1607220271e --- /dev/null +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Based on Raptor2 RPM spec file: +# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec +# The RPM patches have been integrated in the version 2.0.16 +# +# Update: Petr Král (INUITS) +## +easyblock = 'ConfigureMake' + +name = 'Raptor' +version = '2.0.16' +homepage = 'https://librdf.org/raptor/' +description = """Set of parsers and serializers that generate Resource Description Framework +(RDF) triples by parsing syntaxes or serialize the triples into a syntax.""" +# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = ['raptor2-%(version)s.tar.gz'] +checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), + ('cURL', '8.0.1'), + ('ICU', '73.2'), +] + +configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no" + +# fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked' +# see https://github.com/dajobe/raptor/pull/58 +local_sed_replacement = 's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' +prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement + +sanity_check_paths = { + 'files': ['bin/rapper', 'lib/libraptor2.%s' % SHLIB_EXT], + 'dirs': ['include/raptor2/'] +} + +sanity_check_commands = ["rapper --help"] + +moduleclass = 'lib' From 41f451dae6d5dbdbde5f57e694ae8e37fe1837c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 13:12:11 +0200 Subject: [PATCH 242/553] fix PEP8-compliance --- easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb index 1607220271e..979b9b88135 100644 --- a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -41,7 +41,7 @@ configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no # fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked' # see https://github.com/dajobe/raptor/pull/58 -local_sed_replacement = 's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' +local_sed_replacement = r's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement sanity_check_paths = { From df2c01d02ab3fab5863392ddc55051c04ebe2ced Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 14:15:00 +0200 Subject: [PATCH 243/553] adding easyconfigs: IsoQuant-3.5.0-foss-2023a.eb, gffutils-0.13-foss-2023a.eb --- .../g/gffutils/gffutils-0.13-foss-2023a.eb | 47 +++++++++++++++++++ .../i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb | 45 ++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb create mode 100644 easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb new file mode 100644 index 00000000000..2b52f3965bc --- /dev/null +++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'gffutils' +version = '0.13' + +homepage = 'https://github.com/daler/gffutils' +description = """Gffutils is a Python package for working with and manipulating + the GFF and GTF format files typically used for genomic annotations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('pyfaidx', '0.8.1.1'), + ('Biopython', '1.83'), + ('pybedtools', '0.9.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('argh', '0.31.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2edac856ff50126f6e47d884751328c9f466bacbbb6cbfdac322053d94705494'], + }), + ('argcomplete', '3.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b'], + }), + ('simplejson', '3.19.3', { + 'checksums': ['8e086896c36210ab6050f2f9f095a5f1e03c83fa0e7f296d6cba425411364680'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['58e7bb579796fff70e728380ef2d8ffd4a3bc895e53e6529855a0cf87ba6a77a'], + }), +] + +sanity_check_commands = [ + "python -c 'from gffutils import helpers'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..41248bcbf73 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'IsoQuant' +version = '3.5.0' + +homepage = 'https://github.com/ablab/IsoQuant' +description = """IsoQuant is a tool for the genome-based analysis of long RNA reads, + such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify + transcript models with high precision and decent recall. If the reference annotation is given, + IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. + IsoQuant further performs annotated gene, isoform, exon and intron quantification. + If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ablab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['8cbba80b5eb0ed85fe0b519693157eb97820bc1d79ff44435736bf799af85c1f'] + +dependencies = [ + ('Python', '3.11.3'), + ('gffutils', '0.13'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('pyfaidx', '0.8.1.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('PyYAML', '6.0'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['isoquant.py'], + 'dirs': [], +} + +sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"] + +moduleclass = 'bio' From fa86b640f3bcd900b990a2e4d95b6e24ce4c73b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 14:54:29 +0200 Subject: [PATCH 244/553] add missing dependency --- easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb index c77d925c3a0..dd18263d557 100644 --- a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('Pygments', '2.18.0'), + ('GLib', '2.77.1'), ] sanity_check_paths = { From 6635ad9dcc8e5b5d02f525994302109ecaa75820 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 15:42:50 +0200 Subject: [PATCH 245/553] adding easyconfigs: medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb --- .../medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c2ca402d8ba --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,85 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' From a8843e992878dc26846478c027e8b4212b74582a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 20 Aug 2024 15:54:39 +0200 Subject: [PATCH 246/553] Update python-igraph-0.10.6-foss-2022b.eb - add cairo dep Seems on some systems (generoso) it picked system cairo - so it did not fail https://github.com/easybuilders/easybuild-easyconfigs/pull/21141#issuecomment-2298833068 --- .../p/python-igraph/python-igraph-0.10.6-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb index 01e1aa2d9c6..3b61ec3f869 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -20,6 +20,7 @@ dependencies = [ ('Clang', '16.0.4'), ('libxml2', '2.10.3'), ('zlib', '1.2.12'), + ('cairo', '1.17.4'), ] use_pip = True From d35df4bafbcf74893ba81e4f050942e96314f298 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 20 Aug 2024 16:08:35 +0200 Subject: [PATCH 247/553] update cd-hit with sanity_check_commands --- easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb index c4cacfb04bf..bd59609605c 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb @@ -1,4 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version # Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) easyblock = 'MakeCp' @@ -35,4 +36,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + moduleclass = 'bio' From ec12a9fe2e91500dc99f124b378d27d45d590dcb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Aug 2024 17:06:40 +0200 Subject: [PATCH 248/553] Update easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb Co-authored-by: Kenneth Hoste --- .../m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb index c2ca402d8ba..c9ac4870bf5 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), # includes cffi - ('TensorFlow', '2.13.0', versionsuffix), + ('TensorFlow', '2.15.1', versionsuffix), ('Pysam', '0.22.0'), ('SAMtools', '1.18'), ('minimap2', _minimap_ver), From 1bbe45fd783a31a55cd592dc3a7411e5eef5c7fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Aug 2024 17:41:07 +0200 Subject: [PATCH 249/553] adding easyconfigs: VSEARCH-2.28.1-GCC-10.2.0.eb --- .../v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..14ed6e6d975 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.28.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From d2a35a2eac44ae0949523b61f48a3955c15a959c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Aug 2024 18:30:04 +0200 Subject: [PATCH 250/553] adding easyconfigs: longread_umi-0.3.2-foss-2023a.eb, cutadapt-4.9-GCCcore-12.3.0.eb, Filtlong-0.2.1-GCC-12.3.0.eb --- .../c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb | 60 ++++++++++++++ .../f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb | 39 +++++++++ .../longread_umi-0.3.2-foss-2023a.eb | 82 +++++++++++++++++++ 3 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1f54c552c2e --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.9' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Cython', '3.0.8'), # required for dnaio +] + +dependencies = [ + ('pigz', '2.8'), + ('Python', '3.11.3'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # note: newer xopen versions require newer python-isal + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '1.2.1', { + 'checksums': ['4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38'], + }), + (name, version, { + 'checksums': ['da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..25bf2c570f0 --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.13'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..ce954f2edae --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('cutadapt', '4.9'), + ('BCFtools', '1.18'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.1'), + ('gawk', '5.3.0'), + ('medaka', '1.11.3'), + ('minimap2', '2.26'), + ('parallel', '20230722'), + ('Pysam', '0.22.0'), + ('Racon', '1.5.0'), + ('SAMtools', '1.18'), + ('seqtk', '1.4'), + ('VSEARCH', '2.25.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version +local_deps_patch = ( + "sed -i " + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' From 0ccfd57238dbf895a7be37e830682ad80fe1abb7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 20 Aug 2024 19:21:47 +0200 Subject: [PATCH 251/553] update name, version, sources, postinstallcmds, local_pycistopic_preinstallopts --- .../SCENICplus-1.0a1-20240513-foss-2023a.eb | 279 ++++++++++++++++++ 1 file changed, 279 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb new file mode 100644 index 00000000000..dbff79bbe8c --- /dev/null +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -0,0 +1,279 @@ +easyblock = 'PythonBundle' + +name = 'SCENICplus' +version = '1.0a1-20240513' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1'), + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), + ('Sphinx-RTD-Theme', '2.0.0'), + ('scrublet', '0.2.3'), + ('numexpr', '2.9.0'), + ('Kaleido', '0.2.1'), + ('pyfasta', '0.5.2'), + ('gensim', '4.3.2'), +] + +# fix requirements.txt of scenicplus +local_preinstallopts = ( + "sed -i" + " -e '/typing==3.7.4.3/d'" + " -e 's/==.*//g'" + " -e '/pyarrow-hotfix/d'" + " -e '/line-profiler/d'" + " -e '/ndindex/d'" + " -e '/sinfo/d'" + " requirements.txt && " +) +# unpin version restriction and delete typing requirement +local_pycistopic_preinstallopts = ( + "sed -i" + " -e 's/pyscenic>=0.12.0/pyscenic/'" + " -e 's/pandas==1.5/pandas/'" + " -e 's/python-Levenshtein/Levenshtein/'" + " -e 's/python-igraph/igraph/'" + " -e '/typing/d'" + # delete pyscenic and loomxpy req from commit - have versions now + " -e '/pyscenic@git/d'" + " -e '/loomxpy@git/d'" + " requirements.txt && " + "sed -i" + " -e 's/pandas == 1.5/pandas/'" + " -e 's/matplotlib < 3.7/matplotlib/'" + " pyproject.toml && " +) +# delete typing from requirements +local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " +# unpin version restriction and delete poetry.lock +local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " +local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " +local_loomxpy_preinstallopts += "rm poetry.lock && " + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bs4', '0.0.2', { + 'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'], + }), + ('attr', '0.3.2', { + 'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'], + }), + ('attrs', '23.2.0', { + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('lda', '3.0.0', { + 'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'], + }), + ('zope.interface', '6.2', { + 'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'], + }), + ('zope.event', '5.0', { + 'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'], + }), + ('gevent', '24.2.1', { + 'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('suds-community', '1.1.2', { + 'modulename': 'suds', + 'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'], + }), + ('grequests', '0.7.0', { + 'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('easydev', '0.12.1', { + 'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'], + }), + ('bioservices', '1.11.2', { + 'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'], + }), + ('gseapy', '0.10.8', { + 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pybigtools', '0.1.2', { + 'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], + }), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('pyranges', '0.0.111', { + 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], + }), + ('pyrle', '0.0.39', { + 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], + }), + ('pyvis', '0.3.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests_cache', '1.2.0', { + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('scanorama', '1.7.4', { + 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + ('scatac_fragment_tools', '0.1.0', { + 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], + }), + ('snakemake_interface_common', '1.17.1', { + 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], + }), + ('snakemake_interface_report_plugins', '1.0.0', { + 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('globre', '0.1.5', { + 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], + }), + ('bidict', '0.23.1', { + 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], + }), + ('tmtoolkit', '0.12.0', { + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4', { + 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], + }), + ('nbsphinx-link', '1.3.0', { + 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], + }), + ('numpydoc', '1.7.0', { + 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('ansicolors', '1.1.8', { + 'modulename': 'colors', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], + }), + ('papermill', '2.6.0', { + 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('marshmallow', '3.21.1', { + 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], + }), + ('dataclasses_json', '0.6.4', { + 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], + }), + ('loomxpy', '0.4.2', { + 'preinstallopts': local_loomxpy_preinstallopts, + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '2.0a-dca4bb6', { + 'modulename': 'pycisTopic', + 'preinstallopts': local_pycistopic_preinstallopts, + # download commit dca4bb6 to be compatible with pycistarget + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], + 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], + }), + ('pycistarget', '1.0a1-16d14b9', { + 'preinstallopts': local_pycistarget_preinstallopts, + # download commit 16d14b9 to make '$ scenicplus' work + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], + 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], + }), + ('%(namelower)s', version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'], + }), +] + +# copy files to let 'scenicplus init_snakemake' works +postinstallcmds = [ + "cp -r %%(builddir)s/scenicplus/scenicplus-%s*/src/scenicplus/snakemake " + "%%(installdir)s/lib/python%%(pyshortver)s/site-packages/scenicplus" % local_commit +] + +sanity_check_commands = ['scenicplus init_snakemake --help'] + +moduleclass = 'bio' From 00e56aff1ccc692a885560b7a3e66e02b3d2d11b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 08:45:24 +0200 Subject: [PATCH 252/553] adding easyconfigs: medaka-1.12.1-foss-2023a.eb --- .../m/medaka/medaka-1.12.1-foss-2023a.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb new file mode 100644 index 00000000000..f95d01c89d9 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb @@ -0,0 +1,86 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' From f03ea94efe0ddd7efb10e2d96aad0ef7851b115b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 08:45:42 +0200 Subject: [PATCH 253/553] adding easyconfigs: medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb --- .../medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3e055e5d8dd --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,88 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' From 98c7d10918dfadfb6d53ba232450dfd5a6b6ef0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 10:02:41 +0200 Subject: [PATCH 254/553] fix type in configure option to disable VTK Python linking in ParaView 5.12.0 --- .../easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb index 1642881e802..abec428859f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -57,7 +57,7 @@ _copts = [ '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', '-DVTK_OPENGL_HAS_OSMESA=OFF', - '-DVTK_PYTHON_OPTIONAL_LINK=OFFVTK_PYTHON_=OFF'] + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] configopts = ' '.join(_copts) sanity_check_paths = { From c847591f91b846aae0bba5f035f6f66bec6fa79a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 11:27:44 +0200 Subject: [PATCH 255/553] separate PR for VTK-9.3.0-foss-2023a.eb --- .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 98 ------------------- 1 file changed, 98 deletions(-) delete mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb deleted file mode 100644 index 740fd888dfb..00000000000 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ /dev/null @@ -1,98 +0,0 @@ -## -# Authors:: -# * Fotis Georgatos -# * Robert Mijakovic -# Update: Pavel Tománek (Inuits) -## - -easyblock = 'CMakeNinja' - -name = 'VTK' -version = '9.3.0' - -homepage = 'https://www.vtk.org' -description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for - 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several - interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization - algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques - such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] -sources = [ - SOURCE_TAR_GZ, - '%(name)sData-%(version)s.tar.gz', -] -patches = [('vtk-version.egg-info', '.')] -checksums = [ - {'VTK-9.3.0.tar.gz': 'fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9'}, - {'VTKData-9.3.0.tar.gz': 'f82142dd327e995c9536c1003e1370bb4092c96f23edb8119d16d2411ef35dc3'}, - {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, -] - -builddependencies = [ - ('CMake', '3.26.3'), - ('Ninja', '1.11.1'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('XZ', '5.4.2'), - ('libGLU', '9.0.3'), - ('X11', '20230603'), - ('Qt5', '5.15.10'), -] - -separate_build_dir = True - -# OpenGL -configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -# Python -configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " -configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " -configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " -# Other -configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib " -configopts += "-DVTK_QT_VERSION=5 " -configopts += "-DQt5_DIR=$EBROOTQT5 " -configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " -configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" - -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -# Install a egg-info file so VTK is more python friendly, required for mayavi -local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' -postinstallcmds = [ - 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), -] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x - for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] -local_vtk_exec += ['vtkpython'] -local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + - ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], - 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], -} - -sanity_check_commands = [ - "python -c 'import %(namelower)s'", - "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", - # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), - # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 - "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, -] - -moduleclass = 'vis' From fc2c99743c252b08c61e80d3b7a4e138c0ea78d8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 11:30:39 +0200 Subject: [PATCH 256/553] add Qt support --- easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb index 9278837da13..740fd888dfb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -2,6 +2,7 @@ # Authors:: # * Fotis Georgatos # * Robert Mijakovic +# Update: Pavel Tománek (Inuits) ## easyblock = 'CMakeNinja' @@ -42,6 +43,7 @@ dependencies = [ ('XZ', '5.4.2'), ('libGLU', '9.0.3'), ('X11', '20230603'), + ('Qt5', '5.15.10'), ] separate_build_dir = True @@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " From dc043891ddc0c74c14c3377943777d321fafa4ae Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 21 Aug 2024 11:47:05 +0200 Subject: [PATCH 257/553] Update Visit-3.4.1-foss-2023a.eb - add comment to VTK-9.2.6 --- easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb index 7e5eaa8b270..406d78fa312 100644 --- a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -37,6 +37,7 @@ dependencies = [ ('libglvnd', '1.6.0'), ('Qt5', '5.15.10'), ('Qwt', '6.3.0'), + # Visit-3.4.1 needs VTK-9.2.x (not 9.3.x) - https://github.com/visit-dav/visit/issues/19547 ('VTK', '9.2.6'), ('FFmpeg', '6.0'), ] From 4ca72c270d18e5c2157c4ea0144a28e4562b1112 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 11:56:38 +0200 Subject: [PATCH 258/553] add recent version of make as build dependency for Raptor --- easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb index 979b9b88135..61c358020c8 100644 --- a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -28,6 +28,7 @@ checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] builddependencies = [ ('Autotools', '20220317'), ('binutils', '2.40'), + ('make', '4.4.1'), ] dependencies = [ From ca33632d3559a6e4aed6a2e157027ce71ff4a4f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 21 Aug 2024 12:55:12 +0200 Subject: [PATCH 259/553] adding easyconfigs: PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb, Redland-1.0.17-GCC-12.3.0.eb, unixODBC-2.3.12-GCCcore-12.3.0.eb --- .../PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb | 218 ++++++++++++++++++ .../r/Redland/Redland-1.0.17-GCC-12.3.0.eb | 37 +++ .../unixODBC-2.3.12-GCCcore-12.3.0.eb | 30 +++ 3 files changed, 285 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..163a41f725f --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb @@ -0,0 +1,218 @@ +easyblock = 'Bundle' + +name = 'PEcAn' +version = '1.7.2.9000' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/PecanProject/pecan' +description = """Ecosystem science, policy, and management informed by the best available data and models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('PostgreSQL', '16.1'), + ('CDO', '2.2.2'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.2'), + ('UDUNITS', '2.2.28'), + ('texlive', '20230313'), + ('NCO', '5.1.9'), + ('ncview', '2.1.8'), + ('rjags', '4-15', versionsuffix), + ('Redland', '1.0.17'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://pecanproject.r-universe.dev/src/contrib/', # PEcAn sources + ], +} + +local_sed_patterns_duckdb = '1146s/prefix_front_/prefix_front_back.prefix_front_/g;' +local_sed_patterns_duckdb += '1147s/prefix_back_/prefix_front_back.prefix_back_/g' + +exts_list = [ + ('PEcAn.logger', '1.8.1.9000', { + 'checksums': ['3d1d8a6c9afa677dde8a4aaf72809932f0b6b5385ae4a6fc2059b48ed4b09195'], + }), + ('PEcAn.remote', '1.7.2', { + 'checksums': ['59feda08ac6784c5e607a70166e002df96385efbba3b77148b4cf9a0a1e2c9dc'], + }), + ('PEcAn.utils', '1.7.2', { + 'checksums': ['d83ae2a605f7867659d10de952f5db6b947dc3d2bc05633c0f72ced0b4caad17'], + }), + ('PEcAn.DB', version, { + 'checksums': ['f493d6ab100fce139bdb9747c91faff5cf60ff296ee16a82c6bc2366a9722231'], + }), + ('PEcAn.settings', '1.7.2', { + 'checksums': ['ab0dd41e9f421a84e68a16a1e4b290f70d852d23e66a2de1c3e91bf883aa1aeb'], + }), + ('PEcAn.MA', '1.7.2', { + 'checksums': ['bf3a5b6ac8adce4efb6be504cdeb10a71a59b3ac5af72c8d77b59a39c7d90ceb'], + }), + ('PEcAn.emulator', version, { + 'checksums': ['f4465a154e41cfe5a2cc94035ae4a5ddbfd3b5fc54a83bc9578c98a9eb07cff1'], + }), + ('PEcAn.priors', '1.7.2', { + 'checksums': ['001c26275ef23dda369fa2a5b408e481265d29137edeaebd03a30a39b4682edd'], + }), + ('PEcAn.uncertainty', version, { + 'checksums': ['a0d1a3a3d65e06b066d23473def763f5e158b2356ee5fe9e09020fe311e9ef4a'], + }), + ('amerifluxr', '1.0.0', { + 'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'], + }), + ('geonames', '0.999', { + 'checksums': ['1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b'], + }), + ('solartime', '0.0.2', { + 'checksums': ['5dd7a28db2bd4881ab740cd7004b88cd05c61e0954e3a10c8e18ebbe07d3e7d1'], + }), + ('bigleaf', '0.8.2', { + 'checksums': ['e41d82fb6298150c46f57128e959a1f1c6cfa55e916c32544bab7be69b0b6df7'], + }), + ('REddyProc', '1.3.3', { + 'checksums': ['3f673bd24f41813f631bf25139c9595bd91483e898ec31b7207c4eb8b7ff486b'], + }), + ('suntools', '1.0.0', { + 'checksums': ['42b7b39bd23ad48ded002150a0e7798fab94ed9828e5b5fdd8e5e1c9040697e2'], + }), + ('fauxpas', '0.5.2', { + 'checksums': ['84d07361a146b419cb1dcb7751654e3d5f159cf2704faf498e5ea56c8de61ef6'], + }), + ('nneo', '0.1.0', { + 'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'], + }), + ('PEcAn.data.atmosphere', '1.7.2', { + 'checksums': ['1847151588f669e91b35de637c804328efbc606141bf992bee650fd261b70e5a'], + }), + ('redland', '1.0.17-18', { + 'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'], + }), + ('datapack', '1.4.1', { + 'checksums': ['6149733ae90e6bbbb53d5f85ca29cec5f811825e794b56029b7f325de6637493'], + }), + ('dplR', '1.7.7', { + 'checksums': ['0e35a4d2a22773499f9e4592d1a198a08c9842388ce1e5a35394990ed4cdb2bd'], + }), + ('neonUtilities', '2.4.2', { + 'checksums': ['37b4efd0ed3b724de999d08d4d430954a6c717b1d943bc84c513c4fe8dbca057'], + }), + ('storr', '1.2.5', { + 'checksums': ['4224c3991d9c043a45ce530d0698d7f2cdca231b26fe31b45e0db865026e5f63'], + }), + ('thor', '1.1.5', { + 'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'], + }), + ('duckdb', '1.0.0-2', { + 'checksums': ['3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'], + # fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 + 'preinstallopts': "sed -i '%s' src/duckdb/third_party/re2/re2/prog.cc && " % local_sed_patterns_duckdb, + }), + ('duckdbfs', '0.0.4', { + 'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'], + }), + ('neonstore', '0.5.1', { + 'checksums': ['f911e957861d558adead8ca77e4d1575a47dceb9553f1aa9d818460126deab9b'], + }), + ('HDInterval', '0.2.4', { + 'checksums': ['bb07f0edd660a02ed18e578c2798eb8c2db0e181a5e0c3e23db182d13e9494f6'], + }), + ('kknn', '1.3.1', { + 'checksums': ['22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db'], + }), + ('timeSeries', '4032.109', { + 'checksums': ['5e0c47584e0b01ea4011ed5ced217d95f8bb872611f6b029b0797d95eebd731f'], + }), + ('gss', '2.2-7', { + 'checksums': ['3b13144702c570c83462b4ea2ad17f4bd630cff5bf2ab0347a33c7e86a4f3f6a'], + }), + ('fBasics', '4032.96', { + 'checksums': ['e1556909871c836668b10bf90e1676aac6a2892a04663d7ab00c22a64c0b8690'], + }), + ('rmutil', '1.1.10', { + 'checksums': ['819fd7ce695cc742b4594705986eb06764460fc88521ea32de793c49de7ca5f9'], + }), + ('stable', '1.1.6', { + 'checksums': ['2238788a35b5aa9e175ad7b92348640c3dcad68b6ab0a0bc04aeec9084d29da4'], + }), + ('statip', '0.2.3', { + 'checksums': ['56a81a1882856cd1c5711ba133417b64f09071dda356e74280a0dba0db60d54f'], + }), + ('modeest', '2.4.0', { + 'checksums': ['1a949409bf64679d32400d20aa3d53e65a9a20f5bd1a40993b95f81100e0ed20'], + }), + ('runjags', '2.2.2-4', { + 'checksums': ['6f656e4d0620c0806e596ddb4bfec3934534ec17c02da699fcbfd6720a6f424f'], + }), + ('swfscMisc', '1.6.5', { + 'checksums': ['a49cb390643c4079f02986862eb2dfd33db4e6b6498e849bb418f73ffd6882e1'], + }), + ('CDM', '8.2-6', { + 'checksums': ['144a85e36c120e9f8a5bd35c1db50cf089ea4807721ac14460137b9a4b1c98d1'], + }), + ('TAM', '4.2-21', { + 'checksums': ['0d1782e42e89c1863edab12c1861d0e2628ea9ee1a1e37d268f27a3deaf3d568'], + }), + ('pbv', '0.5-47', { + 'checksums': ['e17a04efa96a601ab72172b59f555f36d28bb824f02f363cc5806b05d7d7c792'], + }), + ('sirt', '4.1-15', { + 'checksums': ['c12ffcb83bea5b549c7a34c12561f3e57798b83d68a887c5da0d9a66efac3066'], + }), + ('hoardr', '0.5.4', { + 'checksums': ['4e031ac1317584451c09bc8288ed73fb2d6ceea3c10d29dbb4be08157e489a37'], + }), + ('traits', '0.5.1', { + 'checksums': ['3080887a454d69814cd6cb9683a6750db02cf4c77b40b022ef50d40171ba6aca'], + }), + ('SimilarityMeasures', '1.4', { + 'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'], + }), + ('PEcAn.benchmark', '1.7.2', { + 'checksums': ['c9cf9f299f810e4962476db1afdf6a39de77806fd82b6cb8bb7321e96c350db8'], + }), + ('PEcAn.visualization', '1.7.2', { + 'checksums': ['5d25871d57ded42c7ae7f8dbf0a6907c8b828f6a0463286e6ae178b356a4a848'], + }), + ('PEcAn.data.land', version, { + 'checksums': ['29ed015c1e8a5b993aebc31559aa3f7a4136b1f23e4c13a2d55118e7c541da2f'], + }), + ('MODISTools', '1.1.5', { + 'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'], + }), + ('PEcAn.data.remote', version, { + 'checksums': ['691b9e27cf5afb6bfb32873cca6ba284d0ff303873695e86f7653432aa7c66d4'], + }), + ('SparseGrid', '0.8.2', { + 'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'], + }), + ('lqmm', '1.5.8', { + 'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'], + }), + ('PEcAn.workflow', '1.7.2', { + 'checksums': ['cdd60bf6a99b20aed9792b0cf6648c3f55f4b9bd3a00fd0187b7e7ec56815f0f'], + }), + ('PEcAn.assim.batch', version, { + 'checksums': ['d57b7ce1b0cbef0183bcb689f55f0345575289f1b8741c00cbd026eeaea8a6b9'], + }), + ('%(name)s.all', version, { + 'checksums': ['43e036ab8af9834ae6d7d7f4304adfc6cef08348e3be39ca5e51dcbb1fe21cce'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s.all'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb new file mode 100644 index 00000000000..364d182c058 --- /dev/null +++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Redland' +version = '1.0.17' + +homepage = 'https://librdf.org/raptor' +description = """Redland is a set of free software C libraries that provide support for the Resource Description Framework (RDF).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['de1847f7b59021c16bdc72abb4d8e2d9187cd6124d69156f3326dd34ee043681'] + +dependencies = [ + ('Rasqal', '0.9.33'), + ('Raptor', '2.0.16'), + ('PostgreSQL', '16.1'), + ('MariaDB', '11.6.0'), + ('unixODBC', '2.3.12'), + ('SQLite', '3.42.0'), + ('libtool', '2.4.7'), +] + +sanity_check_paths = { + 'files': [ + 'include/%(namelower)s.h', + 'bin/%(namelower)s-config', + 'bin/%(namelower)s-db-upgrade', + 'lib/librdf.%s' % SHLIB_EXT, + ], + 'dirs': ['share/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9d3f2cfc12f --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.12' + +homepage = "https://www.unixodbc.org" +description = """unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.unixodbc.org/'] +checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec'] + +sanity_check_paths = { + 'files': [ + 'lib/libodbc.%s' % SHLIB_EXT, + 'lib/libodbccr.%s' % SHLIB_EXT, + 'lib/libodbcinst.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'data' From cb60dca8f3444794f0d1869bdb6d0b64fa8d851b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 13:29:44 +0200 Subject: [PATCH 260/553] remove old scenicplus from PR --- .../scenicplus-1.0a1-18072024-foss-2023a.eb | 281 ------------------ 1 file changed, 281 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb deleted file mode 100644 index 37f4c7d76b3..00000000000 --- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb +++ /dev/null @@ -1,281 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scenicplus' -version = '1.0a1-18072024' -local_commit = "fa55dae" - -homepage = 'https://github.com/aertslab/scenicplus' -description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) -using combined or separate single-cell gene expression (scRNA-seq) and single-cell -chromatin accessibility (scATAC-seq) data.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -builddependencies = [ - ('poetry', '1.5.1'), - ('maturin', '1.4.0', '-Rust-1.75.0'), - ('CMake', '3.26.3'), -] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('SciPy-bundle', '2023.07'), - ('Single-cell-python-bundle', '2024.02'), - ('anndata', '0.10.5.post1'), - ('BeautifulSoup', '4.12.2'), - ('h5py', '3.9.0'), - ('python-igraph', '0.11.4'), - ('imageio', '2.33.1'), - ('leidenalg', '0.10.2'), - ('lxml', '4.9.2'), - ('MACS2', '2.2.9.1'), - ('numba', '0.58.1'), - ('polars', '0.20.2'), - ('Arrow', '14.0.1'), - ('plotly.py', '5.16.0'), - ('pybedtools', '0.9.1'), - ('pyBigWig', '0.3.22'), - ('pyGAM', '0.9.1'), - ('Pysam', '0.22.0'), - ('Ray-project', '2.9.1'), - ('scikit-image', '0.22.0'), - ('snakemake', '8.4.2'), - ('statsmodels', '0.14.1'), - ('IPython', '8.14.0'), - ('Pandoc', '3.1.2', '', SYSTEM), - ('ipympl', '0.9.3'), - ('PyTables', '3.8.0'), - ('Sphinx-RTD-Theme', '2.0.0'), - ('scrublet', '0.2.3'), - ('numexpr', '2.9.0'), - ('Kaleido', '0.2.1'), - ('pyfasta', '0.5.2'), - ('gensim', '4.3.2'), -] - -# fix requirements.txt of scenicplus -local_preinstallopts = ( - "sed -i" - " -e '/typing==3.7.4.3/d'" - " -e 's/==.*//g'" - " -e '/pyarrow-hotfix/d'" - " -e '/line-profiler/d'" - " -e '/ndindex/d'" - " -e '/sinfo/d'" - " requirements.txt && " -) -# unpin version restriction and delete typing requirement -local_pycistopic_preinstallopts = ( - "sed -i" - " -e 's/pyscenic>=0.12.0/pyscenic/'" - " -e 's/pandas==1.5/pandas/'" - " -e 's/python-Levenshtein/Levenshtein/'" - " -e 's/python-igraph/igraph/'" - " -e '/typing/d'" - # delete pyscenic and loomxpy req from commit - have versions now - " -e '60,61d'" - " requirements.txt && " - "sed -i" - " -e 's/pandas == 1.5/pandas/'" - " -e 's/matplotlib < 3.7/matplotlib/'" - " pyproject.toml && " -) -# delete typing from requirements -local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " -# unpin version restriction and delete poetry.lock -local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " -local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " -local_loomxpy_preinstallopts += "rm poetry.lock && " - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('bs4', '0.0.2', { - 'checksums': 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['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'], - }), - ('grequests', '0.7.0', { - 'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'], - }), - ('pexpect', '4.9.0', { - 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], - }), - ('colorlog', '6.8.2', { - 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], - }), - ('easydev', '0.12.1', { - 'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'], - }), - ('bioservices', '1.11.2', { - 'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'], - }), - ('gseapy', '0.10.8', { - 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], - }), - ('ncls', '0.0.68', { - 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], - }), - ('pybigtools', '0.1.2', { - 'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], - }), - ('pybiomart', '0.2.0', { - 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], - }), - ('sorted_nearest', '0.0.39', { - 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], - }), - ('pyranges', '0.0.111', { - 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], - }), - ('pyrle', '0.0.39', { - 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], - }), - ('pyvis', '0.3.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], - }), - ('url-normalize', '1.4.3', { - 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], - }), - ('cattrs', '23.2.3', { - 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], - }), - ('requests_cache', '1.2.0', { - 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], - }), - ('scanorama', '1.7.4', { - 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], - }), - ('rich_argparse', '1.4.0', { - 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], - }), - ('scatac_fragment_tools', '0.1.0', { - 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], - }), - ('snakemake_interface_common', '1.17.1', { - 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], - }), - ('snakemake_interface_report_plugins', '1.0.0', { - 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], - }), - ('statistics', '1.0.3.5', { - 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], - }), - ('globre', '0.1.5', { - 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], - }), - ('bidict', '0.23.1', { - 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], - }), - ('tmtoolkit', '0.12.0', { - 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], - }), - ('tspex', '0.6.3', { - 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], - }), - ('plumbum', '1.8.3', { - 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], - }), - ('pandoc', '2.3', { - 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], - }), - ('nbsphinx', '0.9.4', { - 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], - }), - ('nbsphinx-link', '1.3.0', { - 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], - }), - ('numpydoc', '1.7.0', { - 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], - }), - ('pyOpenSSL', '23.2.0', { - 'modulename': 'OpenSSL', - 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], - }), - ('entrypoints', '0.4', { - 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], - }), - ('ansicolors', '1.1.8', { - 'modulename': 'colors', - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], - }), - ('papermill', '2.6.0', { - 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], - }), - ('mypy_extensions', '1.0.0', { - 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], - }), - ('typing_inspect', '0.9.0', { - 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], - }), - ('marshmallow', '3.21.1', { - 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], - }), - ('dataclasses_json', '0.6.4', { - 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], - }), - ('loomxpy', '0.4.2', { - 'preinstallopts': local_loomxpy_preinstallopts, - 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], - }), - ('pycisTopic', '2.0a-dca4bb6', { - 'modulename': 'pycisTopic', - 'preinstallopts': local_pycistopic_preinstallopts, - # download commit dca4bb6 to be compatible with pycistarget - 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], - 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], - 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], - }), - ('pycistarget', '1.0a1-16d14b9', { - 'preinstallopts': local_pycistarget_preinstallopts, - # download commit 16d14b9 to make '$ scenicplus' work - 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], - 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], - 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], - }), - (name, version, { - 'preinstallopts': local_preinstallopts, - 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], - 'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}], - 'checksums': [ - {'scenicplus-1.0a1-18072024-fa55dae.tar.gz': - '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'}, - ], - }), -] - -# copy files to let 'scenicplus init_snakemake' works -postinstallcmds = [ - 'cp -r %(builddir)s/scenicplus/scenicplus-fa55dae55203951c0c42e359b65a28010cd544f6/src/scenicplus/snakemake ' - '%(installdir)s/lib/python%(pyshortver)s/site-packages/scenicplus' -] - -sanity_check_commands = ['scenicplus init_snakemake --help'] - -moduleclass = 'bio' From 669505d3c834a2ce4ca5775451c5c3241cb46c50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 21 Aug 2024 13:34:36 +0200 Subject: [PATCH 261/553] fix line too long error --- easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb index 364d182c058..7217999a898 100644 --- a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb @@ -4,7 +4,8 @@ name = 'Redland' version = '1.0.17' homepage = 'https://librdf.org/raptor' -description = """Redland is a set of free software C libraries that provide support for the Resource Description Framework (RDF).""" +description = """Redland is a set of free software C libraries that + provide support for the Resource Description Framework (RDF).""" toolchain = {'name': 'GCC', 'version': '12.3.0'} From d3495ce7e33faf906034a0df881da3ef980e4d34 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 13:39:17 +0200 Subject: [PATCH 262/553] adding easyconfigs: MATES-0.1.2-20240813-foss-2023a.eb --- .../MATES/MATES-0.1.2-20240813-foss-2023a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb new file mode 100644 index 00000000000..e7e73a89e80 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' From 55331441356f136cf8cfba273af8f2b0bc881848 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 13:54:09 +0200 Subject: [PATCH 263/553] add mates with gpu support --- ...S-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..dbba96ddf2f --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' From de002d6026e0eab8690d1cba7ff79cb896e77704 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 21 Aug 2024 13:59:47 +0200 Subject: [PATCH 264/553] add missing build dependency --- .../easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb index 9d3f2cfc12f..7e5cec281f2 100644 --- a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb @@ -18,6 +18,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://www.unixodbc.org/'] checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec'] +builddependencies = [('binutils', '2.40')] + sanity_check_paths = { 'files': [ 'lib/libodbc.%s' % SHLIB_EXT, From 47c962df1a6aad6aaa2a5ca5e0bea08c76383695 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Aug 2024 14:02:59 +0200 Subject: [PATCH 265/553] make sure that the mpi runner gets built --- .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb | 20 ++++++++++------- .../c/CORSIKA/CORSIKA-77550_fix_include.patch | 22 +++++++++++++++++++ 2 files changed, 34 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb index dc008b79e18..c6f619d9d75 100644 --- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -14,7 +14,11 @@ toolchainopts = {'usempi': True} download_instructions = "Sources have to be requested to the developers" sources = [SOURCELOWER_TAR_GZ] -checksums = ['fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'] +patches = ['%(name)s-%(version)s_fix_include.patch'] +checksums = [ + {'corsika-77550.tar.gz': 'fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'}, + {'CORSIKA-77550_fix_include.patch': 'e858fc4c1fa33d31d050b2fca50e130c23b2d3e4b81b851af34dc3f39e9c709e'}, +] dependencies = [ ("ROOT", "6.30.06"), @@ -24,22 +28,22 @@ dependencies = [ parallel = False # execute ./coconut manually with your own options and extract configure command from top of config.log +_mpi_opts = "--enable-PARALLEL --with-mpirunner-lib=src/parallel --enable-PARALLELIB " configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD " configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS " -configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB " +configopts += _mpi_opts build_cmd = "./coconut" -buildopts = "--batch" +buildopts = "--batch " + _mpi_opts install_cmd = ' && '.join([ - 'mkdir -p %(installdir)s/{bin,data}', - 'mv %(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/', - 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/data/', + 'mkdir -p %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/bin/', ]) sanity_check_paths = { - 'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel', 'data/NUCNUCCS'], - 'dirs': [] + 'files': ['bin/mpi_corsika77550Linux_QGSII_urqmd_thin_coreas_parallel_runner'], + 'dirs': [], } moduleclass = "phys" diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch new file mode 100644 index 00000000000..e7bc3863fae --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch @@ -0,0 +1,22 @@ +Move include out of function to avoid error: +/usr/include/sys/stat.h:453:1: error: nested function ‘stat’ declared ‘extern’ +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -Nur corsika-77550.orig/src/parallel/mpi_runner.c corsika-77550/src/parallel/mpi_runner.c +--- corsika-77550.orig/src/parallel/mpi_runner.c 2024-04-18 18:30:39.000000000 +0200 ++++ corsika-77550/src/parallel/mpi_runner.c 2024-08-09 16:15:39.969688000 +0200 +@@ -99,6 +99,7 @@ + #include + #include + #include "config.h" ++#include + + /////////////////////initializing parameters/////////////////// + //the number of data type block in the MPI message +@@ -1023,7 +1024,6 @@ + strcpy(str2, strtmp); + } + strcpy(statdir,str2); +- #include + struct stat sb; + if (stat(statdir, &sb) == 0 && S_ISDIR(sb.st_mode)) + { From d4c31fa493b87e411027ebeec86ed6931d495375 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 14:03:36 +0200 Subject: [PATCH 266/553] adding easyconfigs: prompt-toolkit-3.0.36-GCCcore-12.3.0.eb --- .../prompt-toolkit-3.0.36-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dfcdad173d1 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' From 348943ac7e5ecb411410b0e449ef57d3d95c77b7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 14:07:00 +0200 Subject: [PATCH 267/553] adding easyconfigs: PyWavelets-1.7.0-foss-2023a.eb --- .../PyWavelets/PyWavelets-1.7.0-foss-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb new file mode 100644 index 00000000000..f68a1a2ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.7.0' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b47250e5bb853e37db5db423bafc82847f4cde0ffdf7aebb06336a993bc174f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('meson-python', '0.13.2'), + ('Cython', '3.0.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' From b6b4d9d52ba0f1d786a2b21ee9e7974a67a721c8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Aug 2024 14:54:28 +0200 Subject: [PATCH 268/553] remove Cython dependency from Python-bundle-PyPI --- .../c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb | 40 +++++++++++++++++++ ...thon-bundle-PyPI-2024.06-GCCcore-13.3.0.eb | 3 -- 2 files changed, 40 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c9e419d570a --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.10' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb index add89b7ae32..01bf9b19b0a 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb @@ -56,9 +56,6 @@ exts_list = [ ('pbr', '6.0.0', { 'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'], }), - ('Cython', '3.0.10', { - 'checksums': ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'], - }), ('six', '1.16.0', { 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], }), From 4c81420765617c74cb9c31e078238ff96e88ef85 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 15:09:42 +0200 Subject: [PATCH 269/553] adding easyconfigs: dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb and patches: dorado-0.7.3_include-fstream.patch --- .../dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb | 80 +++++++++++++++++++ .../dorado/dorado-0.7.3_include-fstream.patch | 27 +++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7aa8f29b002 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,80 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.7.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['dorado-0.7.3_include-fstream.patch'] +checksums = [ + None, + 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch new file mode 100644 index 00000000000..bf8d2346e5d --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include \ No newline at end of file From 2332f84a51642464ad4ba8f75ba2f2bad83fa53d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Aug 2024 15:16:43 +0200 Subject: [PATCH 270/553] add update for VTK-9.3.0-foss-2023b --- easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb index 8a0452f863f..3be42a90bac 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb @@ -42,6 +42,7 @@ dependencies = [ ('XZ', '5.4.4'), ('libGLU', '9.0.3'), ('X11', '20231019'), + ('Qt5', '5.15.13'), ] separate_build_dir = True @@ -57,7 +58,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " From bd321869d56abefae3d20dc7fad2596f0272f52d Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 21 Aug 2024 15:45:43 +0200 Subject: [PATCH 271/553] Use older pydantic in toolchain --- easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb index f3047e4bc6d..f2436367baa 100644 --- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Python', '3.11.5'), ('Python-bundle-PyPI', '2023.10'), ('Pillow', '10.2.0'), - ('pydantic', '2.7.4'), + ('pydantic', '2.6.4'), ('SciPy-bundle', '2023.11'), ] From e88765c60adaabd6e5dfef7569852a237918492f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Aug 2024 15:50:07 +0200 Subject: [PATCH 272/553] add Cython builddep for SciPy-bundle --- .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb | 3 ++- .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb index b80b8631909..99d61098d6b 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb @@ -16,7 +16,8 @@ builddependencies = [ ('Meson', '1.4.0'), ('meson-python', '0.16.0'), ('Ninja', '1.12.1'), - ('pkgconf', '2.2.0'), # required by scipy + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb index cdb7536e15a..2abab977add 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -16,7 +16,8 @@ builddependencies = [ ('Meson', '1.4.0'), ('meson-python', '0.16.0'), ('Ninja', '1.12.1'), - ('pkgconf', '2.2.0'), # required by scipy + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy ] dependencies = [ From bcfc68c25cb301df393924397062658972cd807d Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 21 Aug 2024 14:05:58 +0000 Subject: [PATCH 273/553] adding easyconfigs: SentencePiece-0.2.0-GCC-13.2.0.eb --- .../SentencePiece-0.2.0-GCC-13.2.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..246989eefdc --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.2.0' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('gperftools', '2.13'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9970f0a0afee1648890293321665e5b2efa04eaec9f1671fcf8048f456f5bb86'], +} + +local_external_absl = 'sed -i %(builddir)s/' + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + # using internal protobuf there is no matching pc file so requirement is removed: + 'preconfigopts': 'sed -i s/Requires.private.*// ../sentencepiece-%(version)s/sentencepiece.pc.in &&', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + # Unpredicable where pc files end up; including both lib and lib64 + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help | grep accept_language', # --help has exit code 1, so we check for output text + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From 99abe91b43c1ae70d89f8c8d2a737b710ad1565f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 15:55:44 +0200 Subject: [PATCH 274/553] add missing ihm + modelcif extensions required by AlphaPullDown script convert_to_modelcif.py --- .../AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb index f41935fe51d..f410c438e23 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -61,6 +61,12 @@ exts_list = [ 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), (name, version, { 'sources': [{ 'filename': SOURCE_TAR_GZ, @@ -90,6 +96,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], } -sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] moduleclass = 'bio' From 0b9a9b0395684ade46324441b891c5216518d515 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Aug 2024 16:27:03 +0200 Subject: [PATCH 275/553] add missing ihm + modelcif extensions required by AlphaPullDown script convert_to_modelcif.py --- .../AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb index 72746293174..492a787c919 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb @@ -63,6 +63,12 @@ exts_list = [ 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), (name, version, { 'sources': [{ 'filename': SOURCE_TAR_GZ, @@ -92,6 +98,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], } -sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"] +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] moduleclass = 'bio' From bed9e08628997e5c4d7357992cf75c1e8da6a20b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 21 Aug 2024 17:16:35 +0200 Subject: [PATCH 276/553] update version, add patch file --- ...=> PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb} | 69 +++++++++---------- .../p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch | 16 +++++ 2 files changed, 50 insertions(+), 35 deletions(-) rename easybuild/easyconfigs/p/PEcAn/{PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb => PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb} (72%) create mode 100644 easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb similarity index 72% rename from easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb rename to easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb index 163a41f725f..b5747815246 100644 --- a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'PEcAn' -version = '1.7.2.9000' +version = '1.8.0.9000' versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/PecanProject/pecan' @@ -35,36 +35,33 @@ exts_default_options = { ], } -local_sed_patterns_duckdb = '1146s/prefix_front_/prefix_front_back.prefix_front_/g;' -local_sed_patterns_duckdb += '1147s/prefix_back_/prefix_front_back.prefix_back_/g' - exts_list = [ - ('PEcAn.logger', '1.8.1.9000', { - 'checksums': ['3d1d8a6c9afa677dde8a4aaf72809932f0b6b5385ae4a6fc2059b48ed4b09195'], + ('PEcAn.logger', '1.8.2.9000', { + 'checksums': ['1092f72fa63d58d83ca939a06bfa51ad3b3b4cd94ca4e68202cdb08fd3ada099'], }), - ('PEcAn.remote', '1.7.2', { - 'checksums': ['59feda08ac6784c5e607a70166e002df96385efbba3b77148b4cf9a0a1e2c9dc'], + ('PEcAn.remote', version, { + 'checksums': ['b3c7208c85d37aa6c12ca99182262a9886e57e2591faefd909232b8c89111b20'], }), - ('PEcAn.utils', '1.7.2', { - 'checksums': ['d83ae2a605f7867659d10de952f5db6b947dc3d2bc05633c0f72ced0b4caad17'], + ('PEcAn.utils', version, { + 'checksums': ['524c3231a21a1e5fc48ebc53d17e49c82f018b87c274095cd0362103fe322ec5'], }), ('PEcAn.DB', version, { - 'checksums': ['f493d6ab100fce139bdb9747c91faff5cf60ff296ee16a82c6bc2366a9722231'], + 'checksums': ['9b7e9b40a07879c1265d9ab6087b7448dfd34c3601c64ddcb41511c97399fece'], }), - ('PEcAn.settings', '1.7.2', { - 'checksums': ['ab0dd41e9f421a84e68a16a1e4b290f70d852d23e66a2de1c3e91bf883aa1aeb'], + ('PEcAn.settings', version, { + 'checksums': ['555a7d81eec7e97b8457cef51888087af6b5d7d07f527ca58cbab07ed847fabc'], }), - ('PEcAn.MA', '1.7.2', { - 'checksums': ['bf3a5b6ac8adce4efb6be504cdeb10a71a59b3ac5af72c8d77b59a39c7d90ceb'], + ('PEcAn.MA', '1.7.3.9000', { + 'checksums': ['680290e0ee52526db1242d95c4ca06a1e0ad117337ff721d79387797bc7e40ed'], }), ('PEcAn.emulator', version, { - 'checksums': ['f4465a154e41cfe5a2cc94035ae4a5ddbfd3b5fc54a83bc9578c98a9eb07cff1'], + 'checksums': ['68944ebdf1f37ff84f9b09bf02c709de9eda823728bbdea073a36d7ef19cfb9c'], }), - ('PEcAn.priors', '1.7.2', { - 'checksums': ['001c26275ef23dda369fa2a5b408e481265d29137edeaebd03a30a39b4682edd'], + ('PEcAn.priors', '1.7.3.9000', { + 'checksums': ['e942a31ae02af61b1b8e36d1c5df58f39829b3d0c29421edc151f2f063ff4c1f'], }), ('PEcAn.uncertainty', version, { - 'checksums': ['a0d1a3a3d65e06b066d23473def763f5e158b2356ee5fe9e09020fe311e9ef4a'], + 'checksums': ['65e392536e17e1de2bf8f66c2cd8f46fcb26dcb3294acf0132551b6736722196'], }), ('amerifluxr', '1.0.0', { 'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'], @@ -90,8 +87,8 @@ exts_list = [ ('nneo', '0.1.0', { 'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'], }), - ('PEcAn.data.atmosphere', '1.7.2', { - 'checksums': ['1847151588f669e91b35de637c804328efbc606141bf992bee650fd261b70e5a'], + ('PEcAn.data.atmosphere', version, { + 'checksums': ['28fb884cdeeff6405252352a261c3a884ad33202e556e88cee262aba96e1aea4'], }), ('redland', '1.0.17-18', { 'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'], @@ -112,9 +109,11 @@ exts_list = [ 'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'], }), ('duckdb', '1.0.0-2', { - 'checksums': ['3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'], - # fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 - 'preinstallopts': "sed -i '%s' src/duckdb/third_party/re2/re2/prog.cc && " % local_sed_patterns_duckdb, + 'patches': ['PEcAn-1.8.0.9000_duckdb.patch'], + 'checksums': [ + {'duckdb_1.0.0-2.tar.gz': '3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'}, + {'PEcAn-1.8.0.9000_duckdb.patch': 'fb47b668b23e6c9274ce5365725af71e56f2d99771efdd343dc4283f68ab0c21'}, + ], }), ('duckdbfs', '0.0.4', { 'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'], @@ -176,20 +175,20 @@ exts_list = [ ('SimilarityMeasures', '1.4', { 'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'], }), - ('PEcAn.benchmark', '1.7.2', { - 'checksums': ['c9cf9f299f810e4962476db1afdf6a39de77806fd82b6cb8bb7321e96c350db8'], + ('PEcAn.benchmark', '1.7.3.9000', { + 'checksums': ['2e8b285869b4df148228cdde5de44a67dfe0b584b2a7cd614280134259e33ed4'], }), - ('PEcAn.visualization', '1.7.2', { - 'checksums': ['5d25871d57ded42c7ae7f8dbf0a6907c8b828f6a0463286e6ae178b356a4a848'], + ('PEcAn.visualization', version, { + 'checksums': ['f77dcb756871a419a85e46cde4a1fb0a1993c29cce8578255d5a46db722ece43'], }), ('PEcAn.data.land', version, { - 'checksums': ['29ed015c1e8a5b993aebc31559aa3f7a4136b1f23e4c13a2d55118e7c541da2f'], + 'checksums': ['19c572e95c11362f4714d9c3d9cc7b2d17c2e3a34513c7ed629e7bdb99bdd0ec'], }), ('MODISTools', '1.1.5', { 'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'], }), ('PEcAn.data.remote', version, { - 'checksums': ['691b9e27cf5afb6bfb32873cca6ba284d0ff303873695e86f7653432aa7c66d4'], + 'checksums': ['c097d9395d9dbb6c123f404525cae7fdb1a99b142b32c1a40b0143060444e184'], }), ('SparseGrid', '0.8.2', { 'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'], @@ -197,14 +196,14 @@ exts_list = [ ('lqmm', '1.5.8', { 'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'], }), - ('PEcAn.workflow', '1.7.2', { - 'checksums': ['cdd60bf6a99b20aed9792b0cf6648c3f55f4b9bd3a00fd0187b7e7ec56815f0f'], + ('PEcAn.workflow', version, { + 'checksums': ['91a1849c040089da1088c02469b973a5f301a419237db7c840fe4ca2922f4b9d'], }), ('PEcAn.assim.batch', version, { - 'checksums': ['d57b7ce1b0cbef0183bcb689f55f0345575289f1b8741c00cbd026eeaea8a6b9'], + 'checksums': ['a1403a5a4591791e37e7e48ca9e9d49f66f4270757711b68b72fd38aadd411cb'], }), - ('%(name)s.all', version, { - 'checksums': ['43e036ab8af9834ae6d7d7f4304adfc6cef08348e3be39ca5e51dcbb1fe21cce'], + ('PEcAn.all', version, { + 'checksums': ['6fe594fb890b5680977d1bf58232b941c6d522456e7803e3dc9c4418b92db737'], }), ] diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch new file mode 100644 index 00000000000..940992bf5ba --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch @@ -0,0 +1,16 @@ +Fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 +Source: https://patch-diff.githubusercontent.com/raw/duckdb/duckdb/pull/12344.diff +diff -u src/duckdb/third_party/re2/re2/prog.cc.orig src/duckdb/third_party/re2/re2/prog.cc +--- src/duckdb/third_party/re2/re2/prog.cc.orig 2024-07-19 14:46:13.000000000 +0200 ++++ src/duckdb/third_party/re2/re2/prog.cc 2024-08-21 15:51:17.394266979 +0200 +@@ -1143,8 +1143,8 @@ + const __m256i* bp = reinterpret_cast( + reinterpret_cast(data) + prefix_size_-1); + const __m256i* endfp = fp + size/sizeof(__m256i); +- const __m256i f_set1 = _mm256_set1_epi8(prefix_front_); +- const __m256i b_set1 = _mm256_set1_epi8(prefix_back_); ++ const __m256i f_set1 = _mm256_set1_epi8(prefix_front_back.prefix_front_); ++ const __m256i b_set1 = _mm256_set1_epi8(prefix_front_back.prefix_back_); + do { + const __m256i f_loadu = _mm256_loadu_si256(fp++); + const __m256i b_loadu = _mm256_loadu_si256(bp++); From 16a9662913d59e80baf7185a2d893047dc39a85c Mon Sep 17 00:00:00 2001 From: software Date: Wed, 21 Aug 2024 15:42:17 +0000 Subject: [PATCH 277/553] adding easyconfigs: inferCNV-1.21.0-foss-2023a-R-4.3.2.eb --- .../inferCNV-1.21.0-foss-2023a-R-4.3.2.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..7404bfe1502 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.21.0' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.18' +local_commit = '124eec089e5d9ab5a2a2352461d03db6cdcf0ea0' +github_account = 'broadinstitute' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-15', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-34', { + 'checksums': ['d2047030e9f24c5dc8bbb378867fbcb8e71d1f1c2ab77e9285f79f670568f5f3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c8886c0a7c292e28a5fb0acaab3ae00eb2b3906aa0a1d146d5931819a37daefb'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' From 56cc7623ce00e3c0e661015f0a9c3397a81ffc70 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 22 Aug 2024 11:35:18 +0200 Subject: [PATCH 278/553] adding easyconfigs: FFmpeg-7.0.2-GCCcore-13.3.0.eb, FriBidi-1.0.15-GCCcore-13.3.0.eb, ffnvcodec-12.2.72.0.eb, LAME-3.100-GCCcore-13.3.0.eb, SDL2-2.30.6-GCCcore-13.3.0.eb, x264-20240513-GCCcore-13.3.0.eb, x265-3.6-GCCcore-13.3.0.eb, Yasm-1.3.0-GCCcore-13.3.0.eb --- .../f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb | 30 +++++++++++++ .../f/ffnvcodec/ffnvcodec-12.2.72.0.eb | 32 +++++++++++++ .../l/LAME/LAME-3.100-GCCcore-13.3.0.eb | 36 +++++++++++++++ .../s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb | 26 +++++++++++ .../x/x264/x264-20240513-GCCcore-13.3.0.eb | 33 ++++++++++++++ .../x/x265/x265-3.6-GCCcore-13.3.0.eb | 34 ++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb | 24 ++++++++++ 8 files changed, 260 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..246a8306b76 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '7.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1ed250407ea8f955cca2f1139da3229fbc13032a0802e4b744be195865ff1541'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('ffnvcodec', '12.2.72.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.03'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('x264', '20240513'), + ('LAME', '3.100'), + ('x265', '3.6'), + ('X11', '20240607'), + ('freetype', '2.13.2'), + ('fontconfig', '2.15.0'), + ('FriBidi', '1.0.15'), + ('SDL2', '2.30.6'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a31f21a37dd --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.15' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0bbc7ff633bfa208ae32d7e369cf5a7d20d5d2557a0b067c9aa98bcbf9967587'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb new file mode 100644 index 00000000000..cc4461c3a8b --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.2.72.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c4080545d5b --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [('ncurses', '6.5')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1c8130b397c --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.30.6' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6ef64ca18a19d13df6eb22df9aff19fb0db65610a74cc81dae33a82235cacd4'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('X11', '20240607'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a2a4cccf421 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20240513' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/31e19f92/'] +sources = [{'download_filename': '%(name)s-4613ac3c.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['cf7e66bd0a75f3baba3502b58c80ee388b3d80a9a01be806337dd2214b8a290e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('NASM', '2.16.03'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..307c0abb034 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.6' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['663531f341c5389f460d730e62e10a4fcca3428ca2ca109693867bc5fe2e2807'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5ac8fd8176f --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' From 7f53d3821898b994d5cb2255b23f9aafe0da8493 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 14:33:03 +0200 Subject: [PATCH 279/553] adding easyconfigs: spektral-1.2.0-fosscuda-2020b.eb --- .../spektral/spektral-1.2.0-fosscuda-2020b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..a92e6bd1185 --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.2.0' + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('TensorFlow', '2.5.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 469657c9ab833281e17032ffbbffe35f2e9b84da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 14:59:47 +0200 Subject: [PATCH 280/553] add versionsuffix for spektral 1.2.0 since it depends on TensorFlow 2.5.0 --- ...b.eb => spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/spektral/{spektral-1.2.0-fosscuda-2020b.eb => spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb} (84%) diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb similarity index 84% rename from easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb rename to easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb index a92e6bd1185..75446a8cbff 100644 --- a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -2,6 +2,8 @@ easyblock = 'PythonBundle' name = 'spektral' version = '1.2.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s' % local_tf_version homepage = 'https://graphneural.network' description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" @@ -15,7 +17,7 @@ dependencies = [ ('networkx', '2.5'), ('scikit-learn', '0.23.2'), ('tqdm', '4.56.2'), - ('TensorFlow', '2.5.0'), + ('TensorFlow', local_tf_version), ] use_pip = True From 55d1b0c66473fc2eba945397807aee82d00be3c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 20:24:33 +0200 Subject: [PATCH 281/553] adding easyconfigs: xtb-6.7.1-gfbf-2023b.eb and patches: xtb-6.7.1_fix-dftd4-test.patch, xtb-6.7.1_fix-tblite-pr1072.patch --- .../easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb | 50 ++ .../x/xtb/xtb-6.7.1_fix-dftd4-test.patch | 20 + .../x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch | 528 ++++++++++++++++++ 3 files changed, 598 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb new file mode 100644 index 00000000000..09d459d356b --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.7.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'xtb-6.7.1_fix-tblite-pr1072.patch', + 'xtb-6.7.1_fix-dftd4-test.patch', +] +checksums = [ + {'xtb-6.7.1.tar.gz': '52506a689147cdb4695bf1c666158b6d6d6b31726fecaa5bf53af7f4e3f3d20d'}, + {'xtb-6.7.1_fix-tblite-pr1072.patch': '1f10fef3e94c29926b1f632acc94c3ec92be861ee5c5139104194172726ffe68'}, + {'xtb-6.7.1_fix-dftd4-test.patch': '340e7d5cbc6bbaf0c53d4d292f3624cd67455b7a817818fe2cc8d26f5c34864b'}, +] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +configopts = "-Dlapack='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +pretestopts = 'export OMP_NUM_THREADS=2 && ' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch new file mode 100644 index 00000000000..0405b372a8a --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch @@ -0,0 +1,20 @@ +fix for failing xtb test: + 72/148 dftd4 / param FAIL 1.85s exit status 1 + +from meson-logs/testlog.txt: +# Testing: param + Starting rational-damping ... (1/1) + ... rational-damping [FAILED] + Message: Condition not fullfilled + +see https://github.com/grimme-lab/xtb/pull/1085 +diff --git a/subprojects/dftd4.wrap b/subprojects/dftd4.wrap +index 46dc07ad9..e3e93f459 100644 +--- a/subprojects/dftd4.wrap ++++ b/subprojects/dftd4.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = dftd4 + url = https://github.com/dftd4/dftd4 +-revision = v3.5.0 ++revision = v3.6.0 diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..0684569d3e4 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch @@ -0,0 +1,528 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff --git a/src/dipro.F90 b/src/dipro.F90 +index 42a136364..ab64e0710 100644 +--- a/src/dipro.F90 ++++ b/src/dipro.F90 +@@ -130,6 +130,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff --git a/src/dipro/xtb.F90 b/src/dipro/xtb.F90 +index 95aff7848..4db948a3e 100644 +--- a/src/dipro/xtb.F90 ++++ b/src/dipro/xtb.F90 +@@ -50,11 +50,11 @@ subroutine get_calculator(xcalc, mol, method, error) + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff --git a/src/tblite/calculator.F90 b/src/tblite/calculator.F90 +index 653e6b285..f05087414 100644 +--- a/src/tblite/calculator.F90 ++++ b/src/tblite/calculator.F90 +@@ -150,16 +150,16 @@ subroutine newTBLiteCalculator(env, mol, calc, input) + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + case("ceh") + calc%guess = method + calc%nspin = 1 +- calc%etemp = 5000.0_wp * kt +- call new_ceh_calculator(calc%tblite, struc) ++ calc%etemp = 4000.0_wp * kt ++ call new_ceh_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +@@ -244,18 +244,18 @@ subroutine newTBLiteWavefunction(env, mol, calc, chk) + block + use tblite_context, only : context_type, context_terminal + use tblite_context_terminal, only : escape +- use tblite_ceh_singlepoint, only : ceh_guess ++ use tblite_ceh_singlepoint, only : ceh_singlepoint + use tblite_lapack_solver, only : lapack_solver + use tblite_lapack_solver, only : lapack_algorithm + type(context_type) :: ctx +- ++ + ctx%solver = lapack_solver(lapack_algorithm%gvd) + ctx%terminal = context_terminal(calc%color) + + write (env%unit, '(1x,a)') escape(ctx%terminal%cyan) // "Calculation of CEH charges" // & + & escape(ctx%terminal%reset) +- +- call ceh_guess(ctx, calc%tblite, struc, error, wfn, calc%accuracy, 1) ++ ++ call ceh_singlepoint(ctx, calc%tblite, struc, wfn, calc%accuracy, 1) + end block + end select + end associate +diff --git a/subprojects/mstore.wrap b/subprojects/mstore.wrap +index acf5df9de..0dfe716c0 100644 +--- a/subprojects/mstore.wrap ++++ b/subprojects/mstore.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff --git a/test/unit/test_ptb.F90 b/test/unit/test_ptb.F90 +index 16c14cbe4..5e585f90d 100644 +--- a/test/unit/test_ptb.F90 ++++ b/test/unit/test_ptb.F90 +@@ -186,12 +186,37 @@ subroutine test_ptb_overlap(error) + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ subroutine test_ptb_overlap(error) + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ subroutine test_ptb_overlap_h0(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ subroutine test_ptb_overlap_h0(error) + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ subroutine test_ptb_overlap_SX(error) + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ subroutine test_ptb_overlap_SX(error) + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ subroutine test_ptb_V_ECP(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ subroutine test_ptb_V_ECP(error) + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ subroutine test_ptb_hamiltonian_h0(error) + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -665,15 +794,16 @@ subroutine test_ptb_hamiltonian_h0(error) + & alpha_scal=id_to_atom(mol, ptbData%hamiltonian%kalphah0l)) + allocate (vecp(bas%nao, bas%nao), source=0.0_wp) + ++ ints%hamiltonian = 0.0_wp + call get_hamiltonian(mol, list, bas, ptbData%hamiltonian, ptbData%hamiltonian%kla, auxints%overlap_h0_1, & + & levels, ints%hamiltonian, ptbGlobals%kpol, ptbGlobals%kitr, ptbGlobals%kitocod) + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +838,37 @@ subroutine test_ptb_V_XC(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +926,9 @@ subroutine test_ptb_V_XC(error) + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1114,35 @@ subroutine test_ptb_coulomb_potential(error) + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1226,36 @@ subroutine test_ptb_plus_U_potential(error) + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1275,7 @@ subroutine test_ptb_plus_U_potential(error) + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + From 6f7ebd0c904df72fe5f0bb7fb16ce132537705f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 20:30:45 +0200 Subject: [PATCH 282/553] adding easyconfigs: ORCA-6.0.0-foss-2023b-avx2.eb, ORCA-6.0.0-foss-2023b.eb --- .../o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb | 37 +++++++++++++++++++ .../o/ORCA/ORCA-6.0.0-foss-2023b.eb | 36 ++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb new file mode 100644 index 00000000000..ff3112bb084 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb @@ -0,0 +1,37 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb new file mode 100644 index 00000000000..f28a5a3ff99 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb @@ -0,0 +1,36 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' From fbe578bcdf0917e987fd526045261a8c040878b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Aug 2024 20:51:14 +0200 Subject: [PATCH 283/553] adding easyconfigs: STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb --- ...TAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb new file mode 100644 index 00000000000..a0a119a428c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11b_alpha_2024-02-09' + +homepage = 'https://github.com/dobinlab/STAR_pre_releases' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/dobinlab/STAR_pre_releases/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-2.7.11a_use-external-htslib.patch'] +checksums = [ + {'2.7.11b_alpha_2024-02-09.tar.gz': '7a7bae1f802fc5bc5b270da89e66a824480fb33e21f7ebfbf7ed56e1d4907c1c'}, + {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +builddependencies = [ + ('xxd', '9.0.2112'), +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' From cab6b5585d54dd7cd6af97f5defcfaa90b6cff34 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Thu, 22 Aug 2024 21:50:57 +0000 Subject: [PATCH 284/553] adding easyconfigs: bitsandbytes-0.43.3-foss-2023a.eb --- .../bitsandbytes-0.43.3-foss-2023a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb new file mode 100644 index 00000000000..902b7d717f1 --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', '-CUDA-12.1.1'), + ('SciPy-bundle', '2023.07'), +] + +configopts = '-DCOMPUTE_BACKEND=cuda' +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' From 3c74d87c94ccc2b61e25c02a7865d7cc6a5c5555 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Aug 2024 12:34:11 +0200 Subject: [PATCH 285/553] adding easyconfigs: HERRO-0.1.0_20240808-foss-2023a.eb, duplex-tools-0.3.3-foss-2023a.eb, pod5-file-format-0.3.10-foss-2023a.eb and patches: pod5-file-format-0.3.10_dep_fix.patch --- .../duplex-tools-0.3.3-foss-2023a.eb | 68 ++++ .../HERRO/HERRO-0.1.0_20240808-foss-2023a.eb | 382 ++++++++++++++++++ .../pod5-file-format-0.3.10-foss-2023a.eb | 109 +++++ .../pod5-file-format-0.3.10_dep_fix.patch | 32 ++ 4 files changed, 591 insertions(+) create mode 100644 easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb new file mode 100644 index 00000000000..fe56d08acaa --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +_minimap2_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.4'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('h5py', '3.9.0'), + ('pod5-file-format', '0.3.10'), + ('parasail', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap2_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyfastx', '2.0.1', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'], + }), + (name, version, { + 'source_tmpl': 'duplex_tools-%(version)s.tar.gz', + 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pyfastx --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb new file mode 100644 index 00000000000..d27b48f9a9b --- /dev/null +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -0,0 +1,382 @@ +easyblock = 'Cargo' + +name = 'HERRO' +version = '0.1.0_20240808' +local_commit = 'deccc46' + +homepage = 'https://github.com/lbcb-sci/herro' +description = """ +HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or +R9.4.1 reads (read length of >= 10 kbps is recommended). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/lbcb-sci/herro/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('libffi', '3.4.4'), + ('libnsl', '2.0.1'), + ('SQLite', '3.42.0'), + ('util-linux', '2.39'), + ('zlib', '1.2.13'), + ('ncurses', '6.4'), + ('libreadline', '8.2'), + ('SeqKit', '2.3.1', '', SYSTEM), + ('Tk', '8.6.13'), + ('XZ', '5.4.2'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('h5py', '3.9.0'), + ('duplex-tools', '0.3.3'), + ('PyTorch', '2.1.2'), + ('Pillow', '10.0.0'), + ('zstd', '1.5.5'), + ('parasail', '2.6.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('zstandard', '0.22.0', { + 'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'], + }), + ('Porechop', '20240119', { + 'modulename': 'porechop', + 'source_urls': ['https://github.com/dehui333/Porechop/archive/'], + 'sources': [{'download_filename': 'd2e77c6.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'], + }), +] + +# use tch version 0.14.0 - compatible with PyTorch 2.1 +local_torch_opts = "sed -i 's/tch = \"0.13.0\"/tch = \"0.14.0\"/' Cargo.toml && " +local_torch_opts += 'export LIBTORCH_BYPASS_VERSION_CHECK=1 && export LIBTORCH_USE_PYTORCH=1 && ' +local_torch_opts += 'export LIBTORCH=$EBROOTPYTORCH/lib && RUSTFLAGS="-Ctarget-cpu=native"' +prebuildopts = pretestopts = preinstallopts = local_torch_opts + +# copy scripts to /bin to be easier to run scripts for users +postinstallcmds = [ + 'cp -a %(start_dir)sscripts/* %(installdir)s/bin', + 'rm %(installdir)s/bin/herro-env.yml', + "chmod a+rx %(installdir)s/bin/*.sh", + "chmod a-x %(installdir)s/bin/*.py", +] + +_bins = [ + 'herro', + 'porechop', + 'no_split.sh', + 'postprocess_corrected.sh', + 'create_batched_alignments.sh', + 'porechop_with_split.sh', + 'preprocess.sh', + 'batch.py', + 'create_clusters.py', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["herro --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +modloadmsg = """ +To run scripts from /scripts directory just run .sh +Do not run it as scripts/.sh +For example - run preprocess.sh as: + $ preprocess.sh +""" + +crates = [ + ('adler2', '2.0.0'), + ('aes', '0.8.4'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.86'), + ('approx', '0.5.1'), + ('autocfg', '1.3.0'), + ('base64ct', '1.6.0'), + ('block-buffer', '0.10.4'), + ('buffer-redux', '1.0.2'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('cipher', '0.4.4'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('colorchoice', '1.0.2'), + ('console', '0.15.8'), + ('constant_time_eq', '0.1.5'), + ('cpufeatures', '0.2.13'), + ('crc32fast', '1.4.2'), + ('crossbeam-channel', '0.5.13'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('crypto-common', '0.1.6'), + ('deranged', '0.3.11'), + ('digest', '0.10.7'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('flate2', '1.0.32'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hmac', '0.12.1'), + ('indicatif', '0.17.8'), + ('inout', '0.1.3'), + ('instant', '0.1.13'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jemalloc-sys', '0.5.4+5.3.0-patched'), + ('jemallocator', '0.5.4'), + ('jobserver', '0.1.32'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.158'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.9'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.8.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('npyz', '0.8.3'), + ('npyz-derive', '0.7.0'), + ('num-bigint', '0.4.6'), + ('num-complex', '0.4.6'), + ('num-conv', '0.1.0'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.19'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.19.0'), + ('ordered-float', '4.2.2'), + ('password-hash', '0.4.2'), + ('pbkdf2', '0.11.0'), + ('pest', '2.7.11'), + ('pest_derive', '2.7.11'), + ('pest_generator', '2.7.11'), + ('pest_meta', '2.7.11'), + ('pkg-config', '0.3.30'), + ('portable-atomic', '1.7.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.86'), + ('py_literal', '0.4.0'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rawpointer', '0.2.1'), + ('rustc-hash', '1.1.0'), + ('ryu', '1.0.18'), + ('safetensors', '0.3.3'), + ('serde', '1.0.208'), + ('serde_derive', '1.0.208'), + ('serde_json', '1.0.125'), + ('sha1', '0.10.6'), + ('sha2', '0.10.8'), + ('shlex', '1.3.0'), + ('strsim', '0.10.0'), + ('subtle', '2.6.1'), + ('syn', '1.0.109'), + ('syn', '2.0.75'), + ('tch', '0.14.0'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('torch-sys', '0.14.0'), + ('typenum', '1.17.0'), + ('ucd-trie', '0.1.6'), + ('unicode-ident', '1.0.12'), + ('unicode-width', '0.1.13'), + ('utf8parse', '0.2.2'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), + ('zip', '0.6.6'), + ('zstd', '0.11.2+zstd.1.5.2'), + ('zstd', '0.13.2'), + ('zstd-safe', '5.0.2+zstd.1.5.2'), + ('zstd-safe', '7.2.1'), + ('zstd-sys', '2.0.13+zstd.1.5.6'), +] + +checksums = [ + {'HERRO-0.1.0_20240808.tar.gz': '885f64ab097c89cf8ec8ec38625c6325271997e89636de756aa12fb68aab7598'}, + {'adler2-2.0.0.tar.gz': 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{'safetensors-0.3.3.tar.gz': 'd93279b86b3de76f820a8854dd06cbc33cfa57a417b19c47f6a25280112fb1df'}, + {'serde-1.0.208.tar.gz': 'cff085d2cb684faa248efb494c39b68e522822ac0de72ccf08109abde717cfb2'}, + {'serde_derive-1.0.208.tar.gz': '24008e81ff7613ed8e5ba0cfaf24e2c2f1e5b8a0495711e44fcd4882fca62bcf'}, + {'serde_json-1.0.125.tar.gz': '83c8e735a073ccf5be70aa8066aa984eaf2fa000db6c8d0100ae605b366d31ed'}, + {'sha1-0.10.6.tar.gz': 'e3bf829a2d51ab4a5ddf1352d8470c140cadc8301b2ae1789db023f01cedd6ba'}, + {'sha2-0.10.8.tar.gz': '793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8'}, + {'shlex-1.3.0.tar.gz': '0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64'}, + {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'}, + {'subtle-2.6.1.tar.gz': '13c2bddecc57b384dee18652358fb23172facb8a2c51ccc10d74c157bdea3292'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.75.tar.gz': 'f6af063034fc1935ede7be0122941bafa9bacb949334d090b77ca98b5817c7d9'}, + {'tch-0.14.0.tar.gz': '0ed5dddab3812892bf5fb567136e372ea49f31672931e21cec967ca68aec03da'}, + {'thiserror-1.0.63.tar.gz': 'c0342370b38b6a11b6cc11d6a805569958d54cfa061a29969c3b5ce2ea405724'}, + {'thiserror-impl-1.0.63.tar.gz': 'a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261'}, + {'time-0.3.36.tar.gz': '5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885'}, + {'time-core-0.1.2.tar.gz': 'ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3'}, + {'torch-sys-0.14.0.tar.gz': '803446f89fb877a117503dbfb8375b6a29fa8b0e0f44810fac3863c798ecef22'}, + {'typenum-1.17.0.tar.gz': '42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825'}, + {'ucd-trie-0.1.6.tar.gz': 'ed646292ffc8188ef8ea4d1e0e0150fb15a5c2e12ad9b8fc191ae7a8a7f3c4b9'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unicode-width-0.1.13.tar.gz': '0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d'}, + {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'}, + {'version_check-0.9.5.tar.gz': '0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, + {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb new file mode 100644 index 00000000000..45740411804 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -0,0 +1,109 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.3.10' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.3.10_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'}, + {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'}, +] + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Arrow', '14.0.1'), + ('SciPy-bundle', '2023.07'), + ('zstd', '1.5.5'), + ('flatbuffers', '23.5.26'), + ('pybind11', '2.11.1'), + ('Boost', '1.82.0'), + ('build', '1.0.3'), + ('HDF5', '1.14.0'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('polars', '0.20.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +# unpin polars and h5py versions in pod5 +local_preinstallopts = ( + "sed -i" + " -e 's/polars~=0.19/polars/'" + " -e 's/h5py~=3.10.0/h5py/'" + " pyproject.toml && " +) + +exts_list = [ + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + ('pod5', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['f2dcb1938fcf51c725393345e480c1d12711089d542a27446fb92fbe2e18ae60'], + }), +] + +# create POD5Version.cmake +# python -m setuptools_scm && python -m pod5_make_version shows wrong version +preconfigopts = ( + 'cd %(builddir)s/%(name)s-%(version)s/cmake && ' + 'touch POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_REV 10)">>POD5Version.cmake && ' + 'echo "set(POD5_NUMERIC_VERSION 0.3.10)">>POD5Version.cmake && ' + 'echo "set(POD5_FULL_VERSION 0.3.10)">>POD5Version.cmake && ' +) + +# delete add_subdirectory(third_party/pybind11) from CMakeLists.txt +preconfigopts += "cd %(builddir)s/%(name)s-%(version)s && sed -i '/add_subdirectory(third_party/d' CMakeLists.txt && " +preconfigopts += 'cd %(builddir)s/easybuild_obj && ' + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib" -DZSTD_INCLUDE_DIR="$EBROOTZSTD/include"' + +# install lib_pod5 from wheel - dependency of pod5 +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch new file mode 100644 index 00000000000..a053f870ebe --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -0,0 +1,32 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) +diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt +--- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -3,7 +3,7 @@ + if (ENABLE_CONAN) + find_package(Arrow REQUIRED CONFIG) + find_package(Boost REQUIRED CONFIG) +- find_package(Flatbuffers REQUIRED CONFIG) ++ find_package(FlatBuffers REQUIRED CONFIG) + find_package(zstd REQUIRED CONFIG) + find_package(ZLIB REQUIRED CONFIG) + +@@ -17,7 +17,7 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) + find_package(ZLIB REQUIRED) + +@@ -27,6 +27,7 @@ + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE From 9c0b3627addd0f06520f41b87fd470d700fc9823 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 23 Aug 2024 12:45:53 +0200 Subject: [PATCH 286/553] Update pod5-file-format-0.3.10_dep_fix.patch - update description --- .../p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch index a053f870ebe..b0207d6c4ac 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -1,5 +1,4 @@ -Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' -We want to use our pybind11 instead of the one in git submodules +Flatbuffers uses capital 'B' in 'FlatBuffersConfig.cmake' Author: Petr Král (INUITS) diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt --- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 From fcfb0d5cd6bca9be5b40adc4521388f31a6226b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Aug 2024 13:07:35 +0200 Subject: [PATCH 287/553] adding easyconfigs: SeqKit-2.8.2.eb --- .../easyconfigs/s/SeqKit/SeqKit-2.8.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb new file mode 100644 index 00000000000..820f9abf719 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.8.2' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9cf1e744b785fa673af5a7a1ce2f96d52dc03e14b6537097df86aa6266204556'] + +builddependencies = [ + ('Go', '1.22.1'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' From a2e4f8d4ee03bef5612032c80ea29042c57bb037 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Aug 2024 14:30:05 +0200 Subject: [PATCH 288/553] adding easyconfigs: coxeter-20180226-GCCcore-13.2.0.eb and patches: coxeter-20180226_makefile.patch --- .../coxeter-20180226-GCCcore-13.2.0.eb | 41 +++++++ .../c/coxeter/coxeter-20180226_makefile.patch | 101 ++++++++++++++++++ 2 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1fbcfa900b6 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'coxeter' +version = '20180226' +local_commit = '7b5a1f0' + +homepage = 'https://github.com/tscrim/coxeter' +description = """A library for the study of combinatorial aspects of Coxeter group theory""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit] +sources = [SOURCE_TAR_GZ] +patches = ['coxeter-20180226_makefile.patch'] +checksums = [ + {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'}, + {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'}, +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +preinstallopts = 'mkdir -p "%(installdir)s/bin" "%(installdir)s/lib" && ' +installopts = 'SAGE_LOCAL="%(installdir)s"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'lib/lib%%(name)s3.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + 'share/%(name)s', + ] +} + +sanity_check_commands = ['echo "qq" | coxeter'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch new file mode 100644 index 00000000000..d00d6860689 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch @@ -0,0 +1,101 @@ +Allows installation of files needed for Sagemath +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/main/coxeter-makefile.patch +diff -u makefile.orig makefile +--- makefile.orig 2018-02-26 13:57:36.000000000 +0100 ++++ makefile 2024-08-16 14:15:51.889503570 +0200 +@@ -12,6 +12,7 @@ + gflags = -c $(includedirs) -g + + cflags = $(gflags) # the default setting ++cflags = -c $(includedirs) $(CPPFLAGS) $(CXXFLAGS) -fPIC + + ifdef optimize + NDEBUG = true +@@ -22,18 +23,74 @@ + cflags = $(pflags) + endif + +-cc = g++ ++EXENAME = coxeter ++LIBNAME = coxeter3 ++ifeq ($(UNAME),Darwin) ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .dylib ++ LIBDIR = lib ++ LINKFLAGS = -dynamiclib -Wl,-headerpad_max_install_names,-undefined,dynamic_lookup,-compatibility_version,3.0,-current_version,3.0,-install_name,$(SAGE_LOCAL)/lib/$(LIBPREFIX)$(LIBNAME)$(LIBEXT) ++ LINKLIBS = ++else ++ifeq ($(UNAME),CYGWIN) ++ EXEEXT = .exe ++ LIBPREFIX = cyg ++ LIBEXT = .dll ++ LIBDIR = bin ++ IMPLIB = lib$(LIBNAME).dll.a ++ LINKFLAGS = -shared -Wl,--out-implib=$(IMPLIB) -Wl,--export-all-symbols ++ LINKLIBS = -lc ++else ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .so ++ LIBDIR = lib ++ LINKFLAGS = $(LDFLAGS) -shared -Wl,-soname,libcoxeter3.so ++ LINKLIBS = -lc ++endif ++endif ++LIBRARY = $(LIBPREFIX)$(LIBNAME)$(LIBEXT) + +-all: coxeter #clean ++all: coxeter executable + + coxeter: $(objects) +- $(cc) -o coxeter $(objects) ++ $(CXX) $(LINKFLAGS) -o $(LIBRARY) $(objects) $(LINKLIBS) ++ ++executable: $(objects) ++ $(CXX) $(LDFLAGS) -o $(EXENAME)$(EXEEXT) $(objects) ++ ++DATADIR="$$SAGE_LOCAL/share/coxeter/" ++INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/" ++LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)" ++ ++install: coxeter executable ++ cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/" ++ cp $(LIBRARY) $(LIBRARYDIR) ++ if [ $(UNAME) = "CYGWIN" ]; then \ ++ cp $(IMPLIB) "$$SAGE_LOCAL/lib/"; \ ++ fi ++ ++ mkdir -p $(DATADIR) ++ cp -r coxeter_matrices headers messages $(DATADIR) ++ mkdir -p $(INCLUDEDIR) ++ cp -r *.h *.hpp $(INCLUDEDIR) ++ ++check: coxeter executable ++ $(EXENAME)$(EXEEXT) < test.input > test.output ++ ++ if ! diff test.output.expected test.output > /dev/null; then \ ++ echo >&2 "Error testing coxeter on test.input:"; \ ++ diff test.output.expected test.output; \ ++ exit 1; \ ++ fi ++ rm -f test.output + + clean: + rm -f $(objects) + + %.o:%.cpp +- $(cc) $(cflags) $*.cpp ++ $(CXX) $(cflags) $*.cpp + + # dependencies --- these were generated automatically by make depend on my + # system; they are explicitly copied for portability. Only local dependencies +@@ -43,7 +100,7 @@ + # contents of tmp in lieu of the dependencies listed here. + + %.d:%.cpp +- @$(cc) -MM $*.cpp ++ @$(CXX) -MM $*.cpp + depend: $(dependencies) + + affine.o: affine.cpp affine.h globals.h coxgroup.h coxtypes.h io.h list.h \ From ee8dcee7c9691d80cd34c076ab351ae27b2b2782 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Aug 2024 14:54:47 +0200 Subject: [PATCH 289/553] fix whitespaces --- .../easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb | 4 ++-- .../p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb index d27b48f9a9b..ecef67eed26 100644 --- a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -94,7 +94,7 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in _bins], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } - + sanity_check_commands = ["herro --help"] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -102,7 +102,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} modloadmsg = """ To run scripts from /scripts directory just run .sh Do not run it as scripts/.sh -For example - run preprocess.sh as: +For example - run preprocess.sh as: $ preprocess.sh """ diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb index 45740411804..f0db4069b1c 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -17,7 +17,7 @@ checksums = [ {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'}, {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'}, ] - + builddependencies = [ ('poetry', '1.5.1'), ('CMake', '3.26.3'), @@ -73,7 +73,7 @@ exts_list = [ # create POD5Version.cmake # python -m setuptools_scm && python -m pod5_make_version shows wrong version preconfigopts = ( - 'cd %(builddir)s/%(name)s-%(version)s/cmake && ' + 'cd %(builddir)s/%(name)s-%(version)s/cmake && ' 'touch POD5Version.cmake && ' 'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && ' 'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && ' From d2351dbf30a935911537e96c3f9ae49df42fd7fa Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 23 Aug 2024 15:00:41 +0200 Subject: [PATCH 290/553] Add patch to fix issue 21243 --- .../easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb | 8 +- .../x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch | 487 ++++++++++++++++++ 2 files changed, 494 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb index 97ce290bfe0..81ee768fed0 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb @@ -11,7 +11,13 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'] +patches = [ + 'xtb-6.7.0_fix-tblite-pr1072.patch' +] +checksums = [ + {'xtb-6.7.0.tar.gz': '9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'}, + {'xtb-6.7.0_fix-tblite-pr1072.patch': 'cb8de869fc4a7c6bde44c61a479fc9edb3ccdc47c2a71f15ef124326f8a117e6'}, +] builddependencies = [ ('Meson', '1.1.1'), diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..74e2ea4950e --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch @@ -0,0 +1,487 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff -Naur xtb-6.7.0.orig/src/dipro/xtb.F90 xtb-6.7.0/src/dipro/xtb.F90 +--- xtb-6.7.0.orig/src/dipro/xtb.F90 2024-08-23 13:50:09.000345982 +0200 ++++ xtb-6.7.0/src/dipro/xtb.F90 2024-08-23 14:14:49.499145489 +0200 +@@ -50,11 +50,11 @@ + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff -Naur xtb-6.7.0.orig/src/dipro.F90 xtb-6.7.0/src/dipro.F90 +--- xtb-6.7.0.orig/src/dipro.F90 2024-08-23 13:50:08.996896000 +0200 ++++ xtb-6.7.0/src/dipro.F90 2024-08-23 13:55:44.571958738 +0200 +@@ -130,6 +130,10 @@ + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff -Naur xtb-6.7.0.orig/src/tblite/calculator.F90 xtb-6.7.0/src/tblite/calculator.F90 +--- xtb-6.7.0.orig/src/tblite/calculator.F90 2024-08-23 13:50:09.192101000 +0200 ++++ xtb-6.7.0/src/tblite/calculator.F90 2024-08-23 14:18:13.034251635 +0200 +@@ -144,11 +144,11 @@ + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +diff -Naur xtb-6.7.0.orig/subprojects/mstore.wrap xtb-6.7.0/subprojects/mstore.wrap +--- xtb-6.7.0.orig/subprojects/mstore.wrap 2024-08-23 13:50:09.235197230 +0200 ++++ xtb-6.7.0/subprojects/mstore.wrap 2024-08-23 14:18:50.314014066 +0200 +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff -Naur xtb-6.7.0.orig/test/unit/test_ptb.F90 xtb-6.7.0/test/unit/test_ptb.F90 +--- xtb-6.7.0.orig/test/unit/test_ptb.F90 2024-08-23 13:50:09.260760000 +0200 ++++ xtb-6.7.0/test/unit/test_ptb.F90 2024-08-23 14:34:18.302090669 +0200 +@@ -186,12 +186,37 @@ + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -670,10 +799,10 @@ + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +837,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +925,9 @@ + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1113,35 @@ + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1225,36 @@ + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1274,7 @@ + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + From f5d48ce3410053903a4cf8e75207be586fc60265 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Aug 2024 16:13:41 +0200 Subject: [PATCH 291/553] update patch for pod5 --- .../p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch index b0207d6c4ac..a053f870ebe 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -1,4 +1,5 @@ -Flatbuffers uses capital 'B' in 'FlatBuffersConfig.cmake' +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules Author: Petr Král (INUITS) diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt --- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 From 0576d05b7ea4b091ff3c87c5d04e826d9b4776b5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Aug 2024 16:17:18 +0200 Subject: [PATCH 292/553] adding easyconfigs: nellie-0.3.1-foss-2023a.eb, ome-types-0.5.1.post1-foss-2023a.eb --- .../n/nellie/nellie-0.3.1-foss-2023a.eb | 52 +++++++++++++++++++ .../ome-types-0.5.1.post1-foss-2023a.eb | 52 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb new file mode 100644 index 00000000000..5032e0e6ec5 --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': "sed -i -e 's/numpy==1.26.4/numpy/' -e 's/scipy==1.12.0/scipy/' -e 's/nd2==0.9.0/nd2/' -e 's/pandas==2.2.1/pandas/' -e 's/matplotlib==3.8.3/matplotlib/' -e 's/napari[all]/napari/' setup.cfg && ", + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb new file mode 100644 index 00000000000..0de34e3542b --- /dev/null +++ b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ome-types' +version = '0.5.1.post1' + +homepage = 'https://github.com/tlambert03/ome-types/' +description = """ +ome_types provides a set of python dataclasses and utility functions for parsing +the OME-XML format into fully-typed python objects for interactive or programmatic access in python. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('pydantic', '2.5.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ruff', '0.3.0', { + 'checksums': ['0886184ba2618d815067cf43e005388967b67ab9c80df52b32ec1152ab49f53a'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('untokenize', '0.1.1', { + 'checksums': ['3865dbbbb8efb4bb5eaa72f1be7f3e0be00ea8b7f125c69cbd1f5fda926f37a2'], + }), + ('docformatter', '1.7.5', { + 'checksums': ['ffed3da0daffa2e77f80ccba4f0e50bfa2755e1c10e130102571c890a61b246e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('xsdata', '23.8', { + 'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'], + }), + ('ome_types', version, { + 'checksums': ['cadda5e36ad4d33dad2034fd43f32113a736fe47c67fd9e06bbb8d3858d1dc58'], + }), +] + +moduleclass = 'lib' From 4ee2a2d3c83587cbfe1c4914d465cd5c5ea72a4a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 24 Aug 2024 09:53:20 +0200 Subject: [PATCH 293/553] update configopts --- easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb index 307c0abb034..fc9ad81c0cb 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' From e55798f254fc2ae2c64234b5482a36dcc202a402 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 24 Aug 2024 09:53:45 +0200 Subject: [PATCH 294/553] Use preconfigopts instead of configure_cmd_prefix Co-authored-by: Sam Moors --- easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb index c4080545d5b..1fa3ca78fd9 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb @@ -26,7 +26,7 @@ dependencies = [('ncurses', '6.5')] preconfigopts = "autoconf && " # configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " +preconfigopts += "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], From b2b08049e3ef9d280624bffd39b089f834e498ad Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 26 Aug 2024 11:04:02 +0200 Subject: [PATCH 295/553] update preinstallopts --- easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb index 5032e0e6ec5..34b3ce6299a 100644 --- a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb @@ -44,7 +44,7 @@ exts_list = [ 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], }), (name, version, { - 'preinstallopts': "sed -i -e 's/numpy==1.26.4/numpy/' -e 's/scipy==1.12.0/scipy/' -e 's/nd2==0.9.0/nd2/' -e 's/pandas==2.2.1/pandas/' -e 's/matplotlib==3.8.3/matplotlib/' -e 's/napari[all]/napari/' setup.cfg && ", + 'preinstallopts': local_preinstallopts, 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], }), ] From d49b40557d3cbecf3755832446302e63acada8f3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 26 Aug 2024 11:16:30 +0200 Subject: [PATCH 296/553] update duplex_tools sources --- .../easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb index fe56d08acaa..fb67d050e02 100644 --- a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb @@ -48,7 +48,7 @@ exts_list = [ 'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'], }), (name, version, { - 'source_tmpl': 'duplex_tools-%(version)s.tar.gz', + 'sources': [{'download_filename': 'duplex_tools-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], }), ] From 6279f73668124799c163dfc4fbc66c4fec32766f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Aug 2024 12:05:38 +0200 Subject: [PATCH 297/553] add insight extension to R-bundle-CRAN 2024.06 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index c8376489c57..d239f2596c2 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3436,6 +3436,9 @@ exts_list = [ ('missMDA', '1.19', { 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], }), + ('insight', '0.20.3', { + 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From c1a8df0af156c31ec3745f03332b8f6221ac95d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Aug 2024 12:08:22 +0200 Subject: [PATCH 298/553] adding easyconfigs: BayesOpt-0.9-GCC-12.3.0.eb --- .../b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..ab0e97a41ad --- /dev/null +++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'BayesOpt' +version = '0.9' + +homepage = 'https://rmcantin.github.io/bayesopt' +description = """BayesOpt is an efficient implementation of the Bayesian optimization methodology for +nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rmcantin/bayesopt/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4e60cfac380eccd2d1adc805b752b5bd22a1d8a27dc6aeb630c403adc04f28c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), +] + +sanity_check_paths = { + 'files': ['lib/libbayesopt.a', 'lib/libnlopt.a'], + 'dirs': ['include/bayesopt'], +} + +moduleclass = 'math' From 2e502ae39b1724c81e4e200ff9c0536e49ece880 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Aug 2024 12:22:14 +0200 Subject: [PATCH 299/553] add missing NLopt dependency for BayesOpt --- easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb index ab0e97a41ad..2e20ceba904 100644 --- a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb @@ -19,10 +19,14 @@ builddependencies = [ dependencies = [ ('Boost', '1.82.0'), + ('NLopt', '2.7.1'), ] +# don't build included version of NLopt (use provided dependency) +configopts = "-DNLOPT_BUILD=OFF" + sanity_check_paths = { - 'files': ['lib/libbayesopt.a', 'lib/libnlopt.a'], + 'files': ['lib/libbayesopt.a'], 'dirs': ['include/bayesopt'], } From cfd1b541d24b1fc704c61ec5a3613e50919caf85 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Mon, 26 Aug 2024 12:19:06 +0000 Subject: [PATCH 300/553] Fix cpu and gpu versions of bitsandbytes --- ...sandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++ .../bitsandbytes-0.43.3-foss-2023a.eb | 4 +- 2 files changed, 51 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3b89d58cc47 --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), +] + +configopts = '-DCOMPUTE_BACKEND=cuda' +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb index 902b7d717f1..8a6b11e5a2c 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -20,11 +20,11 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('PyTorch', '2.1.2', '-CUDA-12.1.1'), + ('PyTorch', '2.1.2'), ('SciPy-bundle', '2023.07'), ] -configopts = '-DCOMPUTE_BACKEND=cuda' +# configopts = '-DCOMPUTE_BACKEND=cuda' skipsteps = ['install'] postinstallcmds = [ From a91f271f0acfb03f0ae432ec4d7152a9c96372a1 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Mon, 26 Aug 2024 12:24:31 +0000 Subject: [PATCH 301/553] Remove comments --- .../easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb index 8a6b11e5a2c..e9f92c025a9 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -24,7 +24,6 @@ dependencies = [ ('SciPy-bundle', '2023.07'), ] -# configopts = '-DCOMPUTE_BACKEND=cuda' skipsteps = ['install'] postinstallcmds = [ From 60f891b74fa97c883591e44e4194b38b0fd7a523 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Aug 2024 17:19:02 +0200 Subject: [PATCH 302/553] add back easyconfig for VTK 9.3.0 that shouldn't have been removed --- .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 98 +++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb new file mode 100644 index 00000000000..740fd888dfb --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -0,0 +1,98 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +# Update: Pavel Tománek (Inuits) +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.3.0' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.3.0.tar.gz': 'fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9'}, + {'VTKData-9.3.0.tar.gz': 'f82142dd327e995c9536c1003e1370bb4092c96f23edb8119d16d2411ef35dc3'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XZ', '5.4.2'), + ('libGLU', '9.0.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " +configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From e701ce284117a4ce96aeea93c125eaa0831f0dd7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 26 Aug 2024 17:44:59 +0200 Subject: [PATCH 303/553] adding easyconfigs: NextPolish-1.4.1-GCCcore-12.3.0.eb --- .../NextPolish-1.4.1-GCCcore-12.3.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..857ec88ff80 --- /dev/null +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'MakeCp' + +name = 'NextPolish' +version = '1.4.1' + +homepage = 'https://github.com/Nextomics/NextPolish' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] +sources = [{ + 'download_filename': 'v%(version)s/%(name)s.tgz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('BWA', '0.7.17'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +# fix make -C util - warning: jobserver unavailable +parallel = 1 + +# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 +prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count samtools minimap2/' Makefile && " +prebuildopts += "rm -rf util/bwa && " +prebuildopts += ( + "sed -i" + " -e 's/seq_count bwa_ samtools_/seq_count samtools_/'" + " -e '29d'" # @+make clean -C $(BWADIR) + " -e '18,20d'" # bwa_: @+make -C $(BWADIR) + " -e '1d'" # BWADIR = ./bwa + " util/Makefile && " +) +postinstallcmds = ['cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa'] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] + +sanity_check_paths = { + 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextPolish --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' From c98fb5482ff1a7b2b29b7db945d945a17071cf7b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 27 Aug 2024 10:57:42 +0200 Subject: [PATCH 304/553] adding easyconfigs: nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb --- .../nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..35d0c5778dd --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), + ('CuPy', '13.0.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' From e5bf5862479102f7f066f80628ce023f0efc50e1 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 16:07:43 +0200 Subject: [PATCH 305/553] Install ReFrame the way ReFrame was actually meant to be installed. I.e. with all its deps in the /external subdirectory, and with the reframe command being the only one that can find them (by extending the sys.path). I.e. we no longer add this directory to PYTHONPATH, and we skip various sanity checks for Python packages. Something like python -c "import reframe" is _not_ supposed to work, but "reframe -V" does (because that command sets the right sys.path). --- .../r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6183827a996 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +dependencies = [ + ('Python', '3.11.5'), + ('libxslt', '1.1.38'), + ('libxml2', '2.11.4'), +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' From 0190d40dab9f3a8ed03f73b57fd60791a6ce4b25 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 16:49:04 +0200 Subject: [PATCH 306/553] Add ReFrame 4.6.2 for other toolchains, and list os dependencies there --- .../r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 73 ++++++++++++++++++ .../r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 4 +- .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 76 +++++++++++++++++++ 3 files changed, 152 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2d989755dc2 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), + ('libxml2', '2.11.4'), +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 6183827a996..bf9f13b702f 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -8,10 +8,12 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies dependencies = [ ('Python', '3.11.5'), ('libxslt', '1.1.38'), - ('libxml2', '2.11.4'), + ('libxml2', '2.11.5'), ] use_pip = True diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb new file mode 100644 index 00000000000..13b5404925f --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +osdependencies = [ + ('libxml2'), + ('libxslt'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' From 6415e1eb717e4297bef1cd34533eb8201d54e278 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 16:51:45 +0200 Subject: [PATCH 307/553] Remove setting of RFM_PURGE_ENVIRONMENT for ReFrame at system toolchain level. --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 13b5404925f..a4527f77eb9 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -67,10 +67,4 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running -# any tests by default -modextravars = { - 'RFM_PURGE_ENVIRONMENT': '1', -} - moduleclass = 'devel' From ccd1186e4e18478947658d45e6b55763fe73736b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 17:19:18 +0200 Subject: [PATCH 308/553] Actually change the toolchain version... --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index 2d989755dc2..995f260fbd1 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -6,7 +6,7 @@ version = '4.6.2' homepage = 'https://github.com/reframe-hpc/reframe' description = '''ReFrame is a framework for writing regression tests for HPC systems.''' -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} # Note that for ReFrame's CPU autodetect to work # the system also needs to provide (new enough versions of) these dependencies From bdc1b9447cc578efe4c925178b99c274ed9b3efa Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 18:01:16 +0200 Subject: [PATCH 309/553] Add pip back in as dep. Might need wheel too, let's see --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index a4527f77eb9..2d1448461bc 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -22,6 +22,12 @@ req_py_minver = 6 use_pip = True exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path # so that ReFrame (and only ReFrame) will find & use all of these dependencies. From 2b8e0cd424cd88360db37699c837dd1cf008c80e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 18:09:54 +0200 Subject: [PATCH 310/553] Add setuptools, so that we can install with pyproject.toml instead of setup.py --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 2d1448461bc..47c4afe5e0c 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -28,6 +28,13 @@ exts_list = [ 'use_pip': False, 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False,' + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }) # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path # so that ReFrame (and only ReFrame) will find & use all of these dependencies. From f16a887cacbe1d7e74fcebaab7fd209785629180 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 18:10:47 +0200 Subject: [PATCH 311/553] Forgot comma --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 47c4afe5e0c..db9fa02ede0 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -34,7 +34,7 @@ exts_list = [ 'use_pip': False,' 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], - }) + }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path # so that ReFrame (and only ReFrame) will find & use all of these dependencies. From 71d71b4bb90e007a5d1b3fb17f0eb2753562a7ec Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 18:11:55 +0200 Subject: [PATCH 312/553] Stray quote removed --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index db9fa02ede0..c0195a09783 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -31,7 +31,7 @@ exts_list = [ # Require new enough setuptools to install with e.g. pyproject.toml # 59.6.0 is the latest compatible with Python 3.6 ('setuptools', '59.6.0', { - 'use_pip': False,' + 'use_pip': False, 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), From b19add1d090cd0519995564282cbfd41643cb2c7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 27 Aug 2024 18:14:54 +0200 Subject: [PATCH 313/553] Wheel is still needed, adding back in --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index c0195a09783..b25cee0e9fa 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -35,6 +35,11 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path # so that ReFrame (and only ReFrame) will find & use all of these dependencies. From 4f9e20a85f677c75cb411a041b6cbd035277e9f2 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 27 Aug 2024 11:12:28 -0700 Subject: [PATCH 314/553] update fastp --- .../f/fastp/fastp-0.23.4-GCC-13.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..49b2a29c4f9 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.13'), + ('libdeflate', '1.19'), + ('ISA-L', '2.31.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From bf1b18474e7d4c341848063838313fc90b521465 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 28 Aug 2024 09:35:56 +0200 Subject: [PATCH 315/553] Added builddependency binutils for gmpy2 --- easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb index d919e2ca8e3..45d90e26d6a 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70'] +builddependencies = [ + ('binutils', '2.42') +] + dependencies = [ ('Python', '3.12.3'), ('GMP', '6.3.0'), From 9401f8b94213782f5ca6d7aeb9a6578c9698c3f4 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 28 Aug 2024 11:02:09 +0200 Subject: [PATCH 316/553] add performance, datwizard and bayestestR to R-bundle-CRAN 2024.06 --- .../R-bundle-CRAN-2024.06-foss-2023b.eb | 28 +++++++++---------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index d239f2596c2..72c6dd9e26e 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -588,10 +588,7 @@ exts_list = [ 'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'], }), ('pan', '1.9', { - 'checksums': [ - ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52', - 'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'), - ], + 'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'], }), ('mitml', '0.4-5', { 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], @@ -1603,10 +1600,7 @@ exts_list = [ 'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'], }), ('signal', '1.8-0', { - 'checksums': [ - ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684', - '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'), - ], + 'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'], }), ('tuneR', '1.4.7', { 'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'], @@ -2098,7 +2092,6 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, @@ -2592,8 +2585,8 @@ exts_list = [ 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], }), ('dbarts', '0.9-28', { + 'preinstallopts': '', 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], - 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], @@ -2629,13 +2622,9 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" + 'modulename': False, 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... - 'modulename': False, }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], @@ -3439,6 +3428,15 @@ exts_list = [ ('insight', '0.20.3', { 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], }), + ('datawizard', '0.12.2', { + 'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'], + }), + ('bayestestR', '0.14.0', { + 'checksums': ['fa0f94204b414df05ecf7340b37fbb5fbe6dff2d057e2425a6990b6510054880'], + }), + ('performance', '0.12.2', { + 'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 264581b8bc96990f21429131c45f9d364dccc413 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 28 Aug 2024 11:11:12 +0200 Subject: [PATCH 317/553] remove unnecessary of checksums --- .../R-bundle-CRAN-2024.06-foss-2023b.eb | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 72c6dd9e26e..a15e03469da 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -588,7 +588,10 @@ exts_list = [ 'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'], }), ('pan', '1.9', { - 'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'], + 'checksums': [ + ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52', + 'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'), + ], }), ('mitml', '0.4-5', { 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], @@ -1600,7 +1603,10 @@ exts_list = [ 'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'], }), ('signal', '1.8-0', { - 'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'], + 'checksums': [ + ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684', + '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'), + ], }), ('tuneR', '1.4.7', { 'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'], @@ -2092,6 +2098,7 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, @@ -2585,8 +2592,8 @@ exts_list = [ 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], }), ('dbarts', '0.9-28', { - 'preinstallopts': '', 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], @@ -2622,9 +2629,13 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], From baffea8a827a92c336b76fb4e392b601c8f891ed Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 28 Aug 2024 11:13:52 +0200 Subject: [PATCH 318/553] remove unnecessary changes --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index a15e03469da..3bd3447df1d 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -2098,7 +2098,7 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, From f6989ece375a5d39bc70853d43f2db86c2971969 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 11:39:34 +0200 Subject: [PATCH 319/553] Remove the global sanity_pip_check = True --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index 995f260fbd1..b8f5a73f8c9 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -62,8 +62,6 @@ sanity_check_paths = { sanity_check_commands = ['reframe -V'] -sanity_pip_check = True - # Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running # any tests by default modextravars = { diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index bf9f13b702f..03dd4f7de30 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -62,8 +62,6 @@ sanity_check_paths = { sanity_check_commands = ['reframe -V'] -sanity_pip_check = True - # Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running # any tests by default modextravars = { diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index b25cee0e9fa..c99bbfba4c1 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -83,6 +83,4 @@ sanity_check_paths = { sanity_check_commands = ['reframe -V'] -sanity_pip_check = True - moduleclass = 'devel' From 9bd137c76ebfc1a39c0df9c17663cae9b3b0b901 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 28 Aug 2024 11:43:02 +0200 Subject: [PATCH 320/553] move insight as performance is optional dependency of insight --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 3bd3447df1d..06a928ab8d0 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3436,9 +3436,6 @@ exts_list = [ ('missMDA', '1.19', { 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], }), - ('insight', '0.20.3', { - 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], - }), ('datawizard', '0.12.2', { 'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'], }), @@ -3448,6 +3445,9 @@ exts_list = [ ('performance', '0.12.2', { 'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'], }), + ('insight', '0.20.3', { + 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 34765d2b0f9fba1363259a94fd061e27797466e7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 11:44:46 +0200 Subject: [PATCH 321/553] Add binutils back in at the instruction of the CI checker... --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 4 ++++ .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index b8f5a73f8c9..bdb4139b17e 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -8,6 +8,10 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), +] + # Note that for ReFrame's CPU autodetect to work # the system also needs to provide (new enough versions of) these dependencies dependencies = [ diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 03dd4f7de30..3c6d6af6b48 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -8,6 +8,10 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +builddependencies = [ + ('binutils', '2.40') +] + # Note that for ReFrame's CPU autodetect to work # the system also needs to provide (new enough versions of) these dependencies dependencies = [ From 2ef57c79afe528f929ef857385dd9ee0f6799c90 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 11:45:46 +0200 Subject: [PATCH 322/553] Remove trailing whitespace --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index bdb4139b17e..26018c7bef8 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('libxslt', '1.1.38'), - ('libxml2', '2.11.4'), + ('libxml2', '2.11.4'), ] use_pip = True diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 3c6d6af6b48..5bad59e8703 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), ('libxslt', '1.1.38'), - ('libxml2', '2.11.5'), + ('libxml2', '2.11.5'), ] use_pip = True From 5d1388ad96f235c006d707caacdec9ec8c1aa948 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Aug 2024 12:27:03 +0200 Subject: [PATCH 323/553] don't use %(namelower)s template in name of SCENICplus extension --- .../s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb index dbff79bbe8c..5f88062b0f8 100644 --- a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -260,7 +260,7 @@ exts_list = [ 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], }), - ('%(namelower)s', version, { + ('scenisplus', version, { 'preinstallopts': local_preinstallopts, 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], From 434ae24226e578afdb5405bf0dfe2433977efcb5 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 13:08:45 +0200 Subject: [PATCH 324/553] Whitelist ReFrame to allow not running the sanity_check_pip --- test/easyconfigs/easyconfigs.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4d7b85dac79..b1274497b8a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1086,6 +1086,11 @@ def test_pr_python_packages(self): r'.*-2016[ab]-Python-.*', # mympirun is installed with system Python, pip may not be installed for system Python r'vsc-mympirun.*', + # ReFrame intentionally installs its deps in a %(installdir)s/external subdir, which is added + # to sys.path by the ReFrame command, and is intentionally NOT on the PYTHONPATH. + # Thus, a pip check fails, but this is expected and ok, it is still a working ReFrame installation + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269 for more info + r'ReFrame.*', ] failing_checks = [] From b34d3cb74a0532b6986586ab377da0297185a696 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 28 Aug 2024 13:19:32 +0200 Subject: [PATCH 325/553] Update SCENICplus-1.0a1-20240513-foss-2023a.eb - typo --- .../s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb index 5f88062b0f8..796eb9a63b6 100644 --- a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -260,7 +260,7 @@ exts_list = [ 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], }), - ('scenisplus', version, { + ('scenicplus', version, { 'preinstallopts': local_preinstallopts, 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], From 7af33b2061fa75c3fc2da11e058fc2e8b900cf2f Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 13:22:45 +0200 Subject: [PATCH 326/553] Put additional comments for future clarity --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 4 ++-- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 4 ++-- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 1 + 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index 26018c7bef8..7960a1ae6e4 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -16,8 +16,8 @@ builddependencies = [ # the system also needs to provide (new enough versions of) these dependencies dependencies = [ ('Python', '3.11.3'), - ('libxslt', '1.1.38'), - ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer ] use_pip = True diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 5bad59e8703..0a85c4d2b4e 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -16,8 +16,8 @@ builddependencies = [ # the system also needs to provide (new enough versions of) these dependencies dependencies = [ ('Python', '3.11.5'), - ('libxslt', '1.1.38'), - ('libxml2', '2.11.5'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer ] use_pip = True diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index c99bbfba4c1..fd4a336660e 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -10,6 +10,7 @@ toolchain = SYSTEM allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +# Required by lxml, which is installed by ReFrame's bootstrap installer osdependencies = [ ('libxml2'), ('libxslt'), From e4ec3d8ca28159f3131818093d745de042cf848a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 13:25:03 +0200 Subject: [PATCH 327/553] Correct version that was accidentally changed --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 0a85c4d2b4e..1593844cfac 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer - ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer ] use_pip = True From 2c95bbcad15332323a4f0341fe70f9f24fd5d5e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Aug 2024 15:50:57 +0200 Subject: [PATCH 328/553] remove non-sensical 'import gv' sanity check from TF-COMB easyconfig --- easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb index 2dcd3a55fdf..2c06e8c9c8f 100644 --- a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -45,8 +45,4 @@ exts_list = [ }), ] -sanity_check_commands = [ - "python -c 'import gv'", -] - moduleclass = 'bio' From 98b62f2e810ff86270a1050d82d13ac1f08745c4 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 15:54:36 +0200 Subject: [PATCH 329/553] Add curl as builddep, since ReFrame downloads pip with it in their bootstrap --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 1 + .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index 7960a1ae6e4..84f4c755eb7 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), + ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap ] # Note that for ReFrame's CPU autodetect to work diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 1593844cfac..6393b4e7e52 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -9,7 +9,8 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ - ('binutils', '2.40') + ('binutils', '2.40'), + ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap ] # Note that for ReFrame's CPU autodetect to work From cc8bc38566f2af536932e324c4c3a0830db159e5 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 28 Aug 2024 16:42:33 +0200 Subject: [PATCH 330/553] Fix spaces for inline comments --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 6 +++--- .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb index 84f4c755eb7..9046d5c9362 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -10,15 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap + ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap ] # Note that for ReFrame's CPU autodetect to work # the system also needs to provide (new enough versions of) these dependencies dependencies = [ ('Python', '3.11.3'), - ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer - ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer ] use_pip = True diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb index 6393b4e7e52..e2adb9db1d9 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -10,15 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ ('binutils', '2.40'), - ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap + ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap ] # Note that for ReFrame's CPU autodetect to work # the system also needs to provide (new enough versions of) these dependencies dependencies = [ ('Python', '3.11.5'), - ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer - ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer ] use_pip = True From 17de7b9d5a4eeb4c3d2631286857b774af338150 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Wed, 28 Aug 2024 18:31:28 +0200 Subject: [PATCH 331/553] add to gitignore: *.eb_bak_* *.out .venv/ Such paths should never be committed: - `.eb_bak` files are remnants after `eb --inject-checksums` - `.out` files are log remnants after `eb --job` - `.venv/` are probably created for ad-hoc testing --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index c667a41e000..c2974194435 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,15 @@ .pydevproject .project LICENSE_HEADER +*.eb.bak_* *.pyc *.pyo *.nja +*.out build/ dist/ *egg-info/ +.venv/ *.swp *.ropeproject/ eb-*.log From 11e6ad96ed4ecbd9e04c69cb1f8dd17de3c3f073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Aug 2024 19:01:23 +0200 Subject: [PATCH 332/553] adding easyconfigs: Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb --- .../CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb | 78 ++++++ .../Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb | 43 +++ ...n-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb | 247 ++++++++++++++++++ .../scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb | 53 ++++ ...ib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb | 55 ++++ ...scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb | 69 +++++ 6 files changed, 545 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3ec16f6ab04 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scVelo', '0.3.1'), + ('Seaborn', '0.13.2'), + ('wrapt', '1.15.0'), + ('PyTorch', '2.1.2', versionsuffix), + ('wandb', '0.16.1'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('nam', '0.0.3', { + 'checksums': ['48400d12b5f29fdd1671aebdf78d7f41bcac4f5c8ab7ed48770ee0c4fbc0673b'], + }), + ('python-utils', '3.8.2', { + 'checksums': ['c5d161e4ca58ce3f8c540f035e018850b261a41e7cb98f6ccf8e1deb7174a1f1'], + }), + ('progressbar2', '4.4.1', { + 'modulename': 'progressbar', + 'checksums': ['97d323ba03ad3d017a4d047fd0b2d3e733c5a360c07f87d269f96641c3de729f'], + }), + ('dunamai', '1.19.2', { + 'checksums': ['3be4049890763e19b8df1d52960dbea60b3e263eb0c96144a677ae0633734d2e'], + }), + ('poetry_dynamic_versioning', '1.2.0', { + 'checksums': ['1a7bbdba2530499e73dfc6ac0af19de29020ab4aaa3e507573877114e6b71ed6'], + }), + ('pygpcca', '1.0.4', { + 'preinstallopts': "sed -i 's/jinja2==3.0.3/jinja2>=3.0.3/' requirements.txt && ", + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + }), + ('pygam', '0.9.1', { + 'checksums': ['a321a017bf485ed93fc6233e02621f8e7eab3d4f8971371c9ae9e079c55be01d'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + (name, version, { + 'modulename': 'cellrank', + 'preinstallopts': "sed -i 's/matplotlib>=3.5.0,<3.7.2/matplotlib>=3.5.0/' pyproject.toml && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..43b7ce4b7ef --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..22eca6d4ed4 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,247 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' +versionsuffix = '-CUDA-12.1.1' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2', versionsuffix), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2', versionsuffix), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2', versionsuffix), + ('scArches', '0.6.1', versionsuffix), + ('scib-metrics', '0.5.1', versionsuffix), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..cb33b614f6f --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b021ceb3c20 --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25', versionsuffix), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7a284e4e0c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('jax', '0.4.25', versionsuffix), + ('h5py', '3.9.0'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0', versionsuffix), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From d5acbaf39633a9ea56df14fd2989e01c32b35007 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Wed, 28 Aug 2024 19:32:20 +0200 Subject: [PATCH 333/553] adding patch: HDF5-1.14.3_suppress_fp_exceptions.patch HDF5 v1.14.3 was broken, this patch is the hotfix that was published soon after the release. See: https://github.com/HDFGroup/hdf5/issues/3831 --- .../h/HDF5/HDF5-1.14.3-gompi-2023b.eb | 6 +- .../h/HDF5/HDF5-1.14.3-iimpi-2023b.eb | 6 +- .../HDF5-1.14.3_suppress_fp_exceptions.patch | 223 ++++++++++++++++++ 3 files changed, 233 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb index f2aab3663a3..5cb05f4a4a1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb index 77fa0c12ab9..e180d8619ee 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch new file mode 100644 index 00000000000..420125db46d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch @@ -0,0 +1,223 @@ +See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +Created using +git checkout hdf5-1_14_3 +git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82 +Author: Dana Robinson <43805+derobins@users.noreply.github.com> +Date: Tue Nov 7 08:13:30 2023 -0800 + + Disable FP exceptions in H5T init code (#3837) + + The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. + + Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. + + Fixes #3831 + +diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 +index 328f8d3cec..079f08d96c 100644 +--- a/config/linux-gnulibc1 ++++ b/config/linux-gnulibc1 +@@ -173,10 +173,7 @@ case $FC_BASENAME in + nagfor) + + F9XSUFFIXFLAG="" +- # NOTE: The default is -ieee=stop, which will cause problems +- # when the H5T module performs floating-point type +- # introspection +- AM_FCFLAGS="$AM_FCFLAGS -ieee=full" ++ AM_FCFLAGS="$AM_FCFLAGS" + FSEARCH_DIRS="" + + # Production +diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt +index 200576332b..7de2a56974 100644 +--- a/release_docs/RELEASE.txt ++++ b/release_docs/RELEASE.txt +@@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release + =================================== + Library + ------- ++ - Suppressed floating-point exceptions in H5T init code ++ ++ The floating-point datatype initialization code in H5Tinit_float.c ++ could raise FE_INVALID exceptions while munging bits and performing ++ comparisons that might involve NaN. This was not a problem when the ++ initialization code was executed in H5detect at compile time (prior ++ to 1.14.3), but now that the code is executed at library startup ++ (1.14.3+), these exceptions can be caught by user code, as is the ++ default in the NAG Fortran compiler. ++ ++ Starting in 1.14.4, we now suppress floating-point exceptions while ++ initializing the floating-point types and clear FE_INVALID before ++ restoring the original environment. ++ ++ Fixes GitHub #3831 ++ ++ - Fixed a file handle leak in the core VFD ++ ++ When opening a file with the core VFD and a file image, if the file ++ already exists, the file check would leak the POSIX file handle. ++ ++ Fixes GitHub issue #635 ++ + - Fixed some issues with chunk index metadata not getting read + collectively when collective metadata reads are enabled + +@@ -619,12 +642,6 @@ Known Problems + this release with link errors. As a result, Windows binaries for this release + will not include Fortran. The problem will be addressed in HDF5 1.14.4. + +- IEEE standard arithmetic enables software to raise exceptions such as overflow, +- division by zero, and other illegal operations without interrupting or halting +- the program flow. The HDF5 C library intentionally performs these exceptions. +- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program +- to avoid stopping on an exception. +- + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. +diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c +index 3b9e127fe4..3213f00fec 100644 +--- a/src/H5Tinit_float.c ++++ b/src/H5Tinit_float.c +@@ -51,19 +51,23 @@ + * Function: DETECT_F + * + * Purpose: This macro takes a floating point type like `double' and +- * a base name like `natd' and detects byte order, mantissa +- * location, exponent location, sign bit location, presence or +- * absence of implicit mantissa bit, and exponent bias and +- * initializes a detected_t structure with those properties. ++ * and detects byte order, mantissa location, exponent location, ++ * sign bit location, presence or absence of implicit mantissa ++ * bit, and exponent bias and initializes a detected_t structure ++ * with those properties. ++ * ++ * Note that these operations can raise floating-point ++ * exceptions and building with some compiler options ++ * (especially Fortran) can cause problems. + *------------------------------------------------------------------------- + */ +-#define DETECT_F(TYPE, VAR, INFO) \ ++#define DETECT_F(TYPE, INFO) \ + do { \ +- TYPE _v1, _v2, _v3; \ +- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ +- unsigned char _pad_mask[sizeof(TYPE)]; \ +- unsigned char _byte_mask; \ +- int _i, _j, _last = (-1); \ ++ TYPE _v1, _v2, _v3; \ ++ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ ++ uint8_t _pad_mask[sizeof(TYPE)]; \ ++ uint8_t _byte_mask; \ ++ int _i, _j, _last = -1; \ + \ + memset(&INFO, 0, sizeof(INFO)); \ + INFO.size = sizeof(TYPE); \ +@@ -81,7 +85,7 @@ + _v1 = (TYPE)4.0L; \ + H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \ + for (_i = 0; _i < (int)sizeof(TYPE); _i++) \ +- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \ ++ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \ + _buf1[_i] ^= _byte_mask; \ + H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \ + H5_GCC_CLANG_DIAG_OFF("float-equal") \ +@@ -118,7 +122,7 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)-1.0L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \ + \ + /* Mantissa */ \ + INFO.mpos = 0; \ +@@ -126,12 +130,11 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)1.5L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \ + INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \ + \ + /* Exponent */ \ +- INFO.epos = INFO.mpos + INFO.msize; \ +- \ ++ INFO.epos = INFO.mpos + INFO.msize; \ + INFO.esize = INFO.sign - INFO.epos; \ + \ + _v1 = (TYPE)1.0L; \ +@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d) + herr_t H5_NO_UBSAN + H5T__init_native_float_types(void) + { ++ fenv_t saved_fenv; + H5T_fpoint_det_t det; + H5T_t *dt = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_PACKAGE + ++ /* Turn off floating-point exceptions while initializing to avoid ++ * tripping over signaling NaNs while looking at "don't care" bits. ++ */ ++ if (feholdexcept(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment"); ++ + /* H5T_NATIVE_FLOAT */ + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(float, FLOAT, det); ++ DETECT_F(float, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -497,7 +507,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(double, DOUBLE, det); ++ DETECT_F(double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -528,7 +538,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(long double, LDOUBLE, det); ++ DETECT_F(long double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -561,6 +571,14 @@ H5T__init_native_float_types(void) + H5T_native_order_g = det.order; + + done: ++ /* Clear any FE_INVALID exceptions from NaN handling */ ++ if (feclearexcept(FE_INVALID) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions"); ++ ++ /* Restore the original environment */ ++ if (feupdateenv(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment"); ++ + if (ret_value < 0) { + if (dt != NULL) { + dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); +diff --git a/src/H5private.h b/src/H5private.h +index 14a0ac3225..3aaa0d5245 100644 +--- a/src/H5private.h ++++ b/src/H5private.h +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + #include + #include + #include From 1b99d7e8dbeb93757ee17f5b644c5a628636063a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 29 Aug 2024 10:08:08 +0200 Subject: [PATCH 334/553] add patch file for sage interface --- .../coxeter-20180226-GCCcore-13.2.0.eb | 6 +- .../coxeter-20180226_sage_interface.patch | 89 +++++++++++++++++++ 2 files changed, 94 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb index 1fbcfa900b6..247bb5ac24d 100644 --- a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit] sources = [SOURCE_TAR_GZ] -patches = ['coxeter-20180226_makefile.patch'] +patches = [ + 'coxeter-20180226_makefile.patch', + ('coxeter-20180226_sage_interface.patch', 0), +] checksums = [ {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'}, {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'}, + {'coxeter-20180226_sage_interface.patch': '18ba75e51a944ffccb7fa440b823f68a0aad9066e8edcdd2b52bac6b43404bd3'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch new file mode 100644 index 00000000000..2b4cd427ca9 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch @@ -0,0 +1,89 @@ +Adds sage interface. See https://github.com/tscrim/coxeter/pull/14 +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/git.20180226-4/coxeter-sage.patch +diff -u /dev/null sage.h +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.h 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,23 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#ifndef SAGE_H /* guard against multiple inclusions */ ++#define SAGE_H ++ ++#include "globals.h" ++#include "coxgroup.h" ++#include "coxtypes.h" ++#include "schubert.h" ++#include "list.h" ++ ++namespace sage { ++ using namespace coxeter; ++ using namespace coxtypes; ++ using namespace list; ++ ++ void interval(List& result, CoxGroup& W, const CoxWord& g, const CoxWord& h); ++} ++ ++#endif +diff -u /dev/null sage.cpp +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.cpp 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,56 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#include "sage.h" ++ ++namespace sage { ++ ++ void interval(List& list, CoxGroup& W, const CoxWord& g, const CoxWord& h) ++ ++ /* ++ Returns a list of the elements in the Bruhat interval between g and h. ++ Note that this assumes that g and h are in order. ++ */ ++ { ++ if (not W.inOrder(g,h)) { ++ return; ++ } ++ ++ W.extendContext(h); ++ ++ CoxNbr x = W.contextNumber(g); ++ CoxNbr y = W.contextNumber(h); ++ ++ BitMap b(W.contextSize()); ++ W.extractClosure(b,y); ++ ++ BitMap::ReverseIterator b_rend = b.rend(); ++ List res(0); ++ ++ for (BitMap::ReverseIterator i = b.rbegin(); i != b_rend; ++i) ++ if (not W.inOrder(x,*i)) { ++ BitMap bi(W.contextSize()); ++ W.extractClosure(bi,*i); ++ CoxNbr z = *i; // andnot will invalidate iterator ++ b.andnot(bi); ++ b.setBit(z); // otherwise the decrement will not be correct ++ } else ++ res.append(*i); ++ ++ schubert::NFCompare nfc(W.schubert(),W.ordering()); ++ Permutation a(res.size()); ++ sortI(res,nfc,a); ++ ++ list.setSize(0); ++ for (size_t j = 0; j < res.size(); ++j) { ++ CoxWord w(0); ++ W.schubert().append(w, res[a[j]]); ++ list.append(w); ++ } ++ ++ return; ++ } ++ ++} From 5ea734280a2e15281df21a6898a731d03ed20e7e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 29 Aug 2024 10:45:16 +0200 Subject: [PATCH 335/553] update preconfigopts for POD5Version.cmake --- .../pod5-file-format-0.3.10-foss-2023a.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb index f0db4069b1c..9db2243c96e 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -72,14 +72,15 @@ exts_list = [ # create POD5Version.cmake # python -m setuptools_scm && python -m pod5_make_version shows wrong version +local_ver_sub_minor = version.split('.')[2] preconfigopts = ( - 'cd %(builddir)s/%(name)s-%(version)s/cmake && ' + 'cd %%(builddir)s/%%(name)s-%%(version)s/cmake && ' 'touch POD5Version.cmake && ' - 'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && ' - 'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && ' - 'echo "set(POD5_VERSION_REV 10)">>POD5Version.cmake && ' - 'echo "set(POD5_NUMERIC_VERSION 0.3.10)">>POD5Version.cmake && ' - 'echo "set(POD5_FULL_VERSION 0.3.10)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MAJOR %%(version_major)s)">POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MINOR %%(version_minor)s)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_REV %s)">>POD5Version.cmake && ' + 'echo "set(POD5_NUMERIC_VERSION %%(version)s)">>POD5Version.cmake && ' + 'echo "set(POD5_FULL_VERSION %%(version)s)">>POD5Version.cmake && ' % local_ver_sub_minor ) # delete add_subdirectory(third_party/pybind11) from CMakeLists.txt From 984b840fc5b35c31f99a80aab3869857c4e9b26f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 29 Aug 2024 13:17:09 +0200 Subject: [PATCH 336/553] Update easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb - update postinstallcmds Co-authored-by: Kenneth Hoste --- .../easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb index ecef67eed26..a4057965c49 100644 --- a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -73,7 +73,7 @@ prebuildopts = pretestopts = preinstallopts = local_torch_opts # copy scripts to /bin to be easier to run scripts for users postinstallcmds = [ - 'cp -a %(start_dir)sscripts/* %(installdir)s/bin', + 'cp -a %(start_dir)s/scripts/* %(installdir)s/bin', 'rm %(installdir)s/bin/herro-env.yml', "chmod a+rx %(installdir)s/bin/*.sh", "chmod a-x %(installdir)s/bin/*.py", From a13ac978f1885d5148dfaacd12f1928843b5ab9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 29 Aug 2024 14:30:15 +0200 Subject: [PATCH 337/553] adding easyconfigs: mcqd-1.0.0-GCCcore-13.2.0.eb --- .../m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..efc5b111642 --- /dev/null +++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CmdCp' + +name = 'mcqd' +version = '1.0.0' + +homepage = 'https://gitlab.com/janezkonc/mcqd' +description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +cmds_map = [('.*', 'echo here && pwd && ls -lh && $CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['%(name)s.h'], 'include'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'include/%(name)s.h', + ], + 'dirs': [], +} + +sanity_check_commands = ["command -v %(name)s"] + +moduleclass = 'math' From 649abc544e2561a4a902b70eea8e144324573b32 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 08:25:52 +0200 Subject: [PATCH 338/553] Added ConcurrentVersionsSystem and DBus to the GCCcore-13.3.0 toolchain --- ...ntVersionsSystem-1.11.23-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ .../d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..62826484b73 --- /dev/null +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'ConcurrentVersionsSystem' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of +Source Configuration Management (SCM). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = ['cvs-%(version)s.tar.bz2'] +patches = [ + 'CVS-1.11.23-zlib-1.patch', + 'CVS-1.11.23-getline.patch', +] +checksums = [ + '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9', # cvs-1.11.23.tar.bz2 + # CVS-1.11.23-zlib-1.patch + '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4', + # CVS-1.11.23-getline.patch + '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874', +] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('zlib', '1.3.1') +] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ca182becfcd --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DBus' +version = '1.15.8' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('expat', '2.6.2'), +] + +configopts = '-DENABLE_SYSTEMD=OFF ' +# disable documentation +configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 16b3f16de046daf84590a61854a3c29d22666b0f Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 08:44:19 +0200 Subject: [PATCH 339/553] Added ecBuilds, FLAC (+libogg) in the GCCcore-13.3.0 toolchain. --- .../e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb | 37 +++++++++++++++++++ .../f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb | 30 +++++++++++++++ .../l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb | 25 +++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..97c3992ce77 --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.8.5' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['aa0c44cab0fffec4c0b3542e91ebcc736b3d41b68a068d30c023ec0df5f93425'] + +builddependencies = [('binutils', '2.42')] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f767483f7cd --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..810ddbe1169 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' From f0bf67c9b4c7bd523d8ef57f207507e51c091619 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 30 Aug 2024 07:48:13 +0100 Subject: [PATCH 340/553] correct extension order in R-bundle-CRAN 2024.06 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 06a928ab8d0..3bd3447df1d 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -3436,6 +3436,9 @@ exts_list = [ ('missMDA', '1.19', { 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], }), + ('insight', '0.20.3', { + 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], + }), ('datawizard', '0.12.2', { 'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'], }), @@ -3445,9 +3448,6 @@ exts_list = [ ('performance', '0.12.2', { 'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'], }), - ('insight', '0.20.3', { - 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], - }), ] modextrapaths = {'R_LIBS_SITE': ''} From 94700ab878728fbeadf6e34df956a18a4ac7074e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 09:07:50 +0200 Subject: [PATCH 341/553] Added flatbuffers and flatbuffers-python to the GCCcore-13.3.0 toolchain --- ...atbuffers-python-24.3.25-GCCcore-13.3.0.eb | 27 +++++++++++++++ .../flatbuffers-24.3.25-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6e3bd315965 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..42c0b9a28f1 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4157c5cacdb59737c5d627e47ac26b140e9ee28b1102f812b36068aab728c1ed'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 0a9af9d28f7f45f72e5d8c163042304dbcb2ab0f Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 10:14:21 +0200 Subject: [PATCH 342/553] Added byacc and Guile 2.x.x to the GCCcore-13.3.0 toolchain (dependencies for libmatheval) --- .../byacc-2.0.20240109-GCCcore-13.3.0.eb | 22 ++++++++++ .../g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2cade945ccc --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '2.0.20240109' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://invisible-island.net/archives/byacc/current/'] +sources = ['byacc.tar.gz'] +checksums = ['e5e0c069fb15d454918568f77e90a60221373dd206a3d3c2da1e7daba3bae9ea'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..06a1dc6a05a --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.14' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for +the GNU operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), + ('libtool', '2.4.7'), + ('libreadline', '8.2'), + ('XZ', '5.4.5'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile-%(version_major_minor)s.a", + "include/guile/%(version_major_minor)s/libguile.h"], + 'dirs': [] +} + +moduleclass = 'lang' From db713d732bd607fffc04037431e809d34f4ec80a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 30 Aug 2024 10:27:42 +0200 Subject: [PATCH 343/553] adding easyconfigs: XGBoost-2.1.1-gfbf-2023b.eb --- .../x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb new file mode 100644 index 00000000000..91e9be0529c --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4b1729837f9f1ba88a32ef1be3f8efb860fee6454a68719b196dc88032c23d97'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'ai' From b2544a98444fea2160f8957d48b24a55e128f737 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 10:52:55 +0200 Subject: [PATCH 344/553] Added libmatheval to the GCCcore-13.3.0 toolchain. --- .../l/libmatheval/003-guile2.0.patch | 402 ++++++++++++++++++ .../libmatheval-1.1.11-GCCcore-13.3.0.eb | 45 ++ 2 files changed, 447 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch new file mode 100644 index 00000000000..3f592cadb0d --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch @@ -0,0 +1,402 @@ +Description: Increase precision of floating point tests + guile-2.0 has increased the precision of the floating point maths returns, + so the test suite needs to allow for the correct values to be returned + with higher precision. Thanks to Dave Pigott + Also adapt the configure script to build against guile-2.0 - patch from + Hilo Bengen . + . + libmatheval (1.1.11+dfsg-1.1) unstable; urgency=low + . + * Non-maintainer upload. + * Migrate to guile-2.0 - patch from Hilo Bengen, + extended to support higher precision of return values + by guile-2.0. (Closes: #746013) +Author: Neil Williams +Bug-Debian: https://bugs.debian.org/746013 + +--- + +--- libmatheval-1.1.11+dfsg.orig/configure.in ++++ libmatheval-1.1.11+dfsg/configure.in +@@ -60,10 +60,11 @@ dnl Checks for library functions. + AC_CHECK_FUNCS([bzero memset], [break]) + + dnl Additional Guile feature checks. ++CFLAGS="$CFLAGS $GUILE_CFLAGS" + AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include ]) +-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) + + AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile]) + AC_OUTPUT(libmatheval.pc) +--- libmatheval-1.1.11+dfsg.orig/tests/basics.at ++++ libmatheval-1.1.11+dfsg/tests/basics.at +@@ -62,7 +62,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -70,7 +70,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [0.220966666722528], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [0.22096666672252796], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -78,7 +78,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y f 0.4 -0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [-1.14962406520749], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [-1.1496240652074883], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -86,7 +86,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y-z f 11.2 0.41 -0.66)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [3.99876152571934], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [3.9987615257193383], [ignore]) + + AT_DATA([basics.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/constants.at ++++ libmatheval-1.1.11+dfsg/tests/constants.at +@@ -29,7 +29,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -37,7 +37,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.44269504088896], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4426950408889634], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -45,7 +45,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.434294481903252], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.4342944819032518], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -53,7 +53,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.693147180559945], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6931471805599453], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -61,7 +61,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.30258509299405], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.302585092994046], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -69,7 +69,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [3.14159265358979], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [3.141592653589793], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -77,7 +77,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -85,7 +85,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -93,7 +93,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.318309886183791], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.3183098861837907], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -101,7 +101,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.636619772367581], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6366197723675814], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -109,7 +109,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.12837916709551], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.1283791670955126], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -117,7 +117,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623731], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623730951], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -125,7 +125,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.707106781186548], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7071067811865476], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -133,7 +133,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([constant.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/functions.at ++++ libmatheval-1.1.11+dfsg/tests/functions.at +@@ -29,7 +29,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -80,7 +80,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.841470984807897], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8414709848078965], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -97,7 +97,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.54030230586814], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5403023058681398], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -114,7 +114,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549023], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -131,7 +131,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.642092615934331], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6420926159343306], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -148,7 +148,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.85081571768093], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.8508157176809255], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -165,7 +165,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.18839510577812], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1883951057781212], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -182,7 +182,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -216,7 +216,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -233,7 +233,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -267,7 +267,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -284,7 +284,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438014], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -301,7 +301,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.54308063481524], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5430806348152437], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -318,7 +318,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.761594155955765], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7615941559557649], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -335,7 +335,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.31303528549933], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.3130352854993315], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -352,7 +352,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.648054273663885], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6480542736638855], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -368,7 +368,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.850918128239322], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8509181282393216], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -385,7 +385,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -419,7 +419,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 0.5)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -436,7 +436,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 2)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -470,7 +470,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/numbers.at ++++ libmatheval-1.1.11+dfsg/tests/numbers.at +@@ -53,6 +53,6 @@ AT_DATA([number.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh number.scm], [ignore], [0.644394014977254], [ignore]) ++AT_CHECK([matheval.sh number.scm], [ignore], [0.6443940149772542], [ignore]) + + AT_CLEANUP diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4cea27b91dc --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' # still the latest version available on the ftp mirror + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '003-guile2.0.patch', + 'libmatheval-1.1.11_fix-matheval-test.patch' +] +checksums = [ + {'libmatheval-1.1.11.tar.gz': '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab'}, + {'003-guile2.0.patch': 'd0ad39d54800153cbaa26c01448f040d405f09e9fd57e1357eab170a274a9b5c'}, + {'libmatheval-1.1.11_fix-matheval-test.patch': '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('byacc', '2.0.20240109'), + # guile 2.2.X, 3.0.7 removed scm_num2dbl (among others), which are needed for libmatheval (at least for 1.1.11) + ('Guile', '2.0.14') +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' From 67dd6beac93bdbea7dcb21901d9c23744026a7df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 30 Aug 2024 10:58:48 +0200 Subject: [PATCH 345/553] changes requested in PR --- ...ore-13.2.0.eb => mcqd-1.0.0-GCC-13.2.0.eb} | 20 ++++++++----------- 1 file changed, 8 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/m/mcqd/{mcqd-1.0.0-GCCcore-13.2.0.eb => mcqd-1.0.0-GCC-13.2.0.eb} (54%) diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb similarity index 54% rename from easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb index efc5b111642..87f92553548 100644 --- a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb @@ -6,31 +6,27 @@ version = '1.0.0' homepage = 'https://gitlab.com/janezkonc/mcqd' description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph.""" -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchain = {'name': 'GCC', 'version': '13.2.0'} source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/'] -sources = ['%(name)s-v%(version)s.tar.gz'] +sources = ['mcqd-v%(version)s.tar.gz'] checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d'] -builddependencies = [ - ('binutils', '2.40'), -] - -cmds_map = [('.*', 'echo here && pwd && ls -lh && $CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] +cmds_map = [('.*', '$CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] files_to_copy = [ - (['%(name)s'], 'bin'), - (['%(name)s.h'], 'include'), + (['mcqd'], 'bin'), + (['mcqd.h'], 'include'), ] sanity_check_paths = { 'files': [ - 'bin/%(name)s', - 'include/%(name)s.h', + 'bin/mcqd', + 'include/mcqd.h', ], 'dirs': [], } -sanity_check_commands = ["command -v %(name)s"] +sanity_check_commands = ["command -v mcqd"] moduleclass = 'math' From e6608ff6108ac5a225c722e3d43d56df9fe0692c Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 11:03:59 +0200 Subject: [PATCH 346/553] Added libopus and libgit2 to the GCCcore-13.3.0 toolchain. --- .../l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ .../l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..07da30e2a80 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.8.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c1eaf0cf07cba0e9021920bfba9502140220786ed5d8a8ec6c7ad9174522f8e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '-DREGEX_BACKEND=pcre2' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c09615c86f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' From 04c3043bcaa487db2c20e7d5a55073492ab6c703 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 13:16:49 +0200 Subject: [PATCH 347/553] Added libvorbis and libsndfile to the GCCcore-13.3.0 toolchain. --- .../libsndfile-1.2.2-GCCcore-13.3.0.eb | 39 +++++++++++++++++++ .../libvorbis-1.3.7-GCCcore-13.3.0.eb | 30 ++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e60ad09d1a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e32c5c3a99 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' From 3698b966894a0788ed36e9ef498a7aa54a468453 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 13:31:58 +0200 Subject: [PATCH 348/553] Added libspatialindex and libxslt to the GCCcore-13.3.0 toolchain. --- .../libspatialindex-2.0.0-GCCcore-13.3.0.eb | 25 +++++++++++++ .../libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1752b337b05 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '2.0.0' + +homepage = 'https://libspatialindex.org' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['f1d5a369681fa6ac3301a54db412ccf3180fc17163ebc3252f32c752f77345de'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a38c53ef841 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.42' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], +} + +moduleclass = 'lib' From f2d7b3de0dcb79cb2565140acabc7d9d62be0635 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 14:04:49 +0200 Subject: [PATCH 349/553] Added giflib and libwebp to the GCCcore-13.3.0 toolchain. --- .../g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb | 28 ++++++++++++ .../l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66ef70d59ce --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..70084689c61 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.4.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61f873ec69e3be1b99535634340d5bde750b2e4447caa1db9f61be3fd49ab1e5'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' From 7406dc60d0302c4c0af26d249edf07bdb5546af0 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 14:13:28 +0200 Subject: [PATCH 350/553] Added a moduleclass to byacc --- .../easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb index 2cade945ccc..292636d12e3 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -20,3 +20,5 @@ sanity_check_paths = { 'files': ["bin/yacc"], 'dirs': [] } + +moduleclass = 'lang' From def623c7d60612c2d0f0d31aa27ac4af7e7ac976 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 30 Aug 2024 15:30:33 +0200 Subject: [PATCH 351/553] Add helper_scripts to PATH --- .../ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb index 258c21fef24..db7151ab47f 100644 --- a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb @@ -27,17 +27,20 @@ dependencies = [ ('torchaudio', '0.12.0', '-PyTorch-1.12.0' + versionsuffix), ] -postinstallcmds = ['chmod a+x %(installdir)s/protein_mpnn_run.py'] +postinstallcmds = [ + 'chmod a+x %(installdir)s/protein_mpnn_run.py', + 'chmod a+x %(installdir)s/helper_scripts/*.py' +] sanity_check_paths = { 'files': ['protein_mpnn_run.py'], 'dirs': ['examples'], } -fix_python_shebang_for = ['protein_mpnn_run.py'] +fix_python_shebang_for = ['protein_mpnn_run.py', 'helper_scripts/*.py'] sanity_check_commands = ['protein_mpnn_run.py --help'] -modextrapaths = {'PATH': ''} +modextrapaths = {'PATH': ['', 'helper_scripts']} moduleclass = 'bio' From fc75b68e28885d1c07d9c4fb273ca387c089f6a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 30 Aug 2024 16:47:05 +0200 Subject: [PATCH 352/553] remove exts_default_options from TensorFlow 2.3.1 This is a top-level parameter --- .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 4 +--- .../TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 2cfb8444ca4..daa5022fb1f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -40,9 +40,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 54fdbc44964..7a4a7766ca6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -42,9 +42,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: From 093cbbf29b3cc1a9c458e85477c30f36a8e44295 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 30 Aug 2024 19:42:08 +0200 Subject: [PATCH 353/553] use https --- .../ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb index 62826484b73..b43a426454f 100644 --- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb @@ -15,7 +15,7 @@ Source Configuration Management (SCM). toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] sources = ['cvs-%(version)s.tar.bz2'] patches = [ 'CVS-1.11.23-zlib-1.patch', From a6a5ce548771825825c98218242f39ae3f3a48b5 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 30 Aug 2024 21:26:16 +0200 Subject: [PATCH 354/553] Added LittleCMS and lxml to the GCCcore-13.3.0 toolchain. --- .../LittleCMS-2.16-GCCcore-13.3.0.eb | 26 +++++++++++++++++ .../l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..121d33200a2 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.16' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['d873d34ad8b9b4cea010631f1a6228d2087475e4dc5e763eb81acc23d9d45a51'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libjpeg-turbo', '3.0.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0af2dcbed3f --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '5.3.0' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('libxml2', '2.12.7'), + ('libxslt', '1.1.42'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From df5d54ed5ef88595c3fd94b58f5375bb726e30a2 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Sun, 1 Sep 2024 21:49:03 +0200 Subject: [PATCH 355/553] Added LZO and nano to the GCCcore-13.3.0 toolchain --- .../l/LZO/LZO-2.10-GCCcore-13.3.0.eb | 27 +++++++++++++++++++ .../n/nano/nano-8.1-GCCcore-13.3.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4d8ccd20b1f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64684d1ff42 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '8.1' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6508bfbcfe38153ecbdc1b7d3479323564353f134acc8c501910220371390675'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('ncurses', '6.5')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From 4f3ae736b2a301c5751ace7c72b932aff0ba1ed4 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 2 Sep 2024 08:43:05 +0200 Subject: [PATCH 356/553] Added nettle and nlohmann_json to the GCCcore-13.3.0 toolchain --- .../n/nettle/nettle-3.10-GCCcore-13.3.0.eb | 38 +++++++++++++++++++ .../nlohmann_json-3.11.3-GCCcore-13.3.0.eb | 25 ++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef91cf135fe --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.10' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b4c518adb174e484cb4acea54118f02380c7133771e7e9beb98a0787194ee47c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8be75746afa --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.3' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' From 14b05c0edb653349e8cdc3aa3384cd7db776e147 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Mon, 2 Sep 2024 09:37:56 +0200 Subject: [PATCH 357/553] Fix sanity check --- .../bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb | 2 +- .../b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb index 3b89d58cc47..75c19734a23 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -34,7 +34,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'], + 'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb index e9f92c025a9..8af9e762a99 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -31,7 +31,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'], + 'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 5c1323a3485f8ddb0d9bfe014f6f23c93220f688 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Mon, 2 Sep 2024 09:55:42 +0200 Subject: [PATCH 358/553] Fix syntax error --- .../bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb | 2 +- .../b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb index 75c19734a23..8127a86c558 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -34,7 +34,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb index 8af9e762a99..8b360bb263b 100644 --- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -31,7 +31,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 808838029beb718c92875d4011df85e8c83d9b7c Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 2 Sep 2024 10:51:45 +0200 Subject: [PATCH 359/553] Added Tk and Tkinter to the GCCcore-13.3.0 toolchain (both dependencies of matplotlib) --- .../t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ .../Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb | 25 +++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4069dc5a048 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.14' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['8ffdb720f47a6ca6107eac2dd877e30b0ef7fac14f3a84ebbd0b3612cee41a94'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Tcl', version), + ('X11', '20240607'), + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..00f02ee6424 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.12.3' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'] + +builddependencies = [ + ('binutils', '2.42'), + ('libffi', '3.4.5'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Tk', '8.6.14'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lang' From 62ad0eb9a52dd2dc8fca134815c8dbeea50a8249 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 2 Sep 2024 15:22:15 +0200 Subject: [PATCH 360/553] Added OpenJPEG and Pillow-SIMD (both needed fo matplotlib) to the GCCcore-13.3.0 toolchain. --- .../OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb | 42 ++++++++++++++++ .../Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb | 48 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ee5d1477f8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.2' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90e3896fed910c376aaf79cdd98bdfdaf98c6472efd8e1debf0a854938cbda6a'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e752171a582 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '10.4.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +use_pip = True +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From 5b9dc18218e959e027cead8183bc7fbdc1fb9d81 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 2 Sep 2024 19:22:09 +0200 Subject: [PATCH 361/553] update dorado to properly use openssl from EB and not install external EB libraries into its own lib directory. --- .../dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb | 25 ++++++--- ....7.3_dont_install_external_libraries.patch | 54 +++++++++++++++++++ 2 files changed, 71 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb index 7aa8f29b002..0e32e9616ca 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -20,10 +20,15 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -patches = ['dorado-0.7.3_include-fstream.patch'] +patches = [ + '%(name)s-%(version)s_include-fstream.patch', + '%(name)s-%(version)s_dont_install_external_libraries.patch', +] + checksums = [ None, 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', + '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac', ] builddependencies = [ @@ -45,7 +50,6 @@ dependencies = [ # don't link to OpenSSL static libraries # fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " -preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " # link in the ssl and crypto libs, to fix: # undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " @@ -63,12 +67,17 @@ preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt # cfr. https://github.com/nanoporetech/dorado/issues/779 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " -configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " -configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " -configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " -# add -pthread flag (in addition to -lpthread) to avoid linking error: -# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' -configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) sanity_check_paths = { 'files': ['bin/dorado'], diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch new file mode 100644 index 00000000000..67bd9efee78 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch @@ -0,0 +1,54 @@ +Don't install external libraries in Dorado's lib directory. + +Åke Sandgren, 2024-09-02 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index a84c7524..0791dda8 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + else() + # bundle the libraries from the cuda toolkit + file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}") +- install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) + endif() + endforeach() + +@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) + endif() + endforeach() + FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT}) + RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) + endif() + endforeach() + endif() +@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + find_library(SZ_DLL sz REQUIRED) + get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY) + file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*") +- install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) + + find_library(AEC_DLL aec REQUIRED) + get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY) + file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*") +- install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) + + # If zstd has been dynamically linked, add the .so to the package + get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY) + file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*") +- install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) + + elseif(WIN32) + file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll") From 0a076aabd34a390bedfdd0c20e4b0759c6f877cb Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 2 Sep 2024 21:48:30 +0200 Subject: [PATCH 362/553] Added Qhull to the GCCcore-13.3.0 toolchain (needed for matplotlib) --- .../q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..400fecee609 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' From 37983df04886a9ff9710dc5cb4d7e6a5f83edfee Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Mon, 2 Sep 2024 21:49:52 +0200 Subject: [PATCH 363/553] Added matplotlib to te gfbf 2024a toolchain (plus new patch) --- ...ib-3.9.2-contourpy-fix-pybind-module.patch | 11 +++ .../matplotlib/matplotlib-3.9.2-gfbf-2024a.eb | 79 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch new file mode 100644 index 00000000000..7a4ae1fdcc1 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch @@ -0,0 +1,11 @@ +--- src/wrap.cpp.orig 2024-09-02 21:07:13.893013182 +0200 ++++ src/wrap.cpp 2024-09-02 21:07:39.973005828 +0200 +@@ -18,7 +18,7 @@ + static contourpy::LineType mpl20xx_line_type = contourpy::LineType::SeparateCode; + static contourpy::FillType mpl20xx_fill_type = contourpy::FillType::OuterCode; + +-PYBIND11_MODULE(_contourpy, m, py::mod_gil_not_used()) { ++PYBIND11_MODULE(_contourpy, m) { + m.doc() = + "C++11 extension module wrapped using `pybind11`_.\n\n" + "It should not be necessary to access classes and functions in this extension module " diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb new file mode 100644 index 00000000000..9d460a5f1fc --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.9.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('cppy', '1.2.1'), + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('Tkinter', '%(pyver)s'), + ('Pillow-SIMD', '10.4.0'), + ('Qhull', '2020.2'), +] + +use_pip = True +sanity_pip_check = True + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_configopts = "--config-settings=setup-args='-Dsystem-qhull=true' && " +local_configopts += " --config-settings=setup-args='-Dsystem-freetype=true' && " +local_configopts += "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('Cycler', '0.12.1', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'], + }), + ('kiwisolver', '1.4.5', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.3.0', { + 'patches': ['matplotlib-3.9.2-contourpy-fix-pybind-module.patch'], + 'checksums': [ + {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'}, + {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch': + '1653ea31e98db37734e70552224290277b55ec3aa903aa06884c3579c3da242d'}, + ], + }), + (name, version, { + 'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 8c87ac1a94615359858bec4027577a23adebe207 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 3 Sep 2024 09:58:42 +0200 Subject: [PATCH 364/553] Style corrections for the patch and the easyconfigfile --- .../matplotlib-3.9.2-contourpy-fix-pybind-module.patch | 3 +++ .../easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb | 5 +++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch index 7a4ae1fdcc1..9a34eb1cdae 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch @@ -1,3 +1,6 @@ +Fixes: error: macro "PYBIND11_MODULE" passed 3 arguments, but takes just 2 +Author: Anke Kreuzer (JSC) +diff -ruN src/wrap.cpp.orig src/wrap.cpp --- src/wrap.cpp.orig 2024-09-02 21:07:13.893013182 +0200 +++ src/wrap.cpp 2024-09-02 21:07:39.973005828 +0200 @@ -18,7 +18,7 @@ diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb index 9d460a5f1fc..8e67572cb1a 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -58,11 +58,12 @@ exts_list = [ 'checksums': [ {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'}, {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch': - '1653ea31e98db37734e70552224290277b55ec3aa903aa06884c3579c3da242d'}, + 'a998438a1048524a550bf3bb607197658b13dce56e8e54169e24ce7c3c022a8f'}, ], }), (name, version, { - 'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + #'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'configopts': "%(local_configopts)s", 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], }), ] From 508f5a5c12f0ab6a17cab40a4b3bae208f77c201 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 3 Sep 2024 10:08:39 +0200 Subject: [PATCH 365/553] Deleted unnecessary line --- .../easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb index 8e67572cb1a..33ddf00eb93 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -62,7 +62,6 @@ exts_list = [ ], }), (name, version, { - #'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'configopts': "%(local_configopts)s", 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], }), From 93531deb55017a5362382d3cee6fff7b916f249e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 3 Sep 2024 10:23:16 +0200 Subject: [PATCH 366/553] Update easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fix `libxslt` not found even if it is installed under the name `libsxlt1.1` on Ubuntu 24.04 Co-authored-by: Bob Dröge --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index fd4a336660e..6a16ff28a3a 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -13,7 +13,7 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] # Required by lxml, which is installed by ReFrame's bootstrap installer osdependencies = [ ('libxml2'), - ('libxslt'), + ('libxslt', 'libxslt1.1'), ] # Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg From 3329d72d1cc905ee204161b9c807afca3ed8daaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Sep 2024 10:31:02 +0200 Subject: [PATCH 367/553] {tools}[foss/2023b] Optuna v3.6.1, redis-py v5.0.9 --- .../o/Optuna/Optuna-3.6.1-foss-2023b.eb | 50 +++++++++++++++++++ .../redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb | 38 ++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb new file mode 100644 index 00000000000..35dec40e234 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.6.1' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('SciPy-bundle', '2023.11'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), # optional + ('plotly.py', '5.18.0'), # optional + ('redis-py', '5.0.9'), # optional + ('scikit-learn', '1.4.0'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['146e530b57b4b9afd7526b3e642fbe65491f7e292b405913355f8e438e361ecf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..39e66108872 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.9' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), + ('Redis', '7.2.4'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c107fddbaa40414559ddd21f0a78bc7d466cd6b20a800839ac18b9bb54e5c150'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" From ea2583026118819d3345a2ace8125c200fd780c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 10:47:12 +0200 Subject: [PATCH 368/553] adding easyconfigs: bayesian-optimization-1.5.1-foss-2023a.eb --- .../bayesian-optimization-1.5.1-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb new file mode 100644 index 00000000000..8215f2c822a --- /dev/null +++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bayesian-optimization' +version = '1.5.1' + +homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html' +description = "Pure Python implementation of bayesian global optimization with gaussian processes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorama', '0.4.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'], + }), + ('bayesian_optimization', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'bayes_opt', + 'checksums': ['098946c933d6039073b7ccb0c9f1b4c73ac6e39350043b02e5243b08583c4c5c'], + }), +] + +sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"] + +moduleclass = 'math' From 29cf63cf35bcae3d5ae19f150cfaaa13a9eaa51c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 11:12:44 +0200 Subject: [PATCH 369/553] adding easyconfigs: SharedMeatAxe-1.0.1-GCC-13.2.0.eb --- .../SharedMeatAxe-1.0.1-GCC-13.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..bdc088ddea0 --- /dev/null +++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SharedMeatAxe' +version = '1.0.1' + +homepage = 'https://github.com/simon-king-jena/SharedMeatAxe' +description = """This is an autotoolized shared library version of C MeatAxe 2.4.24, + a set of programs for computing with modular representations.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/simon-king-jena/SharedMeatAxe/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e1e802ef60f3280cdacb3de6d693ebd71b43af93e33c739de2697605c59b1a3b'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf --install && ' + +runtest = 'check' + +local_bins = [ + 'cfcomp', 'genmod', 'mkgraph', 'mkinc', 'orbrep', 'pwkond', 'symnew', 'zad', 'zcl', 'zcv', 'zfr', 'zmo', 'znu', + 'zpr', 'zro', 'zsp', 'zte', 'zuk', 'chop', 'mkcycl', 'mkhom', 'mksub', 'precond', 'rad', 'tcond', 'zbl', 'zcp', + 'zef', 'ziv', 'zmu', 'zor', 'zpt', 'zsc', 'zsy', 'ztr', 'zvp', 'decomp', 'mkdotl', 'mkhom_old', 'mktree', + 'pseudochop', 'soc', 'tuc', 'zcf', 'zct', 'zev', 'zkd', 'zmw', 'zpo', 'zqt', 'zsi', 'ztc', 'zts', +] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins] + ['include/meataxe.h', 'lib/libmtx.%s' % SHLIB_EXT], + 'dirs': [] +} + + +sanity_check_commands = ['mktree --help'] + +moduleclass = 'math' From 47f1a682bdd42a661ce29b2c6e31334a0dab835d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 11:13:35 +0200 Subject: [PATCH 370/553] adding easyconfigs: sirocco-2.1.0-GCC-13.2.0.eb --- .../s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..3819e493fe2 --- /dev/null +++ b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'sirocco' +version = '2.1.0' + +homepage = 'https://github.com/miguelmarco/SIROCCO2/' +description = """C++ library that allows to compute piecewise linear + approximations of the path followed by the root of a complex polynomial""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/miguelmarco/SIROCCO2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fd66ae94d73095f1355389c1d3d94222437bed87579d77667f50548bdd9fa9a'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/sirocco.h', + 'lib/libsirocco.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'math' From 8cf988069bdde5d2b4de7ccffc8dc9032239918e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 11:14:33 +0200 Subject: [PATCH 371/553] adding easyconfigs: tdlib-0.9.3-GCC-13.2.0.eb --- .../t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..7edf36c5ebb --- /dev/null +++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'tdlib' +version = '0.9.3' + +homepage = 'https://github.com/freetdi/tdlib/' +description = """treedec provides tree decomposition algorithms.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/freetdi/tdlib/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Boost', '1.83.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/treedec/combinations.hpp', + ], + 'dirs': [] +} + +moduleclass = 'math' From a0e732d1c483fa66bd26132d308e6e610ef07616 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 12:23:38 +0200 Subject: [PATCH 372/553] adding easyconfigs: pyseer-1.3.12-foss-2023a.eb --- .../p/pyseer/pyseer-1.3.12-foss-2023a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb new file mode 100644 index 00000000000..16cf7b1a00c --- /dev/null +++ b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Borrowed from the BEAR RSG team, University of Birmingham +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'pyseer' +version = '1.3.12' + +homepage = 'https://github.com/mgalardini/pyseer' +description = """pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses + linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population + on a phenotype of interest, while accounting for potentially very strong confounding population structure. + This allows for genome-wide association studies (GWAS) to be performed in clonal organisms + such as bacteria and viruses.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('statsmodels', '0.14.1'), + ('scikit-learn', '1.3.1'), + ('Pysam', '0.22.0'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('glmnet-python', '1.0.2', { + 'source_urls': ['https://github.com/johnlees/glmnet_python/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7a5550514140dabbd27ad4eb1c04db64199d9bb89541e088d9bb162570205e76'], + }), + (name, version, { + 'source_urls': ['https://github.com/mgalardini/pyseer/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aa07fc1bd5346d02123ff36ba64a1ff4dbbb85a21c37a12f35ad7d5be7e21e9c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyseer', 'bin/square_mash'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + '%(namelower)s --help', + 'square_mash --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' From e00100af729eb54a6bfe1dc5fbc7e42e773c4773 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Sep 2024 12:57:15 +0200 Subject: [PATCH 373/553] strip out duplicate empty line from SharedMeatAxe easyconfig --- .../s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb index bdc088ddea0..36923c839cc 100644 --- a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb @@ -33,7 +33,6 @@ sanity_check_paths = { 'dirs': [] } - sanity_check_commands = ['mktree --help'] moduleclass = 'math' From 31ce7fc97a82a6d1960d684fb0052e7fe5cdb218 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Sep 2024 13:10:03 +0200 Subject: [PATCH 374/553] make Python a build dependency only --- easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb index 7edf36c5ebb..63408d65ee7 100644 --- a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb @@ -15,9 +15,6 @@ checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8'] builddependencies = [ ('Autotools', '20220317'), ('Boost', '1.83.0'), -] - -dependencies = [ ('Python', '3.11.5'), ] From 230fae37daf35b286392aba7b9f0592b516517d1 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 3 Sep 2024 13:38:45 +0200 Subject: [PATCH 375/553] Splitting the system toolchain EasyConfig into a different PR, since it shows more issues --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 87 ------------------- 1 file changed, 87 deletions(-) delete mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb deleted file mode 100644 index 6a16ff28a3a..00000000000 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ /dev/null @@ -1,87 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ReFrame' -version = '4.6.2' - -homepage = 'https://github.com/reframe-hpc/reframe' -description = '''ReFrame is a framework for writing regression tests for HPC systems.''' - -toolchain = SYSTEM - -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -# Required by lxml, which is installed by ReFrame's bootstrap installer -osdependencies = [ - ('libxml2'), - ('libxslt', 'libxslt1.1'), -] - -# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg -req_py_majver = 3 -req_py_minver = 6 - -use_pip = True - -exts_list = [ - # stick to pip 21.3.1, which is compatible with Python 3.6 - # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip - ('pip', '21.3.1', { - 'use_pip': False, - 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], - }), - # Require new enough setuptools to install with e.g. pyproject.toml - # 59.6.0 is the latest compatible with Python 3.6 - ('setuptools', '59.6.0', { - 'use_pip': False, - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], - }), - # stick to wheel 0.37.1, which is compatible with Python 3.6 - ('wheel', '0.37.1', { - 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', - 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], - }), - # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame - # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path - # so that ReFrame (and only ReFrame) will find & use all of these dependencies. - # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and - # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that - # a test will pick up on any python deps from ReFrame itself. - # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail - # for this setup. - ('reframe', version, { - # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok - 'download_dep_fail': False, - # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH - # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine - 'sanity_pip_check': False, - # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") - # This step would fail, since the regular python interpreter wouldn't find the additional packages in - # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the - # reframe command. - 'modulename': False, - 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " - "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], - 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], - }), -] - -postinstallcmds = [ - "cp -a tools examples %(installdir)s", - "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", - r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", -] - -sanity_check_paths = { - 'files': ['bin/reframe', - 'share/completions/reframe.bash', - 'share/completions/reframe.fish', - 'share/completions/reframe.tcsh'], - 'dirs': ['external', 'lib', 'tools', 'examples'] -} - -sanity_check_commands = ['reframe -V'] - -moduleclass = 'devel' From d4ba4abf16cf85b53b488173fb8a3eec0aed68dd Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 3 Sep 2024 13:40:57 +0200 Subject: [PATCH 376/553] Add ReFrame 4.6.2 at system toolchain level --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb new file mode 100644 index 00000000000..6a16ff28a3a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' From 893cf70a9964e48b934a7b19ada32563a0aeee80 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 3 Sep 2024 13:56:29 +0200 Subject: [PATCH 377/553] Make two EasyConfigs: one for Python 3.6, and one for Python 3.7 and above, including 3.12 --- .../r/ReFrame/ReFrame-4.6.2-Python-3.6.eb | 90 +++++++++++++++++++ .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 22 +++-- 2 files changed, 103 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb new file mode 100644 index 00000000000..7b48610c6ee --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -0,0 +1,90 @@ +# This EasyConfig is made with older setuptools and wheel versions, so that it still works with Python-3.6.X +# For newer python versions, we suggest to use ReFrame-4.6.2.eb (without suffix) +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' +versionsuffix = '-Python-3.6' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 6a16ff28a3a..c6bbf9aa882 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -16,28 +16,32 @@ osdependencies = [ ('libxslt', 'libxslt1.1'), ] -# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# We use pip, setuptools and wheel compatible with Python 3.7 and above +# Note that ReFrame itself is compatible also with Python 3.6 +# As listed in the python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# To use with Python 3.6, please install ReFrame-4.6.2-Python-3.6.eb instead req_py_majver = 3 -req_py_minver = 6 +req_py_minver = 7 use_pip = True exts_list = [ - # stick to pip 21.3.1, which is compatible with Python 3.6 + # stick to pip 24.0, which is compatible with Python 3.7 # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip - ('pip', '21.3.1', { + ('pip', '24.0', { 'use_pip': False, 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], }), - # Require new enough setuptools to install with e.g. pyproject.toml - # 59.6.0 is the latest compatible with Python 3.6 - ('setuptools', '59.6.0', { + # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore + # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee + # 68.0.0 is the latest compatible with Python 3.7 + ('setuptools', '68.0.0', { 'use_pip': False, 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), - # stick to wheel 0.37.1, which is compatible with Python 3.6 - ('wheel', '0.37.1', { + # stick to wheel 0.42.0, which is compatible with Python 3.7 + ('wheel', '0.42.0', { 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), From 5ff26ab3323581ebd0afa4f8afd36504910216fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:42:51 +0200 Subject: [PATCH 378/553] use correct checksum for pip 24.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index c6bbf9aa882..dcdff5b4b9a 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -30,7 +30,7 @@ exts_list = [ # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip ('pip', '24.0', { 'use_pip': False, - 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + 'checksums': ['ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2'], }), # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee From ed168ec0370d75319f0af68d41111258ef692ccf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:47:41 +0200 Subject: [PATCH 379/553] use correct checksum for setuptools 68.0.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index dcdff5b4b9a..7544d3640ba 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -38,7 +38,7 @@ exts_list = [ ('setuptools', '68.0.0', { 'use_pip': False, 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + 'checksums': ['baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235'], }), # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { From d7e047d98807d392ea488ba5f9efaa7df5563e15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:48:59 +0200 Subject: [PATCH 380/553] use correct filename for wheel 0.42.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 7544d3640ba..1a2416ce023 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -42,7 +42,7 @@ exts_list = [ }), # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { - 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame From 084b306b44df6970b01b301d60b01eeb70463806 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:51:00 +0200 Subject: [PATCH 381/553] use correct checksum for wheel 0.42.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 1a2416ce023..26e331c131e 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -43,7 +43,7 @@ exts_list = [ # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', - 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + 'checksums': ['177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d'], }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path From 423f374762dcdccb8fc0511403466d13e6b623d4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 30 Aug 2024 16:51:12 +0200 Subject: [PATCH 382/553] Move exts_default_options to top-level parameters forPythonBundle ECs It is easier in the top-level and might cause confusion with https://github.com/easybuilders/easybuild-easyblocks/pull/3428 --- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 6 ------ easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb | 7 ++----- easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb | 7 ++----- easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb | 7 ++----- .../g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb | 7 ++----- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 7 +++---- .../OpenStackClient-5.8.0-GCCcore-11.2.0.eb | 7 +++---- .../OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 7 +++---- .../p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb | 7 ++----- .../Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 7 ++----- .../Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 7 ++----- .../Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb | 7 ++----- .../setuptools-rust-1.6.0-GCCcore-12.3.0.eb | 7 ++----- .../setuptools-rust-1.8.0-GCCcore-13.2.0.eb | 7 ++----- .../setuptools-rust-1.9.0-GCCcore-13.3.0.eb | 7 ++----- .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb | 7 ++----- .../v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb | 7 ++----- .../v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb | 7 ++----- 18 files changed, 37 insertions(+), 88 deletions(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba1628..1556b0f9dad 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " use_pip = True -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb index 15b9ad83d78..a19ba324250 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb @@ -17,11 +17,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb index 79b1a625e7e..9ef1de6c8b7 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb index ddc99b99a37..650b15edaa5 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.7', { diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb index d098c3c3cbc..4fae7c08b54 100644 --- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -21,11 +21,8 @@ dependencies = [ ('Python-bundle-PyPI', '2023.06'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Markdown', '3.5.2', { diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e5..50dab938d40 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb index e590dd730ca..d92bda87180 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.37')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 6b695f63279..bdf0b5c45a6 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -15,9 +15,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.39')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -114,7 +114,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c5..96d813edcce 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { - 'use_pip': True -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Logbook', '1.5.3', { @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 6a91bcca5e4..808285d9f26 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.23.1'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-06-26 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index d551945f5e7..d97f7a93c0f 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.24.6'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-10-29 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb index 01bf9b19b0a..42df4fd52a1 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb @@ -28,11 +28,8 @@ dependencies = [ ('virtualenv', '20.26.2'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2024-06-14 diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index 8cbf2db9fe7..b2517ef684c 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.6.3', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb index 669229c8f11..044d56266ae 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.8.0', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb index a8ad0dc7ee9..b763364ba26 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing-extensions', '4.12.2', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 122f3d8d6c8..c36c435d1da 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.6', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb index a0b9921fb5c..2820042ba9d 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.7', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb index 9c6a84c5304..65f1ced6cae 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.8', { From 42c0b3190b5b626a4fa299b4220e3276971684fe Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 12:09:09 +0200 Subject: [PATCH 383/553] Added LMDB to the GCCcore-13.3.0 toolchain --- .../l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a10be56a891 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.42')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' From 6e3465cf36684816d30a8a63316b8a4624bd197f Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 12:12:26 +0200 Subject: [PATCH 384/553] Added NLopt to the GCCcore-13.3.0 toolchain. --- .../n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9bb438dc94 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From 7e0a67b39ad16c5724eb199231b597b68522cf3f Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 12:16:53 +0200 Subject: [PATCH 385/553] Added nsync to the GCCcore-13.3.0 toolchain. --- .../n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7c2035444b --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.29.2' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1d63e967973733d2c97e841e3c05fac4d3fa299f01d14c86f2695594c7a4a2ec'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' From 5ec13aad36b3dfe35b9f0b015feaa5bb34d21970 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 12:25:49 +0200 Subject: [PATCH 386/553] Added OpenEXR to the GCCcore-13.3.0 toolchain. --- .../o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f6e66db69ae --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.4' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['81e6518f2c4656fdeaf18a018f135e96a96e7f66dbe1c1f05860dd94772176cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Imath', '3.1.11'), + ('zlib', '1.3.1') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' From 351afdbec49918eeb20ee8874f4105b8c7dd16d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 4 Sep 2024 12:37:07 +0200 Subject: [PATCH 387/553] adding easyconfigs: LRBinner-0.1-foss-2023a.eb --- .../l/LRBinner/LRBinner-0.1-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb new file mode 100644 index 00000000000..d3ce64d0b9f --- /dev/null +++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'LRBinner' +version = '0.1' + +homepage = 'https://github.com/anuradhawick/LRBinner' +description = "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB. " + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HMMER', '3.4'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tabulate', '0.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f'], + }), + (name, version, { + 'modulename': 'mbcclr_utils', + 'preinstallopts': "sed -i 's/pytorch/torch/g' setup.py && ", + 'source_urls': ['https://github.com/anuradhawick/LRBinner/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['2d77dde8ab1272c432b20eb18a352326c622e929261562ef6d680c6638cc4bd1'], + }), +] + +sanity_check_commands = ['LRBinner --help'] + +moduleclass = 'tools' From 7f717d8d2e9af7dba59c6e1b4bafd2e2aa7abff6 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 4 Sep 2024 12:37:41 +0200 Subject: [PATCH 388/553] remove download_dep_fail --- .../easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb index 39e66108872..b877029e19a 100644 --- a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb @@ -18,7 +18,6 @@ dependencies = [ ('Redis', '7.2.4'), ] -download_dep_fail = True use_pip = True exts_list = [ From 8328d0563441287c92995664f95baeaae4793ee7 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 12:48:19 +0200 Subject: [PATCH 389/553] Added pkgconfig to the GCCcore-13.3.0 toolchain. --- .../pkgconfig-1.5.5-GCCcore-13.3.0-python.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb new file mode 100644 index 00000000000..f66c2f13358 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pkgconf', '2.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From b14673d1c5ca00baf6330ed71f59592861ab3547 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 13:01:50 +0200 Subject: [PATCH 390/553] Added popt to the GCCcore-13.3.0 toolchein. --- .../p/popt/popt-1.19-GCCcore-13.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..91b5c7c74ba --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = '1.19' + +homepage = 'https://github.com/rpm-software-management/popt' +description = 'Popt is a C library for parsing command line parameters.' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x'] +sources = [SOURCE_TAR_GZ] +checksums = ['c25a4838fc8e4c1c8aacb8bd620edb3084a3d63bf8987fdad3ca2758c63240f9'] + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpopt.a', 'lib64/libpopt.a'), ('lib/libpopt.so', 'lib64/libpopt.so')], + 'dirs': [], +} + +moduleclass = 'tools' From 688ee7bbb756a040cbab1f3291235f0a4b50e62c Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 4 Sep 2024 13:17:00 +0200 Subject: [PATCH 391/553] Added PostgreSQL to the GCCcore-13.3.0 toolchain. --- .../PostgreSQL-16.4-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9b4c1f62855 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2e17a90062403e15d6540480fdec50c8b005eb48729a91cb4989ffeb04df193c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 94d34a5af7d222d00f783357a273964ad45c0709 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 4 Sep 2024 13:39:35 +0200 Subject: [PATCH 392/553] Use implementation from https://github.com/easybuilders/easybuild-easyblocks/pull/3431 to set a maximum version --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb index 7b48610c6ee..4e58793cd0a 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -23,6 +23,11 @@ osdependencies = [ req_py_majver = 3 req_py_minver = 6 +# The setuptools in this EasyConfig is the latest that works for Python 3.6, but is too old for Python 3.12 +# See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269#discussion_r1741570244 +max_py_majver = 3 +max_py_minver = 11 + use_pip = True exts_list = [ From 39ab79a3eb6cf416864384afd56a6763f88ade23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 4 Sep 2024 14:49:44 +0200 Subject: [PATCH 393/553] add dependencies --- .../FragGeneScan-1.31-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ .../HDBSCAN-0.8.38.post1-foss-2023a.eb | 27 +++++++++++++ .../l/LRBinner/LRBinner-0.1-foss-2023a.eb | 2 + 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..527ba56e69f --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb new file mode 100644 index 00000000000..b260708eab8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.38.post1' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fbdba2ffb5a99a8b52fa2915658ced6bed59f4d0d5f40b1c673646c928aac0b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb index d3ce64d0b9f..143e59d35c5 100644 --- a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb @@ -18,6 +18,8 @@ dependencies = [ ('tqdm', '4.66.1'), ('Biopython', '1.83'), ('scikit-learn', '1.3.1'), + ('FragGeneScan', '1.31'), + ('HDBSCAN', '0.8.38.post1'), ] use_pip = True From c5412215b3ebbbfcec76d95860d87ed3709a970e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 4 Sep 2024 15:07:38 +0200 Subject: [PATCH 394/553] adding easyconfigs: BRiAl-1.2.12-GCC-13.2.0.eb --- .../b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb new file mode 100644 index 00000000000..c489c77380f --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'BRiAl' +version = '1.2.12' + +homepage = 'https://github.com/BRiAl/BRiAl' +description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.83.0'), + ('m4ri', '20200125'), +] + +configopts = "--with-boost=$EBROOTBOOST " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' From bcba62eb0812eca74327cfdfcde30323ba85199e Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 13:43:57 +0000 Subject: [PATCH 395/553] adding easyconfigs: Abseil-20240722.0-GCCcore-13.3.0.eb --- .../Abseil-20240722.0-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..24951c68814 --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20240722.0' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['f50e5ac311a81382da7fa75b97310e4b9006474f9560ac46f54a9967f07d4ae3'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = "-DABSL_PROPAGATE_CXX_STD=ON " + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['lib/libabsl_base.' + SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' From 738efd053faf839783bcf39e38a4fe18e4781cac Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 15:02:48 +0000 Subject: [PATCH 396/553] adding easyconfigs: Flask-3.0.3-GCCcore-13.3.0.eb --- .../f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b0d0c5a63ae --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '3.0.3' + +homepage = 'https://flask.palletsprojects.com/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.2.0', { + 'checksums': ['e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173'], + }), + ('werkzeug', '3.0.4', { + 'checksums': ['34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('click', '8.1.7', { + 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], + }), + ('blinker', '1.8.2', { + 'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'], + }), + ('flask', version, { + 'checksums': ['ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842'], + }), + ('msgspec', '0.18.6', { + 'checksums': ['a59fc3b4fcdb972d09138cb516dbde600c99d07c38fd9372a6ef500d2d031b4e'], + }), + ('Flask-Cors', '5.0.0', { + 'sources': ['flask_cors-%(version)s.tar.gz'], + 'checksums': ['5aadb4b950c4e93745034594d9f3ea6591f734bb3662e16e255ffbf5e89c88ef'], + }), + ('cachelib', '0.13.0', { + 'checksums': ['209d8996e3c57595bee274ff97116d1d73c4980b2fd9a34c7846cd07fd2e1a48'], + }), + ('Flask-Session', '0.8.0', { + 'sources': ['flask_session-%(version)s.tar.gz'], + 'checksums': ['20e045eb01103694e70be4a49f3a80dbb1b57296a22dc6f44bbf3f83ef0742ff'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' From 015d5a5073297892b02b1b8de69f3a62284947be Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 15:16:24 +0000 Subject: [PATCH 397/553] adding easyconfigs: expecttest-0.2.1-GCCcore-13.3.0.eb --- .../expecttest-0.2.1-GCCcore-13.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a70bf3973ca --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.2.1' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 4e6c8bcddc103717168884e896346b48454cad42 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 4 Sep 2024 17:40:34 +0200 Subject: [PATCH 398/553] adding easyconfigs: Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb, Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb and patches: Triton-2.1.0-disable_rocm_support.patch, Triton-2.1.0-use_eb_env_python_build.patch --- ...0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb | 61 ++++++++++++ .../Triton-2.1.0-disable_rocm_support.patch | 88 ++++++++++++++++++ .../Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb | 56 +++++++++++ ...Triton-2.1.0-use_eb_env_python_build.patch | 93 +++++++++++++++++++ 4 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..947a6afdad5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '17.0.0_20230515' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'c5dede880d17' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ["https://github.com/llvm/llvm-project/archive"], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': 'llvm-project-%s.tar.gz' % version, +}] +checksums = ['6f371f9ac208b8e9dc57fc117b1a9c8565d7ea2bbb49a2768cb9c3c0fee0291d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch new file mode 100644 index 00000000000..13d736b4bfc --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch @@ -0,0 +1,88 @@ +Disable experimental support for AMD GPUs +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/CMakeLists.txt triton-2.1.0/CMakeLists.txt +--- triton-2.1.0.orig/CMakeLists.txt 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/CMakeLists.txt 2024-09-01 10:40:17.863374000 +0200 +@@ -70,7 +70,7 @@ + AMDGPUInfo AMDGPUcodegen + ) + else() +- find_package(LLVM 11 REQUIRED COMPONENTS "nvptx;amdgpu") ++ find_package(LLVM 11 REQUIRED COMPONENTS "nvptx") + endif() + + message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}") +@@ -89,9 +89,7 @@ + LLVMNVPTXCodeGen + LLVMNVPTXDesc + LLVMNVPTXInfo +- LLVMAMDGPUDisassembler + LLVMMCDisassembler +- LLVMAMDGPUCodeGen + LLVMMIRParser + LLVMGlobalISel + LLVMSelectionDAG +@@ -116,10 +114,7 @@ + LLVMObject + LLVMTextAPI + LLVMBitReader +- LLVMAMDGPUAsmParser + LLVMMCParser +- LLVMAMDGPUDesc +- LLVMAMDGPUUtils + LLVMMC + LLVMDebugInfoCodeView + LLVMDebugInfoMSF +@@ -127,7 +122,6 @@ + LLVMRemarks + LLVMBitstreamReader + LLVMBinaryFormat +- LLVMAMDGPUInfo + LLVMSupport + LLVMDemangle + LLVMPasses +diff -ur triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp +--- triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp 2024-09-02 21:27:09.233712000 +0200 +@@ -37,13 +37,6 @@ + + namespace { + +-void init_llvm() { +- LLVMInitializeAMDGPUTarget(); +- LLVMInitializeAMDGPUTargetInfo(); +- LLVMInitializeAMDGPUTargetMC(); +- LLVMInitializeAMDGPUAsmParser(); +- LLVMInitializeAMDGPUAsmPrinter(); +-} + + std::unique_ptr + initialize_module(llvm::Module *module, const std::string &triple, +@@ -155,7 +148,6 @@ + llir_to_amdgcn_and_hsaco(llvm::Module *module, std::string gfx_arch, + std::string gfx_triple, std::string gfx_features) { + +- init_llvm(); + + // verify and store llvm + auto module_obj = llvm::CloneModule(*module); +diff -ur triton-2.1.0.orig/python/src/triton.cc triton-2.1.0/python/src/triton.cc +--- triton-2.1.0.orig/python/src/triton.cc 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/src/triton.cc 2024-09-01 10:41:29.146862440 +0200 +@@ -60,7 +60,6 @@ + enum backend_t { + HOST, + CUDA, +- ROCM, + }; + + void init_triton_runtime(py::module &&m) { +@@ -68,7 +67,6 @@ + py::enum_(m, "backend", py::module_local()) + .value("HOST", HOST) + .value("CUDA", CUDA) +- .value("ROCM", ROCM) + .export_values(); + } + diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a1cdbe87df3 --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonPackage' + +name = 'Triton' +version = '2.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://triton-lang.org/' + +description = """Triton is a language and compiler for parallel programming. It aims to provide a +Python-based programming environment for productively writing custom DNN compute +kernels capable of running at maximal throughput on modern GPU hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'openai' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-disable_rocm_support.patch', + '%(name)s-%(version)s-use_eb_env_python_build.patch', +] +checksums = [ + {'v2.1.0.tar.gz': '4338ca0e80a059aec2671f02bfc9320119b051f378449cf5f56a1273597a3d99'}, + {'Triton-2.1.0-disable_rocm_support.patch': 'e4d7c0947c3287b3f0871a004e8b483963f637c9fa3ef6212ac3a34660de2a7c'}, + {'Triton-2.1.0-use_eb_env_python_build.patch': 'd68bf766c699ad6a778d9449d3bccdadc2f20f1f86ba13e1359ad297b12fbf7c'}, +] + +builddependencies = [ + ('Clang', '17.0.0_20230515', versionsuffix), # this is the exact commit that would be downloaded by Triton + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +start_dir = 'python' + +preinstallopts = 'export LLVM_INCLUDE_DIRS=$EBROOTCLANG/include && ' +preinstallopts += 'export LLVM_LIBRARY_DIR=$EBROOTCLANG/lib && ' +preinstallopts += 'export LLVM_SYSPATH=$EBROOTCLANG && ' +preinstallopts += 'export TRITON_BUILD_WITH_CLANG_LLD=1 && ' + +# make pip print output of cmake +installopts = "-v " + +sanity_pip_check = True + +modluafooter = 'setenv("TRITON_PTXAS_PATH", pathJoin(os.getenv("CUDA_HOME"), "bin", "ptxas"))' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch new file mode 100644 index 00000000000..650134e73be --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch @@ -0,0 +1,93 @@ +Fix Triton cmake build to use dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp +--- triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2024-09-02 19:46:06.574421829 +0200 +@@ -35,6 +35,7 @@ + #endif + #include + #include ++#include // for getenv + + namespace fs = std::filesystem; + +@@ -177,6 +178,7 @@ + } + + if (!funcs.empty()) { ++ std::filesystem::path cuda_home = std::getenv("CUDA_HOME"); + static const std::string libdevice = "libdevice"; + // first search for environmental path + std::string env_path = ::triton::tools::getenv("TRITON_LIBDEVICE_PATH"); +@@ -189,8 +191,7 @@ + // `triton/third_party/cuda/lib/libdevice.10.bc` + static const auto this_library_path = getThisLibraryPath(); + static const auto runtime_path = +- this_library_path.parent_path().parent_path() / "third_party" / "cuda" / +- "lib" / "libdevice.10.bc"; ++ cuda_home / "nvvm" / "libdevice" / "libdevice.10.bc"; + if (fs::exists(runtime_path)) { + externLibs.try_emplace(libdevice, runtime_path.string()); + } else { +diff -ur triton-2.1.0.orig/python/setup.py triton-2.1.0/python/setup.py +--- triton-2.1.0.orig/python/setup.py 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/setup.py 2024-09-02 18:16:58.044760300 +0200 +@@ -202,13 +202,13 @@ + + def build_extension(self, ext): + lit_dir = shutil.which('lit') +- user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ +- os.getenv("HOMEPATH") or None +- if not user_home: +- raise RuntimeError("Could not find user home directory") +- triton_cache_path = os.path.join(user_home, ".triton") ++ # user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ ++ # os.getenv("HOMEPATH") or None ++ # if not user_home: ++ # raise RuntimeError("Could not find user home directory") ++ # triton_cache_path = os.path.join(user_home, ".triton") + # lit is used by the test suite +- thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) ++ # thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) + extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.path))) + # create build directories + if not os.path.exists(self.build_temp): +@@ -216,8 +216,9 @@ + # python directories + python_include_dir = sysconfig.get_path("platinclude") + cmake_args = [ ++ "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON", + "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON", +- "-DLLVM_ENABLE_WERROR=ON", ++ # "-DLLVM_ENABLE_WERROR=ON", + "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir, + "-DTRITON_BUILD_TUTORIALS=OFF", + "-DTRITON_BUILD_PYTHON_MODULE=ON", +@@ -227,7 +228,7 @@ + ] + if lit_dir is not None: + cmake_args.append("-DLLVM_EXTERNAL_LIT=" + lit_dir) +- cmake_args.extend(thirdparty_cmake_args) ++ # cmake_args.extend(thirdparty_cmake_args) + + # configuration + cfg = get_build_type() +@@ -245,7 +246,7 @@ + build_args += ["--", "/m"] + else: + cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg] +- max_jobs = os.getenv("MAX_JOBS", str(2 * os.cpu_count())) ++ max_jobs = os.getenv("MAX_JOBS", str(len(os.sched_getaffinity(0)))) + build_args += ['-j' + max_jobs] + + if check_env_flag("TRITON_BUILD_WITH_CLANG_LLD"): +@@ -262,7 +263,7 @@ + subprocess.check_call(["cmake", "--build", "."] + build_args, cwd=cmake_dir) + + +-download_and_copy_ptxas() ++# download_and_copy_ptxas() + + + setup( From 6d5fb5b515c2ec98c307208bf7ece9ba384269bd Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 15:48:31 +0000 Subject: [PATCH 399/553] adding easyconfigs: hiredis-1.2.0-GCCcore-13.3.0.eb --- .../h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bc3a5a1c715 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 36f0735f0a14fc506b10a7c395634511f287f2d7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 16:03:36 +0000 Subject: [PATCH 400/553] adding easyconfigs: PyYAML-6.0.2-GCCcore-13.3.0.eb --- .../p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..70dfd98dcf4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0.2' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['https://github.com/yaml/pyyaml/archive/refs/tags/%(version)s.tar.gz'] +checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2024.06'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + +moduleclass = 'lib' From d21774ba350a7bd8ec5aef404318e55b465d4e9d Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 16:05:29 +0000 Subject: [PATCH 401/553] adding easyconfigs: YACS-0.1.8-GCCcore-13.3.0.eb --- .../y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ab12a60fca --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' From 67ee0f54f9cf9cf72c5d6d187f7a125c3a7bedeb Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 16:18:23 +0000 Subject: [PATCH 402/553] adding easyconfigs: pretty-yaml-24.7.0-GCCcore-13.3.0.eb --- .../pretty-yaml-24.7.0-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef58228ef61 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' From b4561122d017ab728111b206dfcc8eda59961835 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 4 Sep 2024 18:55:13 +0200 Subject: [PATCH 403/553] add missing dependency --- .../b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb | 1 + .../c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb | 22 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb index c489c77380f..50bbeea16ee 100644 --- a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb @@ -15,6 +15,7 @@ checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] dependencies = [ ('Boost', '1.83.0'), ('m4ri', '20200125'), + ('CUDD', '3.0.0'), ] configopts = "--with-boost=$EBROOTBOOST " diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1f83cad099 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CUDD' +version = '3.0.0' + +homepage = 'https://github.com/ivmai/cudd' +description = """The CUDD package is a package written in C for the manipulation of + decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision + diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce'] + +sanity_check_paths = { + 'files': ['include/cudd.h', 'lib/libcudd.a'], + 'dirs': [], +} + +moduleclass = 'math' From 5a930b443e8e31da57d3ccfa3ed35530c6cfae70 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 4 Sep 2024 16:55:20 +0000 Subject: [PATCH 404/553] adding easyconfigs: ruamel.yaml-0.18.6-GCCcore-13.3.0.eb --- .../ruamel.yaml-0.18.6-GCCcore-13.3.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..48d0b0d8bb5 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.18.6' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.jinja2', '0.2.7', { + 'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + (name, version, { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From b05d0afe9314f401f89ac9b3d2ebe4e76c79c41f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Sep 2024 19:17:33 +0200 Subject: [PATCH 405/553] remove easyconfig for Optax using foss/2023a toolchain --- .../Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index 43b7ce4b7ef..00000000000 --- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Optax' -version = '0.2.2' -versionsuffix = '-CUDA-12.1.1' - -homepage = 'https://github.com/deepmind/optax' -description = """Optax is a gradient processing and optimization library for JAX.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25', versionsuffix), -] - -use_pip = True - -exts_list = [ - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('flit_core', '3.9.0', { - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('chex', '0.1.86', { - 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], - }), - ('optax', version, { - 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], - }), -] - -sanity_pip_check = True - -sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] - -moduleclass = 'lib' From 083be61087c8a75f4f2c919a8662e098bdb8bf40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Sep 2024 20:17:21 +0200 Subject: [PATCH 406/553] don't use ./ in FragGeneScan sanity check commands --- .../f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb index 527ba56e69f..8466e596a3d 100644 --- a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb @@ -31,8 +31,8 @@ sanity_check_paths = { } sanity_check_commands = [ - './run_FragGeneScan.pl help', - './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' + "run_FragGeneScan.pl help", + "run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete", ] moduleclass = 'bio' From 694f27bc29cc117351f2fa170166b50af5512b4b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 4 Sep 2024 19:36:51 +0100 Subject: [PATCH 407/553] adding easyconfigs: OpenFOAM-12-foss-2023a.eb, Zoltan-3.901-foss-2023a.eb and patches: OpenFOAM-12-ThirdParty.patch --- .../o/OpenFOAM/OpenFOAM-12-ThirdParty.patch | 397 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-12-foss-2023a.eb | 38 ++ .../z/Zoltan/Zoltan-3.901-foss-2023a.eb | 46 ++ 3 files changed, 481 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb create mode 100644 easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch new file mode 100644 index 00000000000..e8a0b33adf7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch @@ -0,0 +1,397 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham). +# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +@@ -11,8 +11,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-12-version-12/etc/bashrc OpenFOAM-12/etc/bashrc +--- OpenFOAM-12-version-12/etc/bashrc ++++ OpenFOAM-12/etc/bashrc +@@ -43,12 +43,13 @@ + # + [ "$BASH" ] && bashrcFile=${BASH_SOURCE} + [ "$ZSH_NAME" ] && bashrcFile=$0 +-if [ -n "$bashrcFile" ] +-then +- export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) +-else +- export FOAM_INST_DIR=$HOME/$WM_PROJECT +-fi ++#if [ -n "$bashrcFile" ] ++#then ++# export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) ++#else ++# export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#fi ++# For Easybuild: set by the module + unset bashrcFile + # + # Please set to the appropriate path if the above default is not correct. E.g., +diff -ru OpenFOAM-12-version-12/etc/config.sh/gperftools OpenFOAM-12/etc/config.sh/gperftools +--- OpenFOAM-12-version-12/etc/config.sh/gperftools ++++ OpenFOAM-12/etc/config.sh/gperftools +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-12-version-12/etc/config.sh/metis OpenFOAM-12/etc/config.sh/metis +--- OpenFOAM-12-version-12/etc/config.sh/metis ++++ OpenFOAM-12/etc/config.sh/metis +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the metis installation +-case "$METIS_TYPE" in +-none) +- ;; +-system) +- export METIS_VERSION=system +- export METIS_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$METIS_VERSION" ] +- then +- metisSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/metis-*) +- else +- metisSrcDir=$WM_THIRD_PARTY_DIR/metis-$METIS_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$metisSrcDir" ] +- then +- export METIS_VERSION=${metisSrcDir##*metis-} +- export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/metis-$METIS_VERSION +- fi +- # Clean up +- unset metisSrcDir +- ;; +-esac ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/mpi OpenFOAM-12/etc/config.sh/mpi +--- OpenFOAM-12-version-12/etc/config.sh/mpi ++++ OpenFOAM-12/etc/config.sh/mpi +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-12-version-12/etc/config.sh/paraview OpenFOAM-12/etc/config.sh/paraview +--- OpenFOAM-12-version-12/etc/config.sh/paraview ++++ OpenFOAM-12/etc/config.sh/paraview +@@ -38,117 +38,13 @@ + ) \ + && PATH="$cleaned" + +-# Detect the most recent version of cmake available and add to the PATH +-cmakeDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/cmake-*) +-if [ -n "$cmakeDir" ] +-then +- export PATH=$cmakeDir/bin:$PATH +-fi +-unset cmakeDir +- +-# Set up the paraview environment +-case "$ParaView_TYPE" in +-none) +- ;; +- +-system) +- +- # Look for a paraview installation +- if pvserverExe=$(which pvserver 2> /dev/null) +- then +- paraviewBinDir=$(dirname $pvserverExe) +- paraviewBinDir=$(cd $paraviewBinDir && pwd -P) +- fi +- +- # Set the environment +- if [ -d "$paraviewBinDir" ] +- then +- export ParaView_DIR=$(dirname $paraviewBinDir) +- export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \ +- ldd $paraviewBinDir/paraview | \ +- grep -o "/.*/libpqCore-pv.*.so" | \ +- xargs dirname) +- export ParaView_VERSION=$(unset LD_LIBRARY_PATH && \ +- pvserver --version 2> /dev/null | \ +- awk '{print $NF}') +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the library path +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset pvserverExe paraviewBinDir +- ;; +- +-paraviewopenfoam) +- +- # Look for a paraview installation. The version should be set externally. +- if [ -n "$ParaView_VERSION" ] +- then +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- paraviewDir=/opt/paraviewopenfoam$(echo "$ParaView_MAJOR" | tr -d '.') +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset paraviewDir +- ;; +- +-OpenFOAM | ThirdParty) +- +- # Look for a paraview installation +- if [ -z "$ParaView_VERSION" ] +- then +- paraviewDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/ParaView-*) +- else +- paraviewDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_VERSION=${paraviewDir##*ParaView-} +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$paraviewDir/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r "$paraviewPython" ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- unset paraviewPython +- fi +- +- unset paraviewDir +- ;; +- +-esac ++export ParaView_VERSION=$EBVERSIONPARAVIEW ++export ParaView_MAJOR=${ParaView_VERSION%.*} ++export ParaView_DIR=$EBROOTPARAVIEW ++export ParaView_LIB_DIR=$ParaView_DIR/lib ++export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR ++export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR ++export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH + + # Report + if [ "$FOAM_VERBOSE" ] && [ "$PS1" ] && [ -d "$ParaView_DIR" ] +diff -ru OpenFOAM-12-version-12/etc/config.sh/scotch OpenFOAM-12/etc/config.sh/scotch +--- OpenFOAM-12-version-12/etc/config.sh/scotch ++++ OpenFOAM-12/etc/config.sh/scotch +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the scotch installation +-case "$SCOTCH_TYPE" in +-none) +- ;; +-system) +- export SCOTCH_VERSION=system +- export SCOTCH_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$SCOTCH_VERSION" ] +- then +- scotchSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/scotch_*) +- else +- scotchSrcDir=$WM_THIRD_PARTY_DIR/scotch_$SCOTCH_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$scotchSrcDir" ] +- then +- export SCOTCH_VERSION=${scotchSrcDir##*scotch_} +- export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/scotch_$SCOTCH_VERSION +- fi +- # Clean up +- unset scotchSrcDir +- ;; +-esac ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/zoltan OpenFOAM-12/etc/config.sh/zoltan +--- OpenFOAM-12-version-12/etc/config.sh/zoltan ++++ OpenFOAM-12/etc/config.sh/zoltan +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the zoltan installation +-case "$ZOLTAN_TYPE" in +-none) +- ;; +-system) +- export ZOLTAN_VERSION=system +- export ZOLTAN_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$ZOLTAN_VERSION" ] +- then +- zoltanSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/Zoltan-*) +- else +- zoltanSrcDir=$WM_THIRD_PARTY_DIR/Zoltan-$ZOLTAN_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$zoltanSrcDir" ] +- then +- export ZOLTAN_VERSION=${zoltanSrcDir##*Zoltan-} +- export ZOLTAN_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/Zoltan-$ZOLTAN_VERSION +- fi +- # Clean up +- unset zoltanSrcDir +- ;; +-esac ++export ZOLTAN_VERSION=Zoltan-$EBVERSIONZOLTAN ++export ZOLTAN_ARCH_PATH=$EBROOTZOLTAN + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/settings OpenFOAM-12/etc/config.sh/settings +--- OpenFOAM-12-version-12/etc/config.sh/settings ++++ OpenFOAM-12/etc/config.sh/settings +@@ -63,11 +63,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +@@ -6,15 +6,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(PTSCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- $(if $(PTSCOTCH_LIB_DIR),-L$(PTSCOTCH_LIB_DIR)) \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++#include ++ + extern "C" + { + #include +- #include +- #include "ptscotch.h" + } + +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options OpenFOAM-12/src/parallel/decompose/scotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/scotch/Make/options +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(SCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb new file mode 100644 index 00000000000..ed565315859 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '12' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-12-ThirdParty.patch'] +checksums = [ + {'version-12.tar.gz': 'e59fad54c62e64f1bb89dbaebe5f99a76dc0a6a91d9aad86042a7c4cef6d0744'}, + {'OpenFOAM-12-ThirdParty.patch': 'b8a9abf3b8479d32d87654d833501f54abe57ceb9f06f7d2412a3e52d20108ec'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), + ('Zoltan', '3.901'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb new file mode 100644 index 00000000000..57432d0e0ce --- /dev/null +++ b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Zoltan' +version = '3.901' + +homepage = "https://sandialabs.github.io/Zoltan/" +description = """Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +github_account = 'sandialabs' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030c22d9f7532d3076e40cba1f03a63b2ee961d8cc9a35149af4a3684922a910'] + +dependencies = [ + ('gzip', '1.12'), + ('SCOTCH', '7.0.3'), + ('ParMETIS', '4.0.3'), +] + +preconfigopts = 'mkdir build && cd build &&' +configure_cmd = '../configure' +configopts = ' '.join([ + '--enable-gzip', + '--with-scotch', + '--with-scotch-incdir=$EBROOTSCOTCH/include', + '--with-scotch-libdir=$EBROOTSCOTCH/lib', + '--with-parmetis', + '--with-parmetis-incdir=$EBROOTPARMETIS/include', + '--with-parmetis-libdir=$EBROOTPARMETIS/lib', + '--disable-examples', + '--disable-tests', +]) +prebuildopts = 'cd build &&' +buildopts = 'everything' +preinstallopts = 'cd build &&' + +sanity_check_paths = { + 'files': ['lib/libzoltan.a', 'include/zoltan.h'], + 'dirs': [], +} + +moduleclass = 'cae' From e54970b14ffb1d823f11deb78a83ad972c3d6705 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Thu, 5 Sep 2024 08:59:18 +0200 Subject: [PATCH 408/553] {perf} OTF2: Toolchain Python instead of system MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add Python as a dependency to OTF2 versions to ensure that the toolchain Python is used. To verify, a sanity check is added which ensures that the OTF2 Python module can be loaded. As 'six' is required, newer toolchains also need Python-bundle-PyPI. Signed-off-by: Jan André Reuter --- .../easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb | 9 +++++++-- .../easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb | 8 +++++++- .../easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb | 9 +++++++-- .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb | 9 +++++++-- .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb | 10 ++++++++-- .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb | 10 ++++++++-- 6 files changed, 44 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb index 6e982449e9e..fe8a5244c12 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb index 7c4d60f0514..488b8e0de0d 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.9.6'), ] +local_pyshortver = '3.9' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] -sanity_check_commands = ['%(namelower)s-config --help'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb index 61eba75f5f0..6756aa72eac 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb index 54478bf62fa..f4c842e0450 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.8'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb index 17595d97acb..db786b12a41 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb index 48cbf931ec5..c5108c8daca 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' From d76db40033304ffd748d44a34b61b504bdc530e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Thu, 22 Aug 2024 17:54:50 +0200 Subject: [PATCH 409/553] {perf}[GCCcore/13.3.0,gompi/2024a] Add Score-P with dependencies. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add Score-P 8.4, OTF2 3.0.3, OPARI2 2.0.8, CubeLib 4.8.2, CubeWriter 4.8.2, PAPI 7.1.0, PDT 3.25.2, SIONlib 1.7.7, UCX-CUDA 1.16.0. For OTF2, a patch updates the py-compile file used to fix the removal of the imp module in Python 3.12. This prevents install failures. Signed-off-by: Jan André Reuter --- .../c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb | 52 ++++ .../CubeWriter-4.8.2-GCCcore-13.3.0.eb | 52 ++++ .../o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb | 45 ++++ .../o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb | 55 ++++ .../o/OTF2/otf2-3.0.3-update-py-compile.patch | 252 ++++++++++++++++++ .../p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb | 53 ++++ .../p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb | 40 +++ .../SIONlib-1.7.7-GCCcore-13.3.0-tools.eb | 51 ++++ .../Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb | 57 ++++ .../s/Score-P/Score-P-8.4-gompi-2024a.eb | 55 ++++ ...-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb | 41 +++ ....16.0_link_against_existing_UCX_libs.patch | 93 +++++++ 12 files changed, 846 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6b2414be446 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e030f21ba6c --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright:: Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..503a56951d0 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.8' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..509d81b79af --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,55 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['otf2-3.0.3-update-py-compile.patch'] +checksums = [ + '18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8', # otf2-3.0.3.tar.gz + '5b1dad8788642eaa97bc03003c9329380340ba10649e556a30ce541165cf8da4', # otf2-3.0.3-update-py-compile.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch new file mode 100644 index 00000000000..539726fbf14 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch @@ -0,0 +1,252 @@ +This patch updates the py-compile file used by OTF2 during the install process +to fix the removal of the imp module in Python 3.12 which was long deprecated. +With this, OTF2 can be installed with Python 3.12, which would previously fail +with a module not found error. + +--- build-config/py-compile 2023-02-12 17:32:31.274132086 +0100 ++++ ../../otf2/build-config/py-compile 2024-08-22 17:44:59.939242651 +0200 +@@ -1,7 +1,7 @@ + #!/bin/sh + # py-compile - Compile a Python program + +-scriptversion=2011-06-08.12; # UTC ++scriptversion=2023-03-30.00; # UTC + + # Copyright (C) 2000-2013 Free Software Foundation, Inc. + +@@ -27,7 +27,7 @@ + # bugs to or send patches to + # . + +-if [ -z "$PYTHON" ]; then ++if test -z "$PYTHON"; then + PYTHON=python + fi + +@@ -79,13 +79,20 @@ + ;; + -h|--help) + cat <<\EOF +-Usage: py-compile [--help] [--version] [--basedir DIR] [--destdir DIR] [--silent] FILES..." ++Usage: py-compile [options] FILES... + + Byte compile some python scripts FILES. Use --destdir to specify any + leading directory path to the FILES that you don't want to include in the + byte compiled file. Specify --basedir for any additional path information you + do want to be shown in the byte compiled file. + ++Options: ++ --basedir DIR Prefix all FILES with DIR, and include in error messages. ++ --destdir DIR Prefix all FILES with DIR before compiling. ++ -v, --version Display version information. ++ -h, --help This help screen. ++ --silent Operate silently. ++ + Example: + py-compile --destdir /tmp/pkg-root --basedir /usr/share/test test.py test2.py + +@@ -114,87 +121,165 @@ + shift + done + +-files=$* +-if test -z "$files"; then +- usage_error "no files given" ++if test $# -eq 0; then ++ usage_error "no files given" + fi + + # if basedir was given, then it should be prepended to filenames before + # byte compilation. +-if [ -z "$basedir" ]; then +- pathtrans="path = file" ++if test -z "$basedir"; then ++ pathtrans="path = file" + else +- pathtrans="path = os.path.join('$basedir', file)" ++ pathtrans="path = os.path.join('$basedir', file)" + fi + + # if destdir was given, then it needs to be prepended to the filename to + # byte compile but not go into the compiled file. +-if [ -z "$destdir" ]; then +- filetrans="filepath = path" ++if test -z "$destdir"; then ++ filetrans="filepath = path" + else +- filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++ filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++fi ++ ++python_major=`$PYTHON -c 'import sys; print(sys.version_info[0])'` ++if test -z "$python_major"; then ++ usage_error "could not determine $PYTHON major version" + fi + ++case $python_major in ++[01]) ++ usage_error "python version 0.x and 1.x not supported" ++ ;; ++esac ++ ++python_minor=`$PYTHON -c 'import sys; print(sys.version_info[1])'` ++ ++# NB: When adding support for newer versions, prefer copying & adding new cases ++# rather than try to keep things merged with shell variables. ++ ++# First byte compile (no optimization) all the modules. ++# This works for all currently known Python versions. + $PYTHON -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'c' + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'c', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath), path) +- else: +- py_compile.compile(filepath, filepath + 'c', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" || exit $? ++ sys.stdout.write('\n')" "$@" || exit $? + +-# this will fail for python < 1.5, but that doesn't matter ... ++# Then byte compile w/optimization all the modules. + $PYTHON -O -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'o' + +-# pypy does not use .pyo optimization +-if hasattr(sys, 'pypy_translation_info'): ++# pypy2 does not use .pyo optimization ++if sys.version_info.major <= 2 and hasattr(sys, 'pypy_translation_info'): + sys.exit(0) + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules (optimized versions)...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules (optimized versions) ...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'o', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath, False), path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) ++if not silent: ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ++# Then byte compile w/more optimization. ++# Only do this for Python 3.5+, see https://bugs.gnu.org/38043 for background. ++case $python_major.$python_minor in ++2.*|3.[0-4]) ++ ;; ++*) ++ $PYTHON -OO -c " ++import sys, os, py_compile, importlib ++ ++destpath = importlib.util.cache_from_source ++ ++silent = $silent ++blu = '''$blu''' ++std = '''$std''' ++ ++if not silent: ++ sys.stdout.write('Byte-compiling python modules (more optimized versions)' ++ ' ...\n') ++for file in sys.argv[1:]: ++ $pathtrans ++ $filetrans ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue ++ if not silent: ++ sys.stdout.write(file + ' ') ++ sys.stdout.flush() + else: +- py_compile.compile(filepath, filepath + 'o', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" 2>/dev/null || : ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ;; ++esac + + # Local Variables: + # mode: shell-script diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5c653a9d515 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.42'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..74328c99ae7 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.2' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work +download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " + + "and rename to " + sources[0]) +checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb new file mode 100644 index 00000000000..9d2584de1bb --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..9d7b53221e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb new file mode 100644 index 00000000000..eda406cbe2a --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb @@ -0,0 +1,55 @@ +# Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# * Jan André Reuter +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..34271e18021 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.16.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.16.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'}, + {'UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch': + 'aa5bab38c188276958dd6829da4929ed9ff0b67cd55665b4459521cf3fbbe46d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('UCX', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('GDRCopy', '2.4.1'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch new file mode 100644 index 00000000000..92973cd7f80 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,93 @@ +diff --git a/configure.ac b/configure.ac +index 8d8da54..2765fe0 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -30,13 +30,13 @@ valgrind_libpath="" + AC_USE_SYSTEM_EXTENSIONS + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff --git a/src/ucm/cuda/Makefile.am b/src/ucm/cuda/Makefile.am +index 00bd224..22e719f 100644 +--- a/src/ucm/cuda/Makefile.am ++++ b/src/ucm/cuda/Makefile.am +@@ -9,7 +9,7 @@ if HAVE_CUDA + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la $(CUDA_LIBS) $(CUDART_LIBS) ++libucm_cuda_la_LIBADD = -lucm $(CUDA_LIBS) $(CUDART_LIBS) + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff --git a/src/ucm/rocm/Makefile.am b/src/ucm/rocm/Makefile.am +index f9e183f..dcd1587 100644 +--- a/src/ucm/rocm/Makefile.am ++++ b/src/ucm/rocm/Makefile.am +@@ -10,7 +10,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff --git a/src/uct/cuda/Makefile.am b/src/uct/cuda/Makefile.am +index 00899ab..dcee6b0 100644 +--- a/src/uct/cuda/Makefile.am ++++ b/src/uct/cuda/Makefile.am +@@ -11,8 +11,8 @@ module_LTLIBRARIES = libuct_cuda.la + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la \ ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct \ + $(CUDA_LIBS) $(CUDART_LIBS) $(NVML_LIBS) + + noinst_HEADERS = \ +diff --git a/src/uct/cuda/gdr_copy/Makefile.am b/src/uct/cuda/gdr_copy/Makefile.am +index 47602c7..601cb9f 100644 +--- a/src/uct/cuda/gdr_copy/Makefile.am ++++ b/src/uct/cuda/gdr_copy/Makefile.am +@@ -9,7 +9,7 @@ module_LTLIBRARIES = libuct_cuda_gdrcopy.la + libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(GDR_COPY_CPPFLAGS) + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) + libuct_cuda_gdrcopy_la_LDFLAGS = $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la \ + $(GDR_COPY_LIBS) + +diff --git a/src/uct/rocm/Makefile.am b/src/uct/rocm/Makefile.am +index c7abce1..257e33f 100644 +--- a/src/uct/rocm/Makefile.am ++++ b/src/uct/rocm/Makefile.am +@@ -8,8 +8,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ From d0cbd2e91c75a419bdd7335d48b38ad59265ac21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Thu, 5 Sep 2024 10:00:21 +0200 Subject: [PATCH 410/553] {perf}{GCCcore/13.3.0} OTF2: Use toolchain Python MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb index 509d81b79af..fdf78e0772d 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb @@ -39,17 +39,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), ] +local_pyshortver = '3.12' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' From 31ea36d41b6619f87d34c8ab39fe4322b518896c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 5 Sep 2024 13:35:23 +0200 Subject: [PATCH 411/553] adding easyconfigs: fpylll-0.6.1-foss-2023b.eb, fplll-5.4.5-GCCcore-13.2.0.eb --- .../f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb | 32 +++++++++++++++++++ .../f/fpylll/fpylll-0.6.1-foss-2023b.eb | 26 +++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5184f1f3c1e --- /dev/null +++ b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'fplll' +version = '5.4.5' + +homepage = 'https://github.com/fplll/fplll' +description = """fplll contains implementations of several lattice algorithms. + The implementation relies on floating-point orthogonalization, and the 1982 paper from +Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fplll/fplll/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['76d3778f0326597ed7505bab19493a9bf6b73a5c5ca614e8fb82f42105c57d00'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/fplll', 'lib/libfplll.%s' % SHLIB_EXT, 'include/fplll.h'], + 'dirs': ['share'] +} + +sanity_check_commands = ["fplll --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb new file mode 100644 index 00000000000..5361252deb7 --- /dev/null +++ b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fpylll' +version = '0.6.1' + +homepage = 'https://pypi.org/project/fpylll' +description = "A Python wrapper for fplll." + +# can be moved down to gfbf in more recent toolchain versions +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dfd9529a26c50993a2a716177debd7994312219070574cad31b35b4f0c040a19'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('cysignals', '1.11.4'), + ('fplll', '5.4.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 8dee0734fe2f47d9af1ebf75d4dfbbf6cea181cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 5 Sep 2024 13:36:19 +0200 Subject: [PATCH 412/553] adding easyconfigs: primecountpy-0.1.0-GCCcore-13.2.0.eb, primecount-7.14-GCCcore-13.2.0.eb --- .../primecount-7.14-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ .../primecountpy-0.1.0-GCCcore-13.2.0.eb | 27 ++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..556cc0f1507 --- /dev/null +++ b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'primecount' +version = '7.14' + +homepage = 'https://github.com/kimwalisch/primecount' +description = """primecount is a command-line program and C/C++ library that counts the number of primes ≤ x + (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/kimwalisch/primecount/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d867ac18cc52c0f7014682169988a76f39e4cd56f8ce78fb56e064499b1d66bb'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/primecount', 'include/primecount.h'] + + ['lib/libprimecount.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +sanity_check_commands = ["primecount -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..11244361d59 --- /dev/null +++ b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'primecountpy' +version = '0.1.0' + +homepage = 'https://pypi.org/project/primecountpy' +description = "This is a Cython interface to the C++ library primecount." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Cython', '3.0.10'), + ('cysignals', '1.11.4'), + ('primecount', '7.14'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 42469bb2d883bec568b9e6966b404cd1cedce6a0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 5 Sep 2024 14:07:40 +0200 Subject: [PATCH 413/553] adding easyconfigs: CLUMPP-1.1.2-Linux64.eb --- .../c/CLUMPP/CLUMPP-1.1.2-Linux64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb new file mode 100644 index 00000000000..fb71ad7ff19 --- /dev/null +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'CLUMPP' +version = '1.1.2' +versionsuffix = '-Linux64' + +homepage = 'https://rosenberglab.stanford.edu/clumpp.html' +description = """ +CLUMPP is a program that deals with label switching and multimodality problems +in population-genetic cluster analyses.""" + +toolchain = SYSTEM + +source_urls = ['https://rosenberglab.stanford.edu/software/'] +sources = ['%(name)s_Linux64.%(version)s.tar.gz'] +checksums = ['58cf3fe9e37f890621a76a244362256ffe4dde5e409346ae811d56af26cfe724'] + +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && mv CLUMPP bin/' +] + +sanity_check_paths = { + 'files': ['bin/CLUMPP'], + 'dirs': [], +} + +sanity_check_commands = [ + 'tmpdir=$(mktemp -d) && cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir/ && ' + 'cd $tmpdir && CLUMPP', +] + +moduleclass = 'bio' From a9924f769e2623de5c50086aa3f22a67394f68f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 5 Sep 2024 15:22:01 +0200 Subject: [PATCH 414/553] adding easyconfigs: AGAT-1.4.0-GCC-12.3.0.eb --- .../a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..2677e62fda1 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb @@ -0,0 +1,70 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# Thomas Eylenbosch - Gluo NV +# Update: Petr Král (INUITS) +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '1.4.0' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), + ('Term::ProgressBar', '2.23', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] +moduleclass = 'bio' From 6b56303af3016d3581d0942edaefc119740429ed Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 Sep 2024 15:58:32 +0100 Subject: [PATCH 415/553] add the plugins to OpenFOAM v2406 --- .../easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb index ba59d215581..0e2885c064f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -14,13 +14,20 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] -sources = [SOURCE_TGZ] +sources = [ + SOURCE_TGZ, + { + 'filename': '%(name)s-plugins-%(version)s.tgz', + 'extract_cmd': 'tar --strip-components=1 -C %(installdir)s/%(name)s-%(version)s/ -xzf %s' + } +] patches = [ ('OpenFOAM-v2406-cleanup.patch', 1), ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), ] checksums = [ {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, + {'OpenFOAM-plugins-v2406.tgz': '1d008f86fad06a4a568d194c6e3d5ab52be2b20c83a3b9b1b0230e2de2d0558b'}, {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'}, {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, ] From 184f4ff8f5b6dfcefaedcd7fe05cb53d409fa71a Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 5 Sep 2024 18:02:01 +0200 Subject: [PATCH 416/553] adding easyconfigs: GPyOpt-1.2.6-foss-2023a.eb --- .../g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb new file mode 100644 index 00000000000..ca08a08a88c --- /dev/null +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'GPyOpt' +version = '1.2.6' + +homepage = 'https://sheffieldml.github.io/GPyOpt' +description = "GPyOpt is a Python open-source library for Bayesian Optimization" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.6', { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['4916be6f77f457316bcac8460be9c226026aed81fe7be302b32c0ba74e2ac6dd'], + }), + ('GPy', '1.13.2', { + 'modulename': 'GPy', + 'checksums': ['a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('sobol-seq', '0.2.0', { + 'sources': ['sobol_seq-%(version)s.tar.gz'], + 'checksums': ['e16e701bd7b03ec6ce65b3a64c9205799f6a2d00c2054dd8c4ff4343f3981172'], + }), + ('emcee', '2.2.1', { + 'checksums': ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +local_GPy_file = '%(installdir)s/lib/python%(pyshortver)s/site-packages/GPy/plotting/matplot_dep/plot_definitions.py' + +# Fix GPy with matplotlib>=3.4.0 +# see issue 953 and fix from https://github.com/SheffieldML/GPy/pull/960 +postinstallcmds = [ + 'sed -i ' + '''-e 's|ax._process_unit_info(xdata=X, ydata=y1)|ax._process_unit_info([("x", X), ("y", y1)], convert=False)|' ''' + '''-e 's|ax._process_unit_info(ydata=y2)|ax._process_unit_info([("y", y2)], convert=False)|' %s''' % local_GPy_file, +] + + +sanity_pip_check = True + +moduleclass = 'math' From ebc1c90f62842ff0482dbb2f70cd661b449542f9 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 5 Sep 2024 21:27:20 +0200 Subject: [PATCH 417/553] remove click --- easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb index b0d0c5a63ae..46b9452f48b 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb @@ -33,9 +33,6 @@ exts_list = [ ('asgiref', '3.7.2', { 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], }), - ('click', '8.1.7', { - 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], - }), ('blinker', '1.8.2', { 'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'], }), From 0ca73992ca7533a83a6048d029fece46c07b233c Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 6 Sep 2024 10:38:40 +0000 Subject: [PATCH 418/553] libdap: Update source --- .../easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 6 +++--- .../easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb | 6 +++--- .../easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb | 6 +++--- .../easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb index 237260a43f7..b911c8f3169 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb index 39e628f1d97..39930ab196b 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb @@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index e2bb8f718ab..d43917eb6b0 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6e907ea7a9f878965a3af2a858423450dde389d851fc67a33b0096b8b9b6085'] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index b48c3f1b6bc..5adc0a0f2ee 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e59b48f48bb37b36dcf9618043881e1d4150abd9b2ea3fa7474647c4ad622ccc'] builddependencies = [ ('binutils', '2.37'), From 4e610ab7de6cb389f72f5a64de9aaf903cd10dae Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 6 Sep 2024 12:32:17 +0000 Subject: [PATCH 419/553] Added Autotools as buildep and preconfigopts --- easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb | 2 ++ easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb index b911c8f3169..063ce985f47 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.38'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.38'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb index 39930ab196b..a6dbd52797f 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.40'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.39'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index d43917eb6b0..4a6837a20f1 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.36'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index 5adc0a0f2ee..6e4a0237bff 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.37'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.37'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { From e8cd29fa696c2e467ef75fa6792e22cd4932f639 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:09:00 +0200 Subject: [PATCH 420/553] Update easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index 4a6837a20f1..c1cb33551f7 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), - ('Autotools', '20220317'), + ('Autotools', '20210128'), ] dependencies = [ From 667b2c93c7b659b2e7a3bd6254f2ef89c68e2e8d Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:09:07 +0200 Subject: [PATCH 421/553] Update easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index 6e4a0237bff..1172b66d8f2 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('binutils', '2.37'), ('Bison', '3.7.6'), ('flex', '2.6.4'), - ('Autotools', '20220317'), + ('Autotools', '20210726'), ] dependencies = [ From 9a50608a0d1f7478c2f001e11d38b30a71787509 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 6 Sep 2024 14:15:28 +0100 Subject: [PATCH 422/553] adding easyconfigs: rnamotif-20240904-GCCcore-12.3.0.eb --- .../rnamotif-20240904-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bb1513a04b2 --- /dev/null +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'rnamotif' +version = '20240904' +_commit = '697ee7fda4ff2f5181a33c0c3eac54d7b97409fa' + +homepage = "https://github.com/dacase/rnamotif" +description = """The rnamotif program searchs input sequences for portions that match a given descriptor or "motif". + Matching sequences can also be ranked by various scoring functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'dacase' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['e9432e128ce7f1bfcf4898a36d56435272ad9b4e2d37f1866a95aa159c81fdfe'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + +] + +prebuildopts = 'sed -i "s/CFLAGS= -O2 -Wall/CFLAGS=$CFLAGS/" config.h &&' +pretestopts = 'EFNDATA=%%(builddir)s/%%(name)s-%s/efndata' % _commit +runtest = 'test' + +files_to_copy = [ + (['src/rnamotif', 'src/rmprune', 'src/rmfmt', 'src/rm2ct'], 'bin'), + 'LICENSE', 'efndata', 'Ecoli.trna.example', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['efndata'], +} + +modextravars = {'EFNDATA': 'efndata'} + +moduleclass = 'bio' From 736457464a1f3aaa307083a124d372ca02d195df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Sep 2024 16:01:52 +0200 Subject: [PATCH 423/553] unbundle tensorboard from TensorFlow v2.15.1 --- .../TensorFlow-2.15.1-foss-2023a.eb | 61 ------------------- 1 file changed, 61 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 506cbafd52b..0f3a94f2cc4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -57,7 +57,6 @@ dependencies = [ # - portpicker for tests no longer needed (TF@e85860e838) # - opt_einsum now comes from ml_dtypes exts_list = [ - ('wrapt', '1.14.1', { 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], }), @@ -68,48 +67,6 @@ exts_list = [ 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], }), - ('Werkzeug', '3.0.2', { - 'source_tmpl': SOURCELOWER_TAR_GZ, - 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], - }), - ('tensorboard-data-server', '0.7.2', { - 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', - 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], - }), - ('Markdown', '3.6', { - 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('requests-oauthlib', '2.0.0', { - 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.4.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], - }), - ('cachetools', '5.3.3', { - 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], - }), - ('google-auth', '2.29.0', { - 'modulename': 'google.auth', - 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], - }), - ('google-auth-oauthlib', '1.2.0', { - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('tensorboard', '2.15.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], - }), ('keras', '2.15.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], @@ -128,15 +85,6 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - # Optional profile plugin + dependency - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard-plugin-profile', '2.15.1', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], - }), (name, version, { 'patches': [ 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', @@ -208,13 +156,4 @@ exts_list = [ }), ] -# Taken from tensorboard-2.15.1-gfbf-2023a.eb: -# Relax restriction on protobuf dependency as issue was fixed -# in https://github.com/protocolbuffers/upb/pull/1514 -# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 -postinstallcmds = [ - 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + - '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', -] - moduleclass = 'lib' From 099539e2dd5fa132b5c6c74d66ebd48a7ea0998c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2024 17:00:53 +0200 Subject: [PATCH 424/553] adding easyconfigs: PLINK-1.90-beta-7.4-x86_64.eb --- .../p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb new file mode 100644 index 00000000000..51357650dbb --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.90-beta-7.4-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = SYSTEM + +source_urls = ['https://s3.amazonaws.com/plink1-assets/'] +sources = ['plink_linux_x86_64_20240818.zip'] +checksums = ['0ac294ffcd5d82f5b0d2d7f579ac85a87017f6fc46485b21793f5aff9c719e3d'] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +sanity_check_commands = ["plink --help"] + +moduleclass = 'bio' From 0b7bc593d6a784e7d57ba605c3ef6d295271ce22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 6 Sep 2024 17:10:42 +0200 Subject: [PATCH 425/553] adding easyconfigs: lrcalc-2.1-GCCcore-13.2.0.eb --- .../l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa14572bef6 --- /dev/null +++ b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'lrcalc' +version = '2.1' + +homepage = 'https://sites.math.rutgers.edu/~asbuch/lrcalc/' +description = """The Littlewood-Richardson Calculator is a program + designed to compute Littlewood-Richardson coefficients.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://math.rutgers.edu/~asbuch/lrcalc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': [ + 'bin/lrcalc', + 'lib/liblrcalc.%s' % SHLIB_EXT, + 'include/lrcalc/ivector.h', + ], + 'dirs': [] +} + +sanity_check_commands = ["lrcalc 2>&1 | grep '^Usage:'"] + +moduleclass = 'math' From 0f401ecbd138d5666a7f773f0d8ad7022d37aca4 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 6 Sep 2024 17:41:09 +0200 Subject: [PATCH 426/553] adding easyconfigs: Mercurial-6.8.1-GCCcore-13.3.0.eb --- .../Mercurial-6.8.1-GCCcore-13.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a733004f29a --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'Mercurial' +version = '6.8.1' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['030e8a7a6d590e4eaeb403ee25675615cd80d236f3ab8a0b56dcc84181158b05'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ['hg --help'] + +moduleclass = 'tools' From bf063e5a037c163d90834386f5c8b3b312fa3d5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2024 18:01:39 +0200 Subject: [PATCH 427/553] adding easyconfigs: SNAP-ESA-10.0.0-Java-11.eb --- .../s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb new file mode 100644 index 00000000000..06a2de7582c --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '10.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_linux-%(version)s.sh' +local_varfile = 'SNAP-ESA-8.0-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version_major)s_%(version_minor)s/installers', + 'https://step.esa.int/downloads/%(version_major_minor)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + {'esa-snap_all_linux-10.0.0.sh': 'c928fd886c983fa7c09c09a3c48593542e71b0636d493ae1401b4c964348698a'}, + {'SNAP-ESA-8.0-response.varfile': '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4'}, +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) +dependencies = [ + ('Java', '11'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['rstb', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --help | grep 'Additional module options'", + "gpt -h", +] + +moduleclass = 'geo' From 6c1a16cc45e905347c1ac77e9feac5a762156add Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 6 Sep 2024 18:05:12 +0200 Subject: [PATCH 428/553] Use https for homepage in libmatheval-1.1.11-GCCcore-13.3.0.eb --- .../l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb index 4cea27b91dc..b8bf07966b1 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libmatheval' version = '1.1.11' # still the latest version available on the ftp mirror -homepage = 'http://www.gnu.org/software/libmatheval/' +homepage = 'https://www.gnu.org/software/libmatheval/' description = """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. """ From 7f711b9d3d61842f55a8d6c9d5349d10a263f51b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 19:42:22 +0200 Subject: [PATCH 429/553] use version in byacc sources --- .../b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb index 292636d12e3..fa57e4306e6 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -10,9 +10,9 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -source_urls = ['https://invisible-island.net/archives/byacc/current/'] -sources = ['byacc.tar.gz'] -checksums = ['e5e0c069fb15d454918568f77e90a60221373dd206a3d3c2da1e7daba3bae9ea'] +source_urls = ['https://invisible-island.net/archives/byacc/'] +sources = ['byacc-%s.tgz' % version.split('.')[2]] +checksums = ['f2897779017189f1a94757705ef6f6e15dc9208ef079eea7f28abec577e08446'] builddependencies = [('binutils', '2.42')] From 3a35e90e8e6695d02bdd4cf30751f5a23682a5c9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 22:31:02 +0200 Subject: [PATCH 430/553] adding easyconfigs: fish-3.7.1-GCCcore-13.3.0.eb --- .../f/fish/fish-3.7.1-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bcb975f1857 --- /dev/null +++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'fish' + +version = '3.7.1' + +homepage = 'https://fishshell.com/' +description = """ +fish is a smart and user-friendly command line shell for Linux, macOS, and the rest of the family. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fish-shell/fish-shell/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['614c9f5643cd0799df391395fa6bbc3649427bb839722ce3b114d3bbc1a3b250'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3') +] + +dependencies = [ + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/fish'], + 'dirs': [], +} + +sanity_check_commands = ['fish --version'] + +moduleclass = 'tools' From 51560e74b820a67720e1b66205ff1f720d10287e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 22:35:29 +0200 Subject: [PATCH 431/553] adding easyconfigs: git-annex-10.20240731-GCCcore-13.3.0.eb, GHC-9.10.1-x86_64.eb, Stack-3.1.1-x86_64.eb --- .../easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb | 82 +++++++++++++++++++ .../git-annex-10.20240731-GCCcore-13.3.0.eb | 48 +++++++++++ .../easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb | 26 ++++++ 3 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb new file mode 100644 index 00000000000..d50730bb1b2 --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb @@ -0,0 +1,82 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.10.1' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +components = [ + ('GMP', '6.3.0', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'], + 'configopts': ' --enable-cxx', + 'start_dir': '%(namelower)s-%(version)s', + }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + 'start_dir': '%(namelower)s-%(version)s', + }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['fab143f10f845629cb1b373309b5680667cbaab298cf49827e383ee8a9ddf683'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..89c70af2f45 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240731' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.45.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb new file mode 100644 index 00000000000..0a822a69cbd --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '3.1.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['d096125ea3d987a55d17f7d4f8599ee2fd96bd2d0f033566e28ddfe248f730f9'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' From 35feaf72998556814cd11adbea5d0084964977fb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 22:46:30 +0200 Subject: [PATCH 432/553] adding easyconfigs: METIS-5.1.0-GCCcore-13.3.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..417e4750ef9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' From ab243abe21401004d45cccd3448606dbc070ed1e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 22:50:02 +0200 Subject: [PATCH 433/553] adding easyconfigs: PLY-3.11-GCCcore-13.3.0.eb --- .../p/PLY/PLY-3.11-GCCcore-13.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a5620c426d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 434a6998a91e11948fbe4dd050394c325b96f9e4 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Sep 2024 23:01:33 +0200 Subject: [PATCH 434/553] update easyconfig: GHC-9.10.1-x86_64.eb --- easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb index d50730bb1b2..2074b920ebd 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb @@ -51,7 +51,7 @@ components = [ '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', ], - 'preconfigopts': "export CPPFLAGS='-P' && ", + 'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ", 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', 'start_dir': '%(namelower)s-%(version)s', }), From 16de1658c683710bc8101eb3488528e8e007ded0 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 8 Sep 2024 19:32:40 +0200 Subject: [PATCH 435/553] add Cython builddep --- easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb index 70dfd98dcf4..50b9ad427e6 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb @@ -13,6 +13,7 @@ checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa'] builddependencies = [ ('binutils', '2.42'), + ('Cython', '3.0.10'), ] dependencies = [ ('Python', '3.12.3'), From d86580519347bfa7e87ffc36a5b0be4a212ad159 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 9 Sep 2024 10:43:21 +0200 Subject: [PATCH 436/553] adding easyconfigs: xskillscore-0.0.26-foss-2023a.eb --- .../xskillscore-0.0.26-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb diff --git a/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb new file mode 100644 index 00000000000..c8454e53dbb --- /dev/null +++ b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'xskillscore' +version = '0.0.26' + +homepage = 'https://xskillscore.readthedocs.io' +description = """ +xskillscore is an open source project and Python package that provides verification metrics of +deterministic (and probabilistic from properscoring) forecasts with xarray. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('dask', '2023.9.2'), + ('SciPy-bundle', '2023.07'), + ('statsmodels', '0.14.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('properscoring', '0.1', { + 'checksums': ['b0cc4963cc218b728d6c5f77b3259c8f835ae00e32e82678cdf6936049b93961'], + }), + ('xhistogram', '0.3.2', { + 'checksums': ['56b0751e1469eaed81710f644c8ba5c574b51883baa2feee26a95f2f708f91a1'], + }), + (name, version, { + 'checksums': ['780a424c1ab3eedf526a45ba8e6cf6dca61b17339252115a4e25ea8c5833ada5'], + }), +] + +moduleclass = 'geo' From 524adde76ed4be7075e5b046b55ad1d9416c0e5e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 Sep 2024 11:51:19 +0200 Subject: [PATCH 437/553] adding easyconfigs: MOKIT-1.2.6_20240830-gfbf-2023a.eb --- .../MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb new file mode 100644 index 00000000000..ace55d37c66 --- /dev/null +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'MOKIT' +version = '1.2.6_20240830' +_commit = 'd66560a6a7926e5e21b45cbcc9213aaa26bd997d' + +homepage = 'https://github.com/1234zou/MOKIT' +description = """ +MOKIT offers various utilities and modules to transfer MOs among various quantum chemistry software packages.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +_makefile = 'Makefile.gnu_openblas_conda' +maxparallel = 1 + +default_component_specs = { + 'source_urls': ['https://github.com/1234zou/MOKIT/archive'], + 'checksums': ['b4e7224ac5b56e6d0116f7759a3017c57d527b1d35c32e3b2733904f7f7c4de5'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'MOKIT-%s/src' % _commit, + 'prebuildopts': 'sed -i -e "s/^MKL_FLAGS.*/MKL_FLAGS = $LIBBLAS/" %s && ' % _makefile, + 'buildopts': 'all -f %s' % _makefile, + 'files_to_copy': ['../bin'], + }), + ('mokit', version, { + 'easyblock': 'PythonPackage', + 'start_dir': 'MOKIT-%s' % _commit, + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'mokit'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'fch2inp | grep Example', + 'geom_opt | grep Example', + "python -c 'from mokit.lib.gaussian import load_mol_from_fch'", +] + +sanity_check_paths = { + 'files': ['bin/geom_opt', 'bin/fch2inp'], + 'dirs': ['lib/python3.11/site-packages/mokit'], +} + +moduleclass = 'chem' From a93463e20ada01bcba7667121989a2e0ff2220c4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 9 Sep 2024 11:10:17 +0000 Subject: [PATCH 438/553] adding easyconfigs: rustworkx-0.12.1-foss-2023a.eb --- .../rustworkx/rustworkx-0.12.1-foss-2023a.eb | 170 ++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..2a86b64c9ae --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb @@ -0,0 +1,170 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Rust', '1.75.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + ('num-complex', '0.2.4'), + ('num-complex', '0.4.1'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.13.1'), + ('numpy', '0.17.2'), + ('once_cell', '1.12.0'), + ('parking_lot', '0.11.2'), + ('parking_lot_core', '0.8.5'), + ('petgraph', '0.6.2'), + ('ppv-lite86', '0.2.16'), + ('priority-queue', '1.2.0'), + ('proc-macro2', '1.0.39'), + ('pyo3', '0.17.3'), + ('pyo3-build-config', '0.17.3'), + ('pyo3-ffi', '0.17.3'), + ('pyo3-macros', '0.17.3'), + ('pyo3-macros-backend', '0.17.3'), + ('quick-xml', '0.22.0'), + ('quote', '1.0.18'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.3'), + ('rand_pcg', '0.3.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.5.3'), + ('rayon-core', '1.9.3'), + ('redox_syscall', '0.2.13'), + ('ryu', '1.0.10'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.145'), + ('serde_derive', '1.0.145'), + ('serde_json', '1.0.89'), + ('smallvec', '1.8.0'), + ('syn', '1.0.96'), + ('target-lexicon', '0.12.4'), + ('unicode-ident', '1.0.0'), + ('unindent', '0.1.9'), + ('version_check', '0.9.4'), + ('wasi', '0.10.2+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + {'rustworkx-0.12.1.tar.gz': '13a19a2f64dff086b3bffffb294c4630100ecbc13634b4995d9d36a481ae130e'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'crossbeam-channel-0.5.4.tar.gz': '5aaa7bd5fb665c6864b5f963dd9097905c54125909c7aa94c9e18507cdbe6c53'}, + {'crossbeam-deque-0.8.1.tar.gz': '6455c0ca19f0d2fbf751b908d5c55c1f5cbc65e03c4225427254b46890bdde1e'}, + {'crossbeam-epoch-0.9.8.tar.gz': '1145cf131a2c6ba0615079ab6a638f7e1973ac9c2634fcbeaaad6114246efe8c'}, + {'crossbeam-utils-0.8.8.tar.gz': '0bf124c720b7686e3c2663cf54062ab0f68a88af2fb6a030e87e30bf721fcb38'}, + {'either-1.6.1.tar.gz': 'e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457'}, + {'fixedbitset-0.4.2.tar.gz': '0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80'}, + {'getrandom-0.2.6.tar.gz': '9be70c98951c83b8d2f8f60d7065fa6d5146873094452a1008da8c2f1e4205ad'}, + {'hashbrown-0.11.2.tar.gz': 'ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e'}, + {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'}, + {'indexmap-1.7.0.tar.gz': 'bc633605454125dec4b66843673f01c7df2b89479b32e0ed634e43a91cff62a5'}, + {'indoc-1.0.6.tar.gz': '05a0bd019339e5d968b37855180087b7b9d512c5046fbd244cf8c95687927d6e'}, + {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'}, + {'itoa-1.0.2.tar.gz': '112c678d4050afce233f4f2852bb2eb519230b3cf12f33585275537d7e41578d'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'libc-0.2.126.tar.gz': '349d5a591cd28b49e1d1037471617a32ddcda5731b99419008085f72d5a53836'}, + {'lock_api-0.4.7.tar.gz': '327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53'}, + {'matrixmultiply-0.2.4.tar.gz': '916806ba0031cd542105d916a97c8572e1fa6dd79c9c51e7eb43a09ec2dd84c1'}, + {'memchr-2.5.0.tar.gz': '2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d'}, + {'memoffset-0.6.5.tar.gz': '5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce'}, + {'ndarray-0.13.1.tar.gz': 'ac06db03ec2f46ee0ecdca1a1c34a99c0d188a0d83439b84bf0cb4b386e4ab09'}, + {'num-bigint-0.4.3.tar.gz': 'f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f'}, + {'num-complex-0.2.4.tar.gz': 'b6b19411a9719e753aff12e5187b74d60d3dc449ec3f4dc21e3989c3f554bc95'}, + {'num-complex-0.4.1.tar.gz': '97fbc387afefefd5e9e39493299f3069e14a140dd34dc19b4c1c1a8fddb6a790'}, + {'num-integer-0.1.45.tar.gz': '225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9'}, + {'num-traits-0.2.15.tar.gz': '578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd'}, + {'num_cpus-1.13.1.tar.gz': '19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1'}, + {'numpy-0.17.2.tar.gz': 'a462c1af5ba1fddec1488c4646993a23ae7931f9e170ccba23e9c7c834277797'}, + {'once_cell-1.12.0.tar.gz': '7709cef83f0c1f58f666e746a08b21e0085f7440fa6a29cc194d68aac97a4225'}, + {'parking_lot-0.11.2.tar.gz': '7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99'}, + {'parking_lot_core-0.8.5.tar.gz': 'd76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216'}, + {'petgraph-0.6.2.tar.gz': 'e6d5014253a1331579ce62aa67443b4a658c5e7dd03d4bc6d302b94474888143'}, + {'ppv-lite86-0.2.16.tar.gz': 'eb9f9e6e233e5c4a35559a617bf40a4ec447db2e84c20b55a6f83167b7e57872'}, + {'priority-queue-1.2.0.tar.gz': 'cf40e51ccefb72d42720609e1d3c518de8b5800d723a09358d4a6d6245e1f8ca'}, + {'proc-macro2-1.0.39.tar.gz': 'c54b25569025b7fc9651de43004ae593a75ad88543b17178aa5e1b9c4f15f56f'}, + {'pyo3-0.17.3.tar.gz': '268be0c73583c183f2b14052337465768c07726936a260f480f0857cb95ba543'}, + {'pyo3-build-config-0.17.3.tar.gz': '28fcd1e73f06ec85bf3280c48c67e731d8290ad3d730f8be9dc07946923005c8'}, + {'pyo3-ffi-0.17.3.tar.gz': '0f6cb136e222e49115b3c51c32792886defbfb0adead26a688142b346a0b9ffc'}, + {'pyo3-macros-0.17.3.tar.gz': '94144a1266e236b1c932682136dc35a9dee8d3589728f68130c7c3861ef96b28'}, + {'pyo3-macros-backend-0.17.3.tar.gz': 'c8df9be978a2d2f0cdebabb03206ed73b11314701a5bfe71b0d753b81997777f'}, + {'quick-xml-0.22.0.tar.gz': '8533f14c8382aaad0d592c812ac3b826162128b65662331e1127b45c3d18536b'}, + {'quote-1.0.18.tar.gz': 'a1feb54ed693b93a84e14094943b84b7c4eae204c512b7ccb95ab0c66d278ad1'}, + {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'}, + {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'}, + {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'}, + {'rand_pcg-0.3.1.tar.gz': '59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e'}, + {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'}, + {'rayon-1.5.3.tar.gz': 'bd99e5772ead8baa5215278c9b15bf92087709e9c1b2d1f97cdb5a183c933a7d'}, + {'rayon-core-1.9.3.tar.gz': '258bcdb5ac6dad48491bb2992db6b7cf74878b0384908af124823d118c99683f'}, + {'redox_syscall-0.2.13.tar.gz': '62f25bc4c7e55e0b0b7a1d43fb893f4fa1361d0abe38b9ce4f323c2adfe6ef42'}, + {'ryu-1.0.10.tar.gz': 'f3f6f92acf49d1b98f7a81226834412ada05458b7364277387724a237f062695'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'serde-1.0.145.tar.gz': '728eb6351430bccb993660dfffc5a72f91ccc1295abaa8ce19b27ebe4f75568b'}, + {'serde_derive-1.0.145.tar.gz': '81fa1584d3d1bcacd84c277a0dfe21f5b0f6accf4a23d04d4c6d61f1af522b4c'}, + {'serde_json-1.0.89.tar.gz': '020ff22c755c2ed3f8cf162dbb41a7268d934702f3ed3631656ea597e08fc3db'}, + {'smallvec-1.8.0.tar.gz': 'f2dd574626839106c320a323308629dcb1acfc96e32a8cba364ddc61ac23ee83'}, + {'syn-1.0.96.tar.gz': '0748dd251e24453cb8717f0354206b91557e4ec8703673a4b30208f2abaf1ebf'}, + {'target-lexicon-0.12.4.tar.gz': 'c02424087780c9b71cc96799eaeddff35af2bc513278cda5c99fc1f5d026d3c1'}, + {'unicode-ident-1.0.0.tar.gz': 'd22af068fba1eb5edcb4aea19d382b2a3deb4c8f9d475c589b6ada9e0fd493ee'}, + {'unindent-0.1.9.tar.gz': '52fee519a3e570f7df377a06a1a7775cdbfb7aa460be7e08de2b1f0e69973a44'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 2aff166c8715067650ff83415a1ecc256c47e7fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 9 Sep 2024 13:20:19 +0200 Subject: [PATCH 439/553] replace grpio with tensorboard in TensorFlow v2.15.1 --- .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 0f3a94f2cc4..ebca59072d6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -47,7 +47,7 @@ dependencies = [ ('libpng', '1.6.39'), ('snappy', '1.1.10'), ('zlib', '1.2.13'), - ('grpcio', '1.57.0'), + ('tensorboard', '2.15.1'), ] # Dependencies created and updated using findPythonDeps, see: From 0551a2fab2c7337ba8945e676dfc50de217fa3e1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Sep 2024 15:32:58 +0200 Subject: [PATCH 440/553] adding easyconfigs: PyBullet-3.2.6-gfbf-2023a.eb --- .../p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb new file mode 100644 index 00000000000..71c469fc41f --- /dev/null +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'PyBullet' +version = '3.2.6' + +homepage = 'https://github.com/bulletphysics/bullet3' +description = """Bullet Physics SDK: real-time collision detection and +multi-physics simulation for VR, games, visual effects, robotics, +machine learning etc.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('pybullet', version, { + 'checksums': ['da27525433c88698dc9fd8bc20fa4ae4d07738b4656633659ebd82c2d2884e08'], + }), +] + +moduleclass = 'vis' From 8b1c946254c044cc07411fa3d446c73d8f6ab9af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Sep 2024 18:00:53 +0200 Subject: [PATCH 441/553] adding easyconfigs: LDC-1.39.0-GCCcore-13.2.0.eb --- .../l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f0d3a361152 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.39.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['839bac36f6073318e36f0b163767e03bdbd3f57d99256b97494ac439b59a4562'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '16.0.6'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' From ae8d2a0168b8dc33d0b624a177ca3724ae3846d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 10 Sep 2024 10:28:17 +0200 Subject: [PATCH 442/553] adding easyconfigs: NECAT-0.0.1-foss-2023a.eb --- .../n/NECAT/NECAT-0.0.1-foss-2023a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb new file mode 100644 index 00000000000..33e3bfdd46b --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = """NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%(version)s_update20200803.tar.gz'] +checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] + +builddependencies = [('binutils', '2.40')] + +start_dir = 'src' + +files_to_copy = [ + (['../Linux-amd64/bin/*'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.pl'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' From 23d696d4e92520cfecf6a94b636998444335d659 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Sep 2024 11:01:50 +0200 Subject: [PATCH 443/553] PyBullet: drop download_dep_fail, default in PythonBundle easyblock --- easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb index 71c469fc41f..47fce7ec459 100644 --- a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -16,7 +16,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 1e44aa30fde9755638affe8c18e954e659ffb40b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 10 Sep 2024 11:11:02 +0200 Subject: [PATCH 444/553] add missing dependency --- easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb index 33e3bfdd46b..dbc35f62054 100644 --- a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb @@ -14,6 +14,8 @@ checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] builddependencies = [('binutils', '2.40')] +dependencies = [('Perl', '5.36.1')] + start_dir = 'src' files_to_copy = [ From 184d7ce926bcc53b114596100ac9f6123a0efe1e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Tue, 10 Sep 2024 11:39:17 +0200 Subject: [PATCH 445/553] Added mpifileutils (plus missing deps) and maeparser to the gompi-2024a toolchain --- .../d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb | 39 ++++++++++++++++ .../l/libcircle/libcircle-0.3-gompi-2024a.eb | 38 ++++++++++++++++ .../l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb | 36 +++++++++++++++ .../maeparser/maeparser-1.3.1-gompi-2024a.eb | 26 +++++++++++ .../mpifileutils-0.11.1-gompi-2024a.eb | 45 +++++++++++++++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb new file mode 100644 index 00000000000..5143b629849 --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.5' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c3d672fcf1be81e9afb65ef3f860a7dfe0f1bd79360ac63848acfe4d44439c9'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('lwgrp', '1.0.6'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb new file mode 100644 index 00000000000..1ea2630b327 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb new file mode 100644 index 00000000000..c36ee58b273 --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.6' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['108e622441028b7f88223244c9117d5de18a91fd7c246bfa48802b5c585557d0'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..a757e81653a --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.1' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [('Boost', '1.85.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb new file mode 100644 index 00000000000..f486ed4effd --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('attr', '2.5.2'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.6'), + ('dtcmp', '1.1.5'), + ('libarchive', '3.7.4'), + ('libcircle', '0.3'), +] + +_binaries = [ + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind', + 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries] + +moduleclass = 'tools' From 1fd7655ba65d0366ffc55eb88bf2f51e15941791 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 10 Sep 2024 13:51:37 +0200 Subject: [PATCH 446/553] adding easyconfigs: fonttools-4.53.1-GCCcore-11.3.0.eb, fonttools-4.53.1-GCCcore-12.2.0.eb, fonttools-4.53.1-GCCcore-12.3.0.eb, fonttools-4.53.1-GCCcore-13.2.0.eb, fonttools-4.53.1-GCCcore-13.3.0.eb --- .../fonttools-4.53.1-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ .../fonttools-4.53.1-GCCcore-12.2.0.eb | 26 +++++++++++++++++++ .../fonttools-4.53.1-GCCcore-12.3.0.eb | 26 +++++++++++++++++++ .../fonttools-4.53.1-GCCcore-13.2.0.eb | 26 +++++++++++++++++++ .../fonttools-4.53.1-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 5 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5720e7567a0 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.38'),] +dependencies = [('Python', '3.10.4'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..098066f3c22 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.39'),] +dependencies = [('Python', '3.10.8'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e4089a48e5f --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40'),] +dependencies = [('Python', '3.11.3'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0cfc4e2da74 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40'),] +dependencies = [('Python', '3.11.5'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fb3904198ee --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.42'),] +dependencies = [('Python', '3.12.3'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' From 4de11d81b966fc671187ef06ccee240620a07040 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Sep 2024 14:15:26 +0200 Subject: [PATCH 447/553] adding easyconfigs: slepc4py-3.20.2-foss-2023a.eb --- .../s/slepc4py/slepc4py-3.20.2-foss-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb new file mode 100644 index 00000000000..c161116802d --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.20.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['89ebd1964edd0eb63d4dbfa977d6f35408f4e19a3da290696fd1197901544bd8'] + +dependencies = [ + ('Python', '3.11.3'), + ('SLEPc', '3.20.1'), + ('petsc4py', '3.20.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' From e1ad5234d77914706b73e29d59529f8ee06d6c8b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 10 Sep 2024 14:24:15 +0200 Subject: [PATCH 448/553] Fix style --- .../f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb | 7 ++++--- .../f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb | 7 ++++--- .../f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb | 7 ++++--- .../f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb | 7 ++++--- .../f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb | 7 ++++--- 5 files changed, 20 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb index 5720e7567a0..8453a35a695 100644 --- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb @@ -6,7 +6,8 @@ version = '4.53.1' homepage = 'https://python-markdown.github.io/' description = """ fontTools is a library for manipulating fonts, written in Python. -The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} @@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] -builddependencies = [('binutils', '2.38'),] -dependencies = [('Python', '3.10.4'),] +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb index 098066f3c22..cfaada6dee8 100644 --- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb @@ -6,7 +6,8 @@ version = '4.53.1' homepage = 'https://python-markdown.github.io/' description = """ fontTools is a library for manipulating fonts, written in Python. -The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} @@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] -builddependencies = [('binutils', '2.39'),] -dependencies = [('Python', '3.10.8'),] +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb index e4089a48e5f..bf71a8f341f 100644 --- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb @@ -6,7 +6,8 @@ version = '4.53.1' homepage = 'https://python-markdown.github.io/' description = """ fontTools is a library for manipulating fonts, written in Python. -The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} @@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] -builddependencies = [('binutils', '2.40'),] -dependencies = [('Python', '3.11.3'),] +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb index 0cfc4e2da74..0e8a62e088b 100644 --- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb @@ -6,7 +6,8 @@ version = '4.53.1' homepage = 'https://python-markdown.github.io/' description = """ fontTools is a library for manipulating fonts, written in Python. -The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} @@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] -builddependencies = [('binutils', '2.40'),] -dependencies = [('Python', '3.11.5'),] +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.5')] download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb index fb3904198ee..ed395cfd0ee 100644 --- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb @@ -6,7 +6,8 @@ version = '4.53.1' homepage = 'https://python-markdown.github.io/' description = """ fontTools is a library for manipulating fonts, written in Python. -The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" toolchain = {'name': 'GCCcore', 'version': '13.3.0'} @@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] -builddependencies = [('binutils', '2.42'),] -dependencies = [('Python', '3.12.3'),] +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] download_dep_fail = True sanity_pip_check = True From 6fc9e142fc467a4fe0753eb6aef4506b20c87ea1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 10 Sep 2024 15:27:43 +0200 Subject: [PATCH 449/553] adding easyconfigs: Sagemath-10.4-foss-2023b.eb --- .../s/Sagemath/Sagemath-10.4-foss-2023b.eb | 158 ++++++++++++++++++ 1 file changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb new file mode 100644 index 00000000000..63b4aef04c6 --- /dev/null +++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb @@ -0,0 +1,158 @@ +easyblock = 'PythonBundle' + +name = 'Sagemath' +version = '10.4' + +homepage = 'https://doc.sagemath.org/html/en/index.html' +description = """Sage is open source mathematical software released under the GNU General Public Licence GPLv2+, + and includes packages that have compatible software licenses. + People all around the globe have contributed to the development of Sage. Full documentation is available online.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), + ('Python-bundle-PyPI', '2023.10'), + ('Boost', '1.83.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('ECL', '24.5.10'), + ('FFLAS-FFPACK', '2.5.0'), + ('eclib', '20231212'), + ('GSL', '2.7'), + ('LinBox', '1.7.0'), + ('Singular', '4.4.0'), + ('libpng', '1.6.40'), + ('libgd', '2.3.3'), + ('m4ri', '20200125'), + ('cysignals', '1.11.4'), + ('gmpy2', '2.1.5'), + ('GMP-ECM', '7.0.5'), + ('MPFI', '1.5.4'), + ('cliquer', '1.21'), + ('nauty', '2.8.8'), + ('SYMMETRICA', '2.0'), + ('lcalc', '2.0.5'), + ('gap', '4.13.0'), + ('giac', '1.9.0-99'), + ('m4rie', '20200125'), + ('libhomfly', '1.02r6'), + ('libbraiding', '1.2'), + ('planarity', '3.0.2.0'), + ('rankwidth', '0.9'), + ('BRiAl', '1.2.12'), + ('bliss', '0.77'), + ('coxeter', '20180226'), + ('mcqd', '1.0.0'), + ('SharedMeatAxe', '1.0.1'), + ('sirocco', '2.1.0'), + ('tdlib', '0.9.3'), + ('pkgconfig', '1.5.5', '-python'), + ('matplotlib', '3.8.2'), + ('networkx', '3.2.1'), + ('sympy', '1.12'), + ('IPython', '8.17.2'), + ('Pillow', '10.2.0'), + ('fpylll', '0.6.1'), + ('primecountpy', '0.1.0'), + ('lrcalc', '2.1'), + ('PyZMQ', '25.1.2'), + ('tornado', '6.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cypari2', '2.2.0', { + 'checksums': ['817606bf661b71d33e1d012421907a4f8fb09dd81b7d3e3ae179b3978020bbf1'], + }), + ('memory_allocator', '0.1.4', { + 'checksums': ['d609216b03031967e2b45a804b12ff9029578f4ec019fde42cf6aed6ca09efe4'], + }), + ('sage_setup', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4797ceae2f5f636a756f4121011246445611f7a56bced2df431328fe013c52c7'], + }), + ('conway_polynomials', '0.10', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a354b4ac0a9985da75e2ac6ec6d7de2902396eff48913eeed86a962486171c28'], + }), + ('comm', '0.2.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3'], + }), + ('debugpy', '1.8.5', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55919dce65b471eff25901acf82d328bbd5b833526b6c1364bd5133754777a44'], + }), + ('nest_asyncio', '1.6.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c'], + }), + ('ipykernel', '6.29.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54'], + }), + ('widgetsnbextension', '4.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71'], + }), + ('ipywidgets', '8.1.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245'], + }), + ('jupyter_core', '5.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409'], + }), + ('jupyter_client', '8.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f'], + }), + ('lrcalc', '2.1', { + 'checksums': ['e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9'], + }), + ('%(namelower)s_standard', version, { + 'modulename': 'sage', + 'checksums': ['f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62'], + }), + ('%(namelower)s_bliss', version, { + 'modulename': False, + 'checksums': ['70cccef849908436c2f9f1aabb3992a21c90d3ce99d1a965743f0fdec3735d32'], + }), + ('%(namelower)s_coxeter3', version, { + 'modulename': False, + 'checksums': ['c4f20204b91a696caeb7ad7cf33d2b0398d26d287085b2cb9434e8b067716fca'], + }), + ('%(namelower)s_mcqd', version, { + 'modulename': False, + 'checksums': ['6a140d8b3866ea27aa5966f3aab86a882785862fb00ae37087beb09105b94175'], + }), + ('%(namelower)s_meataxe', version, { + 'modulename': False, + 'checksums': ['5b625333c3168fc2ab55d32ad7e8c41912858bde8010b5aadc70c6450fa967e8'], + }), + ('%(namelower)s_sirocco', version, { + 'modulename': False, + 'checksums': ['499304b3331751d7b0f62de8379afb073d55f144c5f73775da0c5b92160e3a7c'], + }), + ('%(namelower)s_tdlib', version, { + 'modulename': False, + 'checksums': ['018497a1e220d3320a37d1acb3eee59ec820d167c7916e95f0508709a2e31703'], + }), +] + +sanity_check_commands = [ + "sage --help", + "python -c 'from sage.all import *'", +] + +moduleclass = 'math' From 9cc9c7028df5beaafc27830c4c8cb28150591b5a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 10 Sep 2024 16:37:29 +0200 Subject: [PATCH 450/553] python no user site --- .../easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb index ace55d37c66..5b4aedbdadb 100644 --- a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -53,7 +53,7 @@ modextrapaths = { sanity_check_commands = [ 'fch2inp | grep Example', 'geom_opt | grep Example', - "python -c 'from mokit.lib.gaussian import load_mol_from_fch'", + "python -s -c 'from mokit.lib.gaussian import load_mol_from_fch'", ] sanity_check_paths = { From 0a011dc82b76a3407c2328fa3d6125773eb790e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 10 Sep 2024 19:10:59 +0200 Subject: [PATCH 451/553] fix dependency version --- easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb index 63b4aef04c6..dcc9d919c13 100644 --- a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb +++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb @@ -21,7 +21,7 @@ dependencies = [ ('SciPy-bundle', '2023.11'), ('ECL', '24.5.10'), ('FFLAS-FFPACK', '2.5.0'), - ('eclib', '20231212'), + ('eclib', '20240408'), ('GSL', '2.7'), ('LinBox', '1.7.0'), ('Singular', '4.4.0'), From 1736a123b1685836452587a5c51793257570bb2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Sep 2024 19:56:19 +0200 Subject: [PATCH 452/553] remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all --- easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb | 1 - easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb | 1 - 7 files changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f9..9e505b4df5e 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb index 301194a32a4..0661abf0609 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb index 7522f1025e3..57bba400bde 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb index cc914cae6cd..df29a7bda20 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb index 22917f651e9..42e15bb4356 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.4'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb index 249b1170411..6481ba231cd 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.1.0'), - ('Highway', '1.0.7'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb index d374a07304a..3afc7fffd75 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.1.0'), - ('Highway', '1.2.0'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency From 954060586f3caba6ddd538afd17cf1f95337cec6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 08:57:26 +0200 Subject: [PATCH 453/553] adding easyconfigs: NanoStat-1.6.0-foss-2023a.eb, nanoget-1.19.3-foss-2023a.eb, nanomath-1.4.0-foss-2023a.eb --- .../n/NanoStat/NanoStat-1.6.0-foss-2023a.eb | 32 ++++++++++++++++++ .../n/nanoget/nanoget-1.19.3-foss-2023a.eb | 30 +++++++++++++++++ .../n/nanomath/nanomath-1.4.0-foss-2023a.eb | 33 +++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb new file mode 100644 index 00000000000..8f0fa5a053c --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'NanoStat' +version = '1.6.0' + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanoget', '1.19.3'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb new file mode 100644 index 00000000000..2aeb2ceaf26 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.19.3' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb new file mode 100644 index 00000000000..2a2f56955cc --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.4.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math functions for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['ed7a38fbb156d9a68a95c2570fe3c2035321d0a3e234580496750afca4927ced'], + }), +] + +moduleclass = 'math' From 48ab4ab6abc8cbc49010f56444b2f1ebadea22a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:06:23 +0200 Subject: [PATCH 454/553] adding easyconfigs: NanoFilt-2.8.0-foss-2023a.eb --- .../n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb new file mode 100644 index 00000000000..fed069c1e75 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From c1001dec254d845d3735a206895b23ed64643c40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:07:19 +0200 Subject: [PATCH 455/553] adding easyconfigs: NanoLyse-1.2.1-foss-2023a.eb --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb new file mode 100644 index 00000000000..1b21ec42201 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Update: Petr Král (INUITS) +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('minimap2', '2.26'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + (name, version, { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From b26e46e3bad5adae1e4897db20de9f9b1c07f53e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Sep 2024 09:38:41 +0200 Subject: [PATCH 456/553] add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb | 5 ++++- .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 90c7f3f7665..972a8488f6a 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -867,7 +867,10 @@ exts_list = [ 'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'], }), ('bold', '1.3.0', { - 'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'], + 'checksums': [ + ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f', + '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'), + ], }), ('rredlist', '0.7.1', { 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb index 3bd3447df1d..0ff705e9788 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -870,7 +870,10 @@ exts_list = [ 'checksums': ['405c77f191f30ffdbf8c05542ff5dff61059e9c731d2dc5ff0bfccb616314147'], }), ('bold', '1.3.0', { - 'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'], + 'checksums': [ + ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f', + '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'), + ], }), ('rredlist', '0.7.1', { 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], From f0f1e6b727136bd358d2fe0f17a940d777f67ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:51:04 +0200 Subject: [PATCH 457/553] adding easyconfigs: nanoQC-0.9.4-foss-2023a.eb --- .../n/nanoQC/nanoQC-0.9.4-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb new file mode 100644 index 00000000000..d0efa23525d --- /dev/null +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'nanoQC' +version = '0.9.4' + +homepage = 'https://github.com/wdecoster/nanoQC' +description = """Quality control tools for long read sequencing + data aiming to replicate some of the plots made by fastQC.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'nanoQC'} + +sanity_check_commands = ["nanoQC --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From afd298bbfc666f3a707991ca8d2d0b4aa6a536c7 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 11 Sep 2024 12:33:34 +0200 Subject: [PATCH 458/553] Added ccache, PROJ, protobuf(-python), pytest-flakefinder, RDFlib, RapidJSON and Seaborn. --- .../c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb | 49 +++++++++++++++++++ .../p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb | 49 +++++++++++++++++++ .../protobuf-python-5.28.0-GCCcore-13.3.0.eb | 35 +++++++++++++ .../protobuf/protobuf-28.0-GCCcore-13.3.0.eb | 35 +++++++++++++ ...pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb | 24 +++++++++ .../r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb | 35 +++++++++++++ ...RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb | 31 ++++++++++++ .../s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb | 24 +++++++++ 8 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a6b4ee2256 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.10.2' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['108100960bb7e64573ea925af2ee7611701241abb36ce0aae3354528403a7d87'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('zstd', '1.5.6'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1307155f8f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.4.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ffe20170ee2b952207adf8a195e2141eab12cda181e49fdeb54425d98c7171d7'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +dependencies = [ + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), + ('nlohmann_json', '3.11.3'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed4aac1448e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '5.28.0' + +homepage = 'https://github.com/google/protobuf/' +description = "Python Protocol Buffers runtime library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['dde74af0fa774fa98892209992295adbfb91da3fa98c8f67a88afe8f5a349add'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('protobuf', version[2:]), # Major version is only used for the Python bindings +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'google.protobuf'} + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b5f959fc06b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '28.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'protocolbuffers' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['13e7749c30bc24af6ee93e092422f9dc08491c7097efa69461f88eb5f61805ce'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Abseil', '20240722.0'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7a512df4e25 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = "Runs tests multiple times to expose flakiness." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4be8dccf690 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '7.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b296d76e7b7 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240815' +local_commit = '7c73dd7' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['91138ebc9c980e554e6bcf9d13537f9eebf42710e0b956fdca46181ad645f94d'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb new file mode 100644 index 00000000000..de14ff81ce9 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.12.3'), + ('matplotlib', '3.9.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 6772363f449e4f05ac75e63b35c21bbc45a3b9b8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 11 Sep 2024 15:36:16 +0200 Subject: [PATCH 459/553] unbundle tensorboard from TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 62 +------------------ 1 file changed, 1 insertion(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 1d1c871f3d5..7b2f4888b23 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -51,7 +51,7 @@ dependencies = [ ('libpng', '1.6.39'), ('snappy', '1.1.10'), ('zlib', '1.2.13'), - ('grpcio', '1.57.0'), + ('tensorboard', '2.15.1'), ] # Dependencies created and updated using findPythonDeps, see: @@ -71,48 +71,6 @@ exts_list = [ 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], }), - ('Werkzeug', '3.0.2', { - 'source_tmpl': SOURCELOWER_TAR_GZ, - 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], - }), - ('tensorboard-data-server', '0.7.2', { - 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', - 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], - }), - ('Markdown', '3.6', { - 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('requests-oauthlib', '2.0.0', { - 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.4.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], - }), - ('cachetools', '5.3.3', { - 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], - }), - ('google-auth', '2.29.0', { - 'modulename': 'google.auth', - 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], - }), - ('google-auth-oauthlib', '1.2.0', { - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('tensorboard', '2.15.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], - }), ('keras', '2.15.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], @@ -131,15 +89,6 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - # Optional profile plugin + dependency - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard-plugin-profile', '2.15.1', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], - }), (name, version, { 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', @@ -226,13 +175,4 @@ exts_list = [ }), ] -# Taken from tensorboard-2.15.1-gfbf-2023a.eb: -# Relax restriction on protobuf dependency as issue was fixed -# in https://github.com/protocolbuffers/upb/pull/1514 -# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 -postinstallcmds = [ - 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + - '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', -] - moduleclass = 'lib' From 39358586cb3fc549b1fed1f670edeed6c87397df Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 11 Sep 2024 16:46:43 +0200 Subject: [PATCH 460/553] Disable hyperthreading option --- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb index 7ab63c49433..ab96be49230 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb @@ -39,6 +39,8 @@ local_tweak_cfg_cmd = ' '.join([ '-e "s/ -lblas/ $LIBBLAS/g"', # downgrade Fortran compiler error to warning "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + # Disable hyperthreading option + "-e 's/--use-hwthread-cpus//'", "$HOMETEL/configs/systel.easybuild.cfg", ]) From 30c7c9c502fb943271fe1100fa21b4ad9794969e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Sep 2024 18:15:42 +0200 Subject: [PATCH 461/553] add missing Perl dependency for DETONATE v1.11 --- easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index 63246fc43ac..24a8b13835c 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -33,6 +33,7 @@ builddependencies = [ ] dependencies = [ + ('Perl', '5.36.1'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('BamTools', '2.5.2'), From 04ac5d75fe57aaaa19589ade51a2a34c1042c7a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Sep 2024 21:57:48 +0200 Subject: [PATCH 462/553] {phys}[GCC/12.3.0] GATE v9.4, CLHEP v2.4.7.1, Geant4 v11.2.2, Geant4-data v11.2 --- .../c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb | 29 ++++++++++ .../easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb | 29 ++++++++++ .../g/Geant4-data/Geant4-data-11.2.eb | 54 +++++++++++++++++++ .../g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb | 48 +++++++++++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..4bf02eab9a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.7.1' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['1c8304a7772ac6b99195f1300378c6e3ddf4ad07c85d64a04505652abb8a55f9'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb new file mode 100644 index 00000000000..6fd245d2079 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '9.4' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['96c53f6ab1b25c0e540d8f9564bce0049371b378de80a7118a0ff8834c6c117c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Geant4', '11.2.2'), + ('CLHEP', '2.4.7.1'), + ('ROOT', '6.30.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb new file mode 100644 index 00000000000..a085843d7d2 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' +name = 'Geant4-data' +version = '11.2' # version should somewhat match the Geant4 version it should be used in + +homepage = 'https://geant4.web.cern.ch/' +description = """Datasets for Geant4.""" + +toolchain = SYSTEM + +# Pick up the correct sets and versions from cmake/Modules/G4DatasetDefinitions.cmake +# in the Geant source, +# see also https://github.com/Geant4/geant4/blob/v11.2.2/cmake/Modules/G4DatasetDefinitions.cmake +local_datasets = [ + ('G4NDL', '4.7.1', 'G4NDL', 'G4NEUTRONHPDATA'), # NDL + ('G4EMLOW', '8.5', 'G4EMLOW', 'G4LEDATA'), # Low energy electromagnetics + ('PhotonEvaporation', '5.7', 'G4PhotonEvaporation', 'G4LEVELGAMMADATA'), # Photon evaporation + ('RadioactiveDecay', '5.6', 'G4RadioactiveDecay', 'G4RADIOACTIVEDATA'), # Radioisotopes + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS + ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII + ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces + ('G4ABLA', '3.3', 'G4ABLA', 'G4ABLADATA'), # ABLA + ('G4INCL', '1.2', 'G4INCL', 'G4INCLDATA'), # INCL + ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE + ('G4TENDL', '1.4', 'G4TENDL', 'G4PARTICLEHPDATA'), # TENDL +] + +source_urls = ['https://cern.ch/geant4-data/datasets'] +sources = ['%s.%s.tar.gz' % (x[2], x[1]) for x in local_datasets] +checksums = [ + {'G4NDL.4.7.1.tar.gz': 'd3acae48622118d2579de24a54d533fb2416bf0da9dd288f1724df1485a46c7c'}, + {'G4EMLOW.8.5.tar.gz': '66baca49ac5d45e2ac10c125b4fb266225e511803e66981909ce9cd3e9bcef73'}, + {'G4PhotonEvaporation.5.7.tar.gz': '761e42e56ffdde3d9839f9f9d8102607c6b4c0329151ee518206f4ee9e77e7e5'}, + {'G4RadioactiveDecay.5.6.tar.gz': '3886077c9c8e5a98783e6718e1c32567899eeb2dbb33e402d4476bc2fe4f0df1'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, + {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, + {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, + {'G4ABLA.3.3.tar.gz': '1e041b3252ee9cef886d624f753e693303aa32d7e5ef3bba87b34f36d92ea2b1'}, + {'G4INCL.1.2.tar.gz': 'f880b16073ee0a92d7494f3276a6d52d4de1d3677a0d4c7c58700396ed0e1a7e'}, + {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, + {'G4TENDL.1.4.tar.gz': '4b7274020cc8b4ed569b892ef18c2e088edcdb6b66f39d25585ccee25d9721e0'}, +] + +start_dir = '..' + +modextrapaths = {x[3]: x[0] + x[1] for x in local_datasets} + +sanity_check_paths = { + 'files': [], + 'dirs': [x[0] + x[1] for x in local_datasets], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..d4cdf6c78cb --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +name = 'Geant4' +version = '11.2.2' + +homepage = 'https://geant4.web.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = [ + 'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch', +] +checksums = [ + {'geant4-11.2.2.tar.gz': '0b0cfce14e9143079c4440d27ee21f889c4c4172ac5ee7586746b940ffcf812a'}, + {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': + '822265b7cbcaacdffd28b1094786a3c94122aff63338e514d5d3810cdf9218a6'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html + ('CLHEP', '2.4.7.1'), + ('Xerces-C++', '3.2.4'), + ('Qt5', '5.15.10'), + ('Geant4-data', '11.2', '', SYSTEM), +] + +_copts = [ + "-DGEANT4_INSTALL_DATA=OFF", + "-DGEANT4_USE_SYSTEM_ZLIB=ON", + "-DGEANT4_USE_SYSTEM_EXPAT=ON", + "-DGEANT4_USE_SYSTEM_CLHEP=ON", + "-DGEANT4_USE_QT=ON", + "-DGEANT4_USE_GDML=ON", + "-DGEANT4_USE_OPENGL_X11=ON", + "-DGEANT4_USE_RAYTRACER_X11=ON", +] +configopts = ' '.join(_copts) + +moduleclass = 'phys' From c684b96d0e803f4f20f647152e64bfd380a63945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Sep 2024 12:45:48 +0200 Subject: [PATCH 463/553] adding easyconfigs: dub-1.38.1-GCCcore-13.2.0.eb --- .../d/dub/dub-1.38.1-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cfd077260fb --- /dev/null +++ b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'dub' +version = '1.38.1' + +homepage = 'https://github.com/dlang/dub' +description = "Package and build manager for D applications and libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dlang/dub/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a7c9a2f819fdea7359f298cba76e81a24ca1536d756c3b4b98c2480463c37907'] + +builddependencies = [ + ('binutils', '2.40'), + ('LDC', '1.39.0'), +] + +cmds_map = [('.*', "ldmd2 -v -run build.d")] + +files_to_copy = [(['bin/dub'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dub'], + 'dirs': [], +} + +sanity_check_commands = ["dub --help"] + +moduleclass = 'lang' From bd3714e0135d2196db6fb29d545d3618520a218f Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 12 Sep 2024 15:32:24 +0200 Subject: [PATCH 464/553] Added libGLU-9.0.3-GCCcore-13.3.0.eb --- .../l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8a01a3ac439 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] + +dependencies = [('Mesa', '24.1.3')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From ffc017a2ccdf0ced3b566437bfb0f76a423c97d1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 12 Sep 2024 15:49:50 +0200 Subject: [PATCH 465/553] disable buiding docs in fish --- easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb index bcb975f1857..0c7e084ac23 100644 --- a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb @@ -24,6 +24,8 @@ dependencies = [ ('ncurses', '6.5'), ] +configopts = '-DBUILD_DOCS=off ' + sanity_check_paths = { 'files': ['bin/fish'], 'dirs': [], From bfd5bf97147e7df26c34bbdf5edf8434d10c4ed2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 16:07:42 +0200 Subject: [PATCH 466/553] adding easyconfigs: cramino-0.14.5-GCC-12.3.0.eb --- .../c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 348 ++++++++++++++++++ 1 file changed, 348 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..2d7064097e7 --- /dev/null +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -0,0 +1,348 @@ +easyblock = 'Cargo' + +name = 'cramino' +version = '0.14.5' + +homepage = 'https://github.com/wdecoster/cramino' +description = """A tool for quick quality assessment of cram and bam files, intended for long read sequencing.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/cramino/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.14.5.tar.gz': 'd3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032'}, + {'ahash-0.8.9.tar.gz': 'd713b3834d76b85304d4d525563c1276e2e30dc97cc67bfb4585a4a29fc2c89f'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'}, + {'anstream-0.6.12.tar.gz': '96b09b5178381e0874812a9b157f7fe84982617e48f71f4e3235482775e5b540'}, + {'anstyle-1.0.6.tar.gz': 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'1.10.0'), + ('env_filter', '0.1.0'), + ('env_logger', '0.11.2'), + ('equivalent', '1.0.1'), + ('flatbuffers', '23.5.26'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.2.12'), + ('glob', '0.3.1'), + ('half', '2.3.1'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hts-sys', '2.1.1'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '2.2.3'), + ('itertools', '0.12.1'), + ('itoa', '1.0.10'), + ('js-sys', '0.3.68'), + ('lazy_static', '1.4.0'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.15'), + ('linear-map', '1.2.0'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.1'), + ('newtype_derive', '0.1.6'), + ('num', '0.4.1'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-iter', '0.1.44'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.2.3+3.2.1'), + ('openssl-sys', '0.9.100'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('proc-macro2', '1.0.78'), + ('quick-error', '1.2.3'), + ('quote', '1.0.35'), + ('rayon', '1.8.1'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.5'), + ('regex-syntax', '0.8.2'), + ('rust-htslib', '0.46.0'), + ('rustc_version', '0.1.7'), + ('rustc_version', '0.4.0'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('semver', '0.1.20'), + ('semver', '1.0.22'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('static_assertions', '1.1.0'), + ('strsim', '0.11.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.50'), + ('thiserror', '1.0.57'), + ('thiserror-impl', '1.0.57'), + ('tiny-keccak', '2.0.2'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.0'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.91'), + ('wasm-bindgen-backend', '0.2.91'), + ('wasm-bindgen-macro', '0.2.91'), + ('wasm-bindgen-macro-support', '0.2.91'), + ('wasm-bindgen-shared', '0.2.91'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.52.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' From e88c4378baf599d49732fa5019f792bf7f8b5595 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Sep 2024 16:48:24 +0200 Subject: [PATCH 467/553] adding easyconfigs: GObject-Introspection-1.80.1-GCCcore-13.3.0.eb and patches: GObject-Introspection-1.80.1_install-GLib-GIR-files.patch --- ...ect-Introspection-1.80.1-GCCcore-13.3.0.eb | 51 ++++++++++++++++++ ...ection-1.80.1_install-GLib-GIR-files.patch | 52 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4f1620c0db9 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.80.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] +checksums = [ + {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, + {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': + '2920b94cf33a41b424de2fb3a0f04b7a1076fd8f47417fa82cf4703ff1ba95fa'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libffi', '3.4.5'), + ('util-linux', '2.40'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " +configopts = "-Dcairo=enabled" + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch new file mode 100644 index 00000000000..349eecf7c0b --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -0,0 +1,52 @@ +This reverts a commit from upstream +> build: Do not install generated GLib GIR files +> +> GLib 2.79 ships its own introspection data. + +However GObject-Introspection requires (optionally) Cairo, which requires GLib +which requires GLib-Introspection for generating the introspection data. + +So there is a cyclib dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 + +Author: Alexander Grund (TU Dresden) + +diff --git a/gir/meson.build b/gir/meson.build +index 3a016831..312aa886 100644 +--- a/gir/meson.build ++++ b/gir/meson.build +@@ -241,6 +241,8 @@ glib_gir = custom_target('gir-glib', + output: 'GLib-2.0.gir', + depends: [gir_giscanner_pymod, glib_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: glib_command + [ + '--cflags-begin'] + glib_includes + extra_giscanner_cflags + [ +@@ -308,6 +310,8 @@ gobject_gir = custom_target('gir-gobject', + output: 'GObject-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gobject_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gobject_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -360,6 +364,8 @@ uninstalled_gir_files += custom_target('gir-gmodule', + output: 'GModule-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gmodule_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gmodule_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -455,6 +461,8 @@ gio_gir = custom_target('gir-gio', + output: 'Gio-2.0.gir', + depends: [gobject_gir, gir_giscanner_pymod, gio_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gio_command + [ + '--include-uninstalled=' + gobject_gir.full_path(), From 6a10ce129926783d3cae55eb68fe38da279ba451 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Sep 2024 17:04:20 +0200 Subject: [PATCH 468/553] adding easyconfigs: Ghostscript-10.03.1-GCCcore-13.3.0.eb, HarfBuzz-9.0.0-GCCcore-13.3.0.eb, ImageMagick-7.1.1-38-GCCcore-13.3.0.eb, Pango-1.54.0-GCCcore-13.3.0.eb, JasPer-4.2.4-GCCcore-13.3.0.eb and patches: HarfBuzz-9.0.0_fix-subset-test.patch, ImageMagick-7.1.1-38_fix-linking.patch --- .../Ghostscript-10.03.1-GCCcore-13.3.0.eb | 58 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb | 51 ++++++++++++++++ .../HarfBuzz-9.0.0_fix-subset-test.patch | 26 +++++++++ .../ImageMagick-7.1.1-38-GCCcore-13.3.0.eb | 50 ++++++++++++++++ .../ImageMagick-7.1.1-38_fix-linking.patch | 27 +++++++++ .../j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb | 36 ++++++++++++ .../p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb | 41 +++++++++++++ 7 files changed, 289 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..174aec3f515 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.03.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31cd01682ad23a801cc3bbc222a55f07c4ea3e068bdfb447792d54db21a2e8ad'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('LibTIFF', '4.6.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' + +postinstallcmds = [ + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +sanity_check_commands = ["gs --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..40540c3fcdc --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'HarfBuzz' +version = '9.0.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['HarfBuzz-9.0.0_fix-subset-test.patch'] +checksums = [ + {'9.0.0.tar.gz': 'b7e481b109d19aefdba31e9f5888aa0cdfbe7608fed9a43494c060ce1f8a34d2'}, + {'HarfBuzz-9.0.0_fix-subset-test.patch': '1635505c27c312dca507863f2a865eb88d42e35ff4cc241cfa0e90c0ade8b790'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), + ('fonttools', '4.53.1'), # For tests +] + +dependencies = [ + ('GLib', '2.80.4'), + ('ICU', '75.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +configopts = '--default-library=both' # static and shared library +configopts += ' -Dgobject=enabled -Dintrospection=enabled' +configopts += ' -Dglib=enabled' +configopts += ' -Dicu=enabled' +configopts += ' -Dcairo=enabled' +configopts += ' -Dfreetype=enabled' + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch new file mode 100644 index 00000000000..25a2b619fc8 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch @@ -0,0 +1,26 @@ +The test "feature_variation_instance_collect_lookups" fails when run in environments +where the decimal separator is not a dot ("."). +Fix this by using the C locale. +See https://github.com/harfbuzz/harfbuzz/pull/4857 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/subset/run-tests.py b/test/subset/run-tests.py +index 9e09d95d1d9..c0c256d8974 100755 +--- a/test/subset/run-tests.py ++++ b/test/subset/run-tests.py +@@ -135,10 +135,13 @@ def check_ots (path): + + has_ots = has_ots() + ++env = os.environ.copy() ++env['LC_ALL'] = 'C' + process = subprocess.Popen ([hb_subset, '--batch'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, +- stderr=sys.stdout) ++ stderr=sys.stdout, ++ env=env) + + fails = 0 + for path in args: diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..776471b14b2 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-38' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['ImageMagick-7.1.1-38_fix-linking.patch'] +checksums = [ + {'7.1.1-38.tar.gz': '5e449530ccec8b85ae2bfd1ad773184fb7a4737d40fd9439db8a5d4beee4403e'}, + {'ImageMagick-7.1.1-38_fix-linking.patch': '0fbe8e3b6621e3e0d1efec59949fecb45924bc6e65851b9b6399bb3eff8d55d9'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20240607'), + ('Ghostscript', '10.03.1'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.16'), + ('Pango', '1.54.0'), + ('pixman', '0.43.4'), + ('FriBidi', '1.0.15'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch new file mode 100644 index 00000000000..2c9d54a4ac0 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch @@ -0,0 +1,27 @@ +The configure script sets this to a path inside the install location which is empty during build. +However this path(s) is/are used by the compiler/linker to find libraries. `pkg-config` used during configure assumes this is the same during build as on invocation of itself and omits any path already contained in the variable. + +This combination causes build failures due to dependent libraries not being found in the link step unless there happens to be some other way the paths get pulled in. E.g. if HarfBuzz is built using (the deprecated) configure&make it has `*.la` files which contain the required link flags. If HarfBuzz is built using the new Meson build system those files are no longer present and the linker paths will be missing. + +As there doesn't seem to be a specific reason for the variable to be set to an empty directory in the Makefile just remove it. + +See https://github.com/ImageMagick/ImageMagick/pull/7613 + +Author: Alexander Grund (TU Dresden) + +--- + Makefile.in | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/Makefile.in b/Makefile.in +index 47b78566f0c..3a9761cfd5b 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -3288,7 +3288,6 @@ LIBOBJS = @LIBOBJS@ + LIBOPENJP2_CFLAGS = @LIBOPENJP2_CFLAGS@ + LIBOPENJP2_LIBS = @LIBOPENJP2_LIBS@ + LIBRARY_EXTRA_CPPFLAGS = @LIBRARY_EXTRA_CPPFLAGS@ +-LIBRARY_PATH = @LIBRARY_PATH@ + LIBS = @LIBS@ + LIBSTDCLDFLAGS = @LIBSTDCLDFLAGS@ + LIBTOOL = @LIBTOOL@ diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..14ce45ca6ad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.2.4' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['23a3d58cdeacf3abdf9fa1d81dcefee58da6ab330940790c0f27019703bfd2cd'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfbbc1eb16b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.54.0' + +homepage = 'https://pango.gnome.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8a9eed75021ee734d7fc0fdf3a65c3bba51dfefe4ae51a9b414a60c70b2d1ed8'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('HarfBuzz', '9.0.0'), + ('FriBidi', '1.0.15'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 7821c59138199c828095b6da83d37a6e41c57cc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Sep 2024 17:05:36 +0200 Subject: [PATCH 469/553] {bio}[foss/2023b] BiG-SCAPE v1.1.9, HMMER v3.4, FastTree v2.1.11 --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb | 66 ++++++++++++++++ .../FastTree-2.1.11-GCCcore-13.2.0.eb | 42 ++++++++++ .../h/HMMER/HMMER-3.4-gompi-2023b.eb | 78 +++++++++++++++++++ 3 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb new file mode 100644 index 00000000000..87ffb021f06 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.9' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'BiG-SCAPE-1.1.5_use_env_var_for_html.patch', + 'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch', +] +checksums = [ + {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Biopython', '1.84'), + ('scikit-learn', '1.4.0'), + ('networkx', '3.2.1'), + ('HMMER', '3.4'), + ('FastTree', '2.1.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'bigscape'} + +sanity_check_paths = { + 'files': ['bin/bigscape'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'bigscape --help', +] + +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', +} + +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b44229828a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.40')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb new file mode 100644 index 00000000000..bb76dc1e937 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From c6cc0232a089462e57b162169bb4e0b873c860cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 17:39:38 +0200 Subject: [PATCH 470/553] add missing dependency --- easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb index 2d7064097e7..7193a870648 100644 --- a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -336,6 +336,7 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { From 4ff7932b51a185f17e8686d6cd8e1f945c2c6ffe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:00:05 +0200 Subject: [PATCH 471/553] add missing dependencies --- easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb index 7193a870648..49c61ff64fb 100644 --- a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -337,6 +337,8 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), ] sanity_check_paths = { From 545807433e6631ba3fe3c12c85867bdf064ee83c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:41:12 +0200 Subject: [PATCH 472/553] change moduleclass --- easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb index d0efa23525d..264a822a3ca 100644 --- a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -28,4 +28,4 @@ sanity_check_commands = ["nanoQC --help"] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'bio' From 881e8f00be655c2ce5a1c8b169003e7861caa23f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:57:45 +0200 Subject: [PATCH 473/553] adding easyconfigs: phasius-0.2.0-GCC-12.3.0.eb --- .../p/phasius/phasius-0.2.0-GCC-12.3.0.eb | 391 ++++++++++++++++++ 1 file changed, 391 insertions(+) create mode 100644 easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..0999294863b --- /dev/null +++ b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb @@ -0,0 +1,391 @@ +easyblock = 'Cargo' + +name = 'phasius' +version = '0.2.0' + +homepage = 'https://github.com/wdecoster/phasius' +description = """A tool to visualize phase block structure from (many) BAM, + CRAM or VCF files together with BED annotation""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = 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('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '1.9.3'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('lazycell', '1.3.0'), + ('libc', '0.2.158'), + ('libloading', '0.8.5'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.5'), + ('minimal-lexical', '0.2.1'), + ('newtype_derive', '0.1.6'), + ('nom', '7.1.3'), + ('num-conv', '0.1.0'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.3.1+3.3.1'), + ('openssl-sys', '0.9.103'), + ('os_str_bytes', '6.6.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('plotly', '0.9.0'), + ('plotly_derive', '0.9.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.86'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rust-htslib', '0.47.0'), + ('rustc-hash', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.17'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.209'), + ('serde_derive', '1.0.209'), + ('serde_json', '1.0.127'), + ('serde_repr', '0.1.19'), + ('serde_with', '2.3.3'), + ('serde_with_macros', '2.3.3'), + ('shlex', '1.3.0'), + ('strsim', '0.10.0'), + ('strsim', '0.11.1'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.76'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.18'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('typeid', '1.0.2'), + ('unicase', '2.7.0'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.2'), + ('utf8parse', '0.2.2'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), + ('Clang', '16.0.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --version"] + +moduleclass = 'bio' From 48b166808bf877e0e65463fb3b87e670d7a6245a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:59:45 +0200 Subject: [PATCH 474/553] adding easyconfigs: NanoComp-1.24.0-foss-2023a.eb, plotly-orca-1.3.1-GCCcore-12.3.0.eb, joypy-0.2.6-foss-2023a.eb --- .../j/joypy/joypy-0.2.6-foss-2023a.eb | 28 +++++++++++++ .../n/NanoComp/NanoComp-1.24.0-foss-2023a.eb | 42 +++++++++++++++++++ .../plotly-orca-1.3.1-GCCcore-12.3.0.eb | 34 +++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb new file mode 100644 index 00000000000..db6e77ea520 --- /dev/null +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb @@ -0,0 +1,28 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'joypy' +version = '0.2.6' + +homepage = 'https://github.com/sbebo/joypy' +description = "Joyplots in Python with matplotlib & pandas" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_WHL] +checksums = ['fffe882e8281e56e08b374a3148436cb448562ba39e4d566204c7e8ee2caddab'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb new file mode 100644 index 00000000000..94de23b83da --- /dev/null +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoComp' +version = '1.24.0' + +homepage = 'https://github.com/wdecoster/NanoComp' +description = "Comparing runs of Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce02bb38c76137ee00ebcc68b6b2654a4a459993e901aebde436c4d54287b09'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoPlot', '1.43.0'), + ('plotly.py', '5.16.0'), + ('plotly-orca', '1.3.1'), + ('joypy', '0.2.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoComp'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoComp --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcf1a67d7ff --- /dev/null +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'Binary' + +name = 'plotly-orca' +version = '1.3.1' + +homepage = 'https://github.com/plotly/orca' +description = """Orca is an Electron app that generates images and reports of Plotly things like + plotly.js graphs, dash apps, dashboards from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/plotly/orca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/orca'], + 'dirs': ['lib/node_modules/orca'], +} +sanity_check_commands = ['orca --help'] + +moduleclass = 'vis' From 7cfd8073e6cf8d104983f9fb6fbd291c50d45120 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 19:01:10 +0200 Subject: [PATCH 475/553] adding easyconfigs: NanoPlot-1.43.0-foss-2023a.eb --- .../n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb new file mode 100644 index 00000000000..4e547b9963b --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.43.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('plotly.py', '5.16.0'), + ('statsmodels', '0.14.1'), + ('Arrow', '14.0.1'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 8d427bbc6975332d95184a09ac6a6102f981b723 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 19:23:26 +0200 Subject: [PATCH 476/553] add missing dependencies --- easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb index 0999294863b..bc9d066a13d 100644 --- a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb @@ -379,6 +379,8 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), ] sanity_check_paths = { From 2006e7ae337c0feab2e81ef6d7231585842fdc94 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Sep 2024 08:37:12 +0200 Subject: [PATCH 477/553] Fix test_easyconfig_locations when cache is present The test fails if the easyconfig cache file .eb-path-index is present. This is caused by checking all files instead of only easyconfigs. Fix that, directly ignore the TEMPLATE.eb and replace `assertTrue(False` --- test/easyconfigs/easyconfigs.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index dc24739ec01..a4684900718 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1001,14 +1001,13 @@ def test_easyconfig_locations(self): # ignore git/svn dirs & archived easyconfigs if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + # check whether list of .eb files is non-empty, only exception: TEMPLATE.eb + easyconfig_files = [fn for fn in filenames if fn.endswith('eb') and fn != 'TEMPLATE.eb'] if easyconfig_files: # check whether path matches required pattern if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + if not dirpath.endswith('/easybuild/easyconfigs'): + self.fail("There should be no easyconfig files in %s, found %s" % (dirpath, easyconfig_files)) def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" @@ -1029,7 +1028,7 @@ def test_easyconfig_name_clashes(self): duplicates[name] = names[name] if duplicates: - self.assertTrue(False, "EasyConfigs with case-insensitive name clash: %s" % duplicates) + self.fail("EasyConfigs with case-insensitive name clash: %s" % duplicates) @skip_if_not_pr_to_non_main_branch() def test_pr_sha256_checksums(self): From f14cfd24a3040e012e3a95f1038f368a84ca5d78 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Sep 2024 09:16:34 +0200 Subject: [PATCH 478/553] Fix typo in patch --- .../GObject-Introspection-1.80.1-GCCcore-13.3.0.eb | 2 +- .../GObject-Introspection-1.80.1_install-GLib-GIR-files.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb index 4f1620c0db9..83ab6981ae3 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -18,7 +18,7 @@ patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] checksums = [ {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': - '2920b94cf33a41b424de2fb3a0f04b7a1076fd8f47417fa82cf4703ff1ba95fa'}, + 'c1909f1b7fd30784ae789ac0b5e45e0ca3dd2456890b864efa86a2f8c2e563aa'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch index 349eecf7c0b..5c09ded1cb2 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -6,7 +6,7 @@ This reverts a commit from upstream However GObject-Introspection requires (optionally) Cairo, which requires GLib which requires GLib-Introspection for generating the introspection data. -So there is a cyclib dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 +So there is a cyclic dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 Author: Alexander Grund (TU Dresden) From eeee2314626ee9b35b9aff51a8b95ddc017bd8ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Sep 2024 09:55:09 +0200 Subject: [PATCH 479/553] {cae}[foss/2023a] OpenFOAM-Extend v4.1-20210705 --- ...OpenFOAM-Extend-4.1-20210705-foss-2023a.eb | 65 +++++++++++++++++++ ...-4.1-20210705_fix-private-PackedList.patch | 14 ++++ .../ParMGridGen-1.0-gompi-2023a.eb | 40 ++++++++++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb new file mode 100644 index 00000000000..84981fe4760 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb @@ -0,0 +1,65 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +local_commit = 'aa97a0' +version = '4.1-20210705' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + 'git_config': { + 'url': 'https://git.code.sf.net/p/foam-extend/', + 'repo_name': 'foam-extend-4.1', + 'commit': local_commit, + }, +}] +patches = [ + 'OpenFOAM-Extend-3.2-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-4.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', + 'OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch', +] +checksums = [ + # no checksum for OpenFOAM-Extend-4.1-20200408-f2c557.tar.gz since it's created from git repo, + # and hence resuluting tarball won't be exactly the same on all systems + None, + 'f7676a7a12ced7c74caea64c62826a28449fdb2beb8b5be2c4ae7528ffece16e', # OpenFOAM-Extend-3.2-ParMGridGen.patch + '14dcc12ea7191ba42a9c297fcb2f4fbc2c55bf57226029489aa116e2d060b4bf', # OpenFOAM-Extend-3.1_build-qa.patch + 'e71a77b6f39653f9a0d4b0ce6691433c742df74f23402782c69a8b736c98eb7a', # OpenFOAM-Extend-4.1_comp-mpi.patch + # OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch + 'c88b23cd2f5dcf3bd86e02d7ea5dc6719c2049cf4b20e39f1b3262381dee3c50', + # OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch + '47868f35d9a899047be8da451df46e165fc813bc809b96b1c35a0cccddb1a9e6', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('M4', '1.4.19'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('hwloc', '2.9.1'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '7.0.3'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.18'), + # Libccmio v2.6.1, zoltan v3.5 +] + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch new file mode 100644 index 00000000000..84229fdd90a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch @@ -0,0 +1,14 @@ +fix for: +error: class Foam::UList Foam::UList::UList is private within this context +see also https://sourceforge.net/p/foam-extend/tickets/68/ +--- foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H.orig 2024-09-12 21:13:26.103914000 +0200 ++++ foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H 2024-09-12 21:13:53.608924991 +0200 +@@ -147,7 +147,7 @@ + class PackedList + : + public PackedListCore, +- private List ++ public List + { + protected: + diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb new file mode 100644 index 00000000000..bee93301eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://download.sourceforge.net/foam-extend/ThirdParty'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ParMGridGen-%(version)s_malloc_include.patch', + 'ParMGridGen-%(version)s_gompiOpenFOAM-Extend.patch', +] +checksums = [ + '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz + '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch + '60cc46d156e99101b21bde9d23cf6c2db3dcdef1704f1830a7baa0320003c02a', # ParMGridGen-1.0_gompiOpenFOAM-Extend.patch +] + +buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h', 'MGridGen/IMlib/IMlib.h'], 'include'), + (['libmgrid.a', 'libMGridGen.a', 'libparmgrid.a', 'MGridGen/IMlib/libIMlib.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', + 'include/IMlib.h', 'lib/libmgrid.a', 'lib/libMGridGen.a', 'lib/libparmgrid.a', 'lib/libIMlib.a'], + 'dirs': [], +} + +moduleclass = 'math' From 2240b40e1c840f77267dde1bb707eade3ffcba3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Sep 2024 10:46:40 +0200 Subject: [PATCH 480/553] use -Python-2.7.18 as versionsuffix for OpenFOAM-Extend 4.1 --- ... => OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/o/OpenFOAM-Extend/{OpenFOAM-Extend-4.1-20210705-foss-2023a.eb => OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb} (98%) diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb similarity index 98% rename from easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb rename to easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb index 84981fe4760..b65ce71cf76 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb @@ -3,6 +3,7 @@ easyblock = 'EB_OpenFOAM' name = 'OpenFOAM-Extend' local_commit = 'aa97a0' version = '4.1-20210705' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. From 0cc7bb5cf7ecabd958529b72572f2a82733c0a1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Sep 2024 11:22:38 +0200 Subject: [PATCH 481/553] adding easyconfigs: worker-1.6.13-iimpi-2023a.eb --- .../w/worker/worker-1.6.13-iimpi-2023a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb new file mode 100644 index 00000000000..f3b254591f5 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2023a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 85e6c2bbc2fd515a1d4dab607b8d43d0a1ed668f Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 13 Sep 2024 11:37:52 +0200 Subject: [PATCH 482/553] Added TurboVNC-3.1.2-GCCcore-13.3.0.eb, based on TurboVNC-3.0.1-GCCcore-11.3.0.eb. This one leaves out the patch, as the CMakeLists.txt being patched switched to using pkg-config --- .../TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5b532a99e9f --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.1.2' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + '98629cd2b676df5d30df51c69edd97cf99b395c3080cc55e2f997ac33a7d40de', # 3.0.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('libglvnd', '1.7.0'), + ('OpenSSL', '3', '', SYSTEM), +] + +osdependencies = [('pam-devel', 'libpam0g-dev')] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ['rm -rf %(installdir)s/etc/turbovncserver-security.conf'] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' From a0e95b89941f4c1996e07702fed8690234056ab2 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 13 Sep 2024 13:19:36 +0200 Subject: [PATCH 483/553] Added VirtualGL-3.1.1-GCC-13.3.0.eb and its dep pocl-6.0-GCC-13.3.0.eb --- .../easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb | 48 +++++++++++++++++++ .../v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb | 47 ++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..4a188f7473b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb @@ -0,0 +1,48 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '6.0' + +homepage = 'http://portablecl.org' +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + 'de9710223fc1855f833dbbf42ea2681e06aa8ec0464f0201104dc80a74dfd1f2', # v6.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Clang', '18.1.8'), + ('hwloc', '2.10.0'), + ('libtool', '2.4.7'), + ('libxml2', '2.12.7'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..72cd90736a4 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 +# updated by Paul Melis 2022-10-07, 2023-08-18 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.1.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['79c0d76993814d9ed9fdc29908de1cc6da08f41931bc8363084fdfae03f53ce8'] +patches = [] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('pocl', '6.0'), + ('X11', '20240607'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From e898862e93d2b4414edee34dfa57bb64c4a580c1 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 13 Sep 2024 13:35:49 +0200 Subject: [PATCH 484/553] Added ATK and Gdk-Pixbuf after the GObject-Introspection fix. --- .../a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb | 39 ++++++++++++++++ .../Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb | 46 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..506079ce98c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ac4237f4c0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.11' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49dcb402388708647e8c321d56b6fb30f21e51e515d0c5a942268d23052a2f00'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('X11', '20240607'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' From ccd2d8d921cae09496001e344852e721f940ea3c Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Sep 2024 15:14:24 +0000 Subject: [PATCH 485/553] adding easyconfigs: scikit-build-core-0.10.6-GCCcore-13.3.0.eb --- ...scikit-build-core-0.10.6-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..57e6f53d4c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.10.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('CMake', '3.29.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikit_build_core', version, { + 'checksums': ['5397db8f09ee050d145406c11deed06538bb0b261df95f8d2d6aaf8699f0126d'], + }), +] + +moduleclass = 'lib' From 9dfa69f4bead0ff5beedf9e3c545e19449667412 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:38:08 +0200 Subject: [PATCH 486/553] adding easyconfigs: DFTD4-3.7.0-foss-2023a.eb, mctc-lib-0.3.1-GCC-12.3.0.eb, json-fortran-9.0.2-GCC-12.3.0.eb, mstore-0.3.0-GCC-12.3.0.eb, TOML-Fortran-0.4.2-GCC-12.3.0.eb --- .../d/DFTD4/DFTD4-3.7.0-foss-2023a.eb | 49 +++++++++++++++++++ .../json-fortran-9.0.2-GCC-12.3.0.eb | 32 ++++++++++++ .../m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb | 41 ++++++++++++++++ .../m/mstore/mstore-0.3.0-GCC-12.3.0.eb | 37 ++++++++++++++ .../TOML-Fortran-0.4.2-GCC-12.3.0.eb | 24 +++++++++ 5 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb new file mode 100644 index 00000000000..36455d10ffe --- /dev/null +++ b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb @@ -0,0 +1,49 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'DFTD4' +version = '3.7.0' + +homepage = 'https://dftd4.readthedocs.io' +description = """ +The dftd4 project provides an implementation of the generally applicable, charge dependent +London-dispersion correction, termed DFT-D4. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), # New EC + ('mstore', '0.3.0'), # New EC + ('TOML-Fortran', '0.4.2'), # New EC +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'], + 'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..03dceec3b87 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '9.0.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a599a77e406e59cdb7672d780e69156b6ce57cb8ce515d21d1744c4065a85976'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..64ab2ab3bb9 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('json-fortran', '9.0.2'), # New EC +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..a609b4e373b --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..baa1d460ed6 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e66d0e355a8a2e65fd5fc7cd4f00078dfbdbf1b3cc47b60f028c19467df4c337'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 4275401631dfd515bbebd1605b430648d310e199 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:44:49 +0200 Subject: [PATCH 487/553] remove comments --- easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb | 6 +++--- .../easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb index 36455d10ffe..12d97f5a8a4 100644 --- a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb @@ -26,9 +26,9 @@ builddependencies = [ ] dependencies = [ - ('mctc-lib', '0.3.1'), # New EC - ('mstore', '0.3.0'), # New EC - ('TOML-Fortran', '0.4.2'), # New EC + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('TOML-Fortran', '0.4.2'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb index 64ab2ab3bb9..e8ec2b8435d 100644 --- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('json-fortran', '9.0.2'), # New EC + ('json-fortran', '9.0.2'), ] configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] From 166d673f9b3e612fe7c45c1e33a087721e1b4c76 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:53:54 +0200 Subject: [PATCH 488/553] adding easyconfigs: DFTB+-24.1-foss-2023a.eb, libmbd-0.12.6-foss-2023a.eb, ELSI-2.11.0-foss-2023a-PEXSI.eb, NTPoly-3.1.0-foss-2023a.eb and patches: ELSI-2.11.0_bison_3.8_compat.patch --- .../d/DFTB+/DFTB+-24.1-foss-2023a.eb | 93 +++++++++++++++++++ .../e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb | 43 +++++++++ .../e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch | 14 +++ .../l/libmbd/libmbd-0.12.6-foss-2023a.eb | 59 ++++++++++++ .../n/NTPoly/NTPoly-3.1.0-foss-2023a.eb | 28 ++++++ 5 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb new file mode 100644 index 00000000000..c1e713bfa0d --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -0,0 +1,93 @@ +easyblock = 'CMakeMake' + +name = 'DFTB+' +version = '24.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +_external_extract = 'mkdir -p %s && tar -C %s' % (_external_dir, _external_dir) +_external_extract += ' --strip-components=1 -xzf %%s' + +source_urls = ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'] +sources = [ + 'dftbplus-%(version)s.tar.xz', + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'fbe3d62127d86bd8e49ad25a1e5793e6a095e8e7.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('slakos', 'slakos'), + }, + { + # GBSA (gbsa) data for testing + 'source_urls': ['https://github.com/grimme-lab/gbsa-parameters/archive'], + 'download_filename': '6836c4d997e4135e418cfbe273c96b1a3adb13e2.tar.gz', + 'filename': 'gbsa-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('gbsa', 'gbsa'), + }, +] +checksums = [ + {'dftbplus-24.1.tar.xz': '3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'}, + {'slakos-data-24.1.tar.gz': '78a0494c2ff9216d6a9199ba07d632b18b809e0198f43905c044b5748bde488d'}, + {'gbsa-data-24.1.tar.gz': 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('DFTD4', '3.7.0'), + ('ELSI', '2.11.0', '-PEXSI'), + ('libmbd', '0.12.6'), +] + +# Prefer dependencies from EB than bundled sources +configopts = '-DHYBRID_CONFIG_METHODS="Find;Submodule;Fetch" ' +configopts += '-DWITH_MPI=1 -DWITH_OMP=1 -DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DBUILD_SHARED_LIBS=1 -DWITH_API=1 -DWITH_PYTHON=0 ' # Python bindings installed as extension +configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' + +runtest = 'test' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'runtest': False, +} +exts_list = [ + ('dptools', version, { + 'source_tmpl': 'dftbplus-%(version)s.tar.xz', + 'source_urls': ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'], + 'start_dir': 'tools/dptools', + 'checksums': ['3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'], + }), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']] + + ['lib/libdftbplus.%s' % SHLIB_EXT, 'lib/libmpifx.%s' % SHLIB_EXT], + 'dirs': ['include/dftbplus', 'lib/cmake', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import dptools'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb new file mode 100644 index 00000000000..1ac711b9cf5 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -0,0 +1,43 @@ +name = 'ELSI' +version = '2.11.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://gitlab.com/elsi_project/elsi_interface/-/archive/v2.11.0/'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'ELSI-2.11.0_bison_3.8_compat.patch', +] +checksums = [ + {'elsi_interface-v2.11.0.tar.gz': '2e6929827ed9c99a32381ed9da40482e862c28608d59d4f27db7dcbcaed1520d'}, + {'ELSI-2.11.0_bison_3.8_compat.patch': 'a1284f5c0f442129610aa0fb463cc2b54450e3511a2fd6c871fadc21a16e9504'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('ELPA', '2023.05.001'), + ('NTPoly', '3.1.0'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch new file mode 100644 index 00000000000..255ed4a5575 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch @@ -0,0 +1,14 @@ +Make it compatible with Bison 3.7 +Author: Åke Sandgren, 20211020 +Update: Cintia Willemyns (Vrije Universiteit Brussel) +--- elsi_interface-v2.11.0.orig/external/SCOTCH/CMakeLists.txt 2024-09-10 19:01:11.447551000 +0200 ++++ elsi_interface-v2.11.0/external/SCOTCH/CMakeLists.txt 2024-09-10 19:08:44.913993743 +0200 +@@ -56,7 +56,7 @@ + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c + # Versions of bison > 2.X insert a '#include tmp2.h' in tmp2.c. A simple 'mv' will not work. + # The file needs to remain in the directory with the old name. Hence the 'cp' +- COMMAND cp ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h ++ COMMAND ln -s ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h + COMMAND flex -Pscotchyy -o${PROJECT_BINARY_DIR}/generated/tmp1.c ${SCOTCH_DIR}/parser_ll.l + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp1.c ${PROJECT_BINARY_DIR}/generated/parser_ll.c + DEPENDS ${SCOTCH_DIR}/parser_yy.y ${SCOTCH_DIR}/parser_ll.l ${SCOTCH_DIR}/parser_yy.h ${SCOTCH_DIR}/parser_ll.h diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb new file mode 100644 index 00000000000..260ecb98ddb --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ELSI', '2.11.0', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8f7a531ce0e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '3.1.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['71cd6827f20c68e384555dbcfc85422d0690e21d21d7b5d4f7375544a2755271'] + +builddependencies = [('CMake', '3.26.3')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From a73038934f8f5076cc48f8d8e8070c3dd3c2203c Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 18:51:41 +0200 Subject: [PATCH 489/553] fix dftd4 name, add multicharge and remove TOML-Fortran --- .../dftd4-3.7.0-foss-2023a.eb} | 5 ++- .../multicharge-0.3.0-gfbf-2023a.eb | 38 +++++++++++++++++++ .../TOML-Fortran-0.4.2-GCC-12.3.0.eb | 24 ------------ 3 files changed, 41 insertions(+), 26 deletions(-) rename easybuild/easyconfigs/d/{DFTD4/DFTD4-3.7.0-foss-2023a.eb => dftd4/dftd4-3.7.0-foss-2023a.eb} (92%) create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb delete mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb similarity index 92% rename from easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb rename to easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb index 12d97f5a8a4..912ed2baf4a 100644 --- a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb @@ -1,9 +1,10 @@ # A. Domingo (Vrije Universiteit Brussel) # J. Sassmannshausen (Imperial College London/UK) +# C. Willemyns (Vrije Universiteit Brussel) easyblock = 'CMakeNinja' -name = 'DFTD4' +name = 'dftd4' version = '3.7.0' homepage = 'https://dftd4.readthedocs.io' @@ -28,7 +29,7 @@ builddependencies = [ dependencies = [ ('mctc-lib', '0.3.1'), ('mstore', '0.3.0'), - ('TOML-Fortran', '0.4.2'), + ('multicharge', '0.3.0'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb new file mode 100644 index 00000000000..b6debf00815 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -0,0 +1,38 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb deleted file mode 100644 index baa1d460ed6..00000000000 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TOML-Fortran' -version = '0.4.2' - -homepage = 'https://github.com/toml-f/toml-f' -description = 'TOML parser for Fortran projects' - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e66d0e355a8a2e65fd5fc7cd4f00078dfbdbf1b3cc47b60f028c19467df4c337'] - -builddependencies = [ - ('CMake', '3.26.3'), -] - -sanity_check_paths = { - 'files': ['lib/libtoml-f.a'], - 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], -} - -moduleclass = 'tools' From 95d84e1426f1a98bca00bb48160d2672e21ce7d9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 18:59:48 +0200 Subject: [PATCH 490/553] fix dftd4 name --- easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index c1e713bfa0d..c862fcea552 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -51,7 +51,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('DFTD4', '3.7.0'), + ('dftd4', '3.7.0'), ('ELSI', '2.11.0', '-PEXSI'), ('libmbd', '0.12.6'), ] From 21fbc8d3017bbe7b268a51d60eda6f9720370fad Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Fri, 13 Sep 2024 19:20:28 +0200 Subject: [PATCH 491/553] Add missing checksum to multicharge --- .../easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb index b6debf00815..b4ccfa2544f 100644 --- a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] builddependencies = [ ('CMake', '3.26.3'), From 84798df187db79668e55befb2b87cd1f9accb40e Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 13 Sep 2024 22:09:15 +0200 Subject: [PATCH 492/553] add sanity_check_commands --- .../easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb index bb1513a04b2..742dabcaa85 100644 --- a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -37,6 +37,8 @@ sanity_check_paths = { 'dirs': ['efndata'], } +sanity_check_commands = ['rnamotif -h 2>&1 | grep usage'] + modextravars = {'EFNDATA': 'efndata'} moduleclass = 'bio' From d52ec99d0b1a14a3af31df190cb4c04274f09904 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 14 Sep 2024 13:09:48 +0800 Subject: [PATCH 493/553] prepare release notes for EasyBuild v4.9.3 + bump version to 4.9.3 --- RELEASE_NOTES | 103 ++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 104 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e687bf442f8..d9b94b56e35 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,109 @@ The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for incl. 40 different (compiler) toolchains. +v4.9.3 (14 September 2024) +-------------------------- + +update/bugfix release + +- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains +- added example easyconfig files for 108 new software packages: + - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), BayesOpt (#21261), + BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), colorize (#20964), CORSIKA (#20693), + COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), + EGA-QuickView (#20888), EMMAX (#21174), empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), + fish (#21381), flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), + gmpflf (#20882), GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), + ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), jupyter-vscode-proxy (#20876), + langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), + MATES (#21229), MBX (#21155), mcqd (#21283), MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), + napari-denoiseg (#20934), NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), + OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), pyMBE (#21034), pystencils (#20889), + python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), Redland (#21227), Regenie (#15752), rMATS-long (#20916), + Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), + Single-cell-python-bundle (#20116), SIRIUS (#20989), sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), + submitit (#21103), SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), Visit (#20981), + weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) +- added additional easyconfigs for various supported software packages, including: + - AGAT 1.4.0, ANTLR 2.7.7, APOST3D 20240527, APR-util 1.6.3, APR 1.7.4, ASE 3.23.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, AmberTools %s.%s, Arcade-Learning-Environment 0.8.1, Arrow 16.1.0, Autoconf-archive 2023.02.20, absl-py 2.1.0, accelerate 0.33.0, adjustText 0.7.3, affogato 0.3.3, alsa-lib 1.2.11, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BGEN-enkre 1.1.7, BRiAl 1.2.12, Bandage 0.9.0, BayesOpt 0.9, BayesTraits 4.1.2, BeautifulSoup 4.12.3, BioPerl 1.7.8, Biopython 1.84, Bison 3.8.2, Boost.MPI 1.83.0, Boost.Python 1.82.0, Boost 1.55.0, Bowtie 1.3.1, Bowtie 1.3.1, Brunsli 0.1, Brunsli 0.1, bayesian-optimization 1.5.1, bcl-convert 4.2.7-2, beagle-lib 4.0.1, binutils 2.42, biom-format 2.1.16, bitsandbytes 0.43.3, bitsandbytes 0.43.3, bliss 0.77, byacc 2.0.20240109, CD-HIT 4.8.1, CDO 2.3.0, CESM-deps 2, CFITSIO 4.4.1, CGAL 5.6.1, CLANS 2.0.8, CORSIKA 77550, COSTA 2.2.2, CSBDeep 0.7.4, CUDA-Samples 11.8, CUDA-Samples 12.2, CUDA 12.5.0, CUDA 12.6.0, CUDD 3.0.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, Clang 18.1.8, ConcurrentVersionsSystem 1.11.23, Coreutils 9.5, Critic2 1.2, CubeLib 4.8.2, CubeWriter 4.8.2, Cython 3.0.10, cairo 1.18.0, cairomm 1.16.2, cfgrib 0.9.14.0, chewBBACA 3.3.9, code-server 4.90.2, colorize 0.7.7, connected-components-3d 3.14.1, cooler 0.10.2, coxeter 20180226, cppy 1.2.1, crb-blast 0.6.9, crypt4gh 1.7, cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, DB 18.1.40, DB_File 1.859, DBus 1.15.8, DL_POLY_4 5.1.0, DL_POLY_Classic_GUI 1.10, DMTCP 3.0.0, DMTCP 3.0.0, DMTCP 3.0.0, dblatex 0.3.12, dictys 1.1.0, dictys 1.1.0, dorado 0.6.1, dorado 0.7.3, dtcmp 1.1.5, duplex-tools 0.3.3, EGA-QuickView 20240620, EMMAX 20100310, ESIpy 20240709, ESMF 8.6.0, ESMF 8.6.1, ESPResSo 4.2.2, EasyBuild 4.9.2, EvidentialGene 2023.07.15, Exonerate 2.4.0, Extrae 4.2.0, ecBuild 3.8.5, ecCodes 2.27.0, einops 0.7.0, elfutils 0.191, empanada-dl 0.1.7, empanada-napari 1.1.0, expecttest 0.2.1, FFTW.MPI 3.3.10, FFTW.MPI 3.3.10, FFmpeg 7.0.2, FLAC 1.4.3, FLAC 1.4.3, FUSE 3.16.2, FastTree 2.1.11, Filtlong 0.2.1, Flask 3.0.3, Flax 0.8.4, Flax 0.8.4, Flye 2.9.4, FragGeneScan 1.31, FriBidi 1.0.15, fastahack 1.0.0, fastfilters 0.3, fastp 0.23.4, ffnvcodec 12.2.72.0, file 5.43, filevercmp 20191210, fish 3.7.1, flash-attention 2.6.3, flatbuffers-python 24.3.25, flatbuffers 24.3.25, flex 2.6.4, flit 3.9.0, fmt 10.2.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, foss 2024a, fplll 5.4.5, fpylll 0.6.1, fsm-lite 1.0, fsom 20151117, GCC 14.2.0, GCCcore 14.2.0, GDAL 3.9.0, GDMA 2.3.3_20230603, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1, GLibmm 2.75.0, GLibmm 2.77.0, GLibmm 2.78.1, GOATOOLS 1.4.5, GPAW 24.6.0, GPAW 24.6.0, GPflow 2.9.2, GPflow 2.9.2, GPflow 2.9.2, GPyOpt 1.2.6, GROMACS 2023.3, GTS 0.7.6, GeoDict 2024.SP2, GetOrganelle 1.7.7.1, GimmeMotifs 0.17.2, Gubbins 3.3.5, Guile 2.0.14, Guile 3.0.10, Gurobi 11.0.2, Gymnasium 0.29.1, g2lib 3.2.0, gap 4.13.0, gawk 5.3.0, gc 8.2.6, genomepy 0.16.1, gensim 4.3.2, gfbf 2024a, gffutils 0.13, gflags 2.2.2, gh 2.52.0, giflib 5.2.1, git-annex 10.20240731, gmpflf 2024.06, gmpich 2024.06, gmpy2 2.2.0, gompi 2024a, googletest 1.15.2, graph-tool 2.59, graphite2 1.3.14, groff 1.23.0, grpcio 1.57.0, gtk-doc 1.34.0, HDBSCAN 0.8.38.post1, HERRO 0.1.0_20240808, HOMER 4.11.1, HPL 2.3, HPL 2.3, HPL 2.3, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, help2man 1.49.3, hiredis 1.2.0, histolab 0.6.0, histolab 0.7.0, hypothesis 6.103.1, IEnt, IQ-TREE 2.3.5, ITK 5.3.0, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, iimpi 2024a, ilastik-napari 0.2.4, imageio 2.34.1, imbalanced-learn 0.12.3, imkl-FFTW 2024.2.0, imkl 2024.2.0, impi 2021.13.0, inferCNV 1.21.0, intel-compilers 2024.2.0, intel 2024a, intervaltree 0.1, intltool 0.51.0, JsonCpp 1.9.5, JsonCpp 1.9.5, Judy 1.0.5, Julia 1.10.4, jax 0.4.25, jax 0.4.25, jemalloc 5.3.0, json-c 0.17, json-fortran 8.5.2, json-fortran 8.5.2, junos-eznc 2.7.1, jupyter-collaboration 2.1.1, jupyter-vscode-proxy 0.6, Kaleido 0.2.1, Kent_tools 461, Kent_tools 468, kineto 0.4.0, LAME 3.100, LLVM 18.1.8, LMDB 0.9.31, LRBinner 0.1, LZO 2.10, LittleCMS 2.16, langchain-mistralai 0.1.8, langchain-openai 0.1.8, libcircle 0.3, libdap 3.20.11, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, libgit2 1.8.1, libglvnd 1.7.0, libidn2 2.3.4, libmatheval 1.1.11, libogg 1.3.5, libogg 1.3.5, libopus 1.5.2, libopus 1.5.2, libsigc++ 3.6.0, libsigc++ 3.6.0, libsigc++ 3.6.0, libsndfile 1.2.2, libsndfile 1.2.2, libsodium 1.0.20, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libvorbis 1.3.7, libvorbis 1.3.7, libwebp 1.4.0, libxslt 1.1.42, libzip 1.10.1, longread_umi 0.3.2, lrcalc 2.1, lwgrp 1.0.6, lxml 5.3.0, M4 1.4.19, MAGIC 3.0.0, MATES 0.1.2-20240813, MATES 0.1.2-20240813, MBX 1.1.0, MCR R2024a, METIS 5.1.0, MONAI 1.3.0, MPICH 4.2.1, MUMPS 5.6.1, MUMPS 5.7.2, MUMPS 5.7.2, MUSCLE 5.1.0, MariaDB 11.6.0, Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, MeshLab 2023.12, Miniconda3 23.10.0-1, MultiQC 1.22.3, maeparser 1.3.1, makedepend 1.0.9, mallard-ducktype 1.0.2, matplotlib 3.9.2, maturin 1.6.0, mcqd 1.0.0, medaka 1.12.0, medaka 1.12.0, medaka 1.12.1, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, meteogrid 20240627, micro-sam 1.0.1, miniasm 0.3-20191007, miniprot 0.13, ml-collections 0.1.1, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, molmod 1.4.8, molmod 1.4.8, mpifileutils 0.11.1, mrcfile 1.4.3, multichoose 1.0.3, multiprocess 0.70.15, mygene 3.2.2, NCO 5.1.9, NECAT 0.0.1, NLopt 2.7.1, NLopt 2.7.1, NanoCaller 3.6.0, NextPolish 1.4.1, NiBabel 5.2.0, Normaliz 3.10.3, n2v 0.3.3, nano 8.1, nanopolish 0.14.0, napari-denoiseg 0.0.1, ncbi-vdb 3.1.1, nellie 0.3.1, nellie 0.3.1, nettle 3.10, nifty 1.2.1, nlohmann_json 3.11.3, nose3 1.3.8, nsync 1.29.2, numexpr 2.9.0, OPARI2 2.0.8, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, OSU-Micro-Benchmarks 7.4, OSU-Micro-Benchmarks 7.4, OTF2 3.0.3, OpenAI-Gym 0.26.2, OpenEXR 3.2.4, OpenFOAM 10, OpenFOAM 12, OpenFOAM v2406, OpenForceField-Toolkit 0.16.0, OpenJPEG 2.5.2, OpenMM 8.0.0, OpenPGM 5.2.122, OpenSlide 3.4.1, Optax 0.2.2, Optax 0.2.2, Optuna 3.6.1, ome-types 0.5.1.post1, openai-python 1.30.5, openslide-python 1.3.1, orjson 3.9.15, PAPI 7.1.0, PDT 3.25.2, PEcAn 1.8.0.9000, PLY 3.11, PLY 3.11, PaStiX 6.3.2, PaStiX 6.3.2, ParMETIS 4.0.3, ParMETIS 4.0.3, ParaView 5.12.0, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PretextMap 0.1.9, PyAEDT 0.9.9, PyBEL 0.15.5, PyCharm 2024.1.6, PyRosetta 4.release-384, PyTorch-Geometric 2.5.0, PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, pagmo 2.19.0, parallel 20240722, parasail 2.6.2, pixman 0.43.4, pkgconfig 1.5.5, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, primecount 7.14, primecountpy 0.1.0, prompt-toolkit 3.0.36, psycopg 3.2.1, pyBigWig 0.3.22, pyGenomeTracks 3.9, pyMBE 0.8.0, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pydicom 2.4.4, pydot 2.0.0, pyfasta 0.5.2, pygmo 2.19.5, pyperf 2.7.0, pyseer 1.3.12, pyspoa 0.2.1, pystencils 1.3.4, pysteps 1.10.0, python-blosc 1.11.0, python-elf 0.5.1, python-, QuantumESPRESSO 7.3.1, QuantumESPRESSO 7.3.1, Qwt 6.3.0, qnorm 0.8.1, R-bundle-CRAN 2024.06, R 4.4.1, RDKit 2024.03.3, RStudio-Server 2023.09.1+494, RapidJSON 1.1.0-20240409, Raptor 2.0.16, Rasqal 0.9.33, Ray-project 2.9.1, ReFrame 4.6.2, ReFrame 4.6.2, Redland 1.0.17, Regenie 3.1.2, Rust 1.79.0, rMATS-long 1.0.0-20240502, rankwidth 0.9, rapidNJ 2.3.3, redis-py 5.0.9, regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, ruamel.yaml 0.18.6, SCENICplus 1.0a1-20240513, SCOTCH 7.0.4, SDL2 2.30.6, SHAP 0.43.0, SIONlib 1.7.7, SIP 6.8.3, SIRIUS 7.5.2, SKA2 0.3.7, SOCI 4.0.3, SRA-Toolkit 3.1.1, STAR 2.7.11b_alpha_2024-02-09, STREAM 5.10, STRUMPACK 7.1.0, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Sagemath 10.4, Salmon 1.10.3, ScaLAPACK 2.2.0, ScaLAPACK 2.2.0, SciPy-bundle 2024.05, SciPy-bundle 2024.05, Score-P 8.4, Score-P 8.4, SentencePiece 0.2.0, SeqKit 2.8.2, SharedMeatAxe 1.0.1, Single-cell-python-bundle 2024.02, SingleM 0.16.0, SpFFT 1.1.0, Sphinx-RTD-Theme 2.0.0, Sphinx-RTD-Theme 2.0.0, Stable-Baselines3 2.3.2, Stack 3.1.1, SuiteSparse 7.7.0, SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scCustomize 2.1.2, scFEA 1.1-20221109, scib-metrics 0.5.1, scikit-build 0.17.6, scrublet 0.2.3, scvi-tools 1.1.2, scvi-tools 1.1.2, sdsl-lite 2.0.3, segment-anything 1.0, setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, smithwaterman 20160702, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, spglib-python 2.5.0, spglib 2.5.0, spla 1.6.1, spoa 4.1.0, submitit 1.2.0, svist4get 1.3.1, TAMkin 1.2.6, TAMkin 1.2.6, TELEMAC-MASCARET 8p5r0, TF-COMB 1.1, TOBIAS 0.16.1, TensorFlow 2.15.1, Tk 8.6.14, Tkinter 3.12.3, Transrate 1.0.3, Triangle 1.6, Trycycler 0.5.5, tabixpp 1.1.2, tbb 2021.9.0, tdlib 0.9.3, tensorboard 2.15.1, tiktoken 0.7.0, timm 1.0.8, torch-em 0.7.1, UCX-CUDA 1.15.0, UCX-CUDA 1.16.0, Umpire 2024.02.1, Uni-Core 0.0.3, Uni-Core 0.0.3, unixODBC 2.3.12, utf8proc 2.9.0, VBZ-Compression 1.0.3, VSEARCH 2.28.1, VTK 9.2.6, Visit 3.4.1, vcflib 1.0.9, velocyto 0.17.17, vigra 1.11.2, virtualenv 20.26.2, WFA2 2.3.4, WRF 4.5.1, Wayland 1.23.0, weblogo 2.8.2, wget 1.21.4, wradlib 2.0.3, wradlib 2.0.3, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, xtb 6.7.1, xtensor 0.24.7, YACS 0.1.8, Yasm 1.3.0, yell 2.2.2, yelp-tools 42.1, yelp-xsl 42.1, Z3 4.13.0, ZeroMQ 4.3.5, Zoltan 3.901, z5py 2.0.17, zlib 1.3.1 +- minor enhancements, including: + - correct configuration of QuantumESPRESSO for 6.7/6.8/7.0/7.1/7.2/7.3 (#20070) + - add internal CUDA header patch for PSM2 (#20804) + - add support for JupyterHub to TensorBoard (#20823) + - make sure that recent ImageMagick versions pick up the right pkgconf and improve the sanity checks (#20900) + - also install utilities for recent versions of FUSE 3.x (#20918) + - add RISC-V support to x264-20231019/GCCcore-13.2.0 (#20968) + - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970) + - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971) + - add missMDA extension to R-bundle-CRAN versions 2023.12 (#21167) and 2024.06 (#21183) + - add Qt support to VTK 9.3.0 (#21221) + - add insight extension to R-bundle-CRAN 2024.06 (#21260) + - add performance, datwizard and bayestestR to R-bundle-CRAN 2024.06 (#21272) + - add `helper_scripts` to PATH in ProteinMPNN-1.0.1-20230627 (#21289) + - add the plugins to OpenFOAM v2406 (#21332) + - use proper Python dependency for OTF2 (#21325) +- various bug fixes, including: + - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103) + - fix typo in description of SuiteSparse v7.7.0 (#20567) + - add 'pic' flag to IML (#20789) + - add patch to fix build error with numpy with some compilers (#20817) + - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818) + - fix build of OpenBLAS 0.3.24 on A64FX (#20820) + - remove maturin build dependency from langchain-antropic (#20825) + - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841) + - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847) + - skip unreliable memory leak test in PyTorch 2.1.2 (#20874) + - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions (#20879) + - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881) + - add fix for failing test on zen4 to Highway 1.0.4 (#20942) + - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949) + - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951) + - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956) + - set `SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) + - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958) + - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969) + - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) + - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002) + - update homepage in phonopy easyconfigs (#21014) + - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017) + - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028) + - fix download URLs for old Intel software (2018-23) (#21108) + - update source and homepage URLs in Szip easyconfigs (#21129) + - rename source URL in HDF v4.2.16-2 easyconfig (#21130) + - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134) + - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136) + - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143) + - add pkgconf build dependency to scikit-misc v0.3.1 (#21144) + - disable use of MySQL in GDAL (#21156) + - add GPflow v2.9.2 and fix tensorflow-probability to pass pip check (#21172) + - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175) + - remove `Time::HiRes` from `Perl-bundle-CPAN` (#21198) + - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200) + - add missing cairo dependency for python-igraph v0.10.6 (#21211) + - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255) + - add patch for HDF5-1.14.3 to _suppress fp exceptions (#21280) + - correct extension order in R-bundle-CRAN 2024.06 (#21285) + - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297) + - use source tarballs from GitHub for recent libdap easyconfigs (#21334) + - use version in byacc 2.0.20240109 sources (#21344) + - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366) + - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370) + - disable buiding docs in fish (#21381) +- other changes: + - archive outdated example easyconfigs for Fujitsu toolchain (#20781) + - upgrade builddependency rpmrebuild to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) + - switch transformers to use external Safetensor dep (#20864) + - rename ega-quickview to EGA-QuickView (#20888) + - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905) + - whitelist ConfigureMakePythonPackage for sanity_check_paths CI check (#20963) + - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004) + - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038) + - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039) + - remove Cython dependency from Python-bundle-PyPI 2024.06 + standalone easyconfig for Cython 3.0.10 (#21233) + - add Cython builddep for SciPy-bundle (#21235) + - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292) + + v4.9.2 (12 June 2024) --------------------- diff --git a/setup.py b/setup.py index 8d3cd7f76d0..ae4897821b1 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.3.dev0' +VERSION = '4.9.3' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From f82a563b8e1f8118c7c3ab23374d0e28e1691fea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Sep 2024 16:51:56 +0200 Subject: [PATCH 494/553] minor tweaks to 4.9.3 release notes --- RELEASE_NOTES | 132 +++++++++++++++++++++++++++++++------------------- 1 file changed, 83 insertions(+), 49 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d9b94b56e35..590c5db69f2 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for 3,552 different software packages, -incl. 40 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages, +incl. 41 different (compiler) toolchains. v4.9.3 (14 September 2024) @@ -13,100 +13,134 @@ v4.9.3 (14 September 2024) update/bugfix release - added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains -- added example easyconfig files for 108 new software packages: - - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), BayesOpt (#21261), - BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), colorize (#20964), CORSIKA (#20693), - COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), - EGA-QuickView (#20888), EMMAX (#21174), empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), - fish (#21381), flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), - gmpflf (#20882), GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), - ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), jupyter-vscode-proxy (#20876), - langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), - MATES (#21229), MBX (#21155), mcqd (#21283), MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), - napari-denoiseg (#20934), NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), - OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), pyMBE (#21034), pystencils (#20889), - python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), Redland (#21227), Regenie (#15752), rMATS-long (#20916), - Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), - Single-cell-python-bundle (#20116), SIRIUS (#20989), sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), - submitit (#21103), SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), Visit (#20981), - weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) +- new toolchain: gmpflf/2024.06 (#20882) +- added example easyconfig files for 107 new software packages: + - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), + BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), + colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), + dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174), + empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381), + flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), + GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), + ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), + jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), + lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283), + MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934), + NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), + OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), + pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), + Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), + scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989), + sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103), + SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), + Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), + yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) - added additional easyconfigs for various supported software packages, including: - - AGAT 1.4.0, ANTLR 2.7.7, APOST3D 20240527, APR-util 1.6.3, APR 1.7.4, ASE 3.23.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, AmberTools %s.%s, Arcade-Learning-Environment 0.8.1, Arrow 16.1.0, Autoconf-archive 2023.02.20, absl-py 2.1.0, accelerate 0.33.0, adjustText 0.7.3, affogato 0.3.3, alsa-lib 1.2.11, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BGEN-enkre 1.1.7, BRiAl 1.2.12, Bandage 0.9.0, BayesOpt 0.9, BayesTraits 4.1.2, BeautifulSoup 4.12.3, BioPerl 1.7.8, Biopython 1.84, Bison 3.8.2, Boost.MPI 1.83.0, Boost.Python 1.82.0, Boost 1.55.0, Bowtie 1.3.1, Bowtie 1.3.1, Brunsli 0.1, Brunsli 0.1, bayesian-optimization 1.5.1, bcl-convert 4.2.7-2, beagle-lib 4.0.1, binutils 2.42, biom-format 2.1.16, bitsandbytes 0.43.3, bitsandbytes 0.43.3, bliss 0.77, byacc 2.0.20240109, CD-HIT 4.8.1, CDO 2.3.0, CESM-deps 2, CFITSIO 4.4.1, CGAL 5.6.1, CLANS 2.0.8, CORSIKA 77550, COSTA 2.2.2, CSBDeep 0.7.4, CUDA-Samples 11.8, CUDA-Samples 12.2, CUDA 12.5.0, CUDA 12.6.0, CUDD 3.0.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, Clang 18.1.8, ConcurrentVersionsSystem 1.11.23, Coreutils 9.5, Critic2 1.2, CubeLib 4.8.2, CubeWriter 4.8.2, Cython 3.0.10, cairo 1.18.0, cairomm 1.16.2, cfgrib 0.9.14.0, chewBBACA 3.3.9, code-server 4.90.2, colorize 0.7.7, connected-components-3d 3.14.1, cooler 0.10.2, coxeter 20180226, cppy 1.2.1, crb-blast 0.6.9, crypt4gh 1.7, cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, DB 18.1.40, DB_File 1.859, DBus 1.15.8, DL_POLY_4 5.1.0, DL_POLY_Classic_GUI 1.10, DMTCP 3.0.0, DMTCP 3.0.0, DMTCP 3.0.0, dblatex 0.3.12, dictys 1.1.0, dictys 1.1.0, dorado 0.6.1, dorado 0.7.3, dtcmp 1.1.5, duplex-tools 0.3.3, EGA-QuickView 20240620, EMMAX 20100310, ESIpy 20240709, ESMF 8.6.0, ESMF 8.6.1, ESPResSo 4.2.2, EasyBuild 4.9.2, EvidentialGene 2023.07.15, Exonerate 2.4.0, Extrae 4.2.0, ecBuild 3.8.5, ecCodes 2.27.0, einops 0.7.0, elfutils 0.191, empanada-dl 0.1.7, empanada-napari 1.1.0, expecttest 0.2.1, FFTW.MPI 3.3.10, FFTW.MPI 3.3.10, FFmpeg 7.0.2, FLAC 1.4.3, FLAC 1.4.3, FUSE 3.16.2, FastTree 2.1.11, Filtlong 0.2.1, Flask 3.0.3, Flax 0.8.4, Flax 0.8.4, Flye 2.9.4, FragGeneScan 1.31, FriBidi 1.0.15, fastahack 1.0.0, fastfilters 0.3, fastp 0.23.4, ffnvcodec 12.2.72.0, file 5.43, filevercmp 20191210, fish 3.7.1, flash-attention 2.6.3, flatbuffers-python 24.3.25, flatbuffers 24.3.25, flex 2.6.4, flit 3.9.0, fmt 10.2.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, foss 2024a, fplll 5.4.5, fpylll 0.6.1, fsm-lite 1.0, fsom 20151117, GCC 14.2.0, GCCcore 14.2.0, GDAL 3.9.0, GDMA 2.3.3_20230603, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1, GLibmm 2.75.0, GLibmm 2.77.0, GLibmm 2.78.1, GOATOOLS 1.4.5, GPAW 24.6.0, GPAW 24.6.0, GPflow 2.9.2, GPflow 2.9.2, GPflow 2.9.2, GPyOpt 1.2.6, GROMACS 2023.3, GTS 0.7.6, GeoDict 2024.SP2, GetOrganelle 1.7.7.1, GimmeMotifs 0.17.2, Gubbins 3.3.5, Guile 2.0.14, Guile 3.0.10, Gurobi 11.0.2, Gymnasium 0.29.1, g2lib 3.2.0, gap 4.13.0, gawk 5.3.0, gc 8.2.6, genomepy 0.16.1, gensim 4.3.2, gfbf 2024a, gffutils 0.13, gflags 2.2.2, gh 2.52.0, giflib 5.2.1, git-annex 10.20240731, gmpflf 2024.06, gmpich 2024.06, gmpy2 2.2.0, gompi 2024a, googletest 1.15.2, graph-tool 2.59, graphite2 1.3.14, groff 1.23.0, grpcio 1.57.0, gtk-doc 1.34.0, HDBSCAN 0.8.38.post1, HERRO 0.1.0_20240808, HOMER 4.11.1, HPL 2.3, HPL 2.3, HPL 2.3, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, help2man 1.49.3, hiredis 1.2.0, histolab 0.6.0, histolab 0.7.0, hypothesis 6.103.1, IEnt, IQ-TREE 2.3.5, ITK 5.3.0, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, iimpi 2024a, ilastik-napari 0.2.4, imageio 2.34.1, imbalanced-learn 0.12.3, imkl-FFTW 2024.2.0, imkl 2024.2.0, impi 2021.13.0, inferCNV 1.21.0, intel-compilers 2024.2.0, intel 2024a, intervaltree 0.1, intltool 0.51.0, JsonCpp 1.9.5, JsonCpp 1.9.5, Judy 1.0.5, Julia 1.10.4, jax 0.4.25, jax 0.4.25, jemalloc 5.3.0, json-c 0.17, json-fortran 8.5.2, json-fortran 8.5.2, junos-eznc 2.7.1, jupyter-collaboration 2.1.1, jupyter-vscode-proxy 0.6, Kaleido 0.2.1, Kent_tools 461, Kent_tools 468, kineto 0.4.0, LAME 3.100, LLVM 18.1.8, LMDB 0.9.31, LRBinner 0.1, LZO 2.10, LittleCMS 2.16, langchain-mistralai 0.1.8, langchain-openai 0.1.8, libcircle 0.3, libdap 3.20.11, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, libgit2 1.8.1, libglvnd 1.7.0, libidn2 2.3.4, libmatheval 1.1.11, libogg 1.3.5, libogg 1.3.5, libopus 1.5.2, libopus 1.5.2, libsigc++ 3.6.0, libsigc++ 3.6.0, libsigc++ 3.6.0, libsndfile 1.2.2, libsndfile 1.2.2, libsodium 1.0.20, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libvorbis 1.3.7, libvorbis 1.3.7, libwebp 1.4.0, libxslt 1.1.42, libzip 1.10.1, longread_umi 0.3.2, lrcalc 2.1, lwgrp 1.0.6, lxml 5.3.0, M4 1.4.19, MAGIC 3.0.0, MATES 0.1.2-20240813, MATES 0.1.2-20240813, MBX 1.1.0, MCR R2024a, METIS 5.1.0, MONAI 1.3.0, MPICH 4.2.1, MUMPS 5.6.1, MUMPS 5.7.2, MUMPS 5.7.2, MUSCLE 5.1.0, MariaDB 11.6.0, Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, MeshLab 2023.12, Miniconda3 23.10.0-1, MultiQC 1.22.3, maeparser 1.3.1, makedepend 1.0.9, mallard-ducktype 1.0.2, matplotlib 3.9.2, maturin 1.6.0, mcqd 1.0.0, medaka 1.12.0, medaka 1.12.0, medaka 1.12.1, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, meteogrid 20240627, micro-sam 1.0.1, miniasm 0.3-20191007, miniprot 0.13, ml-collections 0.1.1, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, molmod 1.4.8, molmod 1.4.8, mpifileutils 0.11.1, mrcfile 1.4.3, multichoose 1.0.3, multiprocess 0.70.15, mygene 3.2.2, NCO 5.1.9, NECAT 0.0.1, NLopt 2.7.1, NLopt 2.7.1, NanoCaller 3.6.0, NextPolish 1.4.1, NiBabel 5.2.0, Normaliz 3.10.3, n2v 0.3.3, nano 8.1, nanopolish 0.14.0, napari-denoiseg 0.0.1, ncbi-vdb 3.1.1, nellie 0.3.1, nellie 0.3.1, nettle 3.10, nifty 1.2.1, nlohmann_json 3.11.3, nose3 1.3.8, nsync 1.29.2, numexpr 2.9.0, OPARI2 2.0.8, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, OSU-Micro-Benchmarks 7.4, OSU-Micro-Benchmarks 7.4, OTF2 3.0.3, OpenAI-Gym 0.26.2, OpenEXR 3.2.4, OpenFOAM 10, OpenFOAM 12, OpenFOAM v2406, OpenForceField-Toolkit 0.16.0, OpenJPEG 2.5.2, OpenMM 8.0.0, OpenPGM 5.2.122, OpenSlide 3.4.1, Optax 0.2.2, Optax 0.2.2, Optuna 3.6.1, ome-types 0.5.1.post1, openai-python 1.30.5, openslide-python 1.3.1, orjson 3.9.15, PAPI 7.1.0, PDT 3.25.2, PEcAn 1.8.0.9000, PLY 3.11, PLY 3.11, PaStiX 6.3.2, PaStiX 6.3.2, ParMETIS 4.0.3, ParMETIS 4.0.3, ParaView 5.12.0, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PretextMap 0.1.9, PyAEDT 0.9.9, PyBEL 0.15.5, PyCharm 2024.1.6, PyRosetta 4.release-384, PyTorch-Geometric 2.5.0, PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, pagmo 2.19.0, parallel 20240722, parasail 2.6.2, pixman 0.43.4, pkgconfig 1.5.5, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, primecount 7.14, primecountpy 0.1.0, prompt-toolkit 3.0.36, psycopg 3.2.1, pyBigWig 0.3.22, pyGenomeTracks 3.9, pyMBE 0.8.0, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pydicom 2.4.4, pydot 2.0.0, pyfasta 0.5.2, pygmo 2.19.5, pyperf 2.7.0, pyseer 1.3.12, pyspoa 0.2.1, pystencils 1.3.4, pysteps 1.10.0, python-blosc 1.11.0, python-elf 0.5.1, python-, QuantumESPRESSO 7.3.1, QuantumESPRESSO 7.3.1, Qwt 6.3.0, qnorm 0.8.1, R-bundle-CRAN 2024.06, R 4.4.1, RDKit 2024.03.3, RStudio-Server 2023.09.1+494, RapidJSON 1.1.0-20240409, Raptor 2.0.16, Rasqal 0.9.33, Ray-project 2.9.1, ReFrame 4.6.2, ReFrame 4.6.2, Redland 1.0.17, Regenie 3.1.2, Rust 1.79.0, rMATS-long 1.0.0-20240502, rankwidth 0.9, rapidNJ 2.3.3, redis-py 5.0.9, regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, ruamel.yaml 0.18.6, SCENICplus 1.0a1-20240513, SCOTCH 7.0.4, SDL2 2.30.6, SHAP 0.43.0, SIONlib 1.7.7, SIP 6.8.3, SIRIUS 7.5.2, SKA2 0.3.7, SOCI 4.0.3, SRA-Toolkit 3.1.1, STAR 2.7.11b_alpha_2024-02-09, STREAM 5.10, STRUMPACK 7.1.0, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Sagemath 10.4, Salmon 1.10.3, ScaLAPACK 2.2.0, ScaLAPACK 2.2.0, SciPy-bundle 2024.05, SciPy-bundle 2024.05, Score-P 8.4, Score-P 8.4, SentencePiece 0.2.0, SeqKit 2.8.2, SharedMeatAxe 1.0.1, Single-cell-python-bundle 2024.02, SingleM 0.16.0, SpFFT 1.1.0, Sphinx-RTD-Theme 2.0.0, Sphinx-RTD-Theme 2.0.0, Stable-Baselines3 2.3.2, Stack 3.1.1, SuiteSparse 7.7.0, SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scCustomize 2.1.2, scFEA 1.1-20221109, scib-metrics 0.5.1, scikit-build 0.17.6, scrublet 0.2.3, scvi-tools 1.1.2, scvi-tools 1.1.2, sdsl-lite 2.0.3, segment-anything 1.0, setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, smithwaterman 20160702, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, spglib-python 2.5.0, spglib 2.5.0, spla 1.6.1, spoa 4.1.0, submitit 1.2.0, svist4get 1.3.1, TAMkin 1.2.6, TAMkin 1.2.6, TELEMAC-MASCARET 8p5r0, TF-COMB 1.1, TOBIAS 0.16.1, TensorFlow 2.15.1, Tk 8.6.14, Tkinter 3.12.3, Transrate 1.0.3, Triangle 1.6, Trycycler 0.5.5, tabixpp 1.1.2, tbb 2021.9.0, tdlib 0.9.3, tensorboard 2.15.1, tiktoken 0.7.0, timm 1.0.8, torch-em 0.7.1, UCX-CUDA 1.15.0, UCX-CUDA 1.16.0, Umpire 2024.02.1, Uni-Core 0.0.3, Uni-Core 0.0.3, unixODBC 2.3.12, utf8proc 2.9.0, VBZ-Compression 1.0.3, VSEARCH 2.28.1, VTK 9.2.6, Visit 3.4.1, vcflib 1.0.9, velocyto 0.17.17, vigra 1.11.2, virtualenv 20.26.2, WFA2 2.3.4, WRF 4.5.1, Wayland 1.23.0, weblogo 2.8.2, wget 1.21.4, wradlib 2.0.3, wradlib 2.0.3, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, xtb 6.7.1, xtensor 0.24.7, YACS 0.1.8, Yasm 1.3.0, yell 2.2.2, yelp-tools 42.1, yelp-xsl 42.1, Z3 4.13.0, ZeroMQ 4.3.5, Zoltan 3.901, z5py 2.0.17, zlib 1.3.1 + - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, + AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3, + Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109, + CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, + Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, + cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15, + Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4, + FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1, + GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1, + GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2, + gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1, + HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0, + hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1, + imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2, + Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, + libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0, + libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0, + Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2, + maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3, + n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12, + OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, + Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384, + PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, + pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, + primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5, + pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1, + RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9, + regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1, + STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3, + SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0, + SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3, + setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, + spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0, + timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1, + Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, + xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1 - minor enhancements, including: - - correct configuration of QuantumESPRESSO for 6.7/6.8/7.0/7.1/7.2/7.3 (#20070) - - add internal CUDA header patch for PSM2 (#20804) - - add support for JupyterHub to TensorBoard (#20823) - - make sure that recent ImageMagick versions pick up the right pkgconf and improve the sanity checks (#20900) + - add internal CUDA header patch for PSM2 v12.0.1 (#20804) + - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823) + - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900) - also install utilities for recent versions of FUSE 3.x (#20918) - - add RISC-V support to x264-20231019/GCCcore-13.2.0 (#20968) + - add RISC-V support to x264 v20231019 (#20968) - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970) - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971) - - add missMDA extension to R-bundle-CRAN versions 2023.12 (#21167) and 2024.06 (#21183) + - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285) - add Qt support to VTK 9.3.0 (#21221) - - add insight extension to R-bundle-CRAN 2024.06 (#21260) - - add performance, datwizard and bayestestR to R-bundle-CRAN 2024.06 (#21272) - - add `helper_scripts` to PATH in ProteinMPNN-1.0.1-20230627 (#21289) - - add the plugins to OpenFOAM v2406 (#21332) - - use proper Python dependency for OTF2 (#21325) + - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289) + - also build & install the plugins with OpenFOAM v2406 (#21332) - various bug fixes, including: + - fix easyconfigs for recent versions of QuantumESPRESSO (#20070) - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103) - fix typo in description of SuiteSparse v7.7.0 (#20567) - add 'pic' flag to IML (#20789) - - add patch to fix build error with numpy with some compilers (#20817) + - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817) - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818) - fix build of OpenBLAS 0.3.24 on A64FX (#20820) - remove maturin build dependency from langchain-antropic (#20825) - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841) - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847) - skip unreliable memory leak test in PyTorch 2.1.2 (#20874) - - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions (#20879) + - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879) - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881) - add fix for failing test on zen4 to Highway 1.0.4 (#20942) - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949) - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951) - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956) - - set `SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) + - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958) - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969) - - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002) - update homepage in phonopy easyconfigs (#21014) - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017) - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028) - - fix download URLs for old Intel software (2018-23) (#21108) + - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108) - update source and homepage URLs in Szip easyconfigs (#21129) - rename source URL in HDF v4.2.16-2 easyconfig (#21130) - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134) - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136) - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143) - add pkgconf build dependency to scikit-misc v0.3.1 (#21144) - - disable use of MySQL in GDAL (#21156) - - add GPflow v2.9.2 and fix tensorflow-probability to pass pip check (#21172) + - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156) + - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172) - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175) - - remove `Time::HiRes` from `Perl-bundle-CPAN` (#21198) + - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198) - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200) - add missing cairo dependency for python-igraph v0.10.6 (#21211) - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255) - - add patch for HDF5-1.14.3 to _suppress fp exceptions (#21280) - - correct extension order in R-bundle-CRAN 2024.06 (#21285) + - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280) - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297) + - use proper Python dependency for OTF2 (#21325) - use source tarballs from GitHub for recent libdap easyconfigs (#21334) - - use version in byacc 2.0.20240109 sources (#21344) - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366) - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370) - - disable buiding docs in fish (#21381) - other changes: - archive outdated example easyconfigs for Fujitsu toolchain (#20781) - - upgrade builddependency rpmrebuild to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) - - switch transformers to use external Safetensor dep (#20864) - - rename ega-quickview to EGA-QuickView (#20888) + - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) + - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864) - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905) - - whitelist ConfigureMakePythonPackage for sanity_check_paths CI check (#20963) + - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963) + - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004) - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038) - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039) - - remove Cython dependency from Python-bundle-PyPI 2024.06 + standalone easyconfig for Cython 3.0.10 (#21233) - - add Cython builddep for SciPy-bundle (#21235) + - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233) + - add Cython build dependency for SciPy-bundle v2024.05 (#21235) - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292) From 82206bb1c68d8d9ccd551b36efb0a0cc2251147c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Sep 2024 22:51:52 +0200 Subject: [PATCH 495/553] adding easyconfigs: EasyBuild-4.9.3.eb --- .../e/EasyBuild/EasyBuild-4.9.3.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb new file mode 100644 index 00000000000..4059b342213 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.3' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/10/a0/e5484d4078f7450042cd7b7a1af24fd3f8d0cb4818f4578e4c322ba488d8/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ee/40/4f6412917f83429f9389b977903c8905f216cb211c8bf3111f28c3017677/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/13/95/44d1e10ceaaf08219ef50d1d97d500ba3b6b34f2d76dd1ff64def71612dc/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.3.tar.gz': '43bbcaa0a7b075eb6483054428ef4b1279a9fc850301171688f86899eaebfff8'}, + {'easybuild_easyblocks-4.9.3.tar.gz': '4f036be918f88fe2dadba87f15d696e9b4d3f8f06986c675b9fafc77b591649d'}, + {'easybuild_easyconfigs-4.9.3.tar.gz': 'f7f501c87cb16a8eb393f5e98cb3cd5f8e84314901e81ff50f8140681b415676'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 1f374568b1133e89a5faf07c872a531d5681ac46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Sep 2024 23:16:10 +0200 Subject: [PATCH 496/553] bump version to 4.9.4dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ae4897821b1..47b7fc09bd1 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.3' +VERSION = '4.9.4.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 04a1c44abd4ae39fe02e815110731f22aa055bdc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 16 Sep 2024 10:25:51 +0200 Subject: [PATCH 497/553] adding easyconfigs: chopper-0.9.0-GCCcore-12.3.0.eb and patches: chopper-0.9.0_fix_incorrect_version.patch --- .../c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 316 ++++++++++++++++++ .../chopper-0.9.0_fix_incorrect_version.patch | 28 ++ 2 files changed, 344 insertions(+) create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..df0b3abaa21 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,316 @@ +easyblock = 'Cargo' + +name = 'chopper' +version = '0.9.0' + +homepage = 'https://github.com/wdecoster/chopper' +description = """Rust implementation of NanoFilt+NanoLyse, both +originally written in Python. This tool, intended for long read +sequencing such as PacBio or ONT, filters and trims a fastq file. +Filtering is done on average read quality and minimal or maximal read +length, and applying a headcrop (start of read) and tailcrop (end of +read) while printing the reads passing the filter.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'wdecoster' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'chopper-0.9.0_fix_incorrect_version.patch', +] +checksums = [ + {'v0.9.0.tar.gz': 'ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'}, + {'anstyle-1.0.6.tar.gz': 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'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'chopper-0.9.0_fix_incorrect_version.patch': 'b3f3dfa620fbda6d00a73eafc8508a73ac4d96f6edfb0e804b3ff0bc149e37cd'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), +] + +crates = [ + ('adler', '1.0.2'), + ('aho-corasick', '1.1.3'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.82'), + ('approx', '0.5.1'), + ('atty', '0.2.14'), + ('autocfg', '1.2.0'), + ('bio', '1.6.0'), + ('bio-types', '1.0.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('buffer-redux', '1.0.1'), + ('bv', '0.11.1'), + ('bytecount', '0.6.8'), + ('bytemuck', '1.15.0'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', 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('libz-ng-sys', '1.1.15'), + ('libz-sys', '1.1.16'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.2'), + ('minimap2', '0.1.17+minimap2.2.27'), + ('minimap2-sys', '0.1.18+minimap2.2.27'), + ('miniz_oxide', '0.7.2'), + ('multimap', '0.9.1'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('ordered-float', '3.9.2'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pkg-config', '0.3.30'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.81'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rawpointer', '0.2.1'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.15'), + ('ryu', '1.0.17'), + ('safe_arch', '0.7.1'), + ('semver', '0.1.20'), + ('serde', '1.0.198'), + ('serde_derive', '1.0.198'), + ('simba', '0.6.0'), + ('simdutf8', '0.1.4'), + ('statrs', '0.16.0'), + ('strsim', '0.11.1'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.60'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('triple_accel', '0.4.0'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.16'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.52.5'), + ('xz2', '0.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/chopper'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chopper --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch new file mode 100644 index 00000000000..57c15b94db4 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch @@ -0,0 +1,28 @@ +Fix incorrect version number in the 0.9.0 tar file. + +Åke Sandgren, 2024-09-16 +diff --git a/Cargo.lock b/Cargo.lock +index 3e8f1fe..53fa5da 100644 +--- a/Cargo.lock ++++ b/Cargo.lock +@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" + + [[package]] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + dependencies = [ + "approx", + "atty", +diff --git a/Cargo.toml b/Cargo.toml +index f268dce..7f7277a 100644 +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -1,6 +1,6 @@ + [package] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + authors = ["wdecoster "] + edition = "2021" + From 905a8a835ebcb0221d30bcc16699e20cc8616ed1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 12:37:49 +0200 Subject: [PATCH 498/553] account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches --- test/easyconfigs/easyconfigs.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a4684900718..74f98af5cf8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1459,6 +1459,9 @@ def template_easyconfig_test(self, spec): ] failing_checks.extend("Old URL '%s' found" % old_url for old_url in old_urls if old_url in ec.rawtxt) + # Note the use of app.cfg which might contain sources populated by e.g. the Cargo easyblock + sources, patches, checksums = app.cfg['sources'], app.cfg['patches'], app.cfg['checksums'] + # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # easyblocks without a build step @@ -1475,7 +1478,7 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + requires_binutils &= bool(sources or ec['exts_list'] or ec.get('components')) if requires_binutils: # dependencies() returns both build and runtime dependencies @@ -1506,13 +1509,13 @@ def template_easyconfig_test(self, spec): if openssl_osdep: failing_checks.append("OpenSSL should not be listed as OS dependency") - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] + src_cnt = len(sources) + patch_checksums = checksums[src_cnt:] # make sure all patch files are available specdir = os.path.dirname(spec) basedir = os.path.dirname(os.path.dirname(specdir)) - for idx, patch in enumerate(ec['patches']): + for idx, patch in enumerate(patches): patch_dir = specdir if isinstance(patch, str): patch_name = patch @@ -1535,7 +1538,7 @@ def template_easyconfig_test(self, spec): # make sure 'source' step is not being skipped, # since that implies not verifying the checksum - if ec['checksums'] and ('source' in ec['skipsteps']): + if checksums and ('source' in ec['skipsteps']): failing_checks.append("'source' step should not be skipped, since that implies not verifying checksums") for ext in ec.get_ref('exts_list'): From 34ad2d1556fe85c86b3e957f04c77ca9b9787785 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 16 Sep 2024 16:10:58 +0200 Subject: [PATCH 499/553] adding easyconfigs: RepeatMasker-4.1.7-p1-foss-2023a.eb, RMBlast-2.14.1-gompi-2023a.eb, TRF-4.09.1-GCCcore-12.3.0.eb --- .../r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb | 65 +++++++++++++++++++ .../RepeatMasker-4.1.7-p1-foss-2023a.eb | 57 ++++++++++++++++ .../t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb | 30 +++++++++ 3 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb new file mode 100644 index 00000000000..22e6ed85f93 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb @@ -0,0 +1,65 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Update: Petr Král (INUITS) +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.14.1' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.14.1+-src.tar.gz': '712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'}, + {'isb-2.14.1+-rmblast.patch.gz': '9c8091eb2aec97ac83287859d2bfec83cb08c082d5a121cbefe3cc626f933763'}, +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost.MPI', '1.82.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LMDB', '0.9.31'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb new file mode 100644 index 00000000000..90b43c163a0 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.7-p1' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993'] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('TRF', '4.09.1'), + ('h5py', '3.9.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.4'), + ('RMBlast', '2.14.1'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cbf3e47917e --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From f15cafbf3580cd077c444336882c65968a1770b8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:17:21 +0200 Subject: [PATCH 500/553] adding easyconfigs: pytest-workflow-2.1.0-GCCcore-13.3.0.eb, tqdm-4.66.5-GCCcore-13.3.0.eb, typing-extensions-4.11.0-GCCcore-13.3.0.eb --- .../pytest-workflow-2.1.0-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ .../t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb | 24 +++++++++++++ ...typing-extensions-4.11.0-GCCcore-13.3.0.eb | 21 ++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..25aaab957da --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'pytest-workflow' +version = '2.1.0' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('python-isal', '1.7.0'), + ('zlib-ng', '2.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zstandard', '0.23.0', {'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09']}), + ('xopen', '2.0.2', {'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154']}), + (name, version, {'checksums': ['dc86ad9a5f94482aec14926788f6b78b428be68ee0428cbca22f89b6326f8b7a']}), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9d92f49462 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.5' + +homepage = 'https://github.com/tqdm/tqdm' +description = "A fast, extensible progress bar for Python and CLI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..552279e3ffe --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.11.0' + +homepage = 'https://github.com/python/typing_extensions' +description = "Typing Extensions - Backported and Experimental Type Hints for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' From e860d9244185ab88bcff035a5217f50afb0d1768 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:18:47 +0200 Subject: [PATCH 501/553] adding easyconfigs: GitPython-3.1.43-GCCcore-13.3.0.eb, ISA-L-2.31.0-GCCcore-13.3.0.eb, Markdown-3.7-GCCcore-13.3.0.eb, prompt-toolkit-3.0.36-GCCcore-13.3.0.eb, python-isal-1.7.0-GCCcore-13.3.0.eb, versioningit-3.1.2-GCCcore-13.3.0.eb, zlib-ng-2.2.1-GCCcore-13.3.0.eb --- .../GitPython-3.1.43-GCCcore-13.3.0.eb | 33 ++++++++++++ .../i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb | 45 +++++++++++++++++ .../m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb | 24 +++++++++ .../prompt-toolkit-3.0.36-GCCcore-13.3.0.eb | 27 ++++++++++ .../python-isal-1.7.0-GCCcore-13.3.0.eb | 34 +++++++++++++ .../versioningit-3.1.2-GCCcore-13.3.0.eb | 27 ++++++++++ .../z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb | 50 +++++++++++++++++++ 7 files changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..62484b4a3e8 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.43' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42'),] +dependencies = [ + ('Python', '3.12.3'), + ('git', '2.45.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('smmap', '5.0.1', { + 'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62'], + }), + ('gitdb', '4.0.11', { + 'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1e79d2b10db --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.31.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e218b7b2e241cfb8e8b68f54a6e5eed80968cc387c4b1af03708b54e9fb236f1'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [('NASM', '2.16.03')] + +preconfigopts = "autoreconf -i -f &&" + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f5cc55d6ff3 --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.7' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] + +builddependencies = [('binutils', '2.42'),] +dependencies = [('Python', '3.12.3'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cbde894708 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..96885969511 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.7.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('ISA-L', '2.31.0'), +] + +source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')] +sources = ['isal-%(version)s.tar.gz'] +checksums = ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ab4e77dea46 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] +dependencies = [('Python', '3.12.3')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..266b927072a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.1' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['ec6a76169d4214e2e8b737e0850ba4acb806c69eeace6240ed4481b9f5c57cdf'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.0', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From fa048953782740cea16a874946f5dc209644b2a7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:20:24 +0200 Subject: [PATCH 502/553] adding easyconfigs: giflib-5.2.2-GCCcore-13.3.0.eb, Pillow-10.4.0-GCCcore-13.3.0.eb --- .../g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb | 31 +++++++++++++ .../p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d8db77830fe --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.2' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['be7ffbd057cadebe2aa144542fd90c6838c6a083b5e8a9048b8ee3b66b29d5fb'] + +builddependencies = [ + ('binutils', '2.42'), + ('ImageMagick', '7.1.1-38'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..34c086c859a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.4.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['166c1cd4d24309b30d61f79f4a9114b7b2313d7450912277855ff5dfd7cd4a06'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From 6f238ee392ff66428d1a5e09dd2bad1874e3c553 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Sep 2024 08:50:48 +0200 Subject: [PATCH 503/553] fix value for $BIG_SCAPE_HTML_PATH for BiG-SCAPE v1.1.9 --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb index 87ffb021f06..59f7c1a7cd5 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -40,9 +40,11 @@ sanity_pip_check = True options = {'modulename': 'bigscape'} +local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape' + sanity_check_paths = { 'files': ['bin/bigscape'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'dirs': [local_lib_py_bigscape_path], } sanity_check_commands = [ @@ -50,7 +52,7 @@ sanity_check_commands = [ ] modextravars = { - 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path, } modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" From 09d918de048a1a7ff52ae99f68f744a598760899 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 09:05:56 +0200 Subject: [PATCH 504/553] Fix style --- .../g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb | 10 +++------- .../m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb | 4 ++-- 2 files changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb index 62484b4a3e8..e6ca0d7b0aa 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -8,7 +8,7 @@ description = """ GitPython is a python library used to interact with Git reposi toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -builddependencies = [('binutils', '2.42'),] +builddependencies = [('binutils', '2.42')] dependencies = [ ('Python', '3.12.3'), ('git', '2.45.1'), @@ -18,12 +18,8 @@ sanity_pip_check = True use_pip = True exts_list = [ - ('smmap', '5.0.1', { - 'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62'], - }), - ('gitdb', '4.0.11', { - 'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b'], - }), + ('smmap', '5.0.1', {'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62']}), + ('gitdb', '4.0.11', {'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b']}), (name, version, { 'modulename': 'git', 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb index f5cc55d6ff3..04b5629d6bf 100644 --- a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] -builddependencies = [('binutils', '2.42'),] -dependencies = [('Python', '3.12.3'),] +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] download_dep_fail = True sanity_pip_check = True From 4f82480bbc82b2912a3befb929eb044719d0034e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Sep 2024 09:29:54 +0200 Subject: [PATCH 505/553] remove whitespace from empty line in chopper easyconfig --- easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb index df0b3abaa21..b1788fb34f9 100644 --- a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -303,7 +303,6 @@ crates = [ ('windows_x86_64_msvc', '0.52.5'), ('xz2', '0.1.7'), ] - sanity_check_paths = { 'files': ['bin/chopper'], 'dirs': [], From 99107f64310990f97009e53f0119afd324212b9b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 10:03:19 +0200 Subject: [PATCH 506/553] avoid missing symbol in mclust extension of R-4.0.3-foss-2020b --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8b9d1c97fe..9d09c819514 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -57,6 +57,10 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + configopts = "--with-pic --enable-threads --enable-R-shlib" # some recommended packages may fail in a parallel build (e.g. Matrix), and # we're installing them anyway below From 1cfab50d0fa131df4d5108c42cce656c99a1ad78 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 17 Sep 2024 17:14:30 +0200 Subject: [PATCH 507/553] Avoid test-suite fail for ELSI --- easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb index 1ac711b9cf5..a1be84f6de9 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -38,6 +38,10 @@ build_internal_pexsi = True configopts = '-DENABLE_BSEPACK=ON ' +# Tests use 4 MPI ranks, they require a minimum of 4 cores +# Map each MPI process to a single CPU core to avoid tests fails +pretestopts = "export OMPI_MCA_rmaps_base_mapping_policy=slot:PE=1 && " + runtest = True moduleclass = 'math' From 26b7160f205a46edf86305ed85423906ddb3e479 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 17 Sep 2024 16:41:06 +0100 Subject: [PATCH 508/553] adding easyconfigs: CREST-2.12-gfbf-2023b.eb and patches: CREST-2.12-longline.patch --- .../c/CREST/CREST-2.12-gfbf-2023b.eb | 44 +++++++++++++++++++ .../c/CREST/CREST-2.12-longline.patch | 16 +++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb new file mode 100644 index 00000000000..87ae95876bf --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb @@ -0,0 +1,44 @@ +# Author: Jasper Grimm (UoY) +# Update to 2.12: +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.12' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['CREST-2.12-longline.patch'] +checksums = [ + {'v2.12.tar.gz': '390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'}, + {'CREST-2.12-longline.patch': '596ca2bcce3bbdfe99a3849934f41b388fb763a4898240091593b9b6a454fea9'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [('xtb', '6.7.1')] # required to run the program + +# Simple test command just to check if the program is working: +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch new file mode 100644 index 00000000000..c3b84785f5f --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch @@ -0,0 +1,16 @@ +Dealing with a long line, which gfortran does not like +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/crest-2.12.orig/src/qcg/solvtool.f90 b/crest-2.12/src/qcg/solvtool.f90 +index cec514c..f38b576 100644 +--- a/crest-2.12.orig/src/qcg/solvtool.f90 ++++ b/crest-2.12/src/qcg/solvtool.f90 +@@ -3158,7 +3158,8 @@ subroutine check_prog_path_iff(env) + str=trim(str) + open(unit=27, file=str, iostat=ios) + read(27,'(a)',iostat=ios) path +- if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' ++ if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at & ++ https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' + + end subroutine check_prog_path_iff + From 27cbe9bf42c0bd0649750cd5df720c2fba796d8c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Sep 2024 12:38:01 +0200 Subject: [PATCH 509/553] fix build of librosa in somve environments --- easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb index 444e2ba800d..c26fed6c2e3 100644 --- a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb +++ b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb @@ -27,7 +27,6 @@ use_pip = True exts_list = [ ('soxr', '0.3.7', { - 'preinstallopts': 'python -m build && ', 'checksums': ['436ddff00c6eb2c75b79c19cfdca7527b1e31b5fad738652f044045ba6258593'], }), ('audioread', '3.0.1', { From dfd515d50bb3c3e598035cccab7b4de55919d1fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Sep 2024 12:56:22 +0200 Subject: [PATCH 510/553] Fix repeated sanity check runs in manta --- .../m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 4 +--- .../m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb | 2 +- .../m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb | 2 +- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index 4587e8e91df..ff224b45ba2 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -62,9 +62,7 @@ sanity_check_paths = { 'dirs': ['libexec'], } -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb index 8e5943d0213..2d6c80a9b71 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb index 0b2b3af8477..7633e9131e0 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', From a025c619b617c24a2be3a86dcad69d1bb25b477d Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 18 Sep 2024 13:32:29 +0000 Subject: [PATCH 511/553] use eb-built libnsl for git-annex --- .../git-annex-10.20230802-GCCcore-12.2.0.eb | 1 + .../git-annex-10.20230802-GCCcore-12.3.0.eb | 1 + .../git-annex-10.20240731-GCCcore-13.3.0.eb | 1 + .../l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ .../libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb | 28 ++++++++++++++++ 5 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..58d3de407c2 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -16,6 +16,7 @@ dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.38.1', '-nodocs'), + ('libnsl', '2.0.0'), ] sources = [{ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..0e7cce68755 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), + ('libnsl', '2.0.1' ), ] sources = [{ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb index 89c70af2f45..8b981e6ea6c 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.10.1', '-x86_64', SYSTEM), ('Stack', '3.1.1', '-x86_64', SYSTEM), ('git', '2.45.1'), + ('libnsl', '2.0.1'), ] sources = [{ diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ee8ad125324 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libtirpc', '1.3.3'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..30a34609ef9 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.5' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['1e0b0c7231c5fa122e06c0609a76723664d068b0dba3b8219b63e6340b347860'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 199e765b7a77699c90c8069fd967bc0c92df0277 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 18 Sep 2024 13:36:54 +0000 Subject: [PATCH 512/553] correct libtirpc version --- easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb index ee8ad125324..818f1687a15 100644 --- a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('libtirpc', '1.3.3'), + ('libtirpc', '1.3.5'), ] # Provide a symlink for libnsl.so.1, which used to be part of glibc. From b8489cccbd65868ee040eebcf6ab58848d0bf12f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 18 Sep 2024 16:37:52 +0200 Subject: [PATCH 513/553] adding easyconfigs: CREST-3.0.2-foss-2023a.eb --- .../c/CREST/CREST-3.0.2-foss-2023a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb new file mode 100644 index 00000000000..5490dcf0578 --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CREST' +version = '3.0.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/crest-lab', + 'repo_name': 'crest', + 'tag': 'v%s' % version, + 'recursive': True, + }, +}] +checksums = ['010637e0c47a9cb89d8507e5f5ed9e4494f333fe21cd0fd3cbaa983d566eeccc'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('dftd4', '3.7.0'), + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), + ('xtb', '6.6.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' From 7272e21b6dae3abd9680d8f77f0567ccc4708e35 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 18 Sep 2024 16:50:40 +0200 Subject: [PATCH 514/553] remove checksum --- easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb index 5490dcf0578..38fc051e0fb 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = [{ 'recursive': True, }, }] -checksums = ['010637e0c47a9cb89d8507e5f5ed9e4494f333fe21cd0fd3cbaa983d566eeccc'] +checksums = [None] builddependencies = [('CMake', '3.26.3')] From 729d84cee11662133e6fb8d6c1aaa4c26a889b96 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 18 Sep 2024 17:38:46 +0200 Subject: [PATCH 515/553] Fix name of CREST to indicate it is a pre-release --- ...240319-gfbf-2023a.eb => CREST-3.0pre-20240319-gfbf-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/CREST/{CREST-20240319-gfbf-2023a.eb => CREST-3.0pre-20240319-gfbf-2023a.eb} (98%) diff --git a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb similarity index 98% rename from easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb rename to easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb index 7649571fc62..4247fa23773 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb @@ -5,7 +5,7 @@ easyblock = 'CMakeMake' name = 'CREST' -version = '20240319' +version = '3.0pre-20240319' _commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' From 4a91a8842b05c7a0f154f33547d61065f1f5c863 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 19 Sep 2024 07:01:27 +0000 Subject: [PATCH 516/553] correct checksum --- .../easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb index 30a34609ef9..a9fc2a5d749 100644 --- a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_BZ2] -checksums = ['1e0b0c7231c5fa122e06c0609a76723664d068b0dba3b8219b63e6340b347860'] +checksums = ['9b31370e5a38d3391bf37edfa22498e28fe2142467ae6be7a17c9068ec0bf12f'] configopts = '--enable-static --enable-shared --disable-gssapi' From 9c622192222fbe0e615d09c54a1daf24e263b058 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 19 Sep 2024 08:54:09 +0000 Subject: [PATCH 517/553] lint --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 0e7cce68755..5b362fb5873 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), - ('libnsl', '2.0.1' ), + ('libnsl', '2.0.1'), ] sources = [{ From 07f3b358137c09fd8a7b37bfc05181b4f7cee086 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 19 Sep 2024 12:30:50 +0200 Subject: [PATCH 518/553] adding easyconfigs: MPICH-4.2.2-GCC-13.3.0.eb --- .../m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..629c5f4dcbc --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -0,0 +1,21 @@ +name = 'MPICH' +version = '4.2.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] + +dependencies = [ + ('UCX', '1.16.0'), +] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + + +moduleclass = 'mpi' From dabd4a3f99512567b35f88170421b4a6864d8452 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 13:44:13 +0200 Subject: [PATCH 519/553] adding easyconfigs: NanoFilt-2.8.0-foss-2023b.eb --- .../n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb new file mode 100644 index 00000000000..1aef705dc4e --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 2ebaa9b9ab21a438ac5fdf82fd3edbbd3755aeed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 13:45:08 +0200 Subject: [PATCH 520/553] adding easyconfigs: qcat-1.1.0-foss-2023b.eb --- .../q/qcat/qcat-1.1.0-foss-2023b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb new file mode 100644 index 00000000000..347b09bccf3 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' From e984d083f4d8116c13bc2e6ab234708514b3a328 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 13:46:34 +0200 Subject: [PATCH 521/553] adding easyconfigs: CD-HIT-4.8.1-GCC-13.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1a0cf57158 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) +# Update: Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.38.0'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' From 7829eb6998fe3d886225ba1b19ca98d3c34c267d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 13:48:00 +0200 Subject: [PATCH 522/553] adding easyconfigs: minimap2-2.28-GCCcore-13.2.0.eb --- .../minimap2/minimap2-2.28-GCCcore-13.2.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..94f332d290b --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +# Update Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.28' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['ffa5712735d229119f8c05722a0638ae0cc15aeb8938e29a3e52d5da5c92a0b4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From 423df391a7a18d4644d5f952f532facd1bd5fa25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 13:49:08 +0200 Subject: [PATCH 523/553] adding easyconfigs: Racon-1.5.0-GCCcore-13.2.0.eb --- .../r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..de4df21150d --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('git', '2.42.0'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From be3e4102b2f512a31e2b98add3d59bb1101492ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 14:03:00 +0200 Subject: [PATCH 524/553] adding easyconfigs: decona-1.4-20240731-foss-2023a.eb, qcat-1.1.0-foss-2023a.eb --- .../decona/decona-1.4-20240731-foss-2023a.eb | 41 +++++++++++++++++++ .../q/qcat/qcat-1.1.0-foss-2023a.eb | 35 ++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb create mode 100644 easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb new file mode 100644 index 00000000000..3e1eb388a12 --- /dev/null +++ b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'decona' +version = '1.4-20240731' +local_commit = 'f7488ad' + +homepage = 'https://github.com/Saskia-Oosterbroek/decona' +description = "fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Saskia-Oosterbroek/decona/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7504160481ccdd3410fc79348c01a9a3bf0795ad73679cc305e1dcdf3e395962'] + +dependencies = [ + ('Python', '3.11.3'), + ('NanoFilt', '2.8.0'), + ('qcat', '1.1.0'), + ('CD-HIT', '4.8.1'), + ('minimap2', '2.26'), + ('Racon', '1.5.0'), + ('medaka', '1.11.3'), + ('BLAST+', '2.14.1'), +] + +fix_python_shebang_for = ['decona'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['decona'], + 'dirs': [], +} + +sanity_check_commands = ["decona -v | grep 'This is Decona %s'" % version.split('-')[0]] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0c20434dec2 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' From a40c75844c4cf588efced351b7373c67488afb46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 14:27:40 +0200 Subject: [PATCH 525/553] adding easyconfigs: LMDB-0.9.31-GCCcore-13.2.0.eb --- .../l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..946dd8e0961 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' From c371929a82a584ba60fa72fe29be88bd9a52c935 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 16:22:19 +0200 Subject: [PATCH 526/553] adding easyconfigs: awscli-2.17.54-GCCcore-13.2.0.eb --- .../a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9b70b1a9008 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.17.54' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), # required for awscrt +] + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('ruamel.yaml', '0.18.6'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'], + }), + ('botocore', '1.35.22', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'], + }), + ('s3transfer', '0.10.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'], + }), + ('prompt_toolkit', '3.0.47', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'], + }), + ('distro', '1.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'], + }), + ('awscrt', '0.21.5', { + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + 'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'], + }), + # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'` + # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550 + ('urllib3', '1.26.20', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'], + }), + (name, version, { + # version requirements are too strict + 'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' From 100bc746fac841c86af68e76ba344f2ad04d5a9a Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 19 Sep 2024 19:28:29 +0200 Subject: [PATCH 527/553] don't use name template in url --- easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb index 629c5f4dcbc..2b2b2185ecc 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -7,7 +7,7 @@ of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" toolchain = {'name': 'GCC', 'version': '13.3.0'} -source_urls = ['https://www.%(namelower)s.org/static/downloads/%(version)s'] +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] From af0c51f8e3b48ddfbb073442c1d06317e3fcaf07 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 19 Sep 2024 21:06:09 +0200 Subject: [PATCH 528/553] avoid writing to ~/.stack file for git-annex --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- .../g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..efe47052c14 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -29,7 +29,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..9761a2d03a6 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -31,7 +31,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb index 89c70af2f45..b04d3b5f5bb 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -31,7 +31,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ From 57ef341c679aef1f6d41adac979c3846dd153270 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 20 Sep 2024 15:09:38 +0200 Subject: [PATCH 529/553] adding easyconfigs: MCR-R2022b.10.eb, MCR-R2023b.9.eb --- easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb new file mode 100644 index 00000000000..43dcfb25294 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2022b' # runtime version 9.13 +local_update = '10' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['5bcee3f2be7a4ccb6ed0b7d8938eca7b33e4a0d81ec5351d6eb06150a89245eb'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb new file mode 100644 index 00000000000..b6832290ecb --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2023b' # runtime version 23.2 +local_update = '9' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['ef69a624806aa3864d692a88a67d969e3b641ae296b4a091969185ef056f13bd'] + +moduleclass = 'math' From 985ed3c6e5fda49a1197530c0859a295ad4d86e4 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 20 Sep 2024 15:11:44 +0200 Subject: [PATCH 530/553] add sanity_check_commands --- .../g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb index 7b3db4cc18b..fbe1458a01a 100644 --- a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['%s | grep "Info: GOMC"' % x for x in _gomc_exe] + moduleclass = 'chem' From bde569eaea07f752c0adb28bae0a4cdce71b8ed4 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 20 Sep 2024 15:27:11 +0200 Subject: [PATCH 531/553] minor change Co-authored-by: Alex Domingo --- easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb index fb71ad7ff19..3b42e01a2be 100644 --- a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -24,9 +24,15 @@ sanity_check_paths = { 'dirs': [], } +_clumpp_test_cmd = [ + "tmpdir=$(mktemp -d)", + "cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir", + "cd $tmpdir", + "CLUMPP", +] + sanity_check_commands = [ - 'tmpdir=$(mktemp -d) && cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir/ && ' - 'cd $tmpdir && CLUMPP', + " && ".join(_clumpp_test_cmd), ] moduleclass = 'bio' From 364089ed5444765ecfdf949083dcc931673affd9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 20 Sep 2024 15:42:57 +0200 Subject: [PATCH 532/553] Remove broken easyconfig for pre-release --- .../CREST/CREST-3.0pre-20240319-gfbf-2023a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb deleted file mode 100644 index 4247fa23773..00000000000 --- a/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Jasper Grimm (UoY) -# Update to 2.12: -# Author: J. Sassmannshausen (Imperial College London) - -easyblock = 'CMakeMake' - -name = 'CREST' -version = '3.0pre-20240319' -_commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' - -homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' -description = """CREST is an utility/driver program for the xtb program. Originally it was designed - as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, - but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally - the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb - program) and tool for the creation and analysation of structure ensembles. -""" - -toolchain = {'name': 'gfbf', 'version': '2023a'} -toolchainopts = {'opt': True, 'optarch': True, 'extra_fflags': '-ffree-line-length-none'} - -separate_build_dir = False - -github_account = 'grimme-lab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['770b7ca72bc47bc4e1ffd8ca56566df7b03f4d3b702b04ec6b83bad9a125884d'] - -builddependencies = [('CMake', '3.26.3')] - -dependencies = [('xtb', '6.6.1')] # required to run the program - -# Simple test command just to check if the program is working: -test_cmd = 'export PATH=%%(builddir)s/%%(namelower)s-%s:$PATH && ' % _commit -test_cmd += 'cd %%(builddir)s/%%(namelower)s-%s/examples/expl-0/ && ./run.sh ' % _commit - -sanity_check_paths = { - 'files': ['bin/%s' % name.lower()], - 'dirs': [], -} - -sanity_check_commands = ["crest -h", "crest --cite"] - -moduleclass = 'chem' From 927589bdcb88566f9c72b894a2fe3ccfb27e6b3a Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 20 Sep 2024 15:51:19 +0200 Subject: [PATCH 533/553] adding easyconfigs: Panoply-5.5.1.eb --- .../easyconfigs/p/Panoply/Panoply-5.5.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb diff --git a/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb new file mode 100644 index 00000000000..f82b44f3ee5 --- /dev/null +++ b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'Panoply' +version = '5.5.1' + +homepage = 'https://www.giss.nasa.gov/tools/panoply' +description = "Panoply plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets." + + +toolchain = SYSTEM + +source_urls = ['https://www.giss.nasa.gov/tools/panoply/download/'] +sources = ['%(name)sJ-%(version)s.tgz'] +checksums = ['14196be2dd83721e475dfa0b230859b9e102bfdcc62119536ececbf8dcbbbb96'] + +dependencies = [ + ('Java', '11', '', SYSTEM), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mv %(installdir)s/panoply.sh %(installdir)s/bin', + 'sed -i "s,jars,../jars,g" %(installdir)s/bin/panoply.sh', + 'ln -s %(installdir)s/bin/panoply.sh %(installdir)s/bin/panoply', +] + +sanity_check_paths = { + 'files': ['bin/panoply'], + 'dirs': ['jars'] +} + +moduleclass = 'vis' From 819ef0f4897cd2d5effe3c9a2067fa079f201f37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 21:39:59 +0200 Subject: [PATCH 534/553] adding easyconfigs: SignalP-6.0h-foss-2023a-fast.eb --- .../s/SignalP/SignalP-6.0h-foss-2023a-fast.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb new file mode 100644 index 00000000000..8e65da2a7d7 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 012d01b2c6b14db2ab1603a7305e10b9952dcfd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 21:40:14 +0200 Subject: [PATCH 535/553] adding easyconfigs: SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb --- ...ignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb new file mode 100644 index 00000000000..db9e6fe2fb3 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-CUDA-%(cudaver)s-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 68ad2d823fd083d6850a87902927317d76821bf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 21:48:49 +0200 Subject: [PATCH 536/553] {ai}[foss/2023a] face-recognition v1.3.0, dlib v19.24.6 w/ CUDA 12.1.1 --- .../dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++ ...ecognition-1.3.0-foss-2023a-CUDA-12.1.1.eb | 45 +++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..0e7c0ccb880 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'dlib' +version = '19.24.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +# dlib can use BLAS/LAPACK, so using full toolchain +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('Python', '3.11.3'), + ('libjxl', '0.8.2'), + ('X11', '20230603'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " +preinstallopts += "sed -i 's/BLAS_REFERENCE cblas/BLAS_REFERENCE flexiblas/g' dlib/cmake_utils/find_blas.cmake && " + +#installopts = """--global-option="--compiler-flags='$CXXFLAGS'" """ + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..d06d8172e1d --- /dev/null +++ b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'face-recognition' +version = '1.3.0' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/ageitgey/face_recognition' +description = """Recognize and manipulate faces from Python or from the command line with + the world’s simplest face recognition library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('dlib', '19.24.6', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('face-recognition-models', '0.3.0', { + 'sources': ['face_recognition_models-%(version)s.tar.gz'], + 'checksums': ['b79bd200a88c87c9a9d446c990ae71c5a626d1f3730174e6d570157ff1d896cf'], + }), + (name, version, { + 'sources': ['face_recognition-%(version)s.tar.gz'], + 'checksums': ['5e5efdd1686aa566af0d3cc1313b131e4b197657a8ffd03669e6d3fad92705ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/face_detection', 'bin/face_recognition'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "face_detection --help", + "face_recognition --help", +] + +sanity_pip_check = True + +moduleclass = 'ai' From 52c3add6d6ac375b4469cbe49ca129bf3335c721 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 22:00:01 +0200 Subject: [PATCH 537/553] add patch to link dlib with FlexiBLAS --- .../dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb | 6 ++++- .../d/dlib/dlib-19.24.6_FlexiBLAS.patch | 25 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb index 0e7c0ccb880..ff51c90bca5 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb @@ -17,7 +17,11 @@ toolchainopts = {'pic': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d'] +patches = ['dlib-19.24.6_FlexiBLAS.patch'] +checksums = [ + {'dlib-19.24.6.tar.gz': '77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d'}, + {'dlib-19.24.6_FlexiBLAS.patch': '47fb348d5f1cd064a135d33cf49fdef56ade24a64218311743076cb6b313738b'}, +] builddependencies = [ ('CMake', '3.26.3'), diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch new file mode 100644 index 00000000000..bb12f35adbc --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch @@ -0,0 +1,25 @@ +use FlexiBLAS as BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) +diff -ru dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake dlib-19.24.6/dlib/cmake_utils/find_blas.cmake +--- dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake 2024-02-18 14:43:31.000000000 +0100 ++++ dlib-19.24.6/dlib/cmake_utils/find_blas.cmake 2024-09-20 20:35:35.927348475 +0200 +@@ -66,17 +66,15 @@ + + # First, search for libraries via pkg-config, which is the cleanest path + find_package(PkgConfig) +- pkg_check_modules(BLAS_REFERENCE cblas) +- pkg_check_modules(LAPACK_REFERENCE lapack) ++ pkg_check_modules(BLAS_REFERENCE flexiblas) + # Make sure the cblas found by pkgconfig actually has cblas symbols. + SET(CMAKE_REQUIRED_LIBRARIES "${BLAS_REFERENCE_LDFLAGS}") + CHECK_FUNCTION_EXISTS(cblas_ddot PKGCFG_HAVE_CBLAS) + if (BLAS_REFERENCE_FOUND AND LAPACK_REFERENCE_FOUND AND PKGCFG_HAVE_CBLAS) + set(blas_libraries "${BLAS_REFERENCE_LDFLAGS}") +- set(lapack_libraries "${LAPACK_REFERENCE_LDFLAGS}") + set(blas_found 1) + set(lapack_found 1) +- set(REQUIRES_LIBS "${REQUIRES_LIBS} cblas lapack") ++ set(REQUIRES_LIBS "${REQUIRES_LIBS} flexiblas") + message(STATUS "Found BLAS and LAPACK via pkg-config") + return() + endif() From 16d62910720cd11e1b55e1924ea22d64d8ebf277 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 22:29:26 +0200 Subject: [PATCH 538/553] minor cleanup in easyconfig for dlib v19.24.6 --- .../easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb index ff51c90bca5..c3ffb7be647 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb @@ -15,7 +15,6 @@ computing environments.""" toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'pic': True} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['dlib-19.24.6_FlexiBLAS.patch'] checksums = [ @@ -41,8 +40,6 @@ use_pip = True preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " preinstallopts += "sed -i 's/BLAS_REFERENCE cblas/BLAS_REFERENCE flexiblas/g' dlib/cmake_utils/find_blas.cmake && " -#installopts = """--global-option="--compiler-flags='$CXXFLAGS'" """ - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 7875a08513e2dfac29b0b0d85cc8817e136446e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 22:45:52 +0200 Subject: [PATCH 539/553] adding easyconfigs: DeepLoc-2.0-foss-2023a.eb, ONNX-Runtime-1.19.2-foss-2023a.eb, ESM-2-2.0.0-foss-2023a.eb --- .../d/DeepLoc/DeepLoc-2.0-foss-2023a.eb | 59 +++++++++++++++++++ .../e/ESM-2/ESM-2-2.0.0-foss-2023a.eb | 40 +++++++++++++ .../ONNX-Runtime-1.19.2-foss-2023a.eb | 50 ++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb new file mode 100644 index 00000000000..558d3f61871 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2'), + ('ESM-2', '2.0.0'), # for fair-esm + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', '2.2.1'), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb new file mode 100644 index 00000000000..8b461b544cc --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +use_pip = True +sanity_pip_check = True + +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('fair-esm', version, { + 'modulename': "esm, esm.pretrained", + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb new file mode 100644 index 00000000000..440ae5d93e7 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + 'a36511dc07c5c964b916697e42e366fa43c48cdb3d3503578d78cef30417cb84', + local_whl_tmpl % ('aarch64', 'aarch64'): + 'c1dfe4f660a71b31caa81fc298a25f9612815215a47b286236e61d540350d7b6', + }], + 'modulename': 'onnxruntime', + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' From ba1c35b638068d5b07f6c7ab715523a913047b35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2024 22:46:40 +0200 Subject: [PATCH 540/553] adding easyconfigs: DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb, ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb --- .../DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb | 61 +++++++++++++++++ ...X-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb | 67 +++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..379eb0439bb --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('ESM-2', '2.0.0', versionsuffix), # for fair-esm + ('PyTorch', '2.1.2', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..91b8598722a --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + '562fc7c755393eaad9751e56149339dd201ffbfdb3ef5f43ff21d0619ba9045f', + }], + 'modulename': 'onnxruntime', + }), +] + +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + +sanity_pip_check = True + +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' From fa7e7e41a87024ac86c073405793108e3a6ca4b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 10:02:33 +0200 Subject: [PATCH 541/553] prepare release notes for EasyBuild v4.9.4 + bump version to 4.9.4 --- RELEASE_NOTES | 33 +++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 34 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 590c5db69f2..9d2bef5bef9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,39 @@ The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for incl. 41 different (compiler) toolchains. +v4.9.4 (22 september 2024) +-------------------------- + +update/bugfix release + +- added example easyconfig files for XXX new software packages: + - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), + MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), + xskillscore (#21351) +- added additional easyconfigs for various supported software packages, including: + - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0, + GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43, + GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4, + LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0, + NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0, + protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1, + scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2, + VirtualGL 3.1.1, zlib-ng 2.2.1 +- minor enhancements, including: + - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056) + - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337) +- various bug fixes, including: + - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419) + - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429) + - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434) + - fix repeated sanity check runs in manta easyconfigs (#21435) + - fix test_easyconfig_locations when easyconfigs index is present (#21394) + - use proper dependency for libnsl in git-annex (#21441) + - avoid writing into ~/.stack directory during build for git-annex (#21452) +- other changes: + - remove exts_default_options from TensorFlow 2.3.1 (#21290) + + v4.9.3 (14 September 2024) -------------------------- diff --git a/setup.py b/setup.py index 47b7fc09bd1..a2774a7bbe2 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.4.dev0' +VERSION = '4.9.4' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 166f3a68b5e34d20abf63a979ccac7f00a14f966 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 22 Sep 2024 11:23:33 +0200 Subject: [PATCH 542/553] fix test scripts instead of copying files --- .../easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb index 5a8538a55cb..ac13f1e800f 100644 --- a/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb @@ -19,10 +19,11 @@ builddependencies = [ srcdir = 'cmake' -# copy executables into bin directory -test_cmd = 'find -maxdepth 1 -mindepth 1 -type f -executable |xargs -I % cp % ../tinker/bin/ && ' -test_cmd += 'cd ../tinker/test/ && ' -# run all .run scripts in the test directory +test_cmd = 'cd ../tinker/test/ && ' +# fix path to executables in .run test scripts +test_cmd += r"sed -i 's|\.\./bin|../../easybuild_obj|g' *.run && " +# run all .run scripts +# manually compare test results with .log files in test dir # (ifabp succeeds but exits with a memory error) test_cmd += 'for x in *.run; do echo "START TEST: $x" && ./$x; done' From 6d1f4b973a5c2ef81be505bfd3cdcaee5dec5809 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 15:02:27 +0200 Subject: [PATCH 543/553] fix counts in release notes for EasyBuild v4.9.4 --- RELEASE_NOTES | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9d2bef5bef9..457e390f6b9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages, +The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages, incl. 41 different (compiler) toolchains. @@ -12,7 +12,7 @@ v4.9.4 (22 september 2024) update/bugfix release -- added example easyconfig files for XXX new software packages: +- added example easyconfig files for 14 new software packages: - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), xskillscore (#21351) From 39cdebd7bd2cb4a9c170ee22439401316b2e7a25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 18:17:41 +0200 Subject: [PATCH 544/553] adding easyconfigs: EasyBuild-4.9.4.eb --- .../e/EasyBuild/EasyBuild-4.9.4.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb new file mode 100644 index 00000000000..13ee3ee70b1 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.4' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/bd/25/512d9e895a86f4df198274e8a5f6868406d97cc75da9acc5797f78139b52/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/d7/b0/b9289c78fafc21c5c01b225aeee89c69914166742e5f80955d49ed8f9722/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/ed/2c/7b2b22235ffe9310a93cbfef06fb3723466aa8ccc4aca4888b59433e55a6/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.4.tar.gz': '5b380a2e3a359f64f06789c390200b922a840f6b10b441e5163696a34bd9bc27'}, + {'easybuild_easyblocks-4.9.4.tar.gz': '1272f1e294090caafde8cbda72ae344ef400fdd161163781f67b3cffe761dd62'}, + {'easybuild_easyconfigs-4.9.4.tar.gz': 'beee4e098f5fee18f2029d6a0b893549aba26e075b147cc0008cb16fd4c8d982'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 601efee69569e15124fda36aa75165325f25fe2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 19:33:02 +0200 Subject: [PATCH 545/553] bump version to 4.9.5dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a2774a7bbe2..15cbcf7470d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.4' +VERSION = '4.9.5.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From e60a01b44e6ea5c7b928702e11c27c2f699eaedf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 22 Sep 2024 21:08:37 +0100 Subject: [PATCH 546/553] Update RELEASE_NOTES Minor typo fix --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 457e390f6b9..af2e74ae887 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,7 +7,7 @@ The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for incl. 41 different (compiler) toolchains. -v4.9.4 (22 september 2024) +v4.9.4 (22 September 2024) -------------------------- update/bugfix release From 6331d02e2497bca6e5714629e7de2b0996aa2664 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Sep 2024 15:14:03 +0200 Subject: [PATCH 547/553] use -lncurses rather than -ltermcap for Term::ReadLine::GNU Perl extension --- .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 2 ++ .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 2 ++ .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb | 2 ++ easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 ++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 2 ++ 7 files changed, 14 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 7e166bd251f..1c02282d891 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1772,6 +1772,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9f4f7abbc69ea58ab7f24992d47f7391bb4aed6fb701fedaeb1a9f1cdc7fab8a'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 154ff6fee8f..35ab629e89e 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1775,6 +1775,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb index 7ea28abbcbb..cee5ad02ae6 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb @@ -1781,6 +1781,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 87d1215a591..944e2124f79 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1505,6 +1505,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.62', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index ec2e80d1840..497e05a273d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1610,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 11d6a08c241..54c05db3b92 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1603,6 +1603,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 2b37316b16c..3a6727d62a4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1610,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', From a6c88f9d86bab8261c5737003426eecaff184994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Sep 2024 15:40:09 +0200 Subject: [PATCH 548/553] adding easyconfigs: Whisper-20231117-foss-2023a-CUDA-12.1.1.eb --- ...Whisper-20231117-foss-2023a-CUDA-12.1.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..53a2aa183b1 --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20231117' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'checksums': ['7af424181436f1800cc0b7d75cf40ede34e9ddf1ba4983a910832fcf4aade4a4'], + 'modulename': 'whisper', + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai' From 9ea93b473adea990b6a59aaa200546bb7ffee2af Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 23 Sep 2024 17:34:23 +0200 Subject: [PATCH 549/553] Add support to build ALL-0.9.2 with foss-2023b toolchain --- .../easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb new file mode 100644 index 00000000000..33ac11b9620 --- /dev/null +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ALL' +version = '0.9.2' + +homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing' +description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic +domain-based load balancing into particle based simulation codes. The library +is developed in the Simulation Laboratory Molecular Systems of the Jülich +Supercomputing Centre at Forschungszentrum Jülich.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"] +sources = ['loadbalancing-v%(version)s.tar.gz'] +checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Boost', '1.82.0'), # only needed for tests +] + +dependencies = [ + ('VTK', '9.3.0'), +] + +configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' +configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod', + 'lib/libALL.a', 'lib/libALL_fortran.a' + ], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' From 37f7db99861ef133634d7236c91fb62b21a61e77 Mon Sep 17 00:00:00 2001 From: Julian Morillo Date: Mon, 23 Sep 2024 17:41:14 +0200 Subject: [PATCH 550/553] Updated CMAKE and Boost versions in dependencies --- easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb index 33ac11b9620..eb1a53ff8da 100644 --- a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb @@ -17,8 +17,8 @@ sources = ['loadbalancing-v%(version)s.tar.gz'] checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] builddependencies = [ - ('CMake', '3.26.3'), - ('Boost', '1.82.0'), # only needed for tests + ('CMake', '3.27.6'), + ('Boost', '1.83.0'), # only needed for tests ] dependencies = [ From 1f5130f8d8319ef3d096dcd371e0490174e8ce6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 24 Sep 2024 14:36:18 +0200 Subject: [PATCH 551/553] add seqPattern, genomation and ChIPseeker to R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 48c86d2ed02..7d2ebad2d77 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1352,6 +1352,15 @@ exts_list = [ ('plyranges', '1.22.0', { 'checksums': ['fcdcad1082fadd1a365dd2d2cc7d955601b737ecd4a567d888d2b445756297fc'], }), + ('seqPattern', '1.34.0', { + 'checksums': ['6037d3685bab94e2d1f6046bdc19369a786a595ef421e6ce7d8a34408a6f4967'], + }), + ('genomation', '1.34.0', { + 'checksums': ['6c7e40caee1115a28617c2a0a0837c92701dbce7511277c078a5957a50e877ed'], + }), + ('ChIPseeker', '1.38.0', { + 'checksums': ['a0d4710fccda620b750f933916acac6d12999a077e1c17632d8823848a2fa82f'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 71f07dbaaef9fc83692e16a7771099851d5cf957 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 24 Sep 2024 14:43:28 +0200 Subject: [PATCH 552/553] adding easyconfigs: pretty-yaml-24.7.0-GCCcore-12.3.0.eb --- .../pretty-yaml-24.7.0-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7a8779a9412 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' From 728b5b9931432b9416f25d3117c964b7aea3c90e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 24 Sep 2024 15:33:31 +0200 Subject: [PATCH 553/553] adding easyconfigs: AUGUSTUS-3.5.0-foss-2023a.eb, lpsolve-5.5.2.11-GCC-12.3.0.eb --- .../a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb | 74 +++++++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb | 33 +++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..2c31ade2eb0 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb @@ -0,0 +1,74 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('GSL', '2.7'), + ('SAMtools', '1.18'), + ('HTSlib', '1.18'), # also provides tabix + ('BCFtools', '1.18'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '7.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.42.0'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb new file mode 100644 index 00000000000..7681d5bf0a9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math'