{bio}[foss/2020a] GROMACS v2020.1 w/ Python 3.8.2

easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb

@@ -0,0 +1,96 @@
+##
+# 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 <wiktor.jurkowski@gmail.com>
+# * Fotis Georgatos <fotis@cern.ch>
+# * George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# * Kenneth Hoste <kenneth.hoste@ugent.be>
+# * Adam Huffman <adam.huffman@crick.ac.uk>
+# * Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+# License::   MIT/GPL
+# 2019.3 version
+# Contribution from the Crick HPC team
+# uploaded by J. Sassmannshausen
+#
+
+name = 'GROMACS'
+version = '2020.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://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 builds
+for both single and double precision.
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020a'}
+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-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
+    'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch',
+    'GROMACS-%(version)s_dont_override_pythonpath_in_tests.patch',
+    'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch',
+]
+checksums = [
+    'e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf',  # gromacs-2020.1.tar.gz
+    # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
+    '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
+    # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch
+    '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06',
+    # GROMACS-2020.1_dont_override_pythonpath_in_tests.patch
+    'dffcafefeb594864c452cbeea3ee13091168c7ab9cd1f63dc8e9d1663dcb928e',
+    # GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch
+    '564c4e97e0dd05df1f45415ab5cc755c6b157880b26a816f7d6f7f98b318c900',
+]
+
+builddependencies = [
+    ('CMake', '3.16.4'),
+    ('scikit-build', '0.10.0', versionsuffix),
+]
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('networkx', '2.4', versionsuffix),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.1.0.1', {
+        'patches': ['gmxapi-0.1.0.1_drop_cmake_requirement.patch'],
+        'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ",
+        'checksums': [
+            '3371075975117a32ffe44e8972a4a9330da416f0054e00ee587cdffb217497a0',  # gmxapi-0.1.0.1.tar.gz
+            # gmxapi-0.1.0.1_drop_cmake_requirement.patch
+            'c58f1d94e7681bb2931ac90929445dc90f1709a9d8d3be78e55adbda797a2e8c',
+        ],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch

@@ -0,0 +1,15 @@
+Don't overwrite PYTHONPATH when executing tests, add to it instead.
+
+Åke Sandgren, 20200309
+diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt
+--- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt	2020-03-03 17:24:49.000000000 +0100
++++ gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt	2020-03-09 09:18:42.707693465 +0100
+@@ -22,7 +22,7 @@
+ get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir)
+ get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY)
+ add_custom_target(gmxapi_extension_pytest
+-                  COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}
++                  COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}
+                   ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR}
+                   DEPENDS gmxapi_extension _gmxapi
+                   WORKING_DIRECTORY ${PLUGINPATH})

easybuild/easyconfigs/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch

@@ -0,0 +1,39 @@
+Fix search for "gmx" binary to allow for double precision builds.
+
+Åke Sandgren, 20200318
+diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py
+--- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py	2020-03-03 17:24:49.000000000 +0100
++++ gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py	2020-03-18 07:19:09.611507575 +0100
+@@ -156,7 +156,7 @@
+     # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary.
+     #  We should be able to get the GMXRC contents and related hints from a gmxapi
+     #  package resource or from module attributes of a ``gromacs`` stub package.
+-    allowed_command_names = ['gmx', 'gmx_mpi']
++    allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']]
+     command = None
+     for command_name in allowed_command_names:
+         if command is not None:
+diff -ru gromacs-2020.1.orig/python_packaging/src/test/conftest.py gromacs-2020.1/python_packaging/src/test/conftest.py
+--- gromacs-2020.1.orig/python_packaging/src/test/conftest.py	2020-03-03 17:24:49.000000000 +0100
++++ gromacs-2020.1/python_packaging/src/test/conftest.py	2020-03-18 07:19:27.535301581 +0100
+@@ -156,7 +156,7 @@
+     # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary.
+     #  We should be able to get the GMXRC contents and related hints from a gmxapi
+     #  package resource or from module attributes of a ``gromacs`` stub package.
+-    allowed_command_names = ['gmx', 'gmx_mpi']
++    allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']]
+     command = None
+     for command_name in allowed_command_names:
+         if command is not None:
+diff -ru gromacs-2020.1.orig/python_packaging/test/conftest.py gromacs-2020.1/python_packaging/test/conftest.py
+--- gromacs-2020.1.orig/python_packaging/test/conftest.py	2020-03-03 17:24:49.000000000 +0100
++++ gromacs-2020.1/python_packaging/test/conftest.py	2020-03-18 07:19:03.967572439 +0100
+@@ -156,7 +156,7 @@
+     # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary.
+     #  We should be able to get the GMXRC contents and related hints from a gmxapi
+     #  package resource or from module attributes of a ``gromacs`` stub package.
+-    allowed_command_names = ['gmx', 'gmx_mpi']
++    allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']]
+     command = None
+     for command_name in allowed_command_names:
+         if command is not None:

easybuild/easyconfigs/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch

@@ -0,0 +1,16 @@
+Drop the cmake requirement from gmxapi, we take that from the dependencies list.
+
+Åke Sandgren, 20200308
+diff -ru gmxapi-0.1.0.1.orig/setup.py gmxapi-0.1.0.1/setup.py
+--- gmxapi-0.1.0.1.orig/setup.py	2019-12-30 12:08:34.000000000 +0100
++++ gmxapi-0.1.0.1/setup.py	2020-03-08 17:00:54.456270981 +0100
+@@ -152,8 +152,7 @@
+     # TODO: (pending infrastructure and further discussion) Replace with CMake variables from GMXAPI version.
+     version='0.1.0.1',
+     python_requires='>=3.5, <3.9',
+-    setup_requires=['cmake>=3.12',
+-                    'setuptools>=28',
++    setup_requires=['setuptools>=28',
+                     'scikit-build>=0.7'],
+
+     packages=['gmxapi', 'gmxapi.simulation'],