{bio}[foss/2021a] GROMACS v2021.3 w/ Python 3.9.5 + CUDA 11.3.1 + PLUMED v2.7.2

easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.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>
+# * J. Sassmannshausen <Crick HPC team>
+# * Dugan Witherick <dugan.witherick@warwick.ac.uk>
+# License::   MIT/GPL
+
+name = 'GROMACS'
+version = '2021.3'
+_plumedver = '2.7.2'
+versionsuffix = '-CUDA-%%(cudaver)s-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 GPU enabled build, containing both MPI and threadMPI builds.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+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-2019_increase_test_timeout_for_GPU.patch',
+    'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch',
+    'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch',
+    'GROMACS-2021.3_skip_test_for_plumed.patch',
+]
+checksums = [
+    'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6',  # gromacs-2021.3.tar.gz
+    # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
+    '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
+    # GROMACS-2019_increase_test_timeout_for_GPU.patch
+    '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234',
+    # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch
+    'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49',
+    # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch
+    '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb',
+    'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018',  # GROMACS-2021.3_skip_test_for_plumed.patch
+]
+
+builddependencies = [
+    ('CMake', '3.20.1'),
+    ('scikit-build', '0.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('networkx', '2.5.1'),
+    ('CUDA', '11.3.1', '', True),
+    ('PLUMED', _plumedver),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.2.0', {
+        'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ",
+        'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'],
+    }),
+]
+
+# PLUMED-2.7.2 does not officially support GROMACS-2021.3, but seems to work fine
+ignore_plumed_version_check = True
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3_skip_test_for_plumed.patch

@@ -0,0 +1,26 @@
+Skip test checking output of 'mdrun -h' when patched with PLUMED, as it adds an extra option '-hrex'
+Author: Samuel Moors (Vrije Universiteit Brussel)
+diff -ur gromacs-2021.3.orig/src/programs/mdrun/tests/CMakeLists.txt gromacs-2021.3/src/programs/mdrun/tests/CMakeLists.txt
+--- gromacs-2021.3.orig/src/programs/mdrun/tests/CMakeLists.txt	2021-08-18 11:49:23.000000000 +0200
++++ gromacs-2021.3/src/programs/mdrun/tests/CMakeLists.txt	2021-11-16 17:04:47.612357764 +0100
+@@ -51,20 +51,6 @@
+ # To avoid running into test timeouts, some end-to-end tests of mdrun
+ # functionality are split off. This can be rearranged in future as we
+ # see fit.
+-set(testname "MdrunOutputTests")
+-set(exename "mdrun-output-test")
+-
+-gmx_add_gtest_executable(${exename}
+-    CPP_SOURCE_FILES
+-        compressed_x_output.cpp
+-        helpwriting.cpp
+-        outputfiles.cpp
+-        trajectory_writing.cpp
+-        # pseudo-library for code for mdrun
+-        $<TARGET_OBJECTS:mdrun_objlib>
+-    )
+-target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+-gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
+ set(testname "MdrunModulesTests")
+ set(exename "mdrun-modules-test")