From d3d32a1ee2fc1fbb780c39560556f526ea7cbb28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jun 2024 23:09:10 +0200 Subject: [PATCH 1/7] adding easyconfigs: GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb --- .../GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb new file mode 100644 index 00000000000..1044e92dadd --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -0,0 +1,88 @@ +# 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 = '2024.2' +versionsuffix = '-CUDA-%(cudaver)s' + +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 binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +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', +] +checksums = [ + {'gromacs-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('CUDA', '12.5.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +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 f45673ce70c38b049d8ba2a2f12d97f58ef09ba1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Jun 2024 23:02:22 +0200 Subject: [PATCH 2/7] fix long line in GROMACS 2024.2 easyconfig --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index 1044e92dadd..3ed35d7e46e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -74,7 +74,8 @@ exts_default_options = { 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" && ', + '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'], From 5dc10572a05a5cde707a33ebe515b1d0a238fea8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Jun 2024 13:19:12 +0200 Subject: [PATCH 3/7] fix version of GROMACS tarball used for gmxapi extension in easyconfig for GROMACS 2024.2 --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index 3ed35d7e46e..e621e24c6ab 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -76,9 +76,9 @@ 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', + 'sources': ['gromacs-%s.tar.gz' % version], 'start_dir': 'python_packaging/gmxapi', - 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + 'checksums': ['802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'], }), ] From 6da26eca53aff1584bca6177bd00bc0e10296fc2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jul 2024 13:54:00 +0200 Subject: [PATCH 4/7] replace scikit-build with scikit-build-core as build dependency for gmxapi in easyconfig for GROMACS 2024.2 --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index e621e24c6ab..f1362b09b76 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -51,7 +51,7 @@ checksums = [ builddependencies = [ ('CMake', '3.27.6'), - ('scikit-build', '0.17.6'), + ('scikit-build-core', '0.9.3'), ] dependencies = [ From 387edbec20b718788369cb4402d63f330f507bd7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jul 2024 13:57:15 +0200 Subject: [PATCH 5/7] increase test timeout by factor 3 for GROMACS 2024.2 --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index f1362b09b76..becde7400dd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -63,6 +63,10 @@ dependencies = [ ('mpi4py', '3.1.5'), ] +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + exts_defaultclass = 'PythonPackage' exts_default_options = { From 853629184e23f140da084e209cebc6279964af7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Jun 2025 14:09:18 +0200 Subject: [PATCH 6/7] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index becde7400dd..5ebd87791a0 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -71,9 +71,6 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, } exts_list = [ From f1a55b5a8f67d91d5dfcded1bf291478dc24365e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Jun 2025 14:10:17 +0200 Subject: [PATCH 7/7] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb --- .../g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb index 5ebd87791a0..866dacc8670 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb @@ -82,9 +82,4 @@ exts_list = [ 'checksums': ['802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'], }), ] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - moduleclass = 'bio'