From f165d5d3f674ad82d9c9332499e259ab0ae5bddc Mon Sep 17 00:00:00 2001 From: Tanmoy Chakraborty Date: Thu, 12 Mar 2026 17:24:44 +0000 Subject: [PATCH 1/5] adding easyconfigs: GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb --- .../GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb new file mode 100644 index 00000000000..06aadfdddbc --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb @@ -0,0 +1,89 @@ +# 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 = '2025.3' +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 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. +""" + +toolchain = {'name': 'foss', 'version': '2025b'} +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-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'}, + {'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', '4.0.3'), + ('scikit-build-core', '0.11.5'), + ('pybind11', '3.0.0'), +] + +dependencies = [ + ('CUDA', '12.9.1', '', SYSTEM), + ('UCX-CUDA', '1.19.0', versionsuffix), + ('Python', '3.13.5'), + ('SciPy-bundle', '2025.07'), + ('networkx', '3.5'), + ('mpi4py', '4.1.0'), +] +# 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 = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'], + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': [ + {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'}, + {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch': + 'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'}, + ], + }), +] + +moduleclass = 'bio' From def383b80290129ba75c86f6d33ed87bb6aae0d0 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Thu, 12 Mar 2026 17:28:15 +0000 Subject: [PATCH 2/5] Update GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb --- .../g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb index 06aadfdddbc..849fa85610d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb @@ -77,7 +77,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.2', { 'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'], - '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" && ', 'checksums': [ {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'}, {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch': From f71db487cdac3b12fb9a239abfcdf0af3226a158 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Thu, 12 Mar 2026 22:36:40 +0000 Subject: [PATCH 3/5] Update GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb --- .../g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb index 849fa85610d..e6bdeee0173 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb @@ -48,6 +48,8 @@ checksums = [ '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2025.2_workaround-arm-sve512.patch': + 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'}, ] builddependencies = [ From 0ce5dc8584a2dbae05a622cdeb8eb98f7596b6e6 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Thu, 12 Mar 2026 22:50:58 +0000 Subject: [PATCH 4/5] Update GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb --- .../g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb index e6bdeee0173..f5ed5ebb5b5 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb @@ -41,6 +41,7 @@ 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', + 'GROMACS-2025.2_workaround-arm-sve512.patch', ] checksums = [ {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'}, From 3125b2ff2acf67388daf5a10fa683fa2a4928879 Mon Sep 17 00:00:00 2001 From: "Tanmoy Chakraborty, Ph.D." <56235576+tanmoy1989@users.noreply.github.com> Date: Fri, 13 Mar 2026 10:29:48 +0000 Subject: [PATCH 5/5] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb index f5ed5ebb5b5..6fe1617114a 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb @@ -24,8 +24,7 @@ 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. +This is a GPU enabled build, containing both MPI and threadMPI binaries. It also contains the gmxapi extension for the single precision MPI build. """