{bio}[foss/2024a] GROMACS v2024.4 by verdurin · Pull Request #25328 · easybuilders/easybuild-easyconfigs

verdurin · 2026-02-18T17:50:35Z

(created using eb --new-pr)

github-actions · 2026-02-18T17:51:07Z

Updated software `GROMACS-2024.4-foss-2024a.eb`

Diff against GROMACS-2021.0-foss-2023a-20250409-constant-pH-CUDA-12.1.1-PLUMED.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH-CUDA-12.1.1-PLUMED.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH-CUDA-12.1.1-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
index 6f868a8215..56fef165de 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH-CUDA-12.1.1-PLUMED.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
@@ -1,60 +1,85 @@
+# 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>
+# * Christoph Siegert <christoph.siegert@uni-leipzig.de>
+# License::   MIT/GPL
+
 name = 'GROMACS'
-version = '2021.0'
-_date = '-20250409'
-local_commit = '28807b11'
-_cuda_suffix = '-CUDA-%(cudaver)s'
-versionsuffix = f'{_date}-constant-pH{_cuda_suffix}-PLUMED'
-# fork is from v2021.0-beta1, SOVERSION = 6.0.0
-
-homepage = 'https://gitlab.com/gromacs-constantph'
-description = """
-GROMACS constant pH
+version = '2024.4'
 
+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 preliminary version of the GROMACS constant pH code.
-The modified force fields needed for constnat pH.
+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': '2023a'}
-# Currently, separate PME ranks are not supported with MPI
-toolchainopts = {'openmp': True, 'usempi': False}
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'openmp': True, 'usempi': True}
 
-source_urls = ['https://gitlab.com/gromacs-constantph/constantph/-/archive/']
-sources = [{
-    'download_filename': '%s.tar.gz' % local_commit,
-    'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
-}]
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
 patches = [
-    'GROMACS-2021.0-20250409-constant-pH_enable-CUDA-12.1.1.patch',
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+    'GROMACS-2024.1_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'GROMACS-2021.0-28807b11.tar.gz': '88548354e02c872052f2fa662eab5f111421706cb0ea264e94af19e7274d0f78'},
-    {'GROMACS-2021.0-20250409-constant-pH_enable-CUDA-12.1.1.patch':
-     'f1bf5026b92aea6e6ca1265d75aa42976cfa9cf480e6ee5168e935d4380aab3e'},
+    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'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-2024.1_workaround-arm-sve512.patch': '0dfa82a9425322d2b2c250d698ac2065f8c0ce0143df0057e7ec21686d60e5f7'},
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('Doxygen', '1.9.7'),
+    ('CMake', '3.29.3'),
+    ('scikit-build-core', '0.11.1'),
 ]
+
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('PLUMED', '2.9.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('networkx', '3.4.2'),
+    ('mpi4py', '4.0.1'),
+    ('pybind11', '2.12.0'),
 ]
 
-start_dir = 'gromacs-constantph'
+# 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"
 
-plumed = 'patch'
-ignore_plumed_version_check = True
+exts_defaultclass = 'PythonPackage'
 
-# Disable installing the Python gmxapi bindings - python 3.11 not supported
-python_pkg = False
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+}
 
-# Code is not sufficiently covered with tests and some standard GROMACS test might be broken.
-# Thus, make check might end up with errors
-runtest = False
+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" && ',
+        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
+    }),
+]
 
 moduleclass = 'bio'

Diff against GROMACS-2025.2-lmpflf-2025b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
index ec5805ab48..56fef165de 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2024.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -29,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'lmpflf', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -40,31 +40,28 @@ 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',
-    'GROMACS-2025.2_fix-sample_restraint-mpich-launch.patch',
+    'GROMACS-2024.1_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
     {'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-2025.2_workaround-arm-sve512.patch': 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
-    {'GROMACS-2025.2_fix-sample_restraint-mpich-launch.patch':
-     'a910ec50cf296a6bdf8e5d425617d54c13b4ef049b61196487d7dc8a8f674e2c'},
+    {'GROMACS-2024.1_workaround-arm-sve512.patch': '0dfa82a9425322d2b2c250d698ac2065f8c0ce0143df0057e7ec21686d60e5f7'},
 ]
 
 builddependencies = [
-    ('CMake', '4.0.3'),
-    ('scikit-build-core', '0.11.5'),
-    ('pybind11', '3.0.0'),
+    ('CMake', '3.29.3'),
+    ('scikit-build-core', '0.11.1'),
 ]
 
 dependencies = [
-    ('Python', '3.13.5'),
-    ('SciPy-bundle', '2025.07'),
-    ('networkx', '3.5'),
-    ('mpi4py', '4.1.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('networkx', '3.4.2'),
+    ('mpi4py', '4.0.1'),
+    ('pybind11', '2.12.0'),
 ]
 
 # be a bit more forgiving w.r.t. timeouts for GROMACS test suite,
@@ -79,14 +76,9 @@ 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" && ',
-        'checksums': [
-            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
-            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
-             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
-        ],
+        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
     }),
 ]

Diff against GROMACS-2025.2-lfoss-2025b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
index fc29744c2c..56fef165de 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2024a.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2024.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -29,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'lfoss', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -40,28 +40,28 @@ 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',
+    'GROMACS-2024.1_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
     {'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-2025.2_workaround-arm-sve512.patch': 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
+    {'GROMACS-2024.1_workaround-arm-sve512.patch': '0dfa82a9425322d2b2c250d698ac2065f8c0ce0143df0057e7ec21686d60e5f7'},
 ]
 
 builddependencies = [
-    ('CMake', '4.0.3'),
-    ('scikit-build-core', '0.11.5'),
-    ('pybind11', '3.0.0'),
+    ('CMake', '3.29.3'),
+    ('scikit-build-core', '0.11.1'),
 ]
 
 dependencies = [
-    ('Python', '3.13.5'),
-    ('SciPy-bundle', '2025.07'),
-    ('networkx', '3.5'),
-    ('mpi4py', '4.1.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('networkx', '3.4.2'),
+    ('mpi4py', '4.0.1'),
+    ('pybind11', '2.12.0'),
 ]
 
 # be a bit more forgiving w.r.t. timeouts for GROMACS test suite,
@@ -76,14 +76,9 @@ 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" && ',
-        'checksums': [
-            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
-            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
-             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
-        ],
+        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
     }),
 ]

verdurin · 2026-02-19T12:00:59Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-02-19T12:10:10Z

@verdurin: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=25328 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25328 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9761

Test results coming soon (I hope)...

Details

- notification for comment with ID 3926816654 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2026-02-19T12:58:45Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 48 mins 18 secs) (1 easyconfigs in total)
jsczen3c3.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/43c2079b05b5b8d7ab0871c772d6ab0c for a full test report.

Micket

lgtm

Micket · 2026-02-26T17:42:59Z

Test report by @Micket
SUCCESS
Build succeeded for 2 out of 2 (total: 53 mins 20 secs) (1 easyconfigs in total)
vera-r07-01 - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Gold 6338 CPU @ 2.00GHz, 1 x NVIDIA NVIDIA A40, 580.105.08, Python 3.9.21
See https://gist.github.com/Micket/c598e57e2a4d4a34a473356e4f776833 for a full test report.

adding easyconfigs: GROMACS-2024.4-foss-2024a.eb

19dd968

verdurin added the update label Feb 18, 2026

github-actions bot added the 2024a issues & PRs related to 2024a common toolchains label Feb 18, 2026

gkaf89 mentioned this pull request Feb 19, 2026

[BUGFIX:GROMACS] Build with gmxapi distributed with the GROMACS source code #25188

Open

verdurin added 2 commits February 19, 2026 10:32

Use toolchain-compliant version of pybind11

5567078

Fix SciPy-bundle version

9e68ecd

Micket added this to the next release (5.2.2?) milestone Feb 26, 2026

Micket approved these changes Feb 26, 2026

View reviewed changes

Micket merged commit e44f1b6 into easybuilders:develop Feb 27, 2026
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{bio}[foss/2024a] GROMACS v2024.4#25328

{bio}[foss/2024a] GROMACS v2024.4#25328
Micket merged 3 commits intoeasybuilders:developfrom
verdurin:20260218175032_new_pr_GROMACS20244

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Updated software GROMACS-2024.4-foss-2024a.eb

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Updated software `GROMACS-2024.4-foss-2024a.eb`