{bio}[foss/2025a] GROMACS v2025.2 #23566

absrocks · 2025-08-03T13:30:22Z

No description provided.

github-actions · 2025-08-03T13:30:55Z

Updated software `GROMACS-2025.2-foss-2025a.eb`

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

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

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
index 693bdddbf8..5e8fd2c36a 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
@@ -29,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'foss', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -50,14 +50,14 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '4.0.3'),
-    ('scikit-build-core', '0.11.5'),
-    ('pybind11', '3.0.0'),
+    ('CMake', '3.31.3'),
+    ('scikit-build-core', '0.11.1'),
+    ('pybind11', '2.13.6'),
 ]
 
 dependencies = [
-    ('Python', '3.13.5'),
-    ('SciPy-bundle', '2025.07'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
     ('networkx', '3.5'),
     ('mpi4py', '4.1.0'),
 ]

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

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

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
index cd0edce7e0..5e8fd2c36a 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
@@ -1,44 +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 <[email protected]>
+# * Fotis Georgatos <[email protected]>
+# * George Tsouloupas <[email protected]>
+# * Kenneth Hoste <[email protected]>
+# * Adam Huffman <[email protected]>
+# * Ake Sandgren <[email protected]>
+# * J. Sassmannshausen <Crick HPC team>
+# * Dugan Witherick <[email protected]>
+# * Christoph Siegert <[email protected]>
+# License::   MIT/GPL
+
 name = 'GROMACS'
-version = '2021.0'
-_date = '-20250409'
-local_commit = '28807b11'
-versionsuffix = f'{_date}-constant-pH'
-# fork is from v2021.0-beta1, SOVERSION = 6.0.0
+version = '2025.2'
 
-homepage = 'https://gitlab.com/gromacs-constantph'
+homepage = 'https://www.gromacs.org'
 description = """
-GROMACS constant pH
-
 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': '2025a'}
+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,
-}]
-checksums = ['88548354e02c872052f2fa662eab5f111421706cb0ea264e94af19e7274d0f78']
+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-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'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', '3.26.3'),
+    ('CMake', '3.31.3'),
+    ('scikit-build-core', '0.11.1'),
+    ('pybind11', '2.13.6'),
+]
+
+dependencies = [
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('mpi4py', '4.1.0'),
 ]
 
-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"
 
-# this version does not support DOUBLE
-double_precision = False
+exts_defaultclass = 'PythonPackage'
 
-# 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_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'

Diff against GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
index 9a950353a4..5e8fd2c36a 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
@@ -15,9 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
-local_plumedver = '2.9.2'
-versionsuffix = '-PLUMED-%s' % local_plumedver
+version = '2025.2'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -31,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -42,33 +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-2023.3_skip_test_for_plumed.patch',
 ]
 checksums = [
-    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
     {'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-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'},
 ]
 
 builddependencies = [
-    ('CMake', '3.27.6'),
-    ('scikit-build-core', '0.9.3'),
+    ('CMake', '3.31.3'),
+    ('scikit-build-core', '0.11.1'),
+    ('pybind11', '2.13.6'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
-    ('PLUMED', local_plumedver),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('mpi4py', '4.1.0'),
 ]
 
-# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too
-ignore_plumed_version_check = True
-
 # 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"
@@ -81,9 +74,14 @@ 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': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
+        'checksums': [
+            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
+            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
+             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
+        ],
     }),
 ]

…S20252

…cks/easybuild-easyconfigs into 20250802151556_new_pr_GROMACS20252

smoors

thanks a lot for your contribution @absrocks !

smoors · 2025-08-17T19:12:14Z

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb

+    ('SciPy-bundle', '2025.06'),
+    ('networkx', '3.5'),
+    ('mpi4py', '4.1.0'),
+    ('pybind11', '2.13.6'),


this should probably a builddependency instead of a normal dependency

Hijacking this thread, since I've built the same version for the potential 2025b:

== FAILED: Installation ended unsuccessfully: `/data/EasyBuild-develop/software/Python/3.13.5-GCCcore-14.3.0/bin/python -m pip check` failed: gmxapi 0.4.2 requires pybind11, which is not installed.

So we need a hard-dependency.

i don't think it's needed.

in the gmxapi sources on pypi (which are used here) it is listed as an install dependency, but in gmxapi sources included in the GROMACS sources it is only listed as a build dependency.

So we might be able to work around this with a patch.

Patch added in #23699

Added patch from #23699 and added pybind in builddependency

…S20252

Crivella · 2025-09-09T15:32:26Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-09-09T15:40:11Z

@Crivella: 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=23566 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23566 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7899

Test results coming soon (I hope)...

- notification for comment with ID 3271250568 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).

Crivella · 2025-09-09T16:03:27Z

Test report by @Crivella
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.13
See https://gist.github.com/Crivella/2acf85bf6a6fadd32dcacd28889ef5ff for a full test report.

boegelbot · 2025-09-09T16:35:12Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/e2860f509df7da771a81a8736bd7e0b7 for a full test report.

Crivella

LGTM

Crivella · 2025-09-09T17:04:58Z

Going in, thanks @absrocks!

{bio,tools}[foss/2025a] GROMACS v2025.2, networkx v3.5

0486ed7

github-actions bot added the update label Aug 3, 2025

absrocks and others added 4 commits August 3, 2025 09:34

GROMACS-2025.2-foss-2025a.eb preinstallopts format changed

e0ae3ae

Merge branch 'easybuilders:develop' into 20250802151556_new_pr_GROMAC…

6a921bf

…S20252

Merge branch '20250802151556_new_pr_GROMACS20252' of github.com:absro…

4bad6b3

…cks/easybuild-easyconfigs into 20250802151556_new_pr_GROMACS20252

indentation fixed

1e5f83b

Thyre added the 2025a issues & PRs related to 2025a common toolchains label Aug 3, 2025

smoors reviewed Aug 17, 2025

View reviewed changes

absrocks and others added 5 commits August 24, 2025 20:31

Merge branch 'easybuilders:develop' into 20250802151556_new_pr_GROMAC…

b07b144

…S20252

patch added from PR 23699

75c9e91

fixed format

fd00f6c

fixed format

0351071

fixed format

e688835

Crivella approved these changes Sep 9, 2025

View reviewed changes

Crivella changed the title ~~{bio,tools}[foss/2025a] GROMACS v2025.2~~ {bio}[foss/2025a] GROMACS v2025.2 Sep 9, 2025

Crivella added this to the next release (5.1.2) milestone Sep 9, 2025

Crivella merged commit 33787b9 into easybuilders:develop Sep 9, 2025
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{bio}[foss/2025a] GROMACS v2025.2 #23566

{bio}[foss/2025a] GROMACS v2025.2 #23566

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github-actions bot commented Aug 3, 2025 •

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Updated software `GROMACS-2025.2-foss-2025a.eb`