{bio,lib,tools}[foss/2025.07,gfbf/2025.07,gompi/2025.07] GROMACS v2025.2, mpi4py v4.1.0, networkx v3.5 #23699

Thyre · 2025-08-18T15:27:51Z

(created using eb --new-pr)

…i-2025.07.eb, networkx-3.5-gfbf-2025.07.eb

github-actions · 2025-08-18T15:33:27Z

Updated software `GROMACS-2025.2-foss-2025.07.eb`

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-2025.07.eb
index cd0edce7e0..ade8eb6a46 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.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': '2025.07'}
+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', '4.0.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('pybind11', '3.0.0'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('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-2025.07.eb
index 9a950353a4..ade8eb6a46 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-2025.07.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': '2025.07'}
 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', '4.0.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('pybind11', '3.0.0'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
-    ('PLUMED', local_plumedver),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
+    ('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'},
+        ],
     }),
 ]

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

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

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.eb
index cf8db688ea..ade8eb6a46 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
+version = '2025.2'
 
 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': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025.07'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -42,7 +42,7 @@ patches = [
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.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':
@@ -50,15 +50,16 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.27.6'),
-    ('scikit-build-core', '0.9.3'),
+    ('CMake', '4.0.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('pybind11', '3.0.0'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
+    ('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,
@@ -73,9 +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'},
+        ],
     }),
 ]

Updated software `mpi4py-4.1.0-gompi-2025.07.eb`

Diff against mpi4py-4.1.0-gompi-2025a.eb

easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025a.eb

diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025a.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
index 6c242c7cd8..6000e50bac 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025a.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
@@ -7,14 +7,14 @@ homepage = 'https://github.com/mpi4py/mpi4py'
 description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
  the Python programming language, allowing any Python program to exploit multiple processors."""
 
-toolchain = {'name': 'gompi', 'version': '2025a'}
+toolchain = {'name': 'gompi', 'version': '2025.07'}
 
 builddependencies = [
-    ('Cython', '3.1.1'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
+    ('Python', '3.13.5'),
 ]
 
 exts_list = [

Diff against mpi4py-3.1.5-iimpi-2023b.eb

easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-iimpi-2023b.eb

diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-iimpi-2023b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
index e0d06737a7..6000e50bac 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-iimpi-2023b.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
@@ -1,21 +1,25 @@
 easyblock = 'PythonBundle'
 
 name = 'mpi4py'
-version = '3.1.5'
+version = '4.1.0'
 
 homepage = 'https://github.com/mpi4py/mpi4py'
 description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
  the Python programming language, allowing any Python program to exploit multiple processors."""
 
-toolchain = {'name': 'iimpi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2025.07'}
+
+builddependencies = [
+    ('Cython', '3.1.2'),
+]
 
 dependencies = [
-    ('Python', '3.11.5'),
+    ('Python', '3.13.5'),
 ]
 
 exts_list = [
     (name, version, {
-        'checksums': ['a706e76db9255135c2fb5d1ef54cb4f7b0e4ad9e33cbada7de27626205f2a153'],
+        'checksums': ['817492796bce771ccd809a6051cf68d48689815493b567a696ce7679260449cd'],
     }),
 ]

Diff against mpi4py-4.0.1-gompi-2024a.eb

easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
index 7eaa068c6e..6000e50bac 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb
@@ -1,25 +1,25 @@
 easyblock = 'PythonBundle'
 
 name = 'mpi4py'
-version = '4.0.1'
+version = '4.1.0'
 
 homepage = 'https://github.com/mpi4py/mpi4py'
 description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
  the Python programming language, allowing any Python program to exploit multiple processors."""
 
-toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchain = {'name': 'gompi', 'version': '2025.07'}
 
 builddependencies = [
-    ('Cython', '3.0.10'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.13.5'),
 ]
 
 exts_list = [
     (name, version, {
-        'checksums': ['f3174b245775d556f4fddb32519a2066ef0592edc810c5b5a59238f9a0a40c89'],
+        'checksums': ['817492796bce771ccd809a6051cf68d48689815493b567a696ce7679260449cd'],
     }),
 ]

Updated software `networkx-3.5-gfbf-2025.07.eb`

Diff against networkx-3.5-gfbf-2025a.eb

easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025a.eb

diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
index 56a20c2b04..e1f8234ba4 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025a.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
@@ -7,14 +7,14 @@ homepage = 'https://pypi.python.org/pypi/networkx'
 description = """NetworkX is a Python package for the creation, manipulation,
 and study of the structure, dynamics, and functions of complex networks."""
 
-toolchain = {'name': 'gfbf', 'version': '2025a'}
+toolchain = {'name': 'gfbf', 'version': '2025.07'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('SciPy-bundle', '2025.06'),  # required for numpy, scipy, ...
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),  # required for numpy, scipy, ...
 ]
 
 moduleclass = 'tools'

Diff against networkx-3.4.2-gfbf-2024a.eb

easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
index 41707723e8..e1f8234ba4 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
@@ -1,20 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'networkx'
-version = '3.4.2'
+version = '3.5'
 
 homepage = 'https://pypi.python.org/pypi/networkx'
 description = """NetworkX is a Python package for the creation, manipulation,
 and study of the structure, dynamics, and functions of complex networks."""
 
-toolchain = {'name': 'gfbf', 'version': '2024a'}
+toolchain = {'name': 'gfbf', 'version': '2025.07'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1']
+checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),  # required for numpy, scipy, ...
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),  # required for numpy, scipy, ...
 ]
 
 moduleclass = 'tools'

Diff against networkx-3.2.1-gfbf-2023b.eb

easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
index 2d4046a190..e1f8234ba4 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb
@@ -1,20 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'networkx'
-version = '3.2.1'
+version = '3.5'
 
 homepage = 'https://pypi.python.org/pypi/networkx'
 description = """NetworkX is a Python package for the creation, manipulation,
 and study of the structure, dynamics, and functions of complex networks."""
 
-toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchain = {'name': 'gfbf', 'version': '2025.07'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['9f1bb5cf3409bf324e0a722c20bdb4c20ee39bf1c30ce8ae499c8502b0b5e0c6']
+checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),  # required for numpy, scipy, ...
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),  # required for numpy, scipy, ...
 ]
 
 moduleclass = 'tools'

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.eb

boegel · 2025-08-18T15:51:55Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

Thyre · 2025-08-18T15:56:59Z

Test report by @Thyre
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor, 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: 6.16.1-arch1-1), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: 6.16.1-arch1-1), Python 3.13.7
See https://gist.github.com/Thyre/a9229e5f727eed303b045c58ff9a169c for a full test report.

boegelbot · 2025-08-18T16:00:15Z

@boegel: 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=23699 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23699 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7665

Test results coming soon (I hope)...

Details

- notification for comment with ID 3197484838 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).

Thyre · 2025-08-18T16:16:46Z

Test report by @Thyre
FAILED
Build succeeded for 4 out of 5 (3 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.5, AArch64, ARM UNKNOWN, 1 x NVIDIA NVIDIA GH200 480GB, 570.133.20, Python 3.9.21
See https://gist.github.com/Thyre/8b670c04073dc1fc0b361aaf487e5f97 for a full test report.

Thyre · 2025-08-18T16:21:57Z

Test report by @Thyre
FAILED
Build succeeded for 4 out of 5 (3 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.5, AArch64, ARM UNKNOWN, 1 x NVIDIA NVIDIA GH200 480GB, 570.133.20, Python 3.9.21
See https://gist.github.com/Thyre/8b670c04073dc1fc0b361aaf487e5f97 for a full test report.

I'm already running on a node with 1 MPI rank, GROMACS tests seem to not like that...
I'll try again with all the SLURM stuff unset and oversubscription enabled.

Thyre · 2025-08-18T16:24:28Z

Test report by @Thyre
SUCCESS
Build succeeded for 5 out of 5 (3 easyconfigs in total)
Framework - Linux Fedora Linux 42, x86_64, AMD Ryzen AI 7 350 w/ Radeon 860M, 1 x AMD Krackan [Radeon 840M / 860M Graphics] (model: 0x1114, driver: "6.15.9-201.fc42.x86_64"), Python 3.13.5
See https://gist.github.com/Thyre/227e1122b03c2525c5115bb37e827a68 for a full test report.

Thyre · 2025-08-18T16:28:58Z

Test report by @Thyre
SUCCESS
Build succeeded for 5 out of 5 (3 easyconfigs in total)
ZAM054 - Linux Zorin OS 17, x86_64, 12th Gen Intel(R) Core(TM) i7-1260P, 1 x NVIDIA NVIDIA GeForce MX550, 580.65.06, Python 3.10.12
See https://gist.github.com/Thyre/c4ed2986591593662d21c62df9d016bb for a full test report.

Signed-off-by: Jan André Reuter <[email protected]>

boegelbot · 2025-08-18T16:43:12Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jsczen3c1.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/95082a739a46295640ea656a4ca89a22 for a full test report.

Thyre · 2025-08-18T17:50:55Z

Test report by @Thyre
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.5, AArch64, ARM UNKNOWN, 1 x NVIDIA NVIDIA GH200 480GB, 570.133.20, Python 3.9.21
See https://gist.github.com/Thyre/2612bc99ca967b689d81219d26e108cc for a full test report.

Signed-off-by: Jan André Reuter <[email protected]>

Thyre · 2025-08-18T21:35:38Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-08-18T21:40:09Z

@Thyre: 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=23699 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23699 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7700

Test results coming soon (I hope)...

Details

- notification for comment with ID 3198499245 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 · 2025-08-18T22:37:35Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jsczen3c1.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/55d71b094a65825263c727223ace0e99 for a full test report.

smoors

lgtm

smoors · 2025-08-19T06:08:58Z

Going in, thanks @Thyre!

adding easyconfigs: GROMACS-2025.2-foss-2025.07.eb, mpi4py-4.1.0-gomp…

e25d17f

…i-2025.07.eb, networkx-3.5-gfbf-2025.07.eb

Thyre added the update label Aug 18, 2025

Thyre added the 2025b issues & PRs related to 2025b common toolchains label Aug 18, 2025

boegel reviewed Aug 18, 2025

View reviewed changes

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.eb Outdated Show resolved Hide resolved

Fix style of GROMACS 2025.2

f437e31

Signed-off-by: Jan André Reuter <[email protected]>

Drop pybind11 dependency to builddependency

49157ba

Signed-off-by: Jan André Reuter <[email protected]>

smoors modified the milestone: next release (5.1.2) Aug 19, 2025

smoors approved these changes Aug 19, 2025

View reviewed changes

smoors merged commit a7bec53 into easybuilders:develop Aug 19, 2025
5 checks passed

absrocks mentioned this pull request Aug 25, 2025

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

Merged

{bio,lib,tools}[foss/2025.07,gfbf/2025.07,gompi/2025.07] GROMACS v2025.2, mpi4py v4.1.0, networkx v3.5 #23699

{bio,lib,tools}[foss/2025.07,gfbf/2025.07,gompi/2025.07] GROMACS v2025.2, mpi4py v4.1.0, networkx v3.5 #23699

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Updated software `GROMACS-2025.2-foss-2025.07.eb`

Updated software `mpi4py-4.1.0-gompi-2025.07.eb`

Updated software `networkx-3.5-gfbf-2025.07.eb`

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