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

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025.07.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 <[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 = '2025.2'
+
+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': '2025.07'}
+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-2025.2.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', '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'),
+]
+
+# 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'

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2_gmxapi-remove-builddependencies.patch

@@ -0,0 +1,17 @@
+Remove hard-dependencies on packaging and pybind11,
+which are only required for the build, not the actual installation
+
+Author: Jan Reuter (JSC)
+
+diff --color -Naur gmxapi-0.4.2.orig/setup.cfg gmxapi-0.4.2/setup.cfg
+--- gmxapi-0.4.2.orig/setup.cfg	2023-06-01 19:44:02.000000000 +0200
++++ gmxapi-0.4.2/setup.cfg	2025-08-18 21:21:02.611944841 +0200
+@@ -16,8 +16,6 @@
+ packages = find:
+ install_requires = 
+ 	mpi4py
+-	packaging
+-	pybind11
+ 	networkx>=2.0
+ 	numpy>1.7
+

easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025.07.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'mpi4py'
+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': '2025.07'}
+
+builddependencies = [
+    ('Cython', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['817492796bce771ccd809a6051cf68d48689815493b567a696ce7679260449cd'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025.07.eb

@@ -0,0 +1,20 @@
+easyblock = 'PythonPackage'
+
+name = 'networkx'
+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': '2025.07'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),  # required for numpy, scipy, ...
+]
+
+moduleclass = 'tools'