{tools}[lfoss/2025b] GROMACS v2025.2, HPL v2.3, HPCG v3.1, ...

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

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+# 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': 'lfoss', '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-2025.2.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/h/HPCG/HPCG-3.1-lfoss-2025b.eb

@@ -0,0 +1,26 @@
+name = 'HPCG'
+version = '3.1'
+
+homepage = 'https://software.sandia.gov/hpcg'
+description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than
+ the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark."""
+
+toolchain = {'name': 'lfoss', 'version': '2025b'}
+toolchainopts = {'usempi': True, 'openmp': True}
+
+source_urls = ['http://www.hpcg-benchmark.org/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+# Newer compilers require loop's upper-bound variable to be
+# explicitly designated as private/shared/firstprivate/lastprivate
+patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch']
+checksums = [
+    '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4',  # hpcg-3.1.tar.gz
+    # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch
+    '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482',
+]
+
+preconfigopts = 'sed -i "s|-ftree-vectorizer-verbose=0||g" %(start_dir)s/setup/Make.MPI_GCC_OMP && '
+
+runtest = True
+
+moduleclass = 'math'

easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb

@@ -0,0 +1,21 @@
+name = 'HPL'
+version = '2.3'
+
+homepage = 'https://www.netlib.org/benchmark/hpl/'
+description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
+ arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+toolchain = {'name': 'lfoss', 'version': '2025b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+# fix Make dependencies, so parallel build also works
+patches = ['HPL_parallel-make.patch']
+checksums = [
+    '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830',  # hpl-2.3.tar.gz
+    '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6',  # HPL_parallel-make.patch
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.eb

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+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': 'lompi', 'version': '2025b'}
+
+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-lfbf-2025b.eb

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+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': 'lfbf', 'version': '2025b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),  # required for numpy, scipy, ...
+]
+
+moduleclass = 'tools'