{tools}[lfoss/2025b] GROMACS v2025.2, HPL v2.3, HPCG v3.1, ... by Thyre · Pull Request #24517 · easybuilders/easybuild-easyconfigs

Thyre · 2025-11-10T17:03:41Z

(created using eb --new-pr)

Requires:

Implementing a new LLVM based toolchain easybuild-framework#4914
honor (pre)configopts, (pre)buildopts and (pre)testopts in custom easyblock for HPCG easybuild-easyblocks#3986
{lang,toolchain}[lfbf/2025b,system/system] lfbf v2025b, SciPy-bundle v2025.07 #24482
{toolchain}[system/system] lompi v2025b, lmpich v2025b, llvm-compilers v20.1.8 #24481
{toolchain}[lfoss/2025b] Add files for lfoss toolchain 2025b #24514

Test reports:

Success Alder Lake
Success Zen 3
Success Zen 4
Success Zen 5
Success (?) Neoverse V2

…b.eb, HPCG-3.1-lfoss-2025b.eb, mpi4py-4.1.0-lmpich-2025b.eb, networkx-3.5-lfbf-2025b.eb

github-actions · 2025-11-10T17:04:39Z

Updated software `GROMACS-2025.2-lfoss-2025b.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-lfoss-2025b.eb
index 577ba57729..fc29744c2c 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.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': 'lfoss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [

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

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

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
index c8e73fb68d..fc29744c2c 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.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': '2025a'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -52,14 +52,14 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.31.3'),
-    ('scikit-build-core', '0.11.1'),
-    ('pybind11', '2.13.6'),
+    ('CMake', '4.0.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('pybind11', '3.0.0'),
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('SciPy-bundle', '2025.06'),
+    ('Python', '3.13.5'),
+    ('SciPy-bundle', '2025.07'),
     ('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-lfoss-2025b.eb
index cd0edce7e0..fc29744c2c 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.0-foss-2023a-20250409-constant-pH.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
@@ -1,44 +1,90 @@
+# 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'
-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': 'lfoss', 'version': '2025b'}
+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',
+    'GROMACS-2025.2_workaround-arm-sve512.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'},
+    {'GROMACS-2025.2_workaround-arm-sve512.patch': 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
+]
 
 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'

Updated software `HPCG-3.1-lfoss-2025b.eb`

Diff against HPCG-3.1-intel-2025b.eb

easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2025b.eb

diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2025b.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
index fcf40dfd44..aa0cbd8f73 100644
--- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2025b.eb
+++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
@@ -5,7 +5,7 @@ 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': 'intel', 'version': '2025b'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True, 'openmp': True}
 
 source_urls = ['http://www.hpcg-benchmark.org/downloads']
@@ -19,6 +19,8 @@ checksums = [
     '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482',
 ]
 
+preconfigopts = 'sed -i "s|-ftree-vectorizer-verbose=0||g" %(start_dir)s/setup/Make.MPI_GCC_OMP && '
+
 runtest = True
 
 moduleclass = 'math'

Diff against HPCG-3.1-foss-2025b.eb

easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2025b.eb

diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2025b.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
index ba57176586..aa0cbd8f73 100644
--- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2025b.eb
+++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
@@ -5,7 +5,7 @@ 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': 'foss', 'version': '2025b'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True, 'openmp': True}
 
 source_urls = ['http://www.hpcg-benchmark.org/downloads']
@@ -19,6 +19,8 @@ checksums = [
     '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482',
 ]
 
+preconfigopts = 'sed -i "s|-ftree-vectorizer-verbose=0||g" %(start_dir)s/setup/Make.MPI_GCC_OMP && '
+
 runtest = True
 
 moduleclass = 'math'

Diff against HPCG-3.1-intel-2023a.eb

easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb

diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
index 771c57d4d8..aa0cbd8f73 100644
--- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-lfoss-2025b.eb
@@ -5,7 +5,7 @@ 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': 'intel', 'version': '2023a'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True, 'openmp': True}
 
 source_urls = ['http://www.hpcg-benchmark.org/downloads']
@@ -19,6 +19,8 @@ checksums = [
     '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482',
 ]
 
+preconfigopts = 'sed -i "s|-ftree-vectorizer-verbose=0||g" %(start_dir)s/setup/Make.MPI_GCC_OMP && '
+
 runtest = True
 
 moduleclass = 'math'

Updated software `HPL-2.3-lfoss-2025b.eb`

Diff against HPL-2.3-intel-2025b.eb

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

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2025b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
index fe387c1f29..b97550b7b0 100644
--- a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2025b.eb
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
@@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s
  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': 'intel', 'version': '2025b'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']

Diff against HPL-2.3-foss-2025b.eb

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

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2025b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
index e9190d8d63..b97550b7b0 100644
--- a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2025b.eb
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
@@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s
  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': 'foss', 'version': '2025b'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']

Diff against HPL-2.3-foss-2025a.eb

easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2025a.eb

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2025a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
index 0d0af2b6e5..b97550b7b0 100644
--- a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2025a.eb
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-lfoss-2025b.eb
@@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s
  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': 'foss', 'version': '2025a'}
+toolchain = {'name': 'lfoss', 'version': '2025b'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']

Updated software `mpi4py-4.1.0-lompi-2025b.eb`

Diff against mpi4py-4.1.0-iimpi-2025b.eb

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

diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-iimpi-2025b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.eb
index 73e721240a..7df3e52b16 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-iimpi-2025b.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.eb
@@ -7,7 +7,7 @@ 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': '2025b'}
+toolchain = {'name': 'lompi', 'version': '2025b'}
 
 builddependencies = [
     ('Cython', '3.1.2'),

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

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

diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.eb
index 2c89778479..7df3e52b16 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025b.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.eb
@@ -7,7 +7,7 @@ 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': '2025b'}
+toolchain = {'name': 'lompi', 'version': '2025b'}
 
 builddependencies = [
     ('Cython', '3.1.2'),

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-lompi-2025b.eb
index 6c242c7cd8..7df3e52b16 100644
--- a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-gompi-2025a.eb
+++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.1.0-lompi-2025b.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': 'lompi', 'version': '2025b'}
 
 builddependencies = [
-    ('Cython', '3.1.1'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
+    ('Python', '3.13.5'),
 ]
 
 exts_list = [

Updated software `networkx-3.5-lfbf-2025b.eb`

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

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

diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.5-lfbf-2025b.eb
index dc0ed730fd..e63492063d 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025b.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-lfbf-2025b.eb
@@ -7,7 +7,7 @@ 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': '2025b'}
+toolchain = {'name': 'lfbf', 'version': '2025b'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037']

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-lfbf-2025b.eb
index 56a20c2b04..e63492063d 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.5-gfbf-2025a.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-lfbf-2025b.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': 'lfbf', 'version': '2025b'}
 
 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-lfbf-2025b.eb
index 41707723e8..e63492063d 100644
--- a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.5-lfbf-2025b.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': 'lfbf', 'version': '2025b'}
 
 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'

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre · 2025-11-12T11:54:38Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3986
SUCCESS
Build succeeded for 5 out of 5 (total: 46 mins 32 secs) (5 easyconfigs in total)
ZAM054 - Linux Zorin OS 18, x86_64, 12th Gen Intel(R) Core(TM) i7-1260P (skylake), 1 x NVIDIA NVIDIA GeForce MX550, 580.95.05, Python 3.12.3
See https://gist.github.com/Thyre/9a64f628aa72bf849556b793accc5f05 for a full test report.

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre · 2025-11-12T12:50:32Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3986
SUCCESS
Build succeeded for 5 out of 5 (total: 41 mins 11 secs) (5 easyconfigs in total)
datenlager - Linux Ubuntu 24.04, x86_64, AMD Ryzen 7 3700X 8-Core Processor, Python 3.12.3
See https://gist.github.com/Thyre/975f3341ee987b71887857911917ba8b for a full test report.

Thyre · 2025-11-14T09:18:28Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3986
SUCCESS
Build succeeded for 5 out of 5 (total: 44 mins 8 secs) (5 easyconfigs in total)
Framework - Linux Fedora Linux 43, x86_64, AMD Ryzen AI 7 350 w/ Radeon 860M (zen5), 1 x AMD Krackan [Radeon 840M / 860M Graphics] (device id: 0x1114, gfx: gfx1152, driver: Linuxversion6.17.7-300.fc43.x86_64(mockbuild@d49b948bbfce45ee82827ac76e852536)(gcc(GCC)15.2.120251022(RedHat15.2.1-3),GNUldversion2.45-1.fc43)#1SMPPREEMPT_DYNAMICSunNov215:30:09UTC2025), Python 3.14.0
See https://gist.github.com/Thyre/bff450f4e3ddd93d212e412af87185de for a full test report.

Thyre · 2025-11-22T17:45:05Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3986
SUCCESS
Build succeeded for 1 out of 1 (total: 45 secs) (1 easyconfigs in total)
Framework - Linux Fedora Linux 43, x86_64, AMD Ryzen AI 7 350 w/ Radeon 860M (zen5), 1 x AMD Krackan [Radeon 840M / 860M Graphics] (device id: 0x1114, gfx: gfx1152, driver: Linuxversion6.17.7-300.fc43.x86_64(mockbuild@d49b948bbfce45ee82827ac76e852536)(gcc(GCC)15.2.120251022(RedHat15.2.1-3),GNUldversion2.45-1.fc43)#1SMPPREEMPT_DYNAMICSunNov215:30:09UTC2025), Python 3.14.0
See https://gist.github.com/Thyre/c4c1708b5e82f464add836914cd63038 for a full test report.

boegel · 2025-11-23T11:45:42Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3759, easybuilders/easybuild-easyblocks#3986
FAILED
Build succeeded for 1 out of 8 (total: 1 min 53 secs) (5 easyconfigs in total)
aarch64-neoverse-v1-node1.int.aws-rocky88-202310.eessi.io - Linux Rocky Linux 8.10, AArch64, ARM UNKNOWN (neoverse_v1), Python 3.6.8
See https://gist.github.com/boegel/ec6a1e8fb0ec0159b3ff647e4abce041 for a full test report.

Thyre · 2025-11-23T11:52:27Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3759, easybuilders/easybuild-easyblocks#3986
FAILED
Build succeeded for 1 out of 8 (total: 1 min 53 secs) (5 easyconfigs in total) aarch64-neoverse-v1-node1.int.aws-rocky88-202310.eessi.io - Linux Rocky Linux 8.10, AArch64, ARM UNKNOWN (neoverse_v1), Python 3.6.8
See https://gist.github.com/boegel/ec6a1e8fb0ec0159b3ff647e4abce041 for a full test report.

sh: srun: command not found
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 2
slots that were requested by the application:

  xhpcg

This looks to be unrelated I'd guess?

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

…ew_pr_GROMACS20252

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

boegel · 2025-11-23T14:32:18Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3759, easybuilders/easybuild-easyblocks#3986
FAILED
Build succeeded for 3 out of 8 (total: 2 mins 17 secs) (5 easyconfigs in total)
node4226.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/66aeea48507750ec1e158aab4bc8ee8a for a full test report.

Thyre · 2025-11-23T20:54:21Z

Test report by @Thyre
SUCCESS
Build succeeded for 5 out of 5 (total: 27 mins 11 secs) (5 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion6.17.8-arch1-1(linux@archlinux)(gcc(GCC)15.2.120251112,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,14Nov202506:54:20+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion6.17.8-arch1-1(linux@archlinux)(gcc(GCC)15.2.120251112,GNUld(GNUBinutils)2.45.1)#1SMPPREEMPT_DYNAMICFri,14Nov202506:54:20+0000), Python 3.13.7
See https://gist.github.com/Thyre/44f68695b8b91705b916857e6f7d4b04 for a full test report.

Thyre · 2025-11-30T13:58:06Z

GROMACS failing again during the checks with an abort. Maybe too much memory being consumed?

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3579, easybuilders/easybuild-easyblocks#3855, easybuilders/easybuild-easyblocks#3997
FAILED
Build succeeded for 4 out of 5 (total: 11 mins 48 secs) (5 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/17447f0594c9d8ade1b665cc22643da4 for a full test report.

Thyre · 2025-11-30T14:49:30Z

GROMACS alone with less parallelism

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3579, easybuilders/easybuild-easyblocks#3855, easybuilders/easybuild-easyblocks#3997
SUCCESS
Build succeeded for 1 out of 1 (total: 50 mins 13 secs) (1 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/341109184346b78e73ef358e600767d8 for a full test report.

…asyconfigs into 20251110180335_new_pr_GROMACS20252

boegel · 2025-12-07T22:41:06Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (total: 49 mins 48 secs) (5 easyconfigs in total)
node4216.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/794bb675e3ca342b52f508f460a293f6 for a full test report.

boegel · 2025-12-07T22:50:03Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (total: 58 mins 44 secs) (5 easyconfigs in total)
node3551.doduo.os - Linux RHEL 9.6, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.21
See https://gist.github.com/boegel/9877f04c5a8f3086b3868868cc7a80dd for a full test report.

boegel · 2025-12-08T10:03:39Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (total: 33 mins 2 secs) (5 easyconfigs in total)
aarch64-neoverse-v1-node1.int.aws-rocky88-202310.eessi.io - Linux Rocky Linux 8.10, AArch64, ARM UNKNOWN, Python 3.6.8
See https://gist.github.com/boegel/ad1af141bd23df0a1b8ef3b904e41449 for a full test report.

edit: this was on top of a SciPy-bundle/2025.07-lfbf-2025b that was installed with --ignore-test-fail, because of problems with numpy tests, see #24764

boegel

lgtm

boegel · 2025-12-08T13:28:44Z

Going in, thanks @Thyre!

adding easyconfigs: GROMACS-2025.2-lfoss-2025b.eb, HPL-2.3-lfoss-2025…

c7595c4

…b.eb, HPCG-3.1-lfoss-2025b.eb, mpi4py-4.1.0-lmpich-2025b.eb, networkx-3.5-lfbf-2025b.eb

Thyre added the update label Nov 10, 2025

Fix style

2c88d6b

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

Thyre added the 2025b issues & PRs related to 2025b common toolchains label Nov 10, 2025

Fix incorrect toolchain for mpi4py

61adf16

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

github-actions bot removed the 2025b issues & PRs related to 2025b common toolchains label Nov 12, 2025

Thyre added the 2025b issues & PRs related to 2025b common toolchains label Nov 19, 2025

Thyre mentioned this pull request Nov 19, 2025

honor (pre)configopts, (pre)buildopts and (pre)testopts in custom easyblock for HPCG easybuilders/easybuild-easyblocks#3986

Merged

Thyre commented Nov 23, 2025

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

Thyre added 2 commits November 23, 2025 13:14

Merge remote-tracking branch 'upstream/develop' into 20251110180335_n…

efa7de5

…ew_pr_GROMACS20252

Include newest patches for GROMACS

fc6f429

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>

github-actions bot removed the 2025b issues & PRs related to 2025b common toolchains label Nov 23, 2025

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boegel added this to the next release (5.2.0?) milestone Dec 6, 2025

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

e863583

…asyconfigs into 20251110180335_new_pr_GROMACS20252

boegel approved these changes Dec 8, 2025

View reviewed changes

boegel merged commit e7f4925 into easybuilders:develop Dec 8, 2025
8 checks passed

Thyre mentioned this pull request Dec 9, 2025

{tools}[lmpflf/2025b] HPCG v3.1, HPL v2.3, GROMACS v2025.2, ... #24660

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Updated software GROMACS-2025.2-lfoss-2025b.eb

Updated software HPCG-3.1-lfoss-2025b.eb

Updated software HPL-2.3-lfoss-2025b.eb

Updated software mpi4py-4.1.0-lompi-2025b.eb

Updated software networkx-3.5-lfbf-2025b.eb

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Thyre commented Nov 10, 2025 •

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Updated software `GROMACS-2025.2-lfoss-2025b.eb`

Updated software `HPCG-3.1-lfoss-2025b.eb`

Updated software `HPL-2.3-lfoss-2025b.eb`

Updated software `mpi4py-4.1.0-lompi-2025b.eb`

Updated software `networkx-3.5-lfbf-2025b.eb`

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