Add GROMACS easyconfig template with software-commit

easyconfigs/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch

@@ -0,0 +1,68 @@
+Make testing of GMX_THREAD_MPI work.
+Don't drop relevant PYTHONPATH and LD_LIBRARY_PATH settings.
+Make sure OMP_NUM_THREADS is not set so it doesn't fail when -ntomp is set.
+Don't use mpiexec for GMX_THREAD_MPI runs.
+
+Åke Sandgren, 2023-06-27
+diff -ru gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt
+--- gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt	2023-04-21 15:12:07.000000000 +0200
++++ gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt	2023-06-27 08:08:49.967184214 +0200
+@@ -61,7 +61,7 @@
+ endif()
+
+ add_custom_target(gmxapi_pytest
+-                  COMMAND ${PYTHON_EXECUTABLE} -m pytest
++                  COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS ${PYTHON_EXECUTABLE} -m pytest
+                     -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR}
+                   DEPENDS _gmxapi
+                   WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR})
+@@ -70,6 +70,7 @@
+
+ add_dependencies(check gmxapi_pytest)
+
++if (GMX_MPI)
+ if(MPIEXEC_EXECUTABLE)
+     if(NOT GMXAPI_MPI4PY_FOUND)
+         if (MPI_C_COMPILER)
+@@ -107,3 +108,4 @@
+
+     add_dependencies(check gmxapi_pytest_mpi)
+ endif()
++endif()
+diff -ru gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt
+--- gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt	2023-04-21 15:12:07.000000000 +0200
++++ gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt	2023-06-27 09:10:31.134866196 +0200
+@@ -21,15 +21,18 @@
+ get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY)
+ add_custom_target(gmxapi_extension_pytest
+                   COMMAND ${CMAKE_COMMAND}
+-                               -E env PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH}
++                               -E env --unset=OMP_NUM_THREADS LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH}
+                                ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR
+                                ${CMAKE_CURRENT_SOURCE_DIR}
+-                  DEPENDS gmxapi_extension _gmxapi)
++                  DEPENDS gmxapi_extension _gmxapi
++                  WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR})
++
+ # The current test fixtures require the `gmx` tool-wrapper executable.
+ add_dependencies(gmxapi_extension_pytest gmx)
+
+ add_dependencies(check gmxapi_extension_pytest)
+
++if (GMX_MPI)
+ if(MPIEXEC_EXECUTABLE)
+     if(NOT GMXAPI_MPI4PY_FOUND)
+         if (MPI_C_COMPILER)
+@@ -58,10 +61,11 @@
+     #    (https://www.open-mpi.org/doc/v3.0/man1/mpiexec.1.php)
+     add_custom_target(
+         gmxapi_extension_pytest_mpi
+-        COMMAND ${MPIEXEC_EXECUTABLE} -n 4 -x PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH}
++        COMMAND ${MPIEXEC_EXECUTABLE} -n 4 -x PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH}
+             ${PYTHON_EXECUTABLE} -m mpi4py -m pytest -x --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR}
+             DEPENDS gmxapi_extension _gmxapi gmx
+             )
+
+     add_dependencies(check gmxapi_extension_pytest_mpi)
+ endif()
++endif()

easyconfigs/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch

@@ -0,0 +1,14 @@
+Make sure env OMP_NUM_THREADS matches -ntomp argument during testing.
+
+Åke Sandgren, 2023-06-22
+diff -ru gromacs-2023.1.orig/src/testutils/TestMacros.cmake gromacs-2023.1/src/testutils/TestMacros.cmake
+--- gromacs-2023.1.orig/src/testutils/TestMacros.cmake	2023-04-21 15:12:08.000000000 +0200
++++ gromacs-2023.1/src/testutils/TestMacros.cmake	2023-06-22 16:29:28.338270785 +0200
+@@ -288,6 +288,7 @@
+         endif ()
+         set(_cmd ${_prefix_cmd} $<TARGET_FILE:${EXENAME}>)
+         if (ARG_OPENMP_THREADS)
++            set(_cmd "env" "OMP_NUM_THREADS=${ARG_OPENMP_THREADS}" ${_cmd})
+             if (GMX_OPENMP)
+                 list(APPEND _cmd -ntomp ${ARG_OPENMP_THREADS})
+             endif()

easyconfigs/GROMACS-2024.3-foss-2023b-software-commit.eb

@@ -0,0 +1,79 @@
+# 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 = '2024.3'
+versionsuffix = '-%(software_commit)s'
+
+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': '2023b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+github_account = 'gromacs'
+source_urls = ['https://github.com/%(github_account)s/%(name)s/archive/']
+
+
+sources = ['%(software_commit)s.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',
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('scikit-build-core', '0.9.3'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('networkx', '3.2.1'),
+    ('mpi4py', '3.1.5'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

easystacks/gromacs-eb-4.9.4-dev.yml

@@ -0,0 +1,4 @@
+easyconfigs:
+  - GROMACS-2024.3-foss-2023b-software-commit.eb:
+      options:
+        software-commit: d0f934abfd1394621c40858a2c2dd9123451df4e # release 2024.3