new file: g/GROMACS/GROMACS-2023-foss-2022a-CUDA-12.0.0-PLUMED-2.9.0-mpi.eb

modified:   g/GROMACS/GROMACS-2023-foss-2022a-CUDA-12.0.0-PLUMED-2.9.0.eb
	new file:   p/PLUMED/PLUMED-2.9.0-foss-2022a-mpi.eb
	modified:   p/PLUMED/PLUMED-2.9.0-foss-2022a.eb

g/GROMACS/GROMACS-2023-foss-2022a-CUDA-12.0.0-PLUMED-2.9.0-mpi.eb

@@ -0,0 +1,77 @@
+# IT4Innovations
+# LK 2023
+
+name = 'GROMACS'
+version = '2023'
+local_plum_ver = '2.9.0'
+versionsuffix = '-CUDA-12.2.0-PLUMED-2.9.0-mpi'
+
+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 GPU enabled build, containing both MPI and threadMPI binaries.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+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-2023.tar.gz': 'ac92c6da72fbbcca414fd8a8d979e56ecf17c4c1cdabed2da5cfb4e7277b7ba8'},
+    {'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', '3.24.3'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.0.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+    ('PLUMED', local_plum_ver, '-mpi'),
+]
+
+configopts = '-DGMX_MPI=ON'
+
+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" && ',
+        'source_tmpl': 'gromacs-2023.3.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

g/GROMACS/GROMACS-2023-foss-2022a-CUDA-12.0.0-PLUMED-2.9.0.eb

@@ -49,8 +49,6 @@ dependencies = [
     ('PLUMED', local_plum_ver),
 ]
 
-configopts = '-DGMX_MPI=ON'
-
 exts_defaultclass = 'PythonPackage'
 
 exts_default_options = {

p/PLUMED/PLUMED-2.9.0-foss-2022a-mpi.eb

@@ -0,0 +1,65 @@
+# IT4Innovations
+# LK 2023
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.9.0'
+versionsuffix = '-mpi'
+
+homepage = 'https://www.plumed.org'
+description = """PLUMED is an open source library for free energy calculations in molecular systems which
+ works together with some of the most popular molecular dynamics engines. Free energy calculations can be
+ performed as a function of many order parameters with a particular  focus on biological problems, using
+ state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
+ The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['534db9ccb9446844f3e99ecdff091ad79c014ce9c4afe212c1536e19f85ab0d1']
+
+builddependencies = [
+    ('xxd', '8.2.4220'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('GSL', '2.7'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Boost', '1.79.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+configopts += '--enable-asmjit '
+configopts += '--enable-mpi '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'

p/PLUMED/PLUMED-2.9.0-foss-2022a.eb

@@ -37,7 +37,6 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
 configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
 configopts += '--enable-boost_graph --enable-boost_serialization '
 configopts += '--enable-asmjit '
-configopts += '--enable-mpi '
 prebuildopts = 'source sourceme.sh && '
 
 # make sure that ld.gold linker is used