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reset GROMACS easyblock to upstream easybuild-easyblocks-v5.1.2 #29

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Merged
bartoldeman merged 1 commit into from
Dec 18, 2025
Merged

reset GROMACS easyblock to upstream easybuild-easyblocks-v5.1.2 #29

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127 changes: 13 additions & 114 deletions easybuild/easyblocks/g/gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,10 +70,8 @@ def extra_options():
'mpisuffix': ['_mpi', "Suffix to append to MPI-enabled executables (only for GROMACS < 4.6)", CUSTOM],
'mpiexec': ['mpirun', "MPI executable to use when running tests", CUSTOM],
'mpiexec_numproc_flag': ['-np', "Flag to introduce the number of MPI tasks when running tests", CUSTOM],
'mpi_only': [False, "Only build for MPI and skip nompi.", CUSTOM],
'mpi_numprocs': [0, "Number of MPI tasks to use when running tests", CUSTOM],
'ignore_plumed_version_check': [False, "Ignore the version compatibility check for PLUMED", CUSTOM],
'cp2k': [None, "Build with CP2K QM/MM. None is auto-detect. True or False forces behaviour.", CUSTOM],
'plumed': [None, "Try to apply PLUMED patches. None (default) is auto-detect. " +
"True or False forces behaviour.", CUSTOM],
})
Expand Down Expand Up @@ -119,21 +117,9 @@ def get_gromacs_arch(self):
# http://manual.gromacs.org/documentation/2018/install-guide/index.html#simd-support
if 'MIC-AVX512' in optarch and LooseVersion(self.version) >= LooseVersion('2016'):
res = 'AVX_512_KNL'
elif (('AVX512' in optarch or 'MARCH=X86-64-V4' in optarch) and
LooseVersion(self.version) >= LooseVersion('2016')):
if (LooseVersion(self.version) >= LooseVersion('2019') and
LooseVersion(self.version) < LooseVersion('2023') and
comp_fam == toolchain.GCC and get_software_root('imkl') and
re.search(r'GMX_DOUBLE=(1|ON|YES|TRUE)\b', self.cfg['configopts'].upper())):
# Workaround to DOUBLE precision builds being broken for AVX512 in GROMACS 2019.x
# and 2020.x when using toolchains with GCC and MKL.
# With GROMACS 2023.3 under StdEnv/2023 the issue is fixed.
# TODO: test with GROMACS 2021, 2022 under StdEnv/2020 & 2023 to narrow down further.
res = 'AVX2_256'
self.log.info("Falling back to AVX2_256 for GROMACS >= 2019 with GMX_DOUBLE=ON.")
else:
res = 'AVX_512'
elif ('AVX2' in optarch or 'MARCH=X86-64-V3' in optarch) and LooseVersion(self.version) >= LooseVersion('5.0'):
elif 'AVX512' in optarch and LooseVersion(self.version) >= LooseVersion('2016'):
res = 'AVX_512'
elif 'AVX2' in optarch and LooseVersion(self.version) >= LooseVersion('5.0'):
res = 'AVX2_256'
elif 'AVX' in optarch:
res = 'AVX_256'
Expand Down Expand Up @@ -228,65 +214,6 @@ def configure_step(self):
# to avoid that GROMACS finds and uses a system-wide CUDA compiler
self.cfg.update('configopts', "-DGMX_GPU=OFF")

# CP2K detection
# enable CP2K support if CP2K is listed as a dependency
# and CP2K support is either explicitly enabled (cp2k = True) or unspecified ('cp2k' not defined)
cp2k_root = get_software_root('CP2K')
if self.cfg['cp2k'] and not cp2k_root:
msg = "CP2K support has been requested but CP2K is not listed as a dependency."
raise EasyBuildError(msg)
elif cp2k_root and self.cfg['cp2k'] is False:
self.log.info('CP2K was found, but compilation without CP2K has been requested.')
cp2k_root = None

if cp2k_root:
if gromacs_version < LooseVersion('2022'):
msg = 'CP2K support is only available for GROMACS 2022 and newer.'
raise EasyBuildError(msg)
elif LooseVersion(get_software_version('CP2K')) < LooseVersion('8.1'):
msg = 'CP2K support in GROMACS requires CP2K version 8.1 or higher.'
raise EasyBuildError(msg)

if not self.cfg['mpi_only']:
msg = "GROMACS with CP2K support needs to be built with 'mpi_only = True'"
raise EasyBuildError(msg)

if not os.path.exists(os.path.join(cp2k_root, 'lib', 'libcp2k.a')):
msg = 'CP2K needs to be compiled with "library = True".'
raise EasyBuildError(msg)
if not os.path.exists(os.path.join(cp2k_root, 'lib', 'pkgconfig', 'libcp2k.pc')):
msg = "pkg-config is required as a build-dependency for CP2K"
raise EasyBuildError(msg)
if not get_software_root('pkg-config'):
msg = "pkg-config is required as a build-dependency for building GROMACS-CP2K"
raise EasyBuildError(msg)

self.log.info('CP2K support has been enabled.')
# Building with CP2K requires static build w/o gmxapi.
# https://manual.gromacs.org/documentation/2022/install-guide/index.html#building-with-cp2k-qm-mm-support
self.log.info("Building with CP2K QM/MM.")
self.cfg['build_shared_libs'] = False
self.libext = 'a'
cp2k_version = get_software_version('CP2K')
self.cfg.update('configopts', "-DGMX_INSTALL_NBLIB_API=OFF")
self.cfg.update('configopts', "-DGMXAPI=OFF")
self.cfg.update('configopts', "-DGMX_CP2K=ON")
# Ensure that the GROMACS log files report that CP2K was enabled and which version was used.
self.cfg.update('configopts', "-DGMX_VERSION_STRING_OF_FORK=CP2K-{:}".format(cp2k_version))
self.cfg.update('configopts', "-DCP2K_DIR=%s/lib64" % cp2k_root)
cp2k_linker_flags = [
# Need MPI linker flags b/c libcp2k.a is compiled with mpifort.
# These are for OpenMPI (mpifort --showme).
"-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh",
"-L%s/lib/exts/dbcsr" % cp2k_root,
# get depenencies for libcp2k.a:
"$(pkg-config --libs-only-l libcp2k)"
]
if get_software_root('Libint'):
# for some reason libint2 is not discovered by pkg-config:
cp2k_linker_flags.append('-lint2')
self.cfg.update('configopts', '-DCP2K_LINKER_FLAGS="%s"' % " ".join(cp2k_linker_flags))

# PLUMED detection
# enable PLUMED support if PLUMED is listed as a dependency
# and PLUMED support is either explicitly enabled (plumed = True) or unspecified ('plumed' not defined)
Expand Down Expand Up @@ -395,7 +322,7 @@ def configure_step(self):
mpiexec_path, self.cfg.get('mpiexec_numproc_flag'),
mpi_numprocs)

elif gromacs_version >= '2019' and self.cfg['build_shared_libs']:
if gromacs_version >= '2019':
# Building the gmxapi interface requires shared libraries,
# this is handled in the class initialisation so --module-only works
self.cfg.update('configopts', "-DGMXAPI=ON")
Expand Down Expand Up @@ -576,10 +503,8 @@ def test_step(self):
copy_dir('lib', libdir)

orig_runtest = self.cfg['runtest']

if LooseVersion(self.version) < LooseVersion('2019'):
# make very sure OMP_NUM_THREADS is set to 1, to avoid hanging GROMACS regression test
env.setvar('OMP_NUM_THREADS', '1')
# make very sure OMP_NUM_THREADS is set to 1, to avoid hanging GROMACS regression test
env.setvar('OMP_NUM_THREADS', '1')

if self.cfg['runtest'] is None or isinstance(self.cfg['runtest'], bool):
self.cfg['runtest'] = 'check'
Expand Down Expand Up @@ -667,14 +592,6 @@ def get_lib_subdirs(self):
subdir = lib_relpath.split(os.sep)[0:-1]
lib_subdirs.append(os.path.join(*subdir))

if not self.cfg['build_shared_libs'] and len(lib_subdirs) == 0:
for libdir in ['lib', 'lib64']:
if os.path.exists(os.path.join(self.installdir, libdir)):
msg = "Found lib subdirectory: %s but it doesn't contain: %s.\n"
msg += "As building shared libs was disabled, this is probably okay."
lib_subdirs = [libdir]
self.log.info(msg, libdir, libname)

if len(lib_subdirs) == 0:
raise EasyBuildError(f"Failed to determine sub-directory with {libname} in {self.installdir}")

Expand Down Expand Up @@ -738,12 +655,8 @@ def sanity_check_step(self):
else:
mpisuff = '_mpi'

if self.cfg['mpi_only']:
mpi_bins = [binary + mpisuff for binary in mpi_bins]
mpi_libnames = [libname + mpisuff for libname in mpi_libnames]
else:
mpi_bins.extend([binary + mpisuff for binary in mpi_bins])
mpi_libnames.extend([libname + mpisuff for libname in mpi_libnames])
mpi_bins.extend([binary + mpisuff for binary in mpi_bins])
mpi_libnames.extend([libname + mpisuff for libname in mpi_libnames])

suffixes = ['']

Expand Down Expand Up @@ -773,21 +686,10 @@ def sanity_check_step(self):
dirs.extend([os.path.join(ld, 'pkgconfig') for ld in self.lib_subdirs])

custom_paths = {
'files': [os.path.join('bin', b) for b in bin_files],
'files': [os.path.join('bin', b) for b in bin_files] +
[os.path.join(libdir, lib) for libdir in self.lib_subdirs for lib in lib_files],
'dirs': dirs,
}

if self.cfg['build_shared_libs'] or LooseVersion(self.version) <= LooseVersion('2022'):
# only if any libs are actually built
if not self.lib_subdir:
self.lib_subdir = self.get_lib_subdir()

# pkgconfig dir not available for earlier versions, exact version to use here is unclear
if LooseVersion(self.version) >= LooseVersion('4.6'):
custom_paths['dirs'].append(os.path.join(self.lib_subdir, 'pkgconfig'))

custom_paths['files'] = custom_paths['files'] + [os.path.join(self.lib_subdir, lib) for lib in lib_files]

super().sanity_check_step(custom_paths=custom_paths)

def run_all_steps(self, *args, **kwargs):
Expand Down Expand Up @@ -867,12 +769,9 @@ def run_all_steps(self, *args, **kwargs):
if precisions == []:
raise EasyBuildError("No precision selected. At least one of single/double_precision must be unset or True")

if self.cfg['mpi_only']:
mpitypes = ['mpi']
else:
mpitypes = ['nompi']
if self.toolchain.options.get('usempi', None):
mpitypes.append('mpi')
mpitypes = ['nompi']
if self.toolchain.options.get('usempi', None):
mpitypes.append('mpi')

# We need to count the number of variations to build.
versions_built = []
Expand Down