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GROMACS: improve control over PLUMED support (native vs. patching) #3984

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GROMACS: improve control over PLUMED support (native vs. patching) #3984

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5097bd0
EB_GROMACS: finer control over PLUMED support (internal or patching)
ostueker Oct 31, 2025
c394b2f
GROMACS: improve PLUMED patching logic
ostueker Nov 4, 2025
03bbe65
remove print statements added for debugging
ostueker Nov 4, 2025
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57 changes: 40 additions & 17 deletions easybuild/easyblocks/g/gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,8 @@ def extra_options():
'mpiexec_numproc_flag': ['-np', "Flag to introduce the number of MPI tasks when running tests", 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],
'plumed': [None, "Try to apply PLUMED patches. None (default) is auto-detect. " +
'plumed': [None, "Try to enable PLUMED support. None (default) is auto-detect. " +
"'patch' apply PLUMED patches even for GROMACS 2025 and newer." +
"True or False forces behaviour.", CUSTOM],
})
return extra_vars
Expand Down Expand Up @@ -217,41 +218,62 @@ def configure_step(self):
# 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)
# For GROMACS 2025 and newer that means enabling GROMACS' native PLUMED support ('-DGMX_USE_PLUMED=ON')
# unless PLUMED patches are requested with plumed = 'patch'.
# For older versions of GROMACS patches are applied to enable PLUMED support.
plumed_root = get_software_root('PLUMED')
plumed_patches = False
if self.cfg['plumed'] and not plumed_root:
msg = "PLUMED support has been requested but PLUMED is not listed as a dependency."
raise EasyBuildError(msg)
elif plumed_root and self.cfg['plumed'] is False:
self.log.info('PLUMED was found, but compilation without PLUMED has been requested.')
plumed_root = None
elif plumed_root and self.cfg['plumed'] == 'patch':
self.log.info('PLUMED was found, and PLUMED patching has been requested.')
plumed_patches = True
elif plumed_root and self.cfg['plumed'] is True:
msg = 'PLUMED was found, and PLUMED support has been requested.'
if gromacs_version >= '2025':
msg += ' Will use native PLUMED support.'
plumed_patches = False
else:
msg += ' Will apply PLUMED patches.'
plumed_patches = True
self.log.info(msg)

if plumed_root:
self.log.info('PLUMED support has been enabled.')

# Need to check if PLUMED has an engine for this version
engine = 'gromacs-%s' % self.version
if gromacs_version >= '2025' and plumed_patches is False:
self.log.info('Native PLUMED support has been enabled.')
self.cfg.update('configopts', '-DGMX_USE_PLUMED=ON')

res = run_shell_cmd("plumed-patch -l")
if not re.search(engine, res.output):
plumed_ver = get_software_version('PLUMED')
msg = "There is no support in PLUMED version %s for GROMACS %s: %s" % (plumed_ver, self.version,
res.output)
if self.cfg['ignore_plumed_version_check']:
self.log.warning(msg)
else:
raise EasyBuildError(msg)
else:
# Need to check if PLUMED has an engine for this version
engine = 'gromacs-%s' % self.version

res = run_shell_cmd("plumed-patch -l")
if not re.search(engine, res.output):
plumed_ver = get_software_version('PLUMED')
msg = "There is no support in PLUMED version %s for GROMACS %s: %s" % (plumed_ver, self.version,
res.output)
if self.cfg['ignore_plumed_version_check']:
self.log.warning(msg)
else:
raise EasyBuildError(msg)

# PLUMED patching must be done at different stages depending on
# version of GROMACS. Just prepare first part of cmd here
plumed_cmd = "plumed-patch -p -e %s" % engine
# PLUMED patching must be done at different stages depending on
# version of GROMACS. Just prepare first part of cmd here
plumed_cmd = "plumed-patch -p -e %s" % engine

# Ensure that the GROMACS log files report how the code was patched
# during the build, so that any problems are easier to diagnose.
# The GMX_VERSION_STRING_OF_FORK feature is available since 2020.
if (gromacs_version >= '2020' and
'-DGMX_VERSION_STRING_OF_FORK=' not in self.cfg['configopts']):
gromacs_version_string_suffix = 'EasyBuild-%s' % EASYBUILD_VERSION
if plumed_root:
if plumed_patches:
gromacs_version_string_suffix += '-PLUMED-%s' % get_software_version('PLUMED')
self.cfg.update('configopts', '-DGMX_VERSION_STRING_OF_FORK=%s' % gromacs_version_string_suffix)

Expand Down Expand Up @@ -291,7 +313,8 @@ def configure_step(self):
ConfigureMake.configure_step(self)

# Now patch GROMACS for PLUMED between configure and build
if plumed_root:
if plumed_root and plumed_patches:
self.log.info('Applying PLUMED patches to GROMACS.')
run_shell_cmd(plumed_cmd)

else:
Expand Down