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Ignore Python from virtualenvs in GROMACS configure via -DPython3_FIND_VIRTUALENV=STANDARD #3283

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merged 3 commits into from
Sep 18, 2024
Merged

Ignore Python from virtualenvs in GROMACS configure via -DPython3_FIND_VIRTUALENV=STANDARD #3283

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92bb54f
Ignore Python from virtualenvs in GROMACS configure
Flamefire Apr 5, 2024
e6828f9
Remove blank line
Flamefire Apr 5, 2024
1a16588
Merge branch 'easybuilders:develop' into 20240405162525_new_pr_gromacs
Flamefire Jun 6, 2024
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35 changes: 21 additions & 14 deletions easybuild/easyblocks/g/gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,9 @@ def prepare_step(self, *args, **kwargs):
def configure_step(self):
"""Custom configuration procedure for GROMACS: set configure options for configure or cmake."""

if LooseVersion(self.version) >= LooseVersion('4.6'):
gromacs_version = LooseVersion(self.version)

if gromacs_version >= '4.6':
cuda = get_software_root('CUDA')
if cuda:
# CUDA with double precision is currently not supported in GROMACS yet
Expand All @@ -188,10 +190,11 @@ def configure_step(self):
self.log.info("skipping configure step")
return

if LooseVersion(self.version) >= LooseVersion('2021'):
self.cfg.update('configopts', "-DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
if gromacs_version >= '2021':
self.cfg.update('configopts', "-DGMX_GPU=CUDA")
else:
self.cfg.update('configopts', "-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
self.cfg.update('configopts', "-DGMX_GPU=ON")
self.cfg.update('configopts', "-DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)

# Set CUDA capabilities based on template value.
if '-DGMX_CUDA_TARGET_SM' not in self.cfg['configopts']:
Expand Down Expand Up @@ -236,14 +239,14 @@ def configure_step(self):
# 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 (LooseVersion(self.version) >= LooseVersion('2020') and
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:
gromacs_version_string_suffix += '-PLUMED-%s' % get_software_version('PLUMED')
self.cfg.update('configopts', '-DGMX_VERSION_STRING_OF_FORK=%s' % gromacs_version_string_suffix)

if LooseVersion(self.version) < LooseVersion('4.6'):
if gromacs_version < '4.6':
self.log.info("Using configure script for configuring GROMACS build.")

if self.cfg['build_shared_libs']:
Expand All @@ -259,7 +262,7 @@ def configure_step(self):
self.cfg.update('configopts', "--without-x")

# OpenMP is not supported for versions older than 4.5.
if LooseVersion(self.version) >= LooseVersion('4.5'):
if gromacs_version >= '4.5':
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "--enable-threads")
Expand Down Expand Up @@ -310,22 +313,26 @@ def configure_step(self):
mpiexec_path, self.cfg.get('mpiexec_numproc_flag'),
mpi_numprocs)

if LooseVersion(self.version) >= LooseVersion('2019'):
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")

if LooseVersion(self.version) >= LooseVersion('2020'):
if gromacs_version >= '2020':
# build Python bindings if Python is loaded as a dependency
python_root = get_software_root('Python')
if python_root:
self.cfg.update('configopts', "-DGMX_PYTHON_PACKAGE=ON")
bin_python = os.path.join(python_root, 'bin', 'python')
# For find_package(PythonInterp)
self.cfg.update('configopts', "-DPYTHON_EXECUTABLE=%s" % bin_python)
self.cfg.update('configopts', "-DGMX_PYTHON_PACKAGE=ON")
if gromacs_version >= '2021':
# For find_package(Python3) - Ignore virtual envs
self.cfg.update('configopts', "-DPython3_FIND_VIRTUALENV=STANDARD")

# Now patch GROMACS for PLUMED before cmake
if plumed_root:
if LooseVersion(self.version) >= LooseVersion('5.1'):
if gromacs_version >= '5.1':
# Use shared or static patch depending on
# setting of self.cfg['build_shared_libs']
# and adapt cmake flags accordingly as per instructions
Expand Down Expand Up @@ -355,7 +362,7 @@ def configure_step(self):
if self.toolchain.toolchain_family() != toolchain.CRAYPE:
gmx_simd = self.get_gromacs_arch()
if gmx_simd:
if LooseVersion(self.version) < LooseVersion('5.0'):
if gromacs_version < '5.0':
self.cfg.update('configopts', "-DGMX_CPU_ACCELERATION=%s" % gmx_simd)
else:
self.cfg.update('configopts', "-DGMX_SIMD=%s" % gmx_simd)
Expand Down Expand Up @@ -404,7 +411,7 @@ def configure_step(self):
env.setvar('LDFLAGS', "%s -lgfortran -lm" % os.environ.get('LDFLAGS', ''))

# no more GSL support in GROMACS 5.x, see http://redmine.gromacs.org/issues/1472
if LooseVersion(self.version) < LooseVersion('5.0'):
if gromacs_version < '5.0':
# enable GSL when it's provided
if get_software_root('GSL'):
self.cfg.update('configopts', "-DGMX_GSL=ON")
Expand All @@ -424,7 +431,7 @@ def configure_step(self):
out = super(EB_GROMACS, self).configure_step()

# for recent GROMACS versions, make very sure that a decent BLAS, LAPACK and FFT is found and used
if LooseVersion(self.version) >= LooseVersion('4.6.5'):
if gromacs_version >= '4.6.5':
patterns = [
r"Using external FFT library - \S*",
r"Looking for dgemm_ - found",
Expand Down
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