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Update LAMMPS easyblock: v2025 fix + extra tests #3894

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Update LAMMPS easyblock: v2025 fix + extra tests #3894

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811ecb0
Update Python test script to work with LAMMPS 2025+
lorisercole Aug 20, 2025
57204fb
Add accelerator-specific tests
lorisercole Aug 20, 2025
294d28e
Run LAMMPS tests on multiple cores, if possible
lorisercole Aug 20, 2025
3e28f44
Fix small bug when running --dump-env-script
lorisercole Aug 20, 2025
217e21d
Enable Kokkos serial backend
lorisercole Aug 21, 2025
a947538
Enable unit tests
lorisercole Aug 22, 2025
e164235
Reorder & clean lammps easyblock
lorisercole Aug 25, 2025
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115 changes: 95 additions & 20 deletions easybuild/easyblocks/l/lammps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
from easybuild.tools.filetools import copy_dir, copy_file, mkdir, read_file
from easybuild.tools.modules import get_software_root, get_software_version
from easybuild.tools.run import run_shell_cmd
from easybuild.tools.systemtools import AARCH64, get_cpu_architecture, get_shared_lib_ext
from easybuild.tools.systemtools import AARCH64, get_cpu_architecture, get_shared_lib_ext, get_avail_core_count
from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC

from easybuild.easyblocks.generic.cmakemake import CMakeMake
Expand Down Expand Up @@ -359,7 +359,7 @@ def prepare_step(self, *args, **kwargs):
# version 1.3.2 is used in the test suite to check easyblock can be initialised
if self.version != '1.3.2':
# take into account that build directory may not be available (in case of --module-only)
if os.path.exists(self.start_dir) and os.listdir(self.start_dir):
if self.start_dir and os.path.exists(self.start_dir) and os.listdir(self.start_dir):
self.cur_version = translate_lammps_version(self.version, path=self.start_dir)
else:
self.cur_version = translate_lammps_version(self.version, path=self.installdir)
Expand Down Expand Up @@ -471,30 +471,19 @@ def configure_step(self, **kwargs):
# https://docs.lammps.org/Build_basics.html
# https://docs.lammps.org/Build_settings.html
# https://docs.lammps.org/Build_package.html
# https://docs.lammps.org/Build_extras.html
if self.cfg['general_packages']:
for package in self.cfg['general_packages']:
self.cfg.update('configopts', '-D%s%s=on' % (self.pkg_prefix, package))

if self.cfg['user_packages']:
for package in self.cfg['user_packages']:
self.cfg.update('configopts', '-D%s%s=on' % (self.pkg_user_prefix, package))

# Optimization settings
# OPT package
pkg_opt = '-D%sOPT=' % self.pkg_prefix
if pkg_opt not in self.cfg['configopts']:
self.cfg.update('configopts', pkg_opt + 'on')

# grab the architecture so we can check if we have Intel hardware (also used for Kokkos below)
processor_arch, gpu_arch = self.get_kokkos_arch(cuda_cc, self.cfg['kokkos_arch'])

if processor_arch in INTEL_PACKAGE_ARCH_LIST or \
(processor_arch == 'NATIVE' and self.kokkos_cpu_mapping.get(get_cpu_arch()) in INTEL_PACKAGE_ARCH_LIST):
# USER-INTEL enables optimizations on Intel processors. GCC has also partial support for some of them.
pkg_user_intel = '-D%sINTEL=' % self.pkg_user_prefix
if pkg_user_intel not in self.cfg['configopts']:
if self.toolchain.comp_family() in [toolchain.GCC, toolchain.INTELCOMP]:
self.cfg.update('configopts', pkg_user_intel + 'on')

# MPI/OpenMP
if self.toolchain.options.get('usempi', None):
self.cfg.update('configopts', '-DBUILD_MPI=yes')
Expand All @@ -517,11 +506,27 @@ def configure_step(self, **kwargs):
if '-DFFT_PACK=' not in self.cfg['configopts']:
self.cfg.update('configopts', '-DFFT_PACK=array')

# https://lammps.sandia.gov/doc/Build_extras.html
# KOKKOS
# detect the CPU and GPU architecture (used for Intel and Kokkos packages belos)
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Suggested change
# detect the CPU and GPU architecture (used for Intel and Kokkos packages belos)
# detect the CPU and GPU architecture (used for Intel and Kokkos packages below)

processor_arch, gpu_arch = self.get_kokkos_arch(cuda_cc, self.cfg['kokkos_arch'])

# INTEL package
self.pkg_intel = False
if processor_arch in INTEL_PACKAGE_ARCH_LIST or \
(processor_arch == 'NATIVE' and self.kokkos_cpu_mapping.get(get_cpu_arch()) in INTEL_PACKAGE_ARCH_LIST):
# USER-INTEL enables optimizations on Intel processors. GCC has also partial support for some of them.
pkg_user_intel = '-D%sINTEL=' % self.pkg_user_prefix
if pkg_user_intel not in self.cfg['configopts']:
if self.toolchain.comp_family() in [toolchain.GCC, toolchain.INTELCOMP]:
self.cfg.update('configopts', pkg_user_intel + 'on')
self.pkg_intel = True
else:
self.pkg_intel = True

# KOKKOS package
if self.cfg['kokkos']:
print_msg("Using Kokkos package with arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
self.cfg.update('configopts', '-D%sKOKKOS=on' % self.pkg_prefix)
self.cfg.update('configopts', '-D%s_ENABLE_SERIAL=yes' % self.kokkos_prefix)

if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', '-D%s_ENABLE_OPENMP=yes' % self.kokkos_prefix)
Expand Down Expand Up @@ -557,7 +562,7 @@ def configure_step(self, **kwargs):
elif get_software_root("FFTW"):
self.cfg.update('configopts', '-DFFT_KOKKOS=FFTW3')

# CUDA only
# GPU package (cannot be built with KOKKOS+CUDA)
elif self.cuda:
print_msg("Using GPU package (not Kokkos) with arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
self.cfg.update('configopts', '-D%sGPU=on' % self.pkg_prefix)
Expand All @@ -568,6 +573,7 @@ def configure_step(self, **kwargs):
# to lib64)
self.cfg.update('configopts', '-DCMAKE_INSTALL_LIBDIR=lib')

# Python interface
# avoid that pip (ab)uses $HOME/.cache/pip
# cfr. https://pip.pypa.io/en/stable/reference/pip_install/#caching
env.setvar('XDG_CACHE_HOME', tempfile.gettempdir())
Expand Down Expand Up @@ -602,6 +608,23 @@ def configure_step(self, **kwargs):
else:
raise EasyBuildError("Expected to find a Python dependency as sanity check commands rely on it!")

# Testing (PyYAML must be installed)
if self.cfg['runtest'] is None or self.cfg['runtest']:
if LooseVersion(self.cur_version) >= LooseVersion(translate_lammps_version('29Aug2024')):
# Testing of KOKKOS+CUDA builds does not work for version < 22Jul2025
# See: https://github.com/lammps/lammps/issues/405
if LooseVersion(self.cur_version) < LooseVersion(translate_lammps_version('22Jul2025')) \
and self.cfg['kokkos'] and self.cuda:
print_warning("Skipping tests: KOKKOS+CUDA builds have broken testing in LAMMPS < 22Jul2025.")
self.cfg['runtest'] = False
else:
self.cfg['runtest'] = True
if 'PyYAML' not in (dep['name'] for dep in self.cfg.builddependencies()):
raise EasyBuildError("PyYAML not included as build dependency: cannot run tests.")
self.cfg.update('configopts', '-DENABLE_TESTING=on')
else:
self.cfg['runtest'] = False

return super().configure_step()

def install_step(self):
Expand Down Expand Up @@ -648,13 +671,27 @@ def install_step(self):

run_shell_cmd(cmd)

def test_step(self):
"""Filter the ctests that should be run"""
# add flags to test_cmd to ignore some tests
if self.cfg.get('runtest') is True and not self.cfg.get('test_cmd'):
test_cmd = 'ctest'
if LooseVersion(self.cmake_version) >= '3.17.0':
test_cmd += ' --no-tests=error'
test_cmd += ' -LE unstable -E "TestMliapPyUnified|AtomicPairStyle:meam_spline|KSpaceStyle:scafacos.*"'
self.log.debug(f"Running tests using test_cmd = '{test_cmd}' as test_cmd")
self.cfg['test_cmd'] = test_cmd

super().test_step()

def sanity_check_step(self, *args, **kwargs):
"""Run custom sanity checks for LAMMPS files, dirs and commands."""

# Set cur_version when running --sanity-check-only
if self.cur_version is None:
self.cur_version = translate_lammps_version(self.version, path=self.installdir)

# Test some LAMMPS examples
# Output files need to go somewhere (and has to work for --module-only as well)
execution_dir = tempfile.mkdtemp()

Expand All @@ -676,15 +713,53 @@ def sanity_check_step(self, *args, **kwargs):
for check_file in sanity_check_test_inputs
]

# add accelerator-specific tests
if self.pkg_intel: # INTEL package
custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "intel"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)
if self.cfg['kokkos']: # KOKKOS package
if self.cuda: # NOTE: requires a GPU to run
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This is a difficult requirement to meet, we should be able to support a cross-compilation. In EESSI, for example, this is going to cause problems as we must cross-compile for a lot of architectures. You could make it conditional on the nvidia-smi command running successfully?

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See for example

easybuild-easyblocks/easybuild/easyblocks/t/tensorflow.py

Lines 1048 to 1054 in 6a0f356

if not which('nvidia-smi', on_error=IGNORE):
print_warning('Could not find nvidia-smi. Assuming a system without GPUs and skipping GPU tests!')
num_gpus_to_use = 0
elif os.environ.get('CUDA_VISIBLE_DEVICES') == '-1':
print_warning('GPUs explicitely disabled via CUDA_VISIBLE_DEVICES. Skipping GPU tests!')
num_gpus_to_use = 0
else:

custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "kk", "-k", "on", "g", "1"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)
else:
custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "kk", "-k", "on"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)
elif self.cuda: # GPU package
custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "gpu", "-pk", "gpu", "1"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)
if self.toolchain.options.get('openmp', None): # OPENMP package
custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "omp", "-pk", "omp", "2"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)
# OPT package
custom_commands.append(
'from lammps import lammps; l=lammps(cmdargs=["-sf", "opt"]); l.file("%s")' %
os.path.join(self.installdir, "examples", "msst", "in.msst")
)

# mpirun command needs an l.finalize() in the sanity check from LAMMPS 29Sep2021
if LooseVersion(self.cur_version) >= LooseVersion(translate_lammps_version('29Sep2021')):
# This is actually not needed if mpi4py is installed, and can cause a crash in version 2025+
if LooseVersion(self.cur_version) >= LooseVersion(translate_lammps_version('29Sep2021')) and \
LooseVersion(self.cur_version) < LooseVersion(translate_lammps_version('22Jul2025')):
custom_commands = [cmd + '; l.finalize()' for cmd in custom_commands]

custom_commands = ["""python -c '%s'""" % cmd for cmd in custom_commands]

# Execute sanity check commands within an initialized MPI in MPI enabled toolchains
if self.toolchain.options.get('usempi', None):
custom_commands = [self.toolchain.mpi_cmd_for(cmd, 1) for cmd in custom_commands]
# use up to 4 cores, to speed up tests
test_core_cnt = min(self.cfg.parallel, get_avail_core_count(), 4)
self.log.info("Using %s cores for the MPI tests" % test_core_cnt)
custom_commands = [self.toolchain.mpi_cmd_for(cmd, test_core_cnt) for cmd in custom_commands]

custom_commands = ["cd %s && " % execution_dir + cmd for cmd in custom_commands]

Expand Down
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