{chem}[iomkl/2023b] LAMMPS v29Aug2024_update2 w/ kokkos

easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iompi-2023b.eb

@@ -0,0 +1,34 @@
+name = 'HDF5'
+# Note: Odd minor releases are only RCs and should not be used.
+version = '1.14.3'
+
+homepage = 'https://portal.hdfgroup.org/display/support'
+description = """HDF5 is a data model, library, and file format for storing and managing data.
+ It supports an unlimited variety of datatypes, and is designed for flexible
+ and efficient I/O and for high volume and complex data."""
+
+toolchain = {'name': 'iompi', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch']
+checksums = [
+    {'hdf5-1.14.3.tar.gz': (
+        # Folder name changed from hdf5-1.14.3 to hdfsrc and Makefile got deleted
+        '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7',
+        '126b800e9b87f65e7e7ffa58ee006607bab03a8e11e5209ea3d5c0c331321d43',
+    )},
+    {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'},
+]
+
+# replace src include path with installation dir for $H5BLD_CPPFLAGS
+_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g'
+postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-intel-compilers-2023.2.1.eb

@@ -0,0 +1,41 @@
+easyblock = 'CMakeMake'
+
+name = 'kim-api'
+version = '2.3.0'
+
+homepage = 'https://openkim.org/'
+description = """Open Knowledgebase of Interatomic Models.
+
+KIM is an API and OpenKIM is a collection of interatomic models (potentials) for
+atomistic simulations.  This is a library that can be used by simulation programs
+to get access to the models in the OpenKIM database.
+
+This EasyBuild only installs the API, the models can be installed with the
+package openkim-models, or the user can install them manually by running
+    kim-api-collections-management install user MODELNAME
+or
+    kim-api-collections-management install user OpenKIM
+to install them all.
+ """
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'}
+
+source_urls = ['https://s3.openkim.org/kim-api/']
+sources = ['%(name)s-%(version)s.txz']
+checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991']
+
+dependencies = [
+    ('CMake', '3.27.6'),  # Also needed to install models, thus not just a builddependency.
+]
+
+maxparallel = 1
+modextravars = {
+    'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64'
+}
+
+sanity_check_paths = {
+    'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-iomkl-2023b-kokkos.eb

@@ -0,0 +1,186 @@
+name = 'LAMMPS'
+version = '29Aug2024_update2'
+versionsuffix = '-kokkos'
+
+homepage = 'https://www.lammps.org'
+description = """LAMMPS is a classical molecular dynamics code, and an acronym
+for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
+potentials for solid-state materials (metals, semiconductors) and soft matter
+(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
+used to model atoms or, more generically, as a parallel particle simulator at
+the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
+parallel using message-passing techniques and a spatial-decomposition of the
+simulation domain. The code is designed to be easy to modify or extend with new
+functionality.
+"""
+
+toolchain = {'name': 'iomkl', 'version': '2023b'}
+toolchainopts = {'cstd': 'c++17', 'openmp': True, 'usempi': True, 'loose': True}
+
+# 'https://github.com/lammps/lammps/archive/'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['stable_%(version)s.tar.gz']
+patches = [
+    'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch',
+    'lammps-python-venv.patch',
+]
+checksums = [
+    {'stable_29Aug2024_update2.tar.gz': 'f8ca3f021a819ced8658055f7750e235c51b4937ddb621cf1bd7bee08e0b6266'},
+    {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch':
+     '314ab1064af74ddfcf4091dfe9f90fa32cfa4100e8d01fea7b59b019575a7c51'},
+    {'lammps-python-venv.patch': '84d5687aca5df2d288e1c6152843c9f65c6ed11030a1133cceb128c2846fd049'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
+    ('archspec', '0.2.2'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('netCDF', '4.9.2'),
+    ('GSL', '2.7'),
+    ('zlib', '1.2.13'),
+    ('gzip', '1.13'),
+    ('cURL', '8.3.0'),
+    ('HDF5', '1.14.3'),
+    ('PCRE', '8.45'),
+    ('libxml2', '2.11.5'),
+    ('FFmpeg', '6.0'),
+    ('Voro++', '0.4.6'),
+    ('kim-api', '2.3.0'),
+    ('Eigen', '3.4.0'),
+    ('PLUMED', '2.9.2'),
+    ('SciPy-bundle', '2023.11'),
+    # VTK package is auto-disabled if this dep is not available
+    ('VTK', '9.3.0'),
+    # We use a custom build of MDI
+    ('MDI', '1.4.29'),
+    ('mpi4py', '3.1.5'),
+]
+if ARCH == 'x86_64':
+    # TBB and ScaFaCos are an optional dependency when building on Intel arch
+    dependencies += [
+        ('tbb', '2021.13.0'),
+        ('ScaFaCoS', '1.0.4'),
+    ]
+
+# To use additional custom configuration options, use the 'configopts' easyconfig parameter
+# See docs and lammps easyblock for more information.
+# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
+
+# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos,
+# which is claimed to be faster in pure MPI calculations
+# configopts  = "-DKokkos_ENABLE_SERIAL=yes "
+
+
+# packages auto-enabled by easyblock
+# 'GPU'    - if cuda package is present and kokkos is disabled
+# 'KOKKOS' - if kokkos is enabled (by default)
+# 'INTEL'  - if builing on Intel CPU
+# 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
+
+configopts = ' '.join([
+    '-DCMAKE_CXX_STANDARD=17',
+    '-DCMAKE_CXX_STANDARD_REQUIRED=on',
+])
+
+# include the following extra packages into the build
+general_packages = [
+    'AMOEBA',
+    'ASPHERE',
+    'ATC',
+    'AWPMD',
+    'BOCS',
+    'BODY',
+    'BPM',
+    'BROWNIAN',
+    'CG-DNA',
+    'CG-SPICA',
+    'CLASS2',
+    'COLLOID',
+    'COLVARS',
+    'COMPRESS',
+    'CORESHELL',
+    'DIELECTRIC',
+    'DIFFRACTION',
+    'DIPOLE',
+    'DPD-BASIC',
+    'DPD-MESO',
+    'DPD-REACT',
+    'DPD-SMOOTH',
+    'DRUDE',
+    'EFF',
+    'ELECTRODE',
+    'EXTRA-COMPUTE',
+    'EXTRA-DUMP',
+    'EXTRA-FIX',
+    'EXTRA-MOLECULE',
+    'EXTRA-PAIR',
+    'FEP',
+    'GRANULAR',
+    'H5MD',
+    'INTERLAYER',
+    'KIM',
+    'KSPACE',
+    'LATBOLTZ',
+    'LEPTON',
+    'MACHDYN',
+    'MANIFOLD',
+    'MANYBODY',
+    'MC',
+    'MDI',
+    'MEAM',
+    'MGPT',
+    'MISC',
+    'ML-IAP',
+    'ML-PACE',
+    'ML-POD',
+    'ML-RANN',
+    'ML-SNAP',
+    'MOFFF',
+    'MOLECULE',
+    'MOLFILE',
+    'MPIIO',
+    'NETCDF',
+    'OPT',
+    'ORIENT',
+    'PERI',
+    'PHONON',
+    'PLUGIN',
+    'PLUMED',
+    'POEMS',
+    'PTM',
+    'PYTHON',
+    'QEQ',
+    'QTB',
+    'REACTION',
+    'REAXFF',
+    'REPLICA',
+    'RIGID',
+    'SCAFACOS',
+    'SHOCK',
+    'SMTBQ',
+    'SPH',
+    'SPIN',
+    'SRD',
+    'TALLY',
+    'UEF',
+    'VORONOI',
+    'VTK',
+    'YAFF',
+]
+
+# Excluded packages due to requiring additional (non-trivial) deps
+# - ADIOS
+# - LATTE
+# - MESONT (requires very large files downloaded during build)
+# - ML-HDNNP (requires N2P2)
+# - ML-QUIP
+# - MSCG
+# - QMMM (setup seems complex)
+
+runtest = False
+moduleclass = 'chem'

easybuild/easyconfigs/l/LAMMPS/lammps-python-venv.patch

@@ -0,0 +1,40 @@
+Patch Python installation to ensure system packages are used.
+Constrain `build<1.4` for compatibility.
+diff --git a/python/install.py b/python/install.py
+index fd9f95f1bf..42f404224a 100644
+--- a/python/install.py
++++ b/python/install.py
+@@ -97,7 +97,7 @@ shutil.copy(args.lib,'lammps')
+ # create a virtual environment for building the wheel
+ shutil.rmtree('buildwheel', True)
+ try:
+-  txt = subprocess.check_output([sys.executable, '-m', 'venv', 'buildwheel'], stderr=subprocess.STDOUT, shell=False)
++  txt = subprocess.check_output([sys.executable, '-m', 'venv', '--system-site-packages', 'buildwheel'], stderr=subprocess.STDOUT, shell=False)
+   print(txt.decode('UTF-8'))
+ except subprocess.CalledProcessError as err:
+   sys.exit("Failed to create a virtual environment: {0}".format(err.output.decode('UTF-8')))
+diff --git a/python/makewheel.py b/python/makewheel.py
+index f13ad110ce..014756ddbd 100644
+--- a/python/makewheel.py
++++ b/python/makewheel.py
+@@ -23,8 +23,8 @@ sys.real_prefix = sys.prefix
+ sys.prefix = base
+
+ # update pip and install all requirements to build the wheel
+-os.system('python -m pip install --upgrade pip')
+-os.system('python -m pip install --upgrade -r wheel_requirements.txt')
++os.system('python -m pip install pip')
++os.system('python -m pip install -r wheel_requirements.txt')
+
+ print("Building new binary wheel")
+ os.system('python -m build -n --wheel -o .')
+diff --git a/python/wheel_requirements.txt b/python/wheel_requirements.txt
+index dafedeee23..ff4cc9593c 100644
+--- a/python/wheel_requirements.txt
++++ b/python/wheel_requirements.txt
+@@ -1,4 +1,4 @@
+ pip
+-build
++build<1.4
+ wheel
+ setuptools

easybuild/easyconfigs/m/MDI/MDI-1.4.29-iompi-2023b.eb

@@ -0,0 +1,53 @@
+# MDI package for LAMMPS
+# Author: J. Saßmannshausen (Imperial College London)
+
+easyblock = 'CMakeMake'
+name = 'MDI'
+version = '1.4.29'
+
+homepage = 'https://github.com/MolSSI-MDI/MDI_Library'
+description = """The MolSSI Driver Interface (MDI) project provides a
+standardized API for fast, on-the-fly communication between computational
+chemistry codes. This greatly simplifies the process of implementing
+methods that require the cooperation of multiple software packages and
+enables developers to write a single implementation that works across
+many different codes. The API is sufficiently general to support a wide
+variety of techniques, including QM/MM, ab initio MD, machine learning,
+advanced sampling, and path integral MD, while also being straightforwardly
+extensible. Communication between codes is handled by the MDI Library, which
+enables tight coupling between codes using either the MPI or TCP/IP methods.
+"""
+
+toolchain = {'name': 'iompi', 'version': '2023b'}
+
+source_urls = ['https://github.com/MolSSI-%(name)s/MDI_Library/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['6fb9ab2cf01c1a88a183bb481313f3131f0afd041ddea7aeacabe857fbdcb6ad']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+# perform iterative build to get both static and shared libraries
+local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DPython_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts = [
+    local_common_configopts + ' -Dlibtype=STATIC',
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=ON',
+]
+
+modextrapaths = {
+    'LD_LIBRARY_PATH': 'lib/mdi',
+    'LIBRARY_PATH': 'lib/mdi',
+}
+
+sanity_check_paths = {
+    'files': ['lib/mdi/libmdi.a', 'lib/mdi/libmdi.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+bin_lib_subdirs = ['lib/mdi']
+
+moduleclass = 'chem'

easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-iompi-2023b.eb

@@ -0,0 +1,22 @@
+easyblock = 'PythonBundle'
+
+name = 'mpi4py'
+version = '3.1.5'
+
+homepage = 'https://github.com/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors."""
+
+toolchain = {'name': 'iompi', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['a706e76db9255135c2fb5d1ef54cb4f7b0e4ad9e33cbada7de27626205f2a153'],
+    }),
+]
+
+moduleclass = 'lib'