{chem}[foss/2023b] LAMMPS v29Aug2024, MDI v1.4.29, PLUMED v2.9.2, ... w/ kokkos

easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCC-13.2.0.eb

@@ -0,0 +1,43 @@
+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': 'GCC', 'version': '13.2.0'}
+
+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.
+]
+
+parallel = 1
+separate_build_dir = True
+
+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-foss-2023b-kokkos.eb

@@ -0,0 +1,177 @@
+name = 'LAMMPS'
+version = '29Aug2024'
+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': 'foss', 'version': '2023b'}
+toolchainopts = {'openmp': True, 'usempi': 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',
+]
+checksums = [
+    {'stable_29Aug2024.tar.gz': '6112e0cc352c3140a4874c7f74db3c0c8e30134024164509ecf3772b305fde2e'},
+    {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch':
+     '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'},
+]
+
+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'),
+]
+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'
+
+# 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)
+
+moduleclass = 'chem'

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

@@ -0,0 +1,54 @@
+# 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': 'gompi', 'version': '2023b'}
+
+source_urls = ['https://github.com/MolSSI-MDI/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/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb

@@ -0,0 +1,59 @@
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.9.2'
+
+homepage = 'https://www.plumed.org'
+description = """PLUMED is an open source library for free energy calculations in molecular systems which
+ works together with some of the most popular molecular dynamics engines. Free energy calculations can be
+ performed as a function of many order parameters with a particular  focus on biological problems, using
+ state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
+ The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['6fc23fe31074ad6b7a0eb9e2441fce5b3d92514d0d87206594c59c75e4c83d6e']
+
+builddependencies = [
+    ('xxd', '9.1.0307'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('GSL', '2.7'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost', '1.83.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023b.eb

@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'ScaFaCoS'
+version = '1.0.4'
+
+homepage = 'http://www.scafacos.de/'
+description = """ScaFaCoS is a library of scalable fast coulomb solvers."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = [
+    '6634c4202e825e771d1dd75bbe9cac5cee41136c87653fde98fbd634681c1be6',  # scafacos-1.0.1.tar.gz
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [
+    ('GMP', '6.3.0'),
+    ('GSL', '2.7'),
+]
+
+preconfigopts = 'unset F77 && '
+
+configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" '
+configopts += '--enable-shared --enable-static --disable-doc '
+# tell it where to find provided FFTW
+configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib '
+# only include the solvers supported for LAMMPS
+# (for p2nfft we need an additonal dependency)
+configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m '
+
+sanity_check_paths = {
+    'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'],
+    'dirs': [],
+}
+
+moduleclass = 'math'