diff --git a/Custom_EasyBlocks/README.md b/Custom_EasyBlocks/README.md
index 023f3db6b3171001b059926e5df3c081f60ec138..6eca29328f2199f94ced919dc42e0e2add206571 100644
--- a/Custom_EasyBlocks/README.md
+++ b/Custom_EasyBlocks/README.md
@@ -73,6 +73,12 @@ Overview of the custom EasyBlocks.
- __*difference compared to upstream*__ upstream doesn't have such a feature
- __*can not be removed*__ until merged upstream
+## LAMMPS
+- __*added_by*__ d.alvarez
+- __*needed because*__ upstream does not include the changes that we used in the latest stage
+- __*difference compared to upstream*__ various, done by Alan
+- __*can not be removed*__ until merged upstream or the changes here are deprecated (need to be assesed by an expert)
+
## NAMD
- __*added_by*__ d.alvarez
- __*needed because*__ need to disable CUDA support even if CUDA comes as a dependency
diff --git a/Custom_EasyBlocks/lammps.py b/Custom_EasyBlocks/lammps.py
new file mode 100644
index 0000000000000000000000000000000000000000..c058e04ec1f42d715caba41dceb0e4884ff938f2
--- /dev/null
+++ b/Custom_EasyBlocks/lammps.py
@@ -0,0 +1,437 @@
+# -*- coding: utf-8 -*-
+##
+# Copyright 2009-2020 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild. If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+@author: Pavel Grochal (INUITS)
+@author: Kenneth Hoste (Ghent University)
+@author: Alan O'Cais (Juelich Supercomputing Centre)
+"""
+
+import os
+import tempfile
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.framework.easyconfig import CUSTOM, MANDATORY
+from easybuild.tools.build_log import EasyBuildError, print_warning, print_msg
+from easybuild.tools.config import build_option
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
+from easybuild.tools.systemtools import get_shared_lib_ext
+
+from easybuild.easyblocks.generic.cmakemake import CMakeMake
+
+KOKKOS_CPU_ARCH_LIST = [
+ 'AMDAVX', # AMD 64-bit x86 CPU (AVX 1)
+ 'ZEN', # AMD Zen class CPU (AVX 2)
+ 'ZEN2', # AMD Zen2 class CPU (AVX 2)
+ 'ARMV80', # ARMv8.0 Compatible CPU
+ 'ARMV81', # ARMv8.1 Compatible CPU
+ 'ARMV8_THUNDERX', # ARMv8 Cavium ThunderX CPU
+ 'ARMV8_THUNDERX2', # ARMv8 Cavium ThunderX2 CPU
+ 'WSM', # Intel Westmere CPU (SSE 4.2)
+ 'SNB', # Intel Sandy/Ivy Bridge CPU (AVX 1)
+ 'HSW', # Intel Haswell CPU (AVX 2)
+ 'BDW', # Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
+ 'SKX', # Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
+ 'KNC', # Intel Knights Corner Xeon Phi
+ 'KNL', # Intel Knights Landing Xeon Phi
+ 'BGQ', # IBM Blue Gene/Q CPU
+ 'POWER7', # IBM POWER7 CPU
+ 'POWER8', # IBM POWER8 CPU
+ 'POWER9', # IBM POWER9 CPU
+ 'KEPLER30', # NVIDIA Kepler generation CC 3.0 GPU
+ 'KEPLER32', # NVIDIA Kepler generation CC 3.2 GPU
+ 'KEPLER35', # NVIDIA Kepler generation CC 3.5 GPU
+ 'KEPLER37', # NVIDIA Kepler generation CC 3.7 GPU
+ 'MAXWELL50', # NVIDIA Maxwell generation CC 5.0 GPU
+ 'MAXWELL52', # NVIDIA Maxwell generation CC 5.2 GPU
+ 'MAXWELL53', # NVIDIA Maxwell generation CC 5.3 GPU
+ 'PASCAL60', # NVIDIA Pascal generation CC 6.0 GPU
+ 'PASCAL61', # NVIDIA Pascal generation CC 6.1 GPU
+ 'VOLTA70', # NVIDIA Volta generation CC 7.0 GPU
+ 'VOLTA72', # NVIDIA Volta generation CC 7.2 GPU
+ 'TURING75', # NVIDIA Turing generation CC 7.5 GPU
+ 'AMPERE80', # NVIDIA Ampere generation CC 8.0 GPU
+ 'VEGA900', # AMD GPU MI25 GFX900
+ 'VEGA906', # AMD GPU MI50/MI60 GFX906
+ 'INTEL_GEN', #Intel GPUs Gen9+
+]
+
+KOKKOS_CPU_MAPPING = {
+ 'sandybridge': 'SNB',
+ 'ivybridge': 'SNB',
+ 'haswell': 'HSW',
+ 'broadwell': 'BDW',
+ 'skylake_avx512': 'SKX',
+ 'cascadelake': 'SKX',
+ 'knights-landing': 'KNL',
+ 'zen': 'ZEN',
+ 'zen2': 'ZEN2', # KOKKOS doesn't seem to distinguish between zen and zen2 (yet?)
+}
+
+
+KOKKOS_GPU_ARCH_TABLE = {
+ '3.0': 'KEPLER30', # NVIDIA Kepler generation CC 3.0
+ '3.2': 'KEPLER32', # NVIDIA Kepler generation CC 3.2
+ '3.5': 'KEPLER35', # NVIDIA Kepler generation CC 3.5
+ '3.7': 'KEPLER37', # NVIDIA Kepler generation CC 3.7
+ '5.0': 'MAXWELL50', # NVIDIA Maxwell generation CC 5.0
+ '5.2': 'MAXWELL52', # NVIDIA Maxwell generation CC 5.2
+ '5.3': 'MAXWELL53', # NVIDIA Maxwell generation CC 5.3
+ '6.0': 'PASCAL60', # NVIDIA Pascal generation CC 6.0
+ '6.1': 'PASCAL61', # NVIDIA Pascal generation CC 6.1
+ '7.0': 'VOLTA70', # NVIDIA Volta generation CC 7.0
+ '7.2': 'VOLTA72', # NVIDIA Volta generation CC 7.2
+ '7.5': 'TURING75', # NVIDIA Turing generation CC 7.5
+ '8.0': 'AMPERE80', # NVIDIA Ampere generation CC 8.0
+}
+
+PKG_PREFIX = 'PKG_'
+PKG_USER_PREFIX = PKG_PREFIX + 'USER-'
+
+
+class EB_LAMMPS(CMakeMake):
+ """
+ Support for building and installing LAMMPS
+ """
+
+ def __init__(self, *args, **kwargs):
+ """LAMMPS easyblock constructor: determine whether we should build with CUDA support enabled."""
+ super(EB_LAMMPS, self).__init__(*args, **kwargs)
+
+ cuda_dep = 'cuda' in [dep['name'].lower() for dep in self.cfg.dependencies()]
+ cuda_toolchain = hasattr(self.toolchain, 'COMPILER_CUDA_FAMILY')
+ self.cuda = cuda_dep or cuda_toolchain
+
+ @staticmethod
+ def extra_options(**kwargs):
+ """Custom easyconfig parameters for LAMMPS"""
+ extra_vars = CMakeMake.extra_options()
+ extra_vars.update({
+ # see https://developer.nvidia.com/cuda-gpus
+ 'cuda_compute_capabilities': [[], "List of CUDA compute capabilities to build with", CUSTOM],
+ 'general_packages': [None, "List of general packages without '%s' prefix." % PKG_PREFIX, MANDATORY],
+ 'kokkos': [True, "Enable kokkos build.", CUSTOM],
+ 'kokkos_arch': [None, "Set kokkos processor arch manually, if auto-detection doesn't work.", CUSTOM],
+ 'user_packages': [None, "List user packages without '%s' prefix." % PKG_USER_PREFIX, MANDATORY],
+ })
+ extra_vars['separate_build_dir'][0] = True
+ return extra_vars
+
+ def prepare_step(self, *args, **kwargs):
+ """Custom prepare step for LAMMPS."""
+ super(EB_LAMMPS, self).prepare_step(*args, **kwargs)
+
+ # Unset LIBS when using both KOKKOS and CUDA - it will mix lib paths otherwise
+ if self.cfg['kokkos'] and self.cuda:
+ env.unset_env_vars(['LIBS'])
+
+ def configure_step(self, **kwargs):
+ """Custom configuration procedure for LAMMPS."""
+
+ # list of CUDA compute capabilities to use can be specifed in two ways (where (2) overrules (1)):
+ # (1) in the easyconfig file, via the custom cuda_compute_capabilities;
+ # (2) in the EasyBuild configuration, via --cuda-compute-capabilities configuration option;
+ ec_cuda_cc = self.cfg['cuda_compute_capabilities']
+ cfg_cuda_cc = build_option('cuda_compute_capabilities')
+ if cfg_cuda_cc and not isinstance(cfg_cuda_cc, list):
+ raise EasyBuildError("cuda_compute_capabilities in easyconfig should be provided as list of strings, " +
+ "(for example ['8.0', '7.5']). Got %s" % cfg_cuda_cc)
+ cuda_cc = check_cuda_compute_capabilities(cfg_cuda_cc, ec_cuda_cc, cuda=self.cuda)
+
+ # cmake has its own folder
+ self.cfg['srcdir'] = os.path.join(self.start_dir, 'cmake')
+
+ # Enable following packages, if not configured in easyconfig
+ default_options = ['BUILD_DOC', 'BUILD_EXE', 'BUILD_LIB', 'BUILD_TOOLS']
+ for option in default_options:
+ if "-D%s=" % option not in self.cfg['configopts']:
+ self.cfg.update('configopts', '-D%s=on' % option)
+
+ # enable building of shared libraries, if not specified already via configopts
+ if self.cfg['build_shared_libs'] is None and '-DBUILD_SHARED_LIBS=' not in self.cfg['configopts']:
+ self.cfg['build_shared_libs'] = True
+
+ # Enable gzip, libpng and libjpeg-turbo support when its included as dependency
+ deps = [
+ ('gzip', 'GZIP'),
+ ('libpng', 'PNG'),
+ ('libjpeg-turbo', 'JPEG'),
+ ]
+ for dep_name, with_name in deps:
+ with_opt = '-DWITH_%s=' % with_name
+ if with_opt not in self.cfg['configopts']:
+ if get_software_root(dep_name):
+ self.cfg.update('configopts', with_opt + 'yes')
+ else:
+ self.cfg.update('configopts', with_opt + 'no')
+
+ # Disable auto-downloading/building Eigen dependency:
+ if '-DDOWNLOAD_EIGEN3=' not in self.cfg['configopts']:
+ self.cfg.update('configopts', '-DDOWNLOAD_EIGEN3=no')
+
+ # Compiler complains about 'Eigen3_DIR' not being set, but actually it needs 'EIGEN3_INCLUDE_DIR'.
+ # see: https://github.com/lammps/lammps/issues/1110
+ # Enable Eigen when its included as dependency dependency:
+ eigen_root = get_software_root('Eigen')
+ if eigen_root:
+ if '-DEIGEN3_INCLUDE_DIR=' not in self.cfg['configopts']:
+ self.cfg.update('configopts', '-DEIGEN3_INCLUDE_DIR=%s/include/Eigen' % get_software_root('Eigen'))
+ if '-DEigen3_DIR=' not in self.cfg['configopts']:
+ self.cfg.update('configopts', '-DEigen3_DIR=%s/share/eigen3/cmake/' % get_software_root('Eigen'))
+
+ # LAMMPS Configuration Options
+ # https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options
+ if self.cfg['general_packages']:
+ for package in self.cfg['general_packages']:
+ self.cfg.update('configopts', '-D%s%s=on' % (PKG_PREFIX, package))
+
+ if self.cfg['user_packages']:
+ for package in self.cfg['user_packages']:
+ self.cfg.update('configopts', '-D%s%s=on' % (PKG_USER_PREFIX, package))
+
+ # Optimization settings
+ pkg_opt = '-D%sOPT=' % PKG_PREFIX
+ if pkg_opt not in self.cfg['configopts']:
+ self.cfg.update('configopts', pkg_opt + 'on')
+
+ # USER-INTEL enables optimizations on Intel processors. GCC has also partial support for some of them.
+ pkg_user_intel = '-D%sINTEL=' % 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')
+ if self.toolchain.options.get('openmp', None):
+ self.cfg.update('configopts', '-DBUILD_OMP=yes')
+ self.cfg.update('configopts', '-D%sOMP=on' % PKG_USER_PREFIX)
+
+ # FFTW
+ if get_software_root("imkl") or get_software_root("FFTW"):
+ if '-DFFT=' not in self.cfg['configopts']:
+ if get_software_root("imkl"):
+ self.log.info("Using the MKL")
+ self.cfg.update('configopts', '-DFFT=MKL')
+ else:
+ self.log.info("Using FFTW")
+ self.cfg.update('configopts', '-DFFT=FFTW3')
+ if '-DFFT_PACK=' not in self.cfg['configopts']:
+ self.cfg.update('configopts', '-DFFT_PACK=array')
+
+ # https://lammps.sandia.gov/doc/Build_extras.html
+ # KOKKOS
+ if self.cfg['kokkos']:
+ self.cfg.update('configopts', '-D%sKOKKOS=on' % PKG_PREFIX)
+
+ processor_arch, gpu_arch = get_kokkos_arch(cuda_cc, self.cfg['kokkos_arch'], cuda=self.cuda)
+
+ if self.toolchain.options.get('openmp', None):
+ self.cfg.update('configopts', '-DKokkos_ENABLE_OPENMP=yes')
+ self.cfg.update('configopts', '-DKokkos_ARCH_%s=yes' % processor_arch)
+
+ # if KOKKOS and CUDA
+ if self.cuda:
+ nvcc_wrapper_path = os.path.join(self.start_dir, "lib", "kokkos", "bin", "nvcc_wrapper")
+ self.cfg.update('configopts', '-DKokkos_ENABLE_CUDA=yes')
+ self.cfg.update('configopts', '-DKokkos_ARCH_%s=yes' % gpu_arch)
+ self.cfg.update('configopts', '-DCMAKE_CXX_COMPILER="%s"' % nvcc_wrapper_path)
+ self.cfg.update('configopts', '-DCMAKE_CXX_FLAGS="-ccbin $CXX $CXXFLAGS"')
+
+ # CUDA only
+ elif self.cuda:
+ self.cfg.update('configopts', '-D%sGPU=on' % PKG_PREFIX)
+ self.cfg.update('configopts', '-DGPU_API=cuda')
+ self.cfg.update('configopts', '-DGPU_ARCH=%s' % get_cuda_gpu_arch(cuda_cc))
+
+ # 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())
+ self.log.info("Using %s as pip cache directory", os.environ['XDG_CACHE_HOME'])
+
+ return super(EB_LAMMPS, self).configure_step()
+
+ def sanity_check_step(self, *args, **kwargs):
+ """Run custom sanity checks for LAMMPS files, dirs and commands."""
+ check_files = [
+ 'atm', 'balance', 'colloid', 'crack', 'dipole', 'friction',
+ 'hugoniostat', 'indent', 'melt', 'message', 'min', 'msst',
+ 'nemd', 'obstacle', 'pour', 'voronoi',
+ ]
+
+ custom_commands = [
+ # LAMMPS test - you need to call specific test file on path
+ """python -c 'from lammps import lammps; l=lammps(); l.file("%s")'""" %
+ # The path is joined by "build_dir" (start_dir)/examples/filename/in.filename
+ os.path.join(self.start_dir, "examples", "%s" % check_file, "in.%s" % check_file)
+ # And this should be done for every file specified above
+ for check_file in check_files
+ ]
+
+ # 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]
+
+ shlib_ext = get_shared_lib_ext()
+ custom_paths = {
+ 'files': [
+ os.path.join('bin', 'lmp'),
+ os.path.join('include', 'lammps', 'library.h'),
+ os.path.join('lib64', 'liblammps.%s' % shlib_ext),
+ ],
+ 'dirs': [],
+ }
+
+ python = get_software_version('Python')
+ if python:
+ pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
+ pythonpath = os.path.join('lib', 'python%s' % pyshortver, 'site-packages')
+ custom_paths['dirs'].append(pythonpath)
+
+ return super(EB_LAMMPS, self).sanity_check_step(custom_commands=custom_commands, custom_paths=custom_paths)
+
+ def make_module_extra(self):
+ """Add install path to PYTHONPATH"""
+
+ txt = super(EB_LAMMPS, self).make_module_extra()
+
+ python = get_software_version('Python')
+ if python:
+ pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
+ pythonpath = os.path.join('lib', 'python%s' % pyshortver, 'site-packages')
+ txt += self.module_generator.prepend_paths('PYTHONPATH', [pythonpath])
+
+ txt += self.module_generator.prepend_paths('PYTHONPATH', ["lib64"])
+ txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', ["lib64"])
+
+ return txt
+
+
+def get_cuda_gpu_arch(cuda_cc):
+ """Return CUDA gpu ARCH in LAMMPS required format. Example: 'sm_32' """
+ # Get largest cuda supported
+ return 'sm_%s' % str(sorted(cuda_cc, reverse=True)[0]).replace(".", "")
+
+
+def get_kokkos_arch(cuda_cc, kokkos_arch, cuda=None):
+ """
+ Return KOKKOS ARCH in LAMMPS required format, which is either 'CPU_ARCH' or 'CPU_ARCH;GPU_ARCH'.
+
+ see: https://lammps.sandia.gov/doc/Build_extras.html#kokkos
+ """
+ if cuda is None or not isinstance(cuda, bool):
+ cuda = get_software_root('CUDA')
+
+ processor_arch = None
+
+ if kokkos_arch:
+ if kokkos_arch not in KOKKOS_CPU_ARCH_LIST:
+ warning_msg = "Specified CPU ARCH (%s) " % kokkos_arch
+ warning_msg += "was not found in listed options [%s]." % KOKKOS_CPU_ARCH_LIST
+ warning_msg += "Still might work though."
+ print_warning(warning_msg)
+ processor_arch = kokkos_arch
+
+ else:
+ warning_msg = "kokkos_arch not set. Trying to auto-detect CPU arch."
+ print_warning(warning_msg)
+
+ processor_arch = KOKKOS_CPU_MAPPING.get(get_cpu_arch())
+
+ if not processor_arch:
+ error_msg = "Couldn't determine CPU architecture, you need to set 'kokkos_arch' manually."
+ raise EasyBuildError(error_msg)
+
+ print_msg("Determined cpu arch: %s" % processor_arch)
+
+ gpu_arch = None
+ if cuda:
+ # CUDA below
+ for cc in sorted(cuda_cc, reverse=True):
+ gpu_arch = KOKKOS_GPU_ARCH_TABLE.get(str(cc))
+ if gpu_arch:
+ break
+ else:
+ warning_msg = "(%s) GPU ARCH was not found in listed options." % cc
+ print_warning(warning_msg)
+
+ if not gpu_arch:
+ error_msg = "Specified GPU ARCH (%s) " % cuda_cc
+ error_msg += "was not found in listed options [%s]." % KOKKOS_GPU_ARCH_TABLE
+ raise EasyBuildError(error_msg)
+
+ return processor_arch, gpu_arch
+
+
+def check_cuda_compute_capabilities(cfg_cuda_cc, ec_cuda_cc, cuda=None):
+ """
+ Checks if cuda-compute-capabilities is set and prints warning if it gets declared on multiple places.
+
+ :param cfg_cuda_cc: cuda-compute-capabilities from cli config
+ :param ec_cuda_cc: cuda-compute-capabilities from easyconfig
+ :param cuda: boolean to check if cuda should be enabled or not
+ :return: returns preferred cuda-compute-capabilities
+ """
+
+ if cuda is None or not isinstance(cuda, bool):
+ cuda = get_software_root('CUDA')
+
+ cuda_cc = cfg_cuda_cc or ec_cuda_cc or []
+
+ if cuda:
+ if cfg_cuda_cc and ec_cuda_cc:
+ warning_msg = "cuda_compute_capabilities specified in easyconfig (%s)" % ec_cuda_cc
+ warning_msg += " are overruled by "
+ warning_msg += "--cuda-compute-capabilities configuration option (%s)" % cfg_cuda_cc
+ print_warning(warning_msg)
+ elif not cuda_cc:
+ error_msg = "No CUDA compute capabilities specified.\nTo build LAMMPS with Cuda you need to use"
+ error_msg += "the --cuda-compute-capabilities configuration option or the cuda_compute_capabilities "
+ error_msg += "easyconfig parameter to specify a list of CUDA compute capabilities to compile with."
+ raise EasyBuildError(error_msg)
+
+ elif cuda_cc:
+ warning_msg = "Missing CUDA package (in dependencies), "
+ warning_msg += "but 'cuda_compute_capabilities' option was specified."
+ print_warning(warning_msg)
+
+ return cuda_cc
+
+
+def get_cpu_arch():
+ """
+ Checks for CPU architecture via archspec library.
+ https://github.com/archspec/archspec
+ Archspec should be bundled as build-dependency to determine CPU arch.
+ It can't be called directly in code because it gets available only after prepare_step.
+
+ :return: returns detected cpu architecture
+ """
+ out, ec = run_cmd("python -c 'from archspec.cpu import host; print(host())'", simple=False)
+ if ec:
+ raise EasyBuildError("Failed to determine CPU architecture: %s", out)
+ return out.strip()
diff --git a/Golden_Repo/l/LAMMPS/LAMMPS-7Jan2022-gpsmkl-2021b.eb b/Golden_Repo/l/LAMMPS/LAMMPS-7Jan2022-gpsmkl-2021b.eb
new file mode 100644
index 0000000000000000000000000000000000000000..933cfd689cbd5dfe4adf221ee19957cd1a650cb9
--- /dev/null
+++ b/Golden_Repo/l/LAMMPS/LAMMPS-7Jan2022-gpsmkl-2021b.eb
@@ -0,0 +1,163 @@
+# Installation command used:
+# eb --include-easyblocks=$PWD/Custom_EasyBlocks/lammps.py,"$EASYBUILD_INCLUDE_EASYBLOCKS"\\
+# --mpi-cmd-template='echo %(nr_ranks)s && %(cmd)s' \\
+# Golden_Repo/l/LAMMPS/LAMMPS-22Oct2020-intel-para-2020-Python-3.9.6.eb
+name = 'LAMMPS'
+version = '7Jan2022'
+
+homepage = 'https://lammps.sandia.gov/'
+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': 'gpsmkl', 'version': '2021b'}
+toolchainopts = {'openmp': True, 'cstd': 'c++14', 'usempi': True}
+
+# 'https://github.com/lammps/lammps/archive/'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = [
+ 'patch_%(version)s.tar.gz',
+ # Since we are dropping yaff for the time being, drop this too
+ # {'extract_cmd': 'cp %s %(builddir)s', 'filename': 'lammps_vs_yaff_test_single_point_energy.py'},
+]
+checksums = ['fbf6c6814968ae0d772d7b6783079ff4f249a8faeceb39992c344969e9f1edbb']
+
+builddependencies = [
+ ('CMake', '3.21.1', '', SYSTEM),
+ ('pkg-config', '0.29.2'),
+ ('archspec', '0.1.3'),
+]
+dependencies = [
+ ('CUDA', '11.5', '', SYSTEM),
+ ('Python', '3.9.6'),
+ ('libpng', '1.6.37'),
+ ('libjpeg-turbo', '2.1.1'),
+ ('netCDF', '4.8.1'),
+ ('GSL', '2.7'),
+ ('zlib', '1.2.11'),
+ ('gzip', '1.10'),
+ ('cURL', '7.78.0'),
+ ('HDF5', '1.12.1'),
+ ('tbb', '2020.3'),
+ ('PCRE', '8.45'),
+ ('libxml2', '2.9.10'),
+ ('FFmpeg', '4.4.1'),
+ ('Voro++', '0.4.6'),
+ ('kim-api', '2.2.1'),
+ ('Eigen', '3.3.9'),
+ # 'YAFF', # yaff needs an old version of h5py, which needs an old version of HDF5. Let's drop it
+ # ('yaff', '1.6.0'),
+ ('PLUMED', '2.7.2'),
+ ('ScaFaCoS', '1.0.1'),
+ # See below for why this is not included
+ # ('VTK', '8.2.0', local_python_versionsuffix),
+]
+
+# not enabled (yet), needs more work/additional dependencies:
+# ADIOS - https://lammps.sandia.gov/doc/Build_extras.html#user-adios-package
+# AWPMD - https://lammps.sandia.gov/doc/Build_extras.html#user-awpmd-package
+# QMMM - https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-qmmm
+# QUIP - https://lammps.sandia.gov/doc/Build_extras.html#user-quip-package
+# VTK - support is available in the foss version but currently fails to build for intel
+# due to https://software.intel.com/en-us/forums/intel-fortran-compiler/topic/746611
+# see https://github.com/lammps/lammps/issues/1964 for details
+user_packages = [
+ 'ATC',
+ 'BOCS',
+ 'CGDNA',
+ 'CGSDK',
+ 'COLVARS',
+ 'DIFFRACTION',
+ 'DPD',
+ 'DRUDE',
+ 'EFF',
+ 'FEP',
+ 'H5MD',
+ 'LB',
+ 'MANIFOLD',
+ 'MEAMC',
+ 'MESODPD',
+ 'MESONT',
+ 'MGPT',
+ 'MISC',
+ 'MOFFF',
+ 'MOLFILE',
+ 'NETCDF',
+ 'PHONON',
+ 'PLUMED',
+ 'PTM',
+ 'QTB',
+ 'REACTION',
+ 'REAXC',
+ 'SCAFACOS',
+ 'SDPD',
+ 'SMD',
+ 'SMTBQ',
+ 'SPH',
+ 'TALLY',
+ 'UEF',
+ # 'YAFF', # yaff needs an old version of h5py, which needs an old version of HDF5. Let's drop it
+]
+enhance_sanity_check = True
+
+# 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
+
+# Use the bfd linker for C++ (this will only be picked up when using Kokkos)
+preconfigopts = 'export CXXFLAGS="-fuse-ld=bfd $CXXFLAGS" &&'
+# docs require virtualenv (which we don't have)
+configopts = ' -DBUILD_DOC=off -DPKG_USER-INTEL=off '
+
+# auto-enabled by easyblock
+# 'GPU' - if cuda package is present and kokkos is disabled
+# 'KOKKOS' - if kokkos is enabled (by default)
+#
+# not enabled (yet), needs more work/additional dependencies:
+# 'LATTE', - https://lammps.sandia.gov/doc/Build_extras.html#latte-package
+# 'MSCG', - https://lammps.sandia.gov/doc/Build_extras.html#mscg-package
+general_packages = [
+ 'ASPHERE',
+ 'BODY',
+ 'CLASS2',
+ 'COLLOID',
+ 'COMPRESS',
+ 'CORESHELL',
+ 'DIPOLE',
+ 'GRANULAR',
+ 'KIM',
+ 'KSPACE',
+ 'MANYBODY',
+ 'MC',
+ 'MESSAGE',
+ 'MISC',
+ 'MLIAP',
+ 'MOLECULE',
+ 'MPIIO',
+ 'PERI',
+ 'POEMS',
+ 'PYTHON',
+ 'QEQ',
+ 'REPLICA',
+ 'RIGID',
+ 'SHOCK',
+ 'SNAP',
+ 'SPIN',
+ 'SRD',
+ 'VORONOI',
+]
+
+# run short test case to make sure installation doesn't produce blatently incorrect results;
+# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b
+# (requires an MPI context for intel/2020a)
+# Since we are dropping yaff for the time being, drop this too
+# sanity_check_commands = ['cd %(builddir)s && %(mpi_cmd_prefix)s python lammps_vs_yaff_test_single_point_energy.py']
+
+moduleclass = 'chem'
diff --git a/Golden_Repo/s/ScaFaCoS/ScaFaCoS-1.0.1-gpsmpi-2021b.eb b/Golden_Repo/s/ScaFaCoS/ScaFaCoS-1.0.1-gpsmpi-2021b.eb
new file mode 100644
index 0000000000000000000000000000000000000000..d21bbb48327d8ba93735c9a06e25b09c0435f8e1
--- /dev/null
+++ b/Golden_Repo/s/ScaFaCoS/ScaFaCoS-1.0.1-gpsmpi-2021b.eb
@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'ScaFaCoS'
+version = '1.0.1'
+
+homepage = 'http://www.scafacos.de/'
+description = "ScaFaCoS is a library of scalable fast coulomb solvers."
+
+toolchain = {'name': 'gpsmpi', 'version': '2021b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = [
+ '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz
+]
+
+builddependencies = [
+ ('Autotools', '20210726'),
+ ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+ ('GMP', '6.2.1'),
+ ('GSL', '2.7'),
+ ('FFTW', '3.3.10'),
+]
+
+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'
diff --git a/bin/gcc11ize.py b/bin/gcc11ize.py
index 8b8a9ad1539c6630e33dbba3419e225f2c0aeca9..0861124de69e89bd5e62e74812161c647b457984 100755
--- a/bin/gcc11ize.py
+++ b/bin/gcc11ize.py
@@ -14,6 +14,7 @@ releases = {
'AT-SPI2-ATK': ['2.34.2', '2.38.0'],
'AT-SPI2-core': ['2.36.0', '2.40.3'],
'Autotools': ['20200321', '20210726'],
+ 'archspec': ['0.1.0', '0.1.3'],
'binutils': ['2.36.1', '2.37'],
'Bison': ['3.7.6', '3.7.6'],
'Boost': ['1.74.0', '1.78.0'],
@@ -58,13 +59,17 @@ releases = {
'HarfBuzz': ['2.6.7', '2.8.2'],
'HDF5': ['1.10.6', '1.12.1'],
'HTSLib': ['1.1.4', '1.1.4'],
+ 'h5py': ['2.10.0', '3.5.0'],
'ICU': ['67.1', '70.1'],
'ImageMagick': ['7.0.10-25', '7.1.0.13'],
'imkl': ['2021.2.0', '2021.4.0'],
+ 'intel-para': ['2021', '2021b'],
+ 'ipsmpi': ['2021', '2021b'],
'intltool': ['0.51.0', '0.51.0'],
'ispc': ['1.12.0', '1.16.1'],
'JasPer': ['2.0.19', '2.0.33'],
'Java': ['15', '15'],
+ 'kim-api': ['2.1.3', '2.2.1'],
'libcroco': ['0.6.13', '0.6.13'],
'libdrm': ['2.4.106', '2.4.107'],
'libepoxy': ['1.5.4', '1.5.9'],
@@ -85,6 +90,7 @@ releases = {
'NASM': ['2.15.03', '2.15.05'],
'Ninja': ['1.10.0', '1.10.2'],
'NSS': ['3.51', '3.69'],
+ 'netCDF': ['4.7.4', '4.8.1'],
'numactl': ['2.0.13', '2.0.14'],
'OpenEXR': ['2.5.2', '3.1.1'],
'OpenGL': ['2020', '2021b'],
@@ -96,6 +102,7 @@ releases = {
'pkg-config': ['0.29.2', '0.29.2'],
'pkgconfig': ['1.5.4', '1.5.5'],
'PROJ': ['7.1.0', '8.1.0'],
+ 'PLUMED': ['2.6.1', '2.7.2'],
'protobuf': ['3.14.0', '3.17.3'],
'psmpi': ['5.4.9-1', '5.5.0-1'],
'pybind11': ['2.5.0', '2.7.1'],
@@ -156,6 +163,12 @@ def updateFileName(fileName, current, latest):
elif 'gpsmkl' in fileName:
fileName = fileName.replace(
releases['gpsmkl'][0], releases['gpsmkl'][1], 1)
+ elif 'ipsmpi' in fileName:
+ fileName = fileName.replace(
+ releases['ipsmpi'][0], releases['ipsmpi'][1], 1)
+ elif 'intel-para' in fileName:
+ fileName = fileName.replace(
+ releases['intel-para'][0], releases['intel-para'][1], 1)
fileName = fileName.replace(
'-Python-3.8.5', '', 1)
return fileName
@@ -182,6 +195,10 @@ def updateFile(oldName, newName, current, latest):
releases['gomkl'][0], releases['gomkl'][1], 1)
line = line.replace(
releases['gpsmpi'][0], releases['gpsmpi'][1], 1)
+ line = line.replace(
+ releases['ipsmpi'][0], releases['ipsmpi'][1], 1)
+ line = line.replace(
+ releases['intel-para'][0], releases['intel-para'][1], 1)
line = line.replace(
releases['gcccoremkl'][0], releases['gcccoremkl'][1], 1)
if line.startswith('site_contacts'):