add custom easyblock for LAMMPS

.gitignore

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+.idea
 .pydevproject
 .project
 LICENSE_HEADER

easybuild/easyblocks/l/lammps.py

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+##
+# 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)
+"""
+
+import glob
+import os
+import shutil
+import sys
+
+from easybuild.easyblocks.generic.cmakemake import CMakeMake
+from easybuild.framework.easyconfig import CUSTOM, MANDATORY
+from easybuild.tools import toolchain
+from easybuild.tools.build_log import EasyBuildError, print_warning
+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_cpu_features, get_shared_lib_ext
+
+
+KOKKOS_CPU_ARCH_LIST = [
+    'ARMv80',  #  ARMv8.0 Compatible CPU
+    'ARMv81',  #  ARMv8.1 Compatible CPU
+    'ARMv8-ThunderX',  #  ARMv8 Cavium ThunderX CPU
+    'BGQ',  #  IBM Blue Gene/Q CPUs
+    'Power8',  #  IBM POWER8 CPUs
+    'Power9',  #  IBM POWER9 CPUs
+    'SNB',  #  Intel Sandy/Ivy Bridge CPUs
+    'HSW',  #  Intel Haswell CPUs
+    'BDW',  #  Intel Broadwell Xeon E-class CPUs
+    'SKX',  #  Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+    'KNC',  #  Intel Knights Corner Xeon Phi
+    'KNL',  #  Intel Knights Landing Xeon Phi
+]
+
+
+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
+}
+
+
+class EB_LAMMPS(CMakeMake):
+    """
+    Support for building and installing LAMMPS
+    """
+
+    @staticmethod
+    def extra_options():
+        """Custom easyconfig parameters for LAMMPS"""
+
+        extra_vars = {
+            # 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 `PKG_` prefix.", MANDATORY],
+            'kokkos': [True, "Enable kokkos build. (enabled by default)", CUSTOM],
+            'kokkos_arch': [None, "Set kokkos processor arch to specific value, if auto-detection doesn't work.", CUSTOM],
+            'user_packages': [None, "List user packages without `PKG_USER-` prefix.", MANDATORY],
+        }
+        return CMakeMake.extra_options(extra_vars)
+
+    def configure_step(self):
+        """Custom configuration procedure for LAMMPS."""
+
+        cuda = get_software_root('CUDA')
+        # 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')
+        cuda_cc = cfg_cuda_cc or ec_cuda_cc or []
+
+        # cmake has its own folder
+        self.cfg['srcdir'] = os.path.join(self.start_dir, 'cmake')
+
+        # verbose CMake
+        if '-DCMAKE_VERBOSE_MAKEFILE=' not in self.cfg['configopts']:
+            self.cfg.update('configopts','-DCMAKE_VERBOSE_MAKEFILE=yes')
+
+        # Enable following packages, if not configured in easycofig
+        default_options = [
+            'BUILD_DOC', 'BUILD_EXE', 'BUILD_LIB',
+            'BUILD_SHARED_LIBS', 'BUILD_TOOLS',
+        ]
+        for option in default_options:
+            if "-D%s=" % option not in self.cfg['configopts']:
+                self.cfg.update('configopts','-D%s=on' % option)
+
+        # Is there a gzip
+        if '-DWITH_GZIP=' not in self.cfg['configopts']:
+            if get_software_root('gzip'):
+                self.cfg.update('configopts','-DWITH_GZIP=yes')
+            else:
+                self.cfg.update('configopts','-DWITH_GZIP=no')
+
+        # Is there a libpng
+        if '-DWITH_PNG=' not in self.cfg['configopts']:
+            if get_software_root('libpng'):
+                self.cfg.update('configopts','-DWITH_PNG=yes')
+            else:
+                self.cfg.update('configopts','-DWITH_PNG=no')
+
+        # Is there a libjpeg-turbo
+        if '-DWITH_JPEG=' not in self.cfg['configopts']:
+            if get_software_root('libjpeg-turbo'):
+                self.cfg.update('configopts','-DWITH_JPEG=yes')
+            else:
+                self.cfg.update('configopts','-DWITH_JPEG=no')
+
+        # With Eigen dependency:
+        if '-DDOWNLOAD_EIGEN3=' not in self.cfg['configopts']:
+            self.cfg.update('configopts','-DDOWNLOAD_EIGEN3=no')
+        # Compiler complains about 'Eigen3_DIR' not beeing set, but acutally it needs
+        # 'EIGEN3_INCLUDE_DIR'.
+        # see: https://github.com/lammps/lammps/issues/1110
+        if '-DEIGEN3_INCLUDE_DIR=' not in self.cfg['configopts']:
+            if get_software_root('Eigen'):
+                self.cfg.update('configopts','-DEIGEN3_INCLUDE_DIR=%s/include/Eigen' % get_software_root('Eigen'))
+
+        if '-DEigen3_DIR=' not in self.cfg['configopts']:
+            if get_software_root('Eigen'):
+                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', '-DPKG_%s=on' % package)
+
+        if self.cfg['user_packages']:
+            for package in self.cfg['user_packages']:
+                self.cfg.update('configopts', '-DPKG_USER-%s=on' % package)
+
+        # Optimization settings
+        if '-DPKG_OPT=' not in self.cfg['configopts']:
+            self.cfg.update('configopts', '-DPKG_OPT=on')
+
+        if '-DPKG_USR-INTEL=' not in self.cfg['configopts']:
+            self.cfg.update('configopts', '-DPKG_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', '-DPKG_USER-OMP=on')
+
+        # FFT
+        if '-DFFT=' not in self.cfg['configopts']:
+            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']:
+
+            if self.toolchain.options.get('openmp', None):
+                self.cfg.update('configopts', '-DKOKKOS_ENABLE_OPENMP=yes')
+
+            self.cfg.update('configopts', '-DPKG_KOKKOS=on')
+            self.cfg.update('configopts', '-DKOKKOS_ARCH="%s"' % self.get_kokkos_gpu_arch(cuda_cc) )
+
+            # if KOKKOS and CUDA
+            if cuda:
+                self.check_cuda_compute_capabilities(cfg_cuda_cc, ec_cuda_cc, cuda_cc)
+                nvcc_wrapper_path = os.path.join(self.start_dir, "lib","kokkos", "bin", "nvcc_wrapper")
+                # nvcc_wrapper can't find OpenMP for some reason, need to specify OpenMP flags.
+                # https://software.intel.com/en-us/forums/intel-oneapi-base-toolkit/topic/842470
+                self.cfg.update('configopts', '-DOpenMP_CXX_FLAGS="-qopenmp"')
+                self.cfg.update('configopts', '-DOpenMP_CXX_LIB_NAMES="libiomp5"')
+                self.cfg.update('configopts', '-DOpenMP_libiomp5_LIBRARY=$EBROOTICC/lib/intel64_lin/libiomp5.so')
+
+                self.cfg.update('configopts', '-DKOKKOS_ENABLE_CUDA=yes')
+                self.cfg.update('configopts', '-DCMAKE_CXX_COMPILER="%s"' % nvcc_wrapper_path)
+                self.cfg.update('configopts', '-DCMAKE_CXX_FLAGS="-ccbin $CXX $CXXFLAGS"')
+
+        # CUDA only
+        elif cuda:
+            self.cfg.update('configopts', '-DPKG_GPU=on')
+            self.cfg.update('configopts', '-DGPU_API=cuda')
+
+            self.check_cuda_compute_capabilities(cfg_cuda_cc, ec_cuda_cc, cuda_cc)
+            self.cfg.update('configopts', '-DGPU_ARCH=%s' % self.get_cuda_gpu_arch(cuda_cc))
+
+        return super(EB_LAMMPS, self).configure_step()
+
+    # This might be needed - keep it as reference
+    # def build_step(self):
+    #     if self.cfg['kokkos'] and get_software_root('CUDA'):
+    #         self.cfg.update('prebuildopts', 'export NVCC_WRAPPER_DEFAULT_COMPILER=$MPICXX &&')
+    #     return super(EB_LAMMPS, self).build_step()
+
+    def sanity_check_step(self, *args, **kwargs):
+        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
+        ]
+
+        pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
+        pythonpath = os.path.join('lib','python%s' % pyshortver,'site-packages')
+        shlib_ext = get_shared_lib_ext()
+        custom_paths = {
+            'files': [
+                'bin/lmp',
+                'include/lammps/library.h',
+                'lib64/liblammps.%s' % shlib_ext,
+            ],
+            'dirs': [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()
+
+        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, "lib64"])
+        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', ["lib64"])
+
+        return txt
+
+    def get_cuda_gpu_arch(self, cuda_cc):
+        cuda_cc.sort(reverse=True)
+        return 'sm_%' % str(cuda_cc[0]).replace(".", "")
+
+    def get_kokkos_gpu_arch(self, cuda_cc):
+        # see: https://lammps.sandia.gov/doc/Build_extras.html#kokkos
+        cuda = get_software_root('CUDA')
+        processor_arch = None
+
+        if self.cfg['kokkos_arch']:
+            if self.cfg['kokkos_arch'] not in KOKKOS_CPU_ARCH_LIST:
+                warning_msg = "Specified CPU ARCH (%s) " % self.cfg['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 = self.cfg['kokkos_arch']
+
+        else:
+            warning_msg = "kokkos_arch not set. Trying to auto-detect CPU arch."
+            print_warning(warning_msg)
+
+            cpu_arch = self.get_cpu_arch()
+
+            if cpu_arch == "sandybridge" or cpu_arch == "ivybridge":
+                processor_arch = 'SNB'
+            elif cpu_arch == "haswell":
+                processor_arch = 'HSW'
+            elif cpu_arch == "broadwell":
+                processor_arch = 'BDW'
+            elif cpu_arch == "skylake":
+                processor_arch = 'SKX'
+            elif cpu_arch == "knights-landing":
+                processor_arch = 'KNL'
+            else:
+                error_msg = "Couldn't determine CPU architecture, you need to set 'kokkos_arch' manually."
+                raise EasyBuildError(error_msg)
+                exit(1)
+            print("Determined cpu arch: %s" % processor_arch)
+
+        if not cuda:
+            return processor_arch
+
+        # CUDA below
+        cuda_cc.sort(reverse=True)
+        gpu_arch = None
+        for cc in cuda_cc:
+            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 "%s;%s" % (processor_arch, gpu_arch)
+
+    def check_cuda_compute_capabilities(self, cfg_cuda_cc, ec_cuda_cc, cuda_cc):
+        cuda = get_software_root('CUDA')
+
+        if cuda:
+            if cfg_cuda_cc and ec_cuda_cc:
+                warning_msg = "cuda_compute_capabilities specified in easyconfig (%s) are overruled by " % self.ec_cuda_cc
+                warning_msg += "--cuda-compute-capabilities configuration option (%s)" % self.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), but 'cuda_compute_capabilities' option was specified."
+            print_warning(warning_msg)
+
+        return cuda_cc
+
+    def get_cpu_arch(self):
+        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)
+        # transform: 'skylake_avx512\n' => 'skylake'
+        return out.strip().split("_")[0]