From 36d02f60a40190d711df0e4818aecc2f40f1b827 Mon Sep 17 00:00:00 2001
From: easybuild <you@example.com>
Date: Thu, 8 Jun 2023 14:52:19 +0200
Subject: [PATCH] fix
---
easyblocks/a/ansysem.py | 111 ++++
easyblocks/a/aomp.py | 195 +++++++
easyblocks/c/cp2k.py | 970 ++++++++++++++++++++++++++++++++
easyblocks/i/imod.py | 95 ++++
easyblocks/n/nvhpc.py | 312 ++++++++++
easyblocks/o/openfoam.py | 556 ++++++++++++++++++
easyblocks/q/quantumespresso.py | 526 +++++++++++++++++
easyblocks/r/relion.py | 125 ++++
easyblocks/w/wien2k.py | 249 +++++---
9 files changed, 3048 insertions(+), 91 deletions(-)
create mode 100644 easyblocks/a/ansysem.py
create mode 100644 easyblocks/a/aomp.py
create mode 100644 easyblocks/c/cp2k.py
create mode 100644 easyblocks/i/imod.py
create mode 100644 easyblocks/n/nvhpc.py
create mode 100644 easyblocks/o/openfoam.py
create mode 100644 easyblocks/q/quantumespresso.py
create mode 100644 easyblocks/r/relion.py
diff --git a/easyblocks/a/ansysem.py b/easyblocks/a/ansysem.py
new file mode 100644
index 0000000..59e7a48
--- /dev/null
+++ b/easyblocks/a/ansysem.py
@@ -0,0 +1,111 @@
+##
+# 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for installing ANSYS Eletromagnetics
+
+@author: Alexi Rivera (Chalmers University of Technology)
+@author: Mikael OEhman (Chalmers University of Technology)
+"""
+import os
+import glob
+
+from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.run import run_cmd
+
+
+class EB_ANSYSEM(PackedBinary):
+ """Support for installing Ansys Electromagnetics."""
+
+ def __init__(self, *args, **kwargs):
+ """Initialize Ansys Electromagnetics specific variables."""
+ super(EB_ANSYSEM, self).__init__(*args, **kwargs)
+ self.replayfile = None
+
+ def configure_step(self):
+ """Configure Ansys Electromagnetics installation."""
+ licserv = os.getenv('EB_ANSYS_EM_LICENSE_SERVER')
+ licport = os.getenv('EB_ANSYS_EM_LICENSE_SERVER_PORT')
+ licservers = ['', '', '']
+ licservs = licserv.split(',')
+ servercount = len(licservs)
+ licservers[:servercount] = licservs
+ try:
+ self.replayfile = os.path.join(self.builddir, "installer.properties")
+ txt = '\n'.join([
+ "-W Agree.selection=1",
+ "-P installLocation=\"%s\"" % self.installdir,
+ "-W TempDirectory.tempPath=\"/tmp\"",
+ "-W TempDirectory.ChangeTempPermission=\"0\"",
+ "-W LibraryOption.libraryOption=0",
+ "-W LibraryOption.libraryPath=\"\"",
+ "-W LicenseOption.licenseOption=2",
+ "-W LicenseOption.licenseFileName=\"\"",
+ "-W LicenseOption.serverCount=%s" % servercount,
+ "-W LicenseOption.serverName1=\"%s\"" % licservers[0],
+ "-W LicenseOption.serverName2=\"%s\"" % licservers[1],
+ "-W LicenseOption.serverName3=\"%s\"" % licservers[2],
+ "-W LicenseOption.tcpPort=%s" % licport,
+ ])
+ with open(self.replayfile, "w") as f:
+ f.write(txt)
+ except IOError as err:
+ raise EasyBuildError("Failed to create install properties file used for replaying installation: %s", err)
+
+ def install_step(self):
+ """Install Ansys Electromagnetics using its setup tool."""
+ cmd = "./Linux/AnsysEM/disk1/setup.exe -options \"%s\" -silent" % (self.replayfile)
+ run_cmd(cmd, log_all=True, simple=True)
+
+ def make_module_extra(self):
+ """Extra module entries for Ansys Electromagnetics."""
+ idirs = glob.glob(os.path.join(self.installdir, 'AnsysEM*/Linux*/'))
+ if len(idirs) == 1:
+ subdir = os.path.relpath(idirs[0], self.installdir)
+ else:
+ raise EasyBuildError("Failed to locate single install subdirectory AnsysEM*/Linux*/")
+
+ txt = super(EB_ANSYSEM, self).make_module_extra()
+ txt += self.module_generator.prepend_paths('PATH', subdir)
+ # Not sure if these are needed;
+ # txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH',
+ # [os.path.join(ansysdir, 'mainwin540', 'Linux64', 'mw', 'lib-amd64_linux_optimized')])
+ # txt += self.module_generator.prepend_paths('LIBRARY_PATH',
+ # [os.path.join('ansysdir', 'mainwin540', 'Linux64', 'mw', 'lib-amd64_linux_optimized')])
+ return txt
+
+ def sanity_check_step(self):
+ """Custom sanity check for Ansys Electromagnetics."""
+ idirs = glob.glob(os.path.join(self.installdir, 'AnsysEM*/Linux*/'))
+ if len(idirs) == 1:
+ subdir = os.path.relpath(idirs[0], self.installdir)
+ else:
+ raise EasyBuildError("Failed to locate single install subdirectory AnsysEM*/Linux*/")
+
+ custom_paths = {
+ 'files': [os.path.join(subdir, 'ansysedt')],
+ 'dirs': [subdir],
+ }
+ super(EB_ANSYSEM, self).sanity_check_step(custom_paths=custom_paths)
diff --git a/easyblocks/a/aomp.py b/easyblocks/a/aomp.py
new file mode 100644
index 0000000..7dd557c
--- /dev/null
+++ b/easyblocks/a/aomp.py
@@ -0,0 +1,195 @@
+##
+# Copyright 2021-2023 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+Support for building and installing AOMP - AMD OpenMP compiler, implemented as
+an EasyBlock
+
+@author: Jorgen Nordmoen (University Center for Information Technology - UiO)
+"""
+import os
+
+from easybuild.easyblocks.generic.binary import Binary
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.build_log import EasyBuildError, print_warning
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import move_file, remove_file
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.systemtools import AARCH64, POWER, X86_64
+from easybuild.tools.systemtools import get_cpu_architecture, get_shared_lib_ext
+
+AOMP_ALL_COMPONENTS = ['roct', 'rocr', 'project', 'libdevice', 'openmp',
+ 'extras', 'pgmath', 'flang', 'flang_runtime', 'comgr',
+ 'rocminfo', 'vdi', 'hipvdi', 'ocl', 'rocdbgapi',
+ 'rocgdb', 'roctracer', 'rocprofiler']
+AOMP_DEFAULT_COMPONENTS = ['roct', 'rocr', 'project', 'libdevice', 'openmp',
+ 'extras', 'pgmath', 'flang', 'flang_runtime',
+ 'comgr', 'rocminfo']
+AOMP_X86_COMPONENTS = ['vdi', 'hipvdi', 'ocl']
+AOMP_DBG_COMPONENTS = ['rocdbgapi', 'rocgdb']
+AOMP_PROF_COMPONENTS = ['roctracer', 'rocprofiler']
+
+
+class EB_AOMP(Binary):
+ """Support for installing AOMP"""
+
+ @staticmethod
+ def extra_options():
+ extra_vars = Binary.extra_options()
+ extra_vars.update({
+ 'components': [None, "AOMP components to build. Possible components: " +
+ ', '.join(AOMP_ALL_COMPONENTS), CUSTOM],
+ })
+ return extra_vars
+
+ def __init__(self, *args, **kwargs):
+ """Initialize custom class variables for Clang."""
+ super(EB_AOMP, self).__init__(*args, **kwargs)
+ self.cfg['extract_sources'] = True
+ self.cfg['dontcreateinstalldir'] = True
+
+ def configure_step(self):
+ """Configure AOMP build and let 'Binary' install"""
+ # Setup install command
+ self.cfg['install_cmd'] = './aomp/bin/build_aomp.sh'
+ # Setup 'preinstallopts'
+ version_major = self.version.split('-')[0]
+ install_options = [
+ 'AOMP={!s}'.format(self.installdir),
+ 'AOMP_REPOS="{!s}/aomp{!s}"'.format(self.builddir, version_major),
+ 'AOMP_CMAKE={!s}/bin/cmake'.format(get_software_root('CMake')),
+ 'AOMP_CHECK_GIT_BRANCH=0',
+ 'AOMP_APPLY_ROCM_PATCHES=0',
+ 'AOMP_STANDALONE_BUILD=1',
+ ]
+ if self.cfg['parallel']:
+ install_options.append(
+ 'NUM_THREADS={!s}'.format(self.cfg['parallel']))
+ else:
+ install_options.append('NUM_THREADS=1')
+ # Check if CUDA is loaded and alternatively build CUDA backend
+ if get_software_root('CUDA') or get_software_root('CUDAcore'):
+ cuda_root = get_software_root('CUDA') or get_software_root('CUDAcore')
+ install_options.append('AOMP_BUILD_CUDA=1')
+ install_options.append('CUDA="{!s}"'.format(cuda_root))
+ # 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 []
+ if cfg_cuda_cc and ec_cuda_cc:
+ warning_msg = "cuda_compute_capabilities specified in easyconfig (%s) are overruled by " % ec_cuda_cc
+ warning_msg += "--cuda-compute-capabilities configuration option (%s)" % cfg_cuda_cc
+ print_warning(warning_msg)
+ if not cuda_cc:
+ raise EasyBuildError("CUDA module was loaded, "
+ "indicating a build with CUDA, "
+ "but no CUDA compute capability "
+ "was specified!")
+ # Convert '7.0' to '70' format
+ cuda_cc = [cc.replace('.', '') for cc in cuda_cc]
+ cuda_str = ",".join(cuda_cc)
+ install_options.append('NVPTXGPUS="{!s}"'.format(cuda_str))
+ else:
+ # Explicitly disable CUDA
+ install_options.append('AOMP_BUILD_CUDA=0')
+ # Combine install instructions above into 'preinstallopts'
+ self.cfg['preinstallopts'] = ' '.join(install_options)
+ # Setup components for install
+ components = self.cfg.get('components', None)
+ # If no components were defined we use the default
+ if not components:
+ components = AOMP_DEFAULT_COMPONENTS
+ # NOTE: The following has not been tested properly and is therefore
+ # removed
+ #
+ # Add X86 components if correct architecture
+ # if get_cpu_architecture() == X86_64:
+ # components.extend(AOMP_X86_COMPONENTS)
+ # Only build selected components
+ self.cfg['installopts'] = 'select ' + ' '.join(components)
+
+ def post_install_step(self):
+ super(EB_AOMP, self).post_install_step()
+ # The install script will create a symbolic link as the install
+ # directory, this creates problems for EB as it won't remove the
+ # symlink. To remedy this we remove the link here and rename the actual
+ # install directory created by the AOMP install script
+ if os.path.islink(self.installdir):
+ remove_file(self.installdir)
+ else:
+ err_str = "Expected '{!s}' to be a symbolic link" \
+ " that needed to be removed, but it wasn't!"
+ raise EasyBuildError(err_str.format(self.installdir))
+ # Move the actual directory containing the install
+ install_name = '{!s}_{!s}'.format(os.path.basename(self.installdir),
+ self.version)
+ actual_install = os.path.join(os.path.dirname(self.installdir),
+ install_name)
+ if os.path.exists(actual_install) and os.path.isdir(actual_install):
+ move_file(actual_install, self.installdir)
+ else:
+ err_str = "Tried to move '{!s}' to '{!s}', " \
+ " but it either doesn't exist" \
+ " or isn't a directory!"
+ raise EasyBuildError(err_str.format(actual_install,
+ self.installdir))
+
+ def sanity_check_step(self):
+ """Custom sanity check for AOMP"""
+ shlib_ext = get_shared_lib_ext()
+ arch = get_cpu_architecture()
+ # Check architecture explicitly since Clang uses potentially
+ # different names
+ arch_map = {
+ X86_64: 'x86_64',
+ POWER: 'ppc64',
+ AARCH64: 'aarch64',
+ }
+
+ if arch in arch_map:
+ arch = arch_map[arch]
+ else:
+ print_warning("Unknown CPU architecture (%s) for OpenMP offloading!" % arch)
+ custom_paths = {
+ 'files': [
+ "amdgcn/bitcode/hip.bc", "amdgcn/bitcode/opencl.bc", "bin/aompcc",
+ "bin/aompversion", "bin/clang", "bin/flang", "bin/ld.lld", "bin/llvm-config",
+ "bin/mygpu", "bin/opt", "bin/rocminfo", "include/amd_comgr.h",
+ "include/hsa/amd_hsa_common.h", "include/hsa/hsa.h", "include/omp.h",
+ "include/omp_lib.h", "lib/libclang.%s" % shlib_ext, "lib/libflang.%s" % shlib_ext,
+ "lib/libomp.%s" % shlib_ext, "lib/libomptarget.rtl.amdgpu.%s" % shlib_ext,
+ "lib/libomptarget.rtl.%s.%s" % (arch, shlib_ext), "lib/libomptarget.%s" % shlib_ext,
+ ],
+ 'dirs': ["amdgcn", "include/clang", "include/hsa", "include/llvm"],
+ }
+ # If we are building with CUDA support we need to check if it was built properly
+ if get_software_root('CUDA') or get_software_root('CUDAcore'):
+ custom_paths['files'].append("lib/libomptarget.rtl.cuda.%s" % shlib_ext)
+ custom_commands = [
+ 'aompcc --help', 'clang --help', 'clang++ --help', 'flang --help',
+ 'llvm-config --cxxflags',
+ ]
+ super(EB_AOMP, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
diff --git a/easyblocks/c/cp2k.py b/easyblocks/c/cp2k.py
new file mode 100644
index 0000000..1adfd2f
--- /dev/null
+++ b/easyblocks/c/cp2k.py
@@ -0,0 +1,970 @@
+# IT4Innovations 2022
+# JK
+# EasyBlock for CP2K CUDA support
+##
+# Copyright 2009-2021 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for building and installing CP2K, implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Ward Poelmans (Ghent University)
+@author: Luca Marsella (CSCS)
+@author: Damian Alvarez (Forschungszentrum Juelich GmbH)
+@author: Alan O'Cais (Forschungszentrum Juelich GmbH)
+@author: Balazs Hajgato (Free University Brussels (VUB))
+"""
+
+import fileinput
+import glob
+import re
+import os
+import sys
+from distutils.version import LooseVersion
+
+import easybuild.tools.toolchain as toolchain
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.environment import setvar
+from easybuild.tools.filetools import change_dir, copy_dir, copy_file, mkdir, write_file
+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_avail_core_count
+
+
+class EB_CP2K(EasyBlock):
+ """
+ Support for building CP2K
+ - prepare module include files if required
+ - generate custom config file in 'arch' directory
+ - build CP2K
+ - run regression test if desired
+ - install by copying binary executables
+ """
+
+ def __init__(self, *args, **kwargs):
+ super(EB_CP2K, self).__init__(*args, **kwargs)
+
+ self.typearch = None
+
+ # this should be set to False for old versions of GCC (e.g. v4.1)
+ self.compilerISO_C_BINDING = True
+
+ # compiler options that need to be set in Makefile
+ self.debug = ''
+ self.fpic = ''
+
+ # used for both libsmm and libxsmm
+ self.libsmm = ''
+ self.modincpath = ''
+ self.openmp = ''
+
+ self.make_instructions = ''
+
+ @staticmethod
+ def extra_options():
+ extra_vars = {
+ 'extracflags': ['', "Extra CFLAGS to be added", CUSTOM],
+ 'extradflags': ['', "Extra DFLAGS to be added", CUSTOM],
+ 'gpuver': [None, "Value for GPUVER configuration setting, specifies type of GPU to build for", CUSTOM],
+ 'ignore_regtest_fails': [False, ("Ignore failures in regression test "
+ "(should be used with care)"), CUSTOM],
+ 'library': [False, "Also build CP2K as a library", CUSTOM],
+ 'maxtasks': [4, ("Maximum number of CP2K instances run at "
+ "the same time during testing"), CUSTOM],
+ 'modinc': [[], ("List of modinc's to use (*.f90], or 'True' to use "
+ "all found at given prefix"), CUSTOM],
+ 'modincprefix': ['', "Intel MKL prefix for modinc include dir", CUSTOM],
+ 'omp_num_threads': [None, "Value to set $OMP_NUM_THREADS to during testing", CUSTOM],
+ 'plumed': [None, "Enable PLUMED support", CUSTOM],
+ 'runtest': [True, "Build and run CP2K tests", CUSTOM],
+ 'type': ['popt', "Type of build ('popt' or 'psmp')", CUSTOM],
+ 'typeopt': [True, "Enable optimization", CUSTOM],
+ }
+ return EasyBlock.extra_options(extra_vars)
+
+ def _generate_makefile(self, options):
+ """Generate Makefile based on options dictionary and optional make instructions"""
+
+ text = "# Makefile generated by CP2K easyblock in EasyBuild\n"
+ for key, value in sorted(options.items()):
+ text += "%s = %s\n" % (key, value)
+ return text + self.make_instructions
+
+ def configure_step(self):
+ """Configure build
+ - build Libint wrapper
+ - generate Makefile
+ """
+
+ known_types = ['popt', 'psmp']
+ if self.cfg['type'] not in known_types:
+ raise EasyBuildError("Unknown build type specified: '%s', known types are %s",
+ self.cfg['type'], known_types)
+
+ # correct start dir, if needed
+ # recent CP2K versions have a 'cp2k' dir in the unpacked 'cp2k' dir
+ cp2k_path = os.path.join(self.cfg['start_dir'], 'cp2k')
+ if os.path.exists(cp2k_path):
+ self.cfg['start_dir'] = cp2k_path
+ self.log.info("Corrected start_dir to %s" % self.cfg['start_dir'])
+
+ # set compilers options according to toolchain config
+ # full debug: -g -traceback -check all -fp-stack-check
+ # -g links to mpi debug libs
+ if self.toolchain.options['debug']:
+ self.debug = '-g'
+ self.log.info("Debug build")
+ if self.toolchain.options['pic']:
+ self.fpic = "-fPIC"
+ self.log.info("Using fPIC")
+
+ # report on extra flags being used
+ if self.cfg['extracflags']:
+ self.log.info("Using extra CFLAGS: %s" % self.cfg['extracflags'])
+ if self.cfg['extradflags']:
+ self.log.info("Using extra DFLAGS: %s" % self.cfg['extradflags'])
+
+ # lib(x)smm support
+ libsmm = get_software_root('libsmm')
+ libxsmm = get_software_root('libxsmm')
+ if libxsmm:
+ self.cfg.update('extradflags', '-D__LIBXSMM')
+ self.libsmm = '-lxsmm -lxsmmf'
+ self.log.debug('Using libxsmm %s' % libxsmm)
+ elif libsmm:
+ libsmms = glob.glob(os.path.join(libsmm, 'lib', 'libsmm_*nn.a'))
+ dfs = [os.path.basename(os.path.splitext(x)[0]).replace('lib', '-D__HAS_') for x in libsmms]
+ moredflags = ' ' + ' '.join(dfs)
+ self.cfg.update('extradflags', moredflags)
+ self.libsmm = ' '.join(libsmms)
+ self.log.debug('Using libsmm %s (extradflags %s)' % (self.libsmm, moredflags))
+
+ # obtain list of modinc's to use
+ if self.cfg["modinc"]:
+ self.modincpath = self.prepmodinc()
+
+ # set typearch
+ self.typearch = "Linux-x86-64-%s" % self.toolchain.name
+
+ # extra make instructions
+ self.make_instructions = '' # "graphcon.o: graphcon.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
+
+ # compiler toolchain specific configuration
+ comp_fam = self.toolchain.comp_family()
+ if comp_fam == toolchain.INTELCOMP:
+ options = self.configure_intel_based()
+ elif comp_fam == toolchain.GCC:
+ options = self.configure_GCC_based()
+ else:
+ raise EasyBuildError("Don't know how to tweak configuration for compiler family %s" % comp_fam)
+
+ # BLAS/LAPACK/FFTW
+ if get_software_root('imkl'):
+ options = self.configure_MKL(options)
+ else:
+ # BLAS
+ if get_software_root('ACML'):
+ options = self.configure_ACML(options)
+ else:
+ options = self.configure_BLAS_lib(options)
+
+ # FFTW (no MKL involved)
+ if 'fftw3' in os.getenv('LIBFFT', ''):
+ options = self.configure_FFTW3(options)
+
+ # LAPACK
+ if os.getenv('LIBLAPACK_MT', None) is not None:
+ options = self.configure_LAPACK(options)
+
+ if os.getenv('LIBSCALAPACK', None) is not None:
+ options = self.configure_ScaLAPACK(options)
+
+ # PLUMED
+ plumed = get_software_root('PLUMED')
+ if self.cfg['plumed'] and not plumed:
+ raise EasyBuildError("The PLUMED module needs to be loaded to build CP2K with PLUMED support")
+
+ # enable PLUMED support if PLUMED is listed as a dependency
+ # and PLUMED support is either explicitly enabled (plumed = True) or unspecified ('plumed' not defined)
+ if plumed and (self.cfg['plumed'] or self.cfg['plumed'] is None):
+ options['LIBS'] += ' -lplumed'
+ options['DFLAGS'] += ' -D__PLUMED2'
+
+ # ELPA
+ elpa = get_software_root('ELPA')
+ if elpa:
+ options['LIBS'] += ' -lelpa'
+ elpa_inc_dir = os.path.join(elpa, 'include', 'elpa-%s' % get_software_version('ELPA'), 'modules')
+ options['FCFLAGSOPT'] += ' -I%s ' % elpa_inc_dir
+ if LooseVersion(self.version) >= LooseVersion('6.1'):
+ elpa_ver = ''.join(get_software_version('ELPA').split('.')[:2])
+ options['DFLAGS'] += ' -D__ELPA=%s' % elpa_ver
+ elpa_inc_dir = os.path.join(elpa, 'include', 'elpa-%s' % get_software_version('ELPA'), 'elpa')
+ options['FCFLAGSOPT'] += ' -I%s ' % elpa_inc_dir
+ else:
+ options['DFLAGS'] += ' -D__ELPA3'
+
+ # CUDA support
+ # see https://github.com/cp2k/cp2k/blob/master/INSTALL.md#2j-cuda-optional-improved-performance-on-gpu-systems
+ cuda = get_software_root('CUDA')
+ if cuda:
+ # determine CUDA compute capability to use based on --cuda-compute-capabilities in EasyBuild configuration,
+ # or cuda_compute_capabilities easyconfig parameter (fallback);
+ # must be a single value to build CP2K with CUDA support!
+ cuda_cc = build_option('cuda_compute_capabilities') or self.cfg.get('cuda_compute_capabilities')
+ if len(cuda_cc) == 1:
+ cuda_cc = cuda_cc[0]
+ elif cuda_cc:
+ error_msg = "Exactly one CUDA compute capability must be specified, found %d: %s"
+ raise EasyBuildError(error_msg, len(cuda_cc), ', '.join(cuda_cc))
+ else:
+ error_msg = "Exactly one CUDA compute capability must be specified via "
+ error_msg += "--cuda-compute-capabilities or the cuda_compute_capabilities easyconfig parameter."
+ raise EasyBuildError(error_msg)
+
+ # GPUVER must be set, required by the DBCSR component,
+ # see exts/dbcsr/Makefile and the parameters_*.json in src/acc/libsmm_acc/libcusmm/;
+ # determine string value to use based on select CUDA compute capability, unless specified explicitly via
+ # custom 'gpuver' easyconfig parameter
+ gpuver = self.cfg['gpuver']
+
+ if gpuver is None:
+ cuda_cc_lv = LooseVersion(cuda_cc)
+ known_gpuver = [
+ ('7.0', 'V100'),
+ ('6.0', 'P100'),
+ ('3.7', 'K80'),
+ ('3.5', 'K40'),
+ ]
+ for min_cuda_cc, val in known_gpuver:
+ if cuda_cc_lv >= LooseVersion(min_cuda_cc):
+ gpuver = val
+ break
+
+ if gpuver is None:
+ raise EasyBuildError("Failed to determine value for required GPUVER setting!")
+ else:
+ options['GPUVER'] = gpuver
+
+ options['DFLAGS'] += ' -D__ACC -D__DBCSR_ACC -D__PW_CUDA -D__GRID_CUDA'
+ options['LIBS'] += ' -lcudart -lnvrtc -lcuda -lcublas -lcufft -lrt'
+ options['NVCC'] = 'nvcc'
+ options['NVFLAGS'] = ' '.join([
+ options['DFLAGS'],
+ '-O3',
+ '--std=c++11',
+ '-arch sm_%s' % cuda_cc.replace('.', ''),
+ # control host compilers + options
+ "-ccbin='%s'" % os.getenv('CXX'),
+ "-Xcompiler='%s'" % os.getenv('CXXFLAGS'),
+ ])
+
+ # avoid group nesting
+ options['LIBS'] = options['LIBS'].replace('-Wl,--start-group', '').replace('-Wl,--end-group', '')
+
+ options['LIBS'] = "-Wl,--start-group %s -Wl,--end-group" % options['LIBS']
+
+ # specify correct location for 'data' directory in final installation
+ options['DATA_DIR'] = os.path.join(self.installdir, 'data')
+
+ # create arch file using options set
+ archfile = os.path.join(self.cfg['start_dir'], 'arch', '%s.%s' % (self.typearch, self.cfg['type']))
+ txt = self._generate_makefile(options)
+ write_file(archfile, txt)
+ self.log.info("Content of makefile (%s):\n%s" % (archfile, txt))
+
+ def prepmodinc(self):
+ """Prepare list of module files"""
+
+ self.log.debug("Preparing module files")
+
+ imkl = get_software_root('imkl')
+
+ if imkl:
+
+ # prepare modinc target path
+ modincpath = os.path.join(os.path.dirname(os.path.normpath(self.cfg['start_dir'])), 'modinc')
+ self.log.debug("Preparing module files in %s" % modincpath)
+
+ mkdir(modincpath, parents=True)
+
+ # get list of modinc source files
+ modincdir = os.path.join(imkl, self.cfg["modincprefix"], 'include')
+
+ if isinstance(self.cfg["modinc"], list):
+ modfiles = [os.path.join(modincdir, x) for x in self.cfg["modinc"]]
+
+ elif isinstance(self.cfg["modinc"], bool) and self.cfg["modinc"]:
+ modfiles = glob.glob(os.path.join(modincdir, '*.f90'))
+
+ else:
+ raise EasyBuildError("prepmodinc: Please specify either a boolean value or a list of files in modinc "
+ "(found: %s).", self.cfg["modinc"])
+
+ f77 = os.getenv('F77')
+ if not f77:
+ raise EasyBuildError("F77 environment variable not set, can't continue.")
+
+ # create modinc files
+ for f in modfiles:
+ if f77.endswith('ifort'):
+ cmd = "%s -module %s -c %s" % (f77, modincpath, f)
+ elif f77 in ['gfortran', 'mpif77']:
+ cmd = "%s -J%s -c %s" % (f77, modincpath, f)
+ else:
+ raise EasyBuildError("prepmodinc: Unknown value specified for F77 (%s)", f77)
+
+ run_cmd(cmd, log_all=True, simple=True)
+
+ return modincpath
+ else:
+ raise EasyBuildError("Don't know how to prepare modinc, imkl not found")
+
+ def configure_common(self):
+ """Common configuration for all toolchains"""
+
+ # openmp introduces 2 major differences
+ # -automatic is default: -noautomatic -auto-scalar
+ # some mem-bandwidth optimisation
+ if self.cfg['type'] == 'psmp':
+ self.openmp = self.toolchain.get_flag('openmp')
+
+ # determine which opt flags to use
+ if self.cfg['typeopt']:
+ optflags = 'OPT'
+ regflags = 'OPT2'
+ else:
+ optflags = 'NOOPT'
+ regflags = 'NOOPT'
+
+ # make sure a MPI-2 able MPI lib is used
+ mpi2 = False
+ if hasattr(self.toolchain, 'MPI_FAMILY') and self.toolchain.MPI_FAMILY is not None:
+ known_mpi2_fams = [toolchain.MPICH, toolchain.MPICH2, toolchain.MVAPICH2, toolchain.OPENMPI,
+ toolchain.INTELMPI]
+ mpi_fam = self.toolchain.mpi_family()
+ if mpi_fam in known_mpi2_fams:
+ mpi2 = True
+ self.log.debug("Determined MPI2 compatibility based on MPI toolchain component: %s" % mpi_fam)
+ else:
+ self.log.debug("Cannot determine MPI2 compatibility based on MPI toolchain component: %s" % mpi_fam)
+ else:
+ # can't use toolchain.mpi_family, because of system toolchain
+ mpi2libs = ['impi', 'MVAPICH2', 'OpenMPI', 'MPICH2', 'MPICH']
+ for mpi2lib in mpi2libs:
+ if get_software_root(mpi2lib):
+ mpi2 = True
+ self.log.debug("Determined MPI2 compatibility based on loaded MPI module: %s")
+ else:
+ self.log.debug("MPI-2 supporting MPI library %s not loaded.")
+
+ if not mpi2:
+ raise EasyBuildError("CP2K needs MPI-2, no known MPI-2 supporting library loaded?")
+
+ cppflags = os.getenv('CPPFLAGS')
+ ldflags = os.getenv('LDFLAGS')
+ cflags = os.getenv('CFLAGS')
+ fflags = os.getenv('FFLAGS')
+ fflags_lowopt = re.sub('-O[0-9]', '-O1', fflags)
+ options = {
+ 'CC': os.getenv('MPICC'),
+ 'CPP': '',
+ 'FC': '%s %s' % (os.getenv('MPIF90'), self.openmp),
+ 'LD': '%s %s' % (os.getenv('MPIF90'), self.openmp),
+ 'AR': 'ar -r',
+ 'CPPFLAGS': '',
+
+ 'FPIC': self.fpic,
+ 'DEBUG': self.debug,
+
+ 'FCFLAGS': '$(FCFLAGS%s)' % optflags,
+ 'FCFLAGS2': '$(FCFLAGS%s)' % regflags,
+
+ 'CFLAGS': ' %s %s %s $(FPIC) $(DEBUG) %s ' % (cflags, cppflags, ldflags, self.cfg['extracflags']),
+ 'DFLAGS': ' -D__parallel -D__BLACS -D__SCALAPACK -D__FFTSG %s' % self.cfg['extradflags'],
+
+ 'LIBS': os.getenv('LIBS', ''),
+
+ 'FCFLAGSNOOPT': '$(DFLAGS) $(CFLAGS) -O0 $(FREE) $(FPIC) $(DEBUG)',
+ 'FCFLAGSOPT': '%s $(FREE) $(SAFE) $(FPIC) $(DEBUG)' % fflags,
+ 'FCFLAGSOPT2': '%s $(FREE) $(SAFE) $(FPIC) $(DEBUG)' % fflags_lowopt,
+ }
+
+ libint = get_software_root('LibInt')
+ if libint:
+ options['DFLAGS'] += ' -D__LIBINT'
+
+ libintcompiler = "%s %s" % (os.getenv('CC'), os.getenv('CFLAGS'))
+
+ # Build libint-wrapper, if required
+ libint_wrapper = ''
+
+ # required for old versions of GCC
+ if not self.compilerISO_C_BINDING:
+ options['DFLAGS'] += ' -D__HAS_NO_ISO_C_BINDING'
+
+ # determine path for libint_tools dir
+ libinttools_paths = ['libint_tools', 'tools/hfx_tools/libint_tools']
+ libinttools_path = None
+ for path in libinttools_paths:
+ path = os.path.join(self.cfg['start_dir'], path)
+ if os.path.isdir(path):
+ libinttools_path = path
+ change_dir(libinttools_path)
+ if not libinttools_path:
+ raise EasyBuildError("No libinttools dir found")
+
+ # build libint wrapper
+ cmd = "%s -c libint_cpp_wrapper.cpp -I%s/include" % (libintcompiler, libint)
+ if not run_cmd(cmd, log_all=True, simple=True):
+ raise EasyBuildError("Building the libint wrapper failed")
+ libint_wrapper = '%s/libint_cpp_wrapper.o' % libinttools_path
+
+ # determine Libint libraries based on major version number
+ libint_maj_ver = get_software_version('Libint').split('.')[0]
+ if libint_maj_ver == '1':
+ libint_libs = "$(LIBINTLIB)/libderiv.a $(LIBINTLIB)/libint.a $(LIBINTLIB)/libr12.a"
+ elif libint_maj_ver == '2':
+ libint_libs = "$(LIBINTLIB)/libint2.a"
+ else:
+ raise EasyBuildError("Don't know how to handle libint version %s", libint_maj_ver)
+ self.log.info("Using Libint version %s" % (libint_maj_ver))
+
+ options['LIBINTLIB'] = '%s/lib' % libint
+ options['LIBS'] += ' %s -lstdc++ %s' % (libint_libs, libint_wrapper)
+
+ # add Libint include dir to $FCFLAGS
+ options['FCFLAGS'] += ' -I' + os.path.join(libint, 'include')
+
+ else:
+ # throw a warning, since CP2K without Libint doesn't make much sense
+ self.log.warning("Libint module not loaded, so building without Libint support")
+
+ libxc = get_software_root('libxc')
+ if libxc:
+ cur_libxc_version = get_software_version('libxc')
+ if LooseVersion(self.version) >= LooseVersion('6.1'):
+ libxc_min_version = '4.0.3'
+ options['DFLAGS'] += ' -D__LIBXC'
+ else:
+ libxc_min_version = '2.0.1'
+ options['DFLAGS'] += ' -D__LIBXC2'
+
+ if LooseVersion(cur_libxc_version) < LooseVersion(libxc_min_version):
+ raise EasyBuildError("This version of CP2K is not compatible with libxc < %s" % libxc_min_version)
+
+ if LooseVersion(cur_libxc_version) >= LooseVersion('4.0.3'):
+ # cfr. https://www.cp2k.org/howto:compile#k_libxc_optional_wider_choice_of_xc_functionals
+ options['LIBS'] += ' -L%s/lib -lxcf03 -lxc' % libxc
+ elif LooseVersion(cur_libxc_version) >= LooseVersion('2.2'):
+ options['LIBS'] += ' -L%s/lib -lxcf90 -lxc' % libxc
+ else:
+ options['LIBS'] += ' -L%s/lib -lxc' % libxc
+ self.log.info("Using Libxc-%s" % cur_libxc_version)
+ else:
+ self.log.info("libxc module not loaded, so building without libxc support")
+
+ return options
+
+ def configure_intel_based(self):
+ """Configure for Intel based toolchains"""
+
+ # based on guidelines available at
+ # http://software.intel.com/en-us/articles/build-cp2k-using-intel-fortran-compiler-professional-edition/
+ intelurl = ''.join(["http://software.intel.com/en-us/articles/",
+ "build-cp2k-using-intel-fortran-compiler-professional-edition/"])
+
+ options = self.configure_common()
+
+ extrainc = ''
+ if self.modincpath:
+ extrainc = '-I%s' % self.modincpath
+
+ options.update({
+ # -Vaxlib : older options
+ 'FREE': '-fpp -free',
+
+ # SAFE = -assume protect_parens -fp-model precise -ftz # causes problems, so don't use this
+ 'SAFE': '-assume protect_parens -no-unroll-aggressive',
+
+ 'INCFLAGS': '$(DFLAGS) -I$(INTEL_INC) -I$(INTEL_INCF) %s' % extrainc,
+
+ 'LDFLAGS': '$(INCFLAGS) ',
+ 'OBJECTS_ARCHITECTURE': 'machine_intel.o',
+ })
+
+ options['DFLAGS'] += ' -D__INTEL'
+
+ options['FCFLAGSOPT'] += ' $(INCFLAGS) -heap-arrays 64'
+ options['FCFLAGSOPT2'] += ' $(INCFLAGS) -heap-arrays 64'
+
+ ifortver = LooseVersion(get_software_version('ifort'))
+
+ # Required due to memory leak that occurs if high optimizations are used (from CP2K 7.1 intel-popt-makefile)
+ if ifortver >= LooseVersion("2018.5"):
+ self.make_instructions += "mp2_optimize_ri_basis.o: mp2_optimize_ri_basis.F\n" \
+ "\t$(FC) -c $(subst O2,O0,$(FCFLAGSOPT)) $<\n"
+ self.log.info("Optimization level of mp2_optimize_ri_basis.F was decreased to '-O0'")
+
+ # RHEL8 intel/2020a lots of CPASSERT failed (due to high optimization in cholesky decomposition)
+ if ifortver >= LooseVersion("2019"):
+ self.make_instructions += "cp_fm_cholesky.o: cp_fm_cholesky.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
+ self.log.info("Optimization flags for cp_fm_cholesky.F is set to '%s'", options['FCFLAGSOPT2'])
+
+ # -i-static has been deprecated prior to 2013, but was still usable. From 2015 it is not.
+ if ifortver < LooseVersion("2013"):
+ options['LDFLAGS'] += ' -i-static '
+ else:
+ options['LDFLAGS'] += ' -static-intel '
+
+ # Otherwise it fails on linking, since there are 2 definitions of main
+ if LooseVersion(self.version) >= LooseVersion('4.1'):
+ options['LDFLAGS'] += ' -nofor-main '
+
+ failmsg = "CP2K won't build correctly with the Intel %%s compilers prior to %%s, see %s" % intelurl
+
+ if ifortver >= LooseVersion("2011") and ifortver < LooseVersion("2012"):
+
+ # don't allow using Intel compiler 2011 prior to release 8, because of known issue (see Intel URL)
+ if ifortver >= LooseVersion("2011.8"):
+ # add additional make instructions to Makefile
+ self.make_instructions += "et_coupling.o: et_coupling.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
+ self.make_instructions += "qs_vxc_atom.o: qs_vxc_atom.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
+
+ else:
+ raise EasyBuildError(failmsg, "v12", "v2011.8")
+
+ elif ifortver >= LooseVersion("11"):
+ if LooseVersion(get_software_version('ifort')) >= LooseVersion("11.1.072"):
+ self.make_instructions += "qs_vxc_atom.o: qs_vxc_atom.F\n\t$(FC) -c $(FCFLAGS2) $<\n"
+
+ else:
+ raise EasyBuildError(failmsg, "v11", "v11.1.072")
+
+ else:
+ raise EasyBuildError("Intel compilers version %s not supported yet.", ifortver)
+
+ return options
+
+ def configure_GCC_based(self):
+ """Configure for GCC based toolchains"""
+ options = self.configure_common()
+
+ options.update({
+ # need this to prevent "Unterminated character constant beginning" errors
+ 'FREE': '-ffree-form -ffree-line-length-none',
+
+ 'LDFLAGS': '$(FCFLAGS)',
+ 'OBJECTS_ARCHITECTURE': 'machine_gfortran.o',
+ })
+
+ options['DFLAGS'] += ' -D__GFORTRAN'
+
+ options['FCFLAGSOPT'] += ' $(DFLAGS) $(CFLAGS) -fmax-stack-var-size=32768'
+ options['FCFLAGSOPT2'] += ' $(DFLAGS) $(CFLAGS)'
+
+ gcc_version = get_software_version('GCCcore') or get_software_version('GCC')
+ if LooseVersion(gcc_version) >= LooseVersion('10.0') and LooseVersion(self.version) <= LooseVersion('7.1'):
+ # -fallow-argument-mismatch is required for CP2K 7.1 (and older) when compiling with GCC 10.x & more recent,
+ # see https://github.com/cp2k/cp2k/issues/1157, https://github.com/cp2k/dbcsr/issues/351,
+ # https://github.com/cp2k/dbcsr/commit/58ee9709545deda8524cab804bf1f88a61a864ac and
+ # https://gcc.gnu.org/legacy-ml/gcc-patches/2019-10/msg01861.html
+ options['FCFLAGSOPT'] += ' -fallow-argument-mismatch'
+ options['FCFLAGSOPT2'] += ' -fallow-argument-mismatch'
+
+ return options
+
+ def configure_ACML(self, options):
+ """Configure for AMD Math Core Library (ACML)"""
+
+ openmp_suffix = ''
+ if self.openmp:
+ openmp_suffix = '_mp'
+
+ options['ACML_INC'] = '%s/gfortran64%s/include' % (get_software_root('ACML'), openmp_suffix)
+ options['CFLAGS'] += ' -I$(ACML_INC) -I$(FFTW_INC)'
+ options['DFLAGS'] += ' -D__FFTACML'
+
+ blas = os.getenv('LIBBLAS', '')
+ blas = blas.replace('gfortran64', 'gfortran64%s' % openmp_suffix)
+ options['LIBS'] += ' %s %s %s' % (self.libsmm, os.getenv('LIBSCALAPACK', ''), blas)
+
+ return options
+
+ def configure_BLAS_lib(self, options):
+ """Configure for BLAS library."""
+ options['LIBS'] += ' %s %s' % (self.libsmm, os.getenv('LIBBLAS', ''))
+ return options
+
+ def configure_MKL(self, options):
+ """Configure for Intel Math Kernel Library (MKL)"""
+
+ options['INTEL_INC'] = '$(MKLROOT)/include'
+ options['DFLAGS'] += ' -D__FFTW3'
+
+ extra = ''
+ if self.modincpath:
+ extra = '-I%s' % self.modincpath
+ options['CFLAGS'] += ' -I$(INTEL_INC) %s $(FPIC) $(DEBUG)' % extra
+
+ options['LIBS'] += ' %s %s' % (self.libsmm, os.getenv('LIBSCALAPACK', ''))
+
+ fftw_root = get_software_root('FFTW')
+ if fftw_root:
+ libfft = '-lfftw3'
+ if self.cfg['type'] == 'psmp':
+ libfft += ' -lfftw3_omp'
+
+ options['CFLAGS'] += ' -I$(INTEL_INCF)'
+ options['INTEL_INCF'] = os.path.join(fftw_root, 'include')
+ options['LIBS'] += ' -L%s %s' % (os.path.join(fftw_root, 'lib'), libfft)
+
+ else:
+ # only use Intel FFTW wrappers if FFTW is not loaded
+ options['CFLAGS'] += ' -I$(INTEL_INCF)'
+ options['DFLAGS'] += ' -D__FFTMKL'
+ options['INTEL_INCF'] = '$(INTEL_INC)/fftw'
+ options['LIBS'] = '%s %s' % (os.getenv('LIBFFT', ''), options['LIBS'])
+
+ return options
+
+ def configure_FFTW3(self, options):
+ """Configure for FFTW3"""
+
+ options.update({
+ 'FFTW_INC': os.getenv('FFT_INC_DIR', ''), # GCC
+ 'FFTW3INC': os.getenv('FFT_INC_DIR', ''), # Intel
+ 'FFTW3LIB': os.getenv('FFT_LIB_DIR', ''), # Intel
+ })
+
+ options['DFLAGS'] += ' -D__FFTW3'
+ if self.cfg['type'] == 'psmp':
+ libfft = os.getenv('LIBFFT_MT', '')
+ else:
+ libfft = os.getenv('LIBFFT', '')
+ options['LIBS'] += ' -L%s %s' % (os.getenv('FFT_LIB_DIR', '.'), libfft)
+
+ return options
+
+ def configure_LAPACK(self, options):
+ """Configure for LAPACK library"""
+ options['LIBS'] += ' %s' % os.getenv('LIBLAPACK_MT', '')
+ return options
+
+ def configure_ScaLAPACK(self, options):
+ """Configure for ScaLAPACK library"""
+
+ options['LIBS'] += ' %s' % os.getenv('LIBSCALAPACK', '')
+
+ return options
+
+ def build_step(self):
+ """Start the actual build
+ - go into makefiles dir
+ - patch Makefile
+ -build_and_install
+ """
+
+ if LooseVersion(self.version) < LooseVersion('7.0'):
+ makefiles = os.path.join(self.cfg['start_dir'], 'makefiles')
+ change_dir(makefiles)
+
+ # modify makefile for parallel build
+ parallel = self.cfg['parallel']
+ if parallel:
+
+ try:
+ for line in fileinput.input('Makefile', inplace=1, backup='.orig.patchictce'):
+ line = re.sub(r"^PMAKE\s*=.*$", "PMAKE\t= $(SMAKE) -j %s" % parallel, line)
+ sys.stdout.write(line)
+ except IOError as err:
+ raise EasyBuildError("Can't modify/write Makefile in %s: %s", makefiles, err)
+
+ # update make options with MAKE
+ self.cfg.update('buildopts', 'MAKE="make -j %s"' % self.cfg['parallel'])
+
+ # update make options with ARCH and VERSION
+ self.cfg.update('buildopts', 'ARCH=%s VERSION=%s' % (self.typearch, self.cfg['type']))
+
+ cmd = "make %s" % self.cfg['buildopts']
+
+ # clean first
+ run_cmd(cmd + " clean", log_all=True, simple=True, log_output=True)
+
+ # build and install
+ if self.cfg['library']:
+ cmd += ' libcp2k'
+ run_cmd(cmd + " all", log_all=True, simple=True, log_output=True)
+
+ def test_step(self):
+ """Run regression test."""
+
+ if self.cfg['runtest']:
+
+ # we need to specify location of 'data' directory in *build* dir,
+ # since we've configured CP2K to look into the installation directory
+ # (where 'data' will be copied to in install step)
+ setvar('CP2K_DATA_DIR', os.path.join(self.cfg['start_dir'], 'data'))
+
+ if not build_option('mpi_tests'):
+ self.log.info("Skipping testing of CP2K since MPI testing is disabled")
+ return
+
+ if self.cfg['omp_num_threads']:
+ setvar('OMP_NUM_THREADS', self.cfg['omp_num_threads'])
+
+ # change to root of build dir
+ change_dir(self.builddir)
+
+ # use regression test reference output if available
+ # try and find an unpacked directory that starts with 'LAST-'
+ regtest_refdir = None
+ for d in os.listdir(self.builddir):
+ if d.startswith("LAST-"):
+ regtest_refdir = d
+ break
+
+ # location of do_regtest script
+ cfg_fn = 'cp2k_regtest.cfg'
+
+ regtest_script = os.path.join(self.cfg['start_dir'], 'tools', 'regtesting', 'do_regtest')
+ regtest_cmd = [regtest_script, '-nobuild', '-config', cfg_fn]
+ if LooseVersion(self.version) < LooseVersion('7.1'):
+ # -nosvn option was removed in CP2K 7.1
+ regtest_cmd.insert(1, '-nosvn')
+
+ # older version of CP2K
+ if not os.path.exists(regtest_script):
+ regtest_script = os.path.join(self.cfg['start_dir'], 'tools', 'do_regtest')
+ regtest_cmd = [regtest_script, '-nocvs', '-quick', '-nocompile', '-config', cfg_fn]
+
+ regtest_cmd = ' '.join(regtest_cmd)
+
+ # patch do_regtest so that reference output is used
+ if regtest_refdir:
+ self.log.info("Using reference output available in %s" % regtest_refdir)
+ try:
+ for line in fileinput.input(regtest_script, inplace=1, backup='.orig.refout'):
+ line = re.sub(r"^(dir_last\s*=\${dir_base})/.*$", r"\1/%s" % regtest_refdir, line)
+ sys.stdout.write(line)
+ except IOError as err:
+ raise EasyBuildError("Failed to modify '%s': %s", regtest_script, err)
+
+ else:
+ self.log.info("No reference output found for regression test, just continuing without it...")
+
+ # prefer using 4 cores, since some tests require/prefer square (n^2) numbers or powers of 2 (2^n)
+ test_core_cnt = min(self.cfg['parallel'], 4)
+ if get_avail_core_count() < test_core_cnt:
+ raise EasyBuildError("Cannot run MPI tests as not enough cores (< %s) are available", test_core_cnt)
+ else:
+ self.log.info("Using %s cores for the MPI tests" % test_core_cnt)
+
+ # configure regression test
+ cfg_txt = '\n'.join([
+ 'FORT_C_NAME="%(f90)s"',
+ 'dir_base=%(base)s',
+ 'cp2k_version=%(cp2k_version)s',
+ 'dir_triplet=%(triplet)s',
+ 'export ARCH=${dir_triplet}',
+ 'cp2k_dir=%(cp2k_dir)s',
+ 'leakcheck="YES"',
+ 'maxtasks=%(maxtasks)s',
+ 'cp2k_run_prefix="%(mpicmd_prefix)s"',
+ ]) % {
+ 'f90': os.getenv('F90'),
+ 'base': os.path.dirname(os.path.normpath(self.cfg['start_dir'])),
+ 'cp2k_version': self.cfg['type'],
+ 'triplet': self.typearch,
+ 'cp2k_dir': os.path.basename(os.path.normpath(self.cfg['start_dir'])),
+ 'maxtasks': self.cfg['maxtasks'],
+ 'mpicmd_prefix': self.toolchain.mpi_cmd_for('', test_core_cnt),
+ }
+
+ write_file(cfg_fn, cfg_txt)
+ self.log.debug("Contents of %s: %s" % (cfg_fn, cfg_txt))
+
+ # run regression test
+ (regtest_output, ec) = run_cmd(regtest_cmd, log_all=True, simple=False, log_output=True)
+
+ if ec == 0:
+ self.log.info("Regression test output:\n%s" % regtest_output)
+ else:
+ raise EasyBuildError("Regression test failed (non-zero exit code): %s", regtest_output)
+
+ # pattern to search for regression test summary
+ re_pattern = r"number\s+of\s+%s\s+tests\s+(?P<cnt>[0-9]+)"
+
+ # find total number of tests
+ regexp = re.compile(re_pattern % "", re.M | re.I)
+ res = regexp.search(regtest_output)
+ tot_cnt = None
+ if res:
+ tot_cnt = int(res.group('cnt'))
+ else:
+ raise EasyBuildError("Finding total number of tests in regression test summary failed")
+
+ # function to report on regtest results
+ def test_report(test_result):
+ """Report on tests with given result."""
+
+ postmsg = ''
+
+ test_result = test_result.upper()
+ regexp = re.compile(re_pattern % test_result, re.M | re.I)
+
+ cnt = None
+ res = regexp.search(regtest_output)
+ if not res:
+ raise EasyBuildError("Finding number of %s tests in regression test summary failed",
+ test_result.lower())
+ else:
+ cnt = int(res.group('cnt'))
+
+ logmsg = "Regression test reported %s / %s %s tests"
+ logmsg_values = (cnt, tot_cnt, test_result.lower())
+
+ # failed tests indicate problem with installation
+ # wrong tests are only an issue when there are excessively many
+ if (test_result == "FAILED" and cnt > 0) or (test_result == "WRONG" and (cnt / tot_cnt) > 0.1):
+ if self.cfg['ignore_regtest_fails']:
+ self.log.warning(logmsg, *logmsg_values)
+ self.log.info("Ignoring failures in regression test, as requested.")
+ else:
+ raise EasyBuildError(logmsg, *logmsg_values)
+ elif test_result == "CORRECT" or cnt == 0:
+ self.log.info(logmsg, *logmsg_values)
+ else:
+ self.log.warning(logmsg, *logmsg_values)
+
+ return postmsg
+
+ # number of failed/wrong tests, will report error if count is positive
+ self.postmsg += test_report("FAILED")
+ self.postmsg += test_report("WRONG")
+
+ # there are no more 'new' tests from CP2K 8.1 onwards
+ if LooseVersion(self.version) < LooseVersion('8.0'):
+ # number of new tests, will be high if a non-suitable regtest reference was used
+ # will report error if count is positive (is that what we want?)
+ self.postmsg += test_report("NEW")
+
+ # number of correct tests: just report
+ test_report("CORRECT")
+
+ def install_step(self):
+ """Install built CP2K
+ - copy from exe to bin
+ - copy data dir (if exists)
+ - copy tests
+ """
+
+ # copy executables
+ exedir = os.path.join(self.cfg['start_dir'], 'exe', self.typearch)
+ targetdir = os.path.join(self.installdir, 'bin')
+ copy_dir(exedir, targetdir)
+
+ # copy libraries and include files, not sure what is strictly required so we take everything
+ if self.cfg['library']:
+ libdir = os.path.join(self.cfg['start_dir'], 'lib', self.typearch, self.cfg['type'])
+ targetdir = os.path.join(self.installdir, 'lib')
+ copy_dir(libdir, targetdir)
+ # Also need to populate the include directory
+ targetdir = os.path.join(self.installdir, 'include')
+ libcp2k_header = os.path.join(self.cfg['start_dir'], 'src', 'start', 'libcp2k.h')
+ target_header = os.path.join(targetdir, os.path.basename(libcp2k_header))
+ copy_file(libcp2k_header, target_header)
+ # include all .mod files for fortran users (don't know the exact list so take everything)
+ mod_path = os.path.join(self.cfg['start_dir'], 'obj', self.typearch, self.cfg['type'])
+ for mod_file in glob.glob(os.path.join(mod_path, '*.mod')):
+ target_mod = os.path.join(targetdir, os.path.basename(mod_file))
+ copy_file(mod_file, target_mod)
+
+ # copy data dir
+ datadir = os.path.join(self.cfg['start_dir'], 'data')
+ targetdir = os.path.join(self.installdir, 'data')
+ if os.path.exists(targetdir):
+ self.log.info("Won't copy data dir. Destination directory %s already exists" % targetdir)
+ elif os.path.exists(datadir):
+ copy_dir(datadir, targetdir)
+ else:
+ self.log.info("Won't copy data dir. Source directory %s does not exist" % datadir)
+
+ # copy tests
+ srctests = os.path.join(self.cfg['start_dir'], 'tests')
+ targetdir = os.path.join(self.installdir, 'tests')
+ if os.path.exists(targetdir):
+ self.log.info("Won't copy tests. Destination directory %s already exists" % targetdir)
+ else:
+ copy_dir(srctests, targetdir)
+
+ # copy regression test results
+ if self.cfg['runtest']:
+ try:
+ testdir = os.path.dirname(os.path.normpath(self.cfg['start_dir']))
+ for d in os.listdir(testdir):
+ if d.startswith('TEST-%s-%s' % (self.typearch, self.cfg['type'])):
+ path = os.path.join(testdir, d)
+ target = os.path.join(self.installdir, d)
+ copy_dir(path, target)
+ self.log.info("Regression test results dir %s copied to %s" % (d, self.installdir))
+ break
+ except (OSError, IOError) as err:
+ raise EasyBuildError("Failed to copy regression test results dir: %s", err)
+
+ def sanity_check_step(self):
+ """Custom sanity check for CP2K"""
+
+ cp2k_type = self.cfg['type']
+ custom_paths = {
+ 'files': ["bin/%s.%s" % (x, cp2k_type) for x in ["cp2k", "cp2k_shell"]],
+ 'dirs': ["tests"]
+ }
+ if self.cfg['library']:
+ custom_paths['files'].append(os.path.join('lib', 'libcp2k.a'))
+ custom_paths['files'].append(os.path.join('include', 'libcp2k.h'))
+ custom_paths['files'].append(os.path.join('include', 'libcp2k.mod'))
+ super(EB_CP2K, self).sanity_check_step(custom_paths=custom_paths)
+
+ def make_module_extra(self):
+ """Set up a CP2K_DATA_DIR environment variable to find CP2K provided basis sets"""
+
+ txt = super(EB_CP2K, self).make_module_extra()
+
+ # also define $CP2K_DATA_DIR in module,
+ # even though CP2K was already configured to pick up 'data' from install dir
+ # this could be useful for users to access the 'data' dir in a documented way (and it doesn't hurt)
+ datadir = os.path.join(self.installdir, 'data')
+ if os.path.exists(datadir):
+ txt += self.module_generator.set_environment('CP2K_DATA_DIR', datadir)
+
+ return txt
+
diff --git a/easyblocks/i/imod.py b/easyblocks/i/imod.py
new file mode 100644
index 0000000..93b019d
--- /dev/null
+++ b/easyblocks/i/imod.py
@@ -0,0 +1,95 @@
+##
+# Copyright 2013-2022 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),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for building and installing IMOD, implemented as an easyblock
+
+@author: Benjamin Roberts (Landcare Research NZ Ltd)
+"""
+import os
+import shutil
+
+from easybuild.easyblocks.generic.binary import Binary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import remove_dir
+from easybuild.tools.run import run_cmd
+
+
+class EB_IMOD(Binary):
+ """Support for building/installing IMOD."""
+
+ def install_step(self):
+ """Install IMOD using install script."""
+
+ # -dir: Choose location of installation directory
+ # -skip: do not attempt to deploy resource files in /etc
+ # -yes: do not prompt for confirmation
+ script = '{0}_{1}{2}.sh'.format(self.name.lower(), self.version, self.cfg['versionsuffix'])
+ cmd = "bash {0} -dir {1} -script {1} -skip -yes".format(script, self.installdir)
+ run_cmd(cmd, log_all=True, simple=True)
+
+ # The assumption by the install script is that installdir will be something
+ # like /usr/local. So it creates, within the specified install location, a
+ # number of additional directories within which to install IMOD. We will,
+ # therefore, move the contents of these directories up and throw away the
+ # directories themselves. Doing so apparently is not a problem so long as
+ # IMOD_DIR is correctly set in the module.
+ link_to_remove = os.path.join(self.installdir, self.name)
+ dir_to_remove = os.path.join(self.installdir, "{0}_{1}".format(self.name.lower(), self.version))
+ try:
+ for entry in os.listdir(dir_to_remove):
+ shutil.move(os.path.join(dir_to_remove, entry), self.installdir)
+ if os.path.realpath(link_to_remove) != os.path.realpath(dir_to_remove):
+ raise EasyBuildError("Something went wrong: %s doesn't point to %s", link_to_remove, dir_to_remove)
+ remove_dir(dir_to_remove)
+ os.remove(link_to_remove)
+ except OSError as err:
+ raise EasyBuildError("Failed to clean up install dir: %s", err)
+
+ def sanity_check_step(self):
+ """Custom sanity check for IMOD."""
+ custom_paths = {
+ 'files': ['bin/imod', 'IMOD-linux.sh', 'IMOD-linux.sh', 'installIMOD'],
+ 'dirs': ['lib'],
+ }
+ super(EB_IMOD, self).sanity_check_step(custom_paths=custom_paths)
+
+ def make_module_extra(self):
+ """Define IMOD specific variables in generated module file."""
+ txt = super(EB_IMOD, self).make_module_extra()
+ txt += self.module_generator.set_environment('IMOD_DIR', self.installdir)
+ txt += self.module_generator.set_environment('IMOD_PLUGIN_DIR',
+ os.path.join(self.installdir, 'lib', 'imodplug'))
+ txt += self.module_generator.set_environment('IMOD_QTLIBDIR', os.path.join(self.installdir, 'qtlib'))
+ if os.getenv('JAVA_HOME') is None:
+ raise EasyBuildError("$JAVA_HOME is not defined for some reason -- check environment")
+ else:
+ txt += self.module_generator.set_environment('IMOD_JAVADIR', os.getenv('JAVA_HOME'))
+ txt += self.module_generator.set_environment('FOR_DISABLE_STACK_TRACE', '1')
+ txt += self.module_generator.set_alias('subm', "submfg $* &")
+ txt += self.module_generator.msg_on_load("Please set the environment variable $IMOD_CALIB_DIR if appropriate.\n")
+
+ txt += self.module_generator.msg_on_load("bash users run: 'source $EBROOTIMOD/IMOD-linux.sh\n")
+ txt += self.module_generator.msg_on_load("csh users run: 'source $EBROOTIMOD/IMOD-linux.csh'\n")
+ return txt
diff --git a/easyblocks/n/nvhpc.py b/easyblocks/n/nvhpc.py
new file mode 100644
index 0000000..06a6f9e
--- /dev/null
+++ b/easyblocks/n/nvhpc.py
@@ -0,0 +1,312 @@
+##
+# Copyright 2015-2023 Bart Oldeman
+# Copyright 2016-2023 Forschungszentrum Juelich
+#
+# This file is triple-licensed under GPLv2 (see below), MIT, and
+# BSD three-clause licenses.
+#
+# 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for installing NVIDIA HPC SDK compilers, based on the easyblock for PGI compilers
+
+@author: Bart Oldeman (McGill University, Calcul Quebec, Compute Canada)
+@author: Damian Alvarez (Forschungszentrum Juelich)
+@author: Andreas Herten (Forschungszentrum Juelich)
+"""
+import os
+import fileinput
+import re
+import stat
+import sys
+import platform
+
+from distutils.version import LooseVersion
+from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.filetools import adjust_permissions, write_file
+from easybuild.tools.run import run_cmd
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.config import build_option
+from easybuild.tools.build_log import EasyBuildError, print_warning
+
+
+# contents for siterc file to make PGI/NVHPC pick up $LIBRARY_PATH
+# cfr. https://www.pgroup.com/support/link.htm#lib_path_ldflags
+SITERC_LIBRARY_PATH = """
+# get the value of the environment variable LIBRARY_PATH
+variable LIBRARY_PATH is environment(LIBRARY_PATH);
+
+# split this value at colons, separate by -L, prepend 1st one by -L
+variable library_path is
+default($if($LIBRARY_PATH,-L$replace($LIBRARY_PATH,":", -L)));
+
+# add the -L arguments to the link line
+append LDLIBARGS=$library_path;
+
+# also include the location where libm & co live on Debian-based systems
+# cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/919
+append LDLIBARGS=-L/usr/lib/x86_64-linux-gnu;
+"""
+
+
+class EB_NVHPC(PackedBinary):
+ """
+ Support for installing the NVIDIA HPC SDK (NVHPC) compilers
+ """
+
+ @staticmethod
+ def extra_options():
+ extra_vars = {
+ 'default_cuda_version': [None, "CUDA Version to be used as default (10.2 or 11.0 or ...)", CUSTOM],
+ 'module_add_cuda': [False, "Add NVHPC's CUDA to module", CUSTOM],
+ 'module_add_math_libs': [False, "Add NVHPC's math libraries to module", CUSTOM],
+ 'module_add_nccl': [False, "Add NVHPC's NCCL library to module", CUSTOM],
+ 'module_add_nvshmem': [False, "Add NVHPC's NVSHMEM library to module", CUSTOM],
+ 'module_add_profilers': [False, "Add NVHPC's NVIDIA Profilers to module", CUSTOM],
+ 'module_byo_compilers': [False, "BYO Compilers: Remove compilers from module", CUSTOM],
+ 'module_nvhpc_own_mpi': [False, "Add NVHPC's packaged OpenMPI to module", CUSTOM]
+ }
+ return PackedBinary.extra_options(extra_vars)
+
+ def __init__(self, *args, **kwargs):
+ """Easyblock constructor, define custom class variables specific to NVHPC."""
+ super(EB_NVHPC, self).__init__(*args, **kwargs)
+
+ # Ideally we should be using something like `easybuild.tools.systemtools.get_cpu_architecture` here, however,
+ # on `ppc64le` systems this function returns `POWER` instead of `ppc64le`. Since this path needs to reflect
+ # `arch` (https://easybuild.readthedocs.io/en/latest/version-specific/easyconfig_templates.html) the same
+ # procedure from `templates.py` was reused here:
+ architecture = 'Linux_%s' % platform.uname()[4]
+ self.nvhpc_install_subdir = os.path.join(architecture, self.version)
+
+ def install_step(self):
+ """Install by running install command."""
+
+ # EULA for NVHPC must be accepted via --accept-eula-for EasyBuild configuration option,
+ # or via 'accept_eula = True' in easyconfig file
+ self.check_accepted_eula(more_info='https://docs.nvidia.com/hpc-sdk/eula/index.html')
+
+ default_cuda_version = self.cfg['default_cuda_version']
+ if default_cuda_version is None:
+ module_cuda_version_full = get_software_version('CUDA')
+ if module_cuda_version_full is not None:
+ default_cuda_version = '.'.join(module_cuda_version_full.split('.')[:2])
+ else:
+ error_msg = "A default CUDA version is needed for installation of NVHPC. "
+ error_msg += "It can not be determined automatically and needs to be added manually. "
+ error_msg += "You can edit the easyconfig file, "
+ error_msg += "or use 'eb --try-amend=default_cuda_version=<version>'."
+ raise EasyBuildError(error_msg)
+
+ # Parse default_compute_capability from different sources (CLI has priority)
+ ec_default_compute_capability = self.cfg['cuda_compute_capabilities']
+ cfg_default_compute_capability = build_option('cuda_compute_capabilities')
+ if cfg_default_compute_capability is not None:
+ default_compute_capability = cfg_default_compute_capability
+ elif ec_default_compute_capability and ec_default_compute_capability is not None:
+ default_compute_capability = ec_default_compute_capability
+ else:
+ error_msg = "A default Compute Capability is needed for installation of NVHPC."
+ error_msg += "Please provide it either in the easyconfig file like 'cuda_compute_capabilities=\"7.0\"',"
+ error_msg += "or use 'eb --cuda-compute-capabilities=7.0' from the command line."
+ raise EasyBuildError(error_msg)
+
+ # Extract first element of default_compute_capability list, if it is a list
+ if isinstance(default_compute_capability, list):
+ _before_default_compute_capability = default_compute_capability
+ default_compute_capability = _before_default_compute_capability[0]
+ if len(_before_default_compute_capability) > 1:
+ warning_msg = "Replaced list of compute capabilities {} ".format(_before_default_compute_capability)
+ warning_msg += "with first element of list: {}".format(default_compute_capability)
+ print_warning(warning_msg)
+
+ # Remove dot-divider for CC; error out if it is not a string
+ if isinstance(default_compute_capability, str):
+ default_compute_capability = default_compute_capability.replace('.', '')
+ else:
+ raise EasyBuildError("Unexpected non-string value encountered for compute capability: %s",
+ default_compute_capability)
+
+ nvhpc_env_vars = {
+ 'NVHPC_INSTALL_DIR': self.installdir,
+ 'NVHPC_SILENT': 'true',
+ 'NVHPC_DEFAULT_CUDA': str(default_cuda_version), # 10.2, 11.0
+ 'NVHPC_STDPAR_CUDACC': str(default_compute_capability), # 70, 80; single value, no list!
+ }
+ cmd = "%s ./install" % ' '.join(['%s=%s' % x for x in sorted(nvhpc_env_vars.items())])
+ run_cmd(cmd, log_all=True, simple=True)
+
+ # make sure localrc uses GCC in PATH, not always the system GCC, and does not use a system g77 but gfortran
+ install_abs_subdir = os.path.join(self.installdir, self.nvhpc_install_subdir)
+ compilers_subdir = os.path.join(install_abs_subdir, "compilers")
+ makelocalrc_folder = os.path.join(compilers_subdir, "bin")
+ makelocalrc_filename = os.path.join(compilers_subdir, "bin", "makelocalrc")
+ for line in fileinput.input(makelocalrc_filename, inplace='1', backup='.orig'):
+ line = re.sub(r"^PATH=/", r"#PATH=/", line)
+ sys.stdout.write(line)
+
+ if LooseVersion(self.version) >= LooseVersion('22.9'):
+ cmd = "%s -x %s" % (makelocalrc_filename, makelocalrc_folder)
+ else:
+ cmd = "%s -x %s -g77 /" % (makelocalrc_filename, makelocalrc_folder)
+ run_cmd(cmd, log_all=True, simple=True)
+
+ # If an OS libnuma is NOT found, makelocalrc creates symbolic links to libpgnuma.so
+ # If we use the EB libnuma, delete those symbolic links to ensure they are not used
+ if get_software_root("numactl"):
+ for filename in ["libnuma.so", "libnuma.so.1"]:
+ path = os.path.join(compilers_subdir, "lib", filename)
+ if os.path.islink(path):
+ os.remove(path)
+
+ if LooseVersion(self.version) < LooseVersion('21.3'):
+ # install (or update) siterc file to make NVHPC consider $LIBRARY_PATH
+ siterc_path = os.path.join(compilers_subdir, 'bin', 'siterc')
+ write_file(siterc_path, SITERC_LIBRARY_PATH, append=True)
+ self.log.info("Appended instructions to pick up $LIBRARY_PATH to siterc file at %s: %s",
+ siterc_path, SITERC_LIBRARY_PATH)
+
+ # The cuda nvvp tar file has broken permissions
+ adjust_permissions(self.installdir, stat.S_IWUSR, add=True, onlydirs=True)
+
+ def sanity_check_step(self):
+ """Custom sanity check for NVHPC"""
+ prefix = self.nvhpc_install_subdir
+ compiler_names = ['nvc', 'nvc++', 'nvfortran']
+
+ files = [os.path.join(prefix, 'compilers', 'bin', x) for x in compiler_names]
+ if LooseVersion(self.version) < LooseVersion('21.3'):
+ files.append(os.path.join(prefix, 'compilers', 'bin', 'siterc'))
+
+ custom_paths = {
+ 'files': files,
+ 'dirs': [os.path.join(prefix, 'compilers', 'bin'), os.path.join(prefix, 'compilers', 'lib'),
+ os.path.join(prefix, 'compilers', 'include'), os.path.join(prefix, 'compilers', 'man')]
+ }
+ custom_commands = ["%s -v" % compiler for compiler in compiler_names]
+ super(EB_NVHPC, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
+
+ def _nvhpc_extended_components(self, dirs, basepath, env_vars_dirs):
+ """
+ Extends `dirs` dict of key:environment_variables, value:list_of_directories with additional vars and dirs.
+ The dictionary key for a new env var will be created if it doesn't exist.
+ Also, the relative path specified in the `env_vars_dirs` dict is absolutized with the `basepath` prefix.
+ """
+ for env_var, folders in sorted(env_vars_dirs.items()):
+ if env_var not in dirs:
+ dirs[env_var] = []
+ if not isinstance(folders, list):
+ folders = [folders]
+ for folder in folders:
+ dirs[env_var].append(os.path.join(basepath, folder))
+
+ def make_module_req_guess(self):
+ """Prefix subdirectories in NVHPC install dir considered for environment variables defined in module file."""
+ dirs = super(EB_NVHPC, self).make_module_req_guess()
+ for key in dirs:
+ dirs[key] = [os.path.join(self.nvhpc_install_subdir, 'compilers', d) for d in dirs[key]]
+
+ # $CPATH should not be defined in module for NVHPC, it causes problems
+ # cfr. https://github.com/easybuilders/easybuild-easyblocks/issues/830
+ if 'CPATH' in dirs:
+ self.log.info("Removing $CPATH entry: %s", dirs['CPATH'])
+ del dirs['CPATH']
+
+ # EasyBlock option parsing follows:
+ # BYO Compilers:
+ # Use NVHPC's libraries and tools with other, external compilers
+ if self.cfg['module_byo_compilers']:
+ if 'PATH' in dirs:
+ del dirs["PATH"]
+ # Own MPI:
+ # NVHPC is shipped with a compiled OpenMPI installation
+ # Enable it by setting according environment variables
+ if self.cfg['module_nvhpc_own_mpi']:
+ self.nvhpc_mpi_basedir = os.path.join(self.nvhpc_install_subdir, "comm_libs", "mpi")
+ env_vars_dirs = {
+ 'PATH': 'bin',
+ 'CPATH': 'include',
+ 'LD_LIBRARY_PATH': 'lib'
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_mpi_basedir, env_vars_dirs)
+ # Math Libraries:
+ # NVHPC is shipped with math libraries (in a dedicated folder)
+ # Enable them by setting according environment variables
+ if self.cfg['module_add_math_libs']:
+ self.nvhpc_math_basedir = os.path.join(self.nvhpc_install_subdir, "math_libs")
+ env_vars_dirs = {
+ 'CPATH': 'include',
+ 'LD_LIBRARY_PATH': 'lib64'
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_math_basedir, env_vars_dirs)
+ # GPU Profilers:
+ # NVHPC is shipped with NVIDIA's GPU profilers (Nsight Compute/Nsight Systems)
+ # Enable them by setting the according environment variables
+ if self.cfg['module_add_profilers']:
+ self.nvhpc_profilers_basedir = os.path.join(self.nvhpc_install_subdir, "profilers")
+ env_vars_dirs = {
+ 'PATH': ['Nsight_Compute', 'Nsight_Systems/bin']
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_profilers_basedir, env_vars_dirs)
+ # NCCL:
+ # NVHPC is shipped with NCCL
+ # Enable it by setting the according environment variables
+ if self.cfg['module_add_nccl']:
+ self.nvhpc_nccl_basedir = os.path.join(self.nvhpc_install_subdir, "comm_libs", "nccl")
+ env_vars_dirs = {
+ 'CPATH': 'include',
+ 'LD_LIBRARY_PATH': 'lib'
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_nccl_basedir, env_vars_dirs)
+ # NVSHMEM:
+ # NVHPC is shipped with NVSHMEM
+ # Enable it by setting the according environment variables
+ if self.cfg['module_add_nvshmem']:
+ self.nvhpc_nvshmem_basedir = os.path.join(self.nvhpc_install_subdir, "comm_libs", "nvshmem")
+ env_vars_dirs = {
+ 'CPATH': 'include',
+ 'LD_LIBRARY_PATH': 'lib'
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_nvshmem_basedir, env_vars_dirs)
+ # CUDA:
+ # NVHPC is shipped with CUDA (possibly multiple versions)
+ # Rather use this CUDA than an external CUDA (via $CUDA_HOME) by setting according environment variables
+ if self.cfg['module_add_cuda']:
+ self.nvhpc_cuda_basedir = os.path.join(self.nvhpc_install_subdir, "cuda")
+ env_vars_dirs = {
+ 'PATH': 'bin',
+ 'LD_LIBRARY_PATH': 'lib64',
+ 'CPATH': 'include'
+ }
+ self._nvhpc_extended_components(dirs, self.nvhpc_cuda_basedir, env_vars_dirs)
+ return dirs
+
+ def make_module_extra(self):
+ """Add environment variable for NVHPC location"""
+ txt = super(EB_NVHPC, self).make_module_extra()
+ txt += self.module_generator.set_environment('NVHPC', self.installdir)
+ if LooseVersion(self.version) >= LooseVersion('22.7'):
+ # NVHPC 22.7+ requires the variable NVHPC_CUDA_HOME for external CUDA. CUDA_HOME has been deprecated.
+ if not self.cfg['module_add_cuda'] and get_software_root('CUDA'):
+ txt += self.module_generator.set_environment('NVHPC_CUDA_HOME', os.getenv('CUDA_HOME'))
+ return txt
diff --git a/easyblocks/o/openfoam.py b/easyblocks/o/openfoam.py
new file mode 100644
index 0000000..04f0fb3
--- /dev/null
+++ b/easyblocks/o/openfoam.py
@@ -0,0 +1,556 @@
+##
+# Copyright 2009-2023 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for building and installing OpenFOAM, implemented as an easyblock
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Xavier Besseron (University of Luxembourg)
+@author: Ward Poelmans (Ghent University)
+@author: Balazs Hajgato (Free University Brussels (VUB))
+"""
+
+import glob
+import os
+import re
+import shutil
+import stat
+import tempfile
+from distutils.version import LooseVersion
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.easyblocks.generic.cmakemake import setup_cmake_env
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions, apply_regex_substitutions, mkdir
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd, run_cmd_qa
+from easybuild.tools.systemtools import get_shared_lib_ext, get_cpu_architecture, AARCH64, POWER
+
+
+class EB_OpenFOAM(EasyBlock):
+ """Support for building and installing OpenFOAM."""
+
+ def __init__(self, *args, **kwargs):
+ """Specify that OpenFOAM should be built in install dir."""
+
+ super(EB_OpenFOAM, self).__init__(*args, **kwargs)
+
+ self.build_in_installdir = True
+
+ self.openfoamdir = None
+ self.thrdpartydir = None
+
+ # version may start with 'v' for some variants of OpenFOAM
+ # we need to strip this off to avoid problems when comparing LooseVersion instances in Python 3
+ clean_version = self.version.strip('v+')
+
+ # take into account versions like '4.x',
+ # assume it's equivalent to a very recent minor version (.99)
+ if '.x' in clean_version:
+ clean_version = clean_version.replace('.x', '.99')
+
+ self.looseversion = LooseVersion(clean_version)
+
+ self.is_extend = 'extend' in self.name.lower()
+ self.is_dot_com = self.looseversion >= LooseVersion('1606')
+ self.is_dot_org = self.looseversion <= LooseVersion('100')
+
+ if self.is_extend:
+ if self.looseversion >= LooseVersion('3.0'):
+ self.openfoamdir = 'foam-extend-%s' % self.version
+ else:
+ self.openfoamdir = 'OpenFOAM-%s-ext' % self.version
+ else:
+ self.openfoamdir = '-'.join([self.name, '-'.join(self.version.split('-')[:2])])
+ self.log.debug("openfoamdir: %s" % self.openfoamdir)
+
+ # Set build type to requested value
+ if self.toolchain.options['debug']:
+ self.build_type = 'Debug'
+ else:
+ self.build_type = 'Opt'
+
+ # determine values for wm_compiler and wm_mplib
+ comp_fam = self.toolchain.comp_family()
+ if comp_fam == toolchain.GCC: # @UndefinedVariable
+ self.wm_compiler = 'Gcc'
+ self.wm_mplib = "OPENMPI"
+ elif comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
+ self.wm_compiler = 'Icc'
+ self.wm_mplib = "INTELMPI"
+ else:
+ raise EasyBuildError("Unknown compiler family, don't know how to set WM_COMPILER")
+
+ def extract_step(self):
+ """Extract sources as expected by the OpenFOAM(-Extend) build scripts."""
+ super(EB_OpenFOAM, self).extract_step()
+ # make sure that the expected subdir is really there after extracting
+ # if not, the build scripts (e.g., the etc/bashrc being sourced) will likely fail
+ openfoam_installdir = os.path.join(self.installdir, self.openfoamdir)
+ if not os.path.exists(openfoam_installdir):
+ self.log.warning("Creating expected directory %s, and moving everything there" % openfoam_installdir)
+ try:
+ contents_installdir = os.listdir(self.installdir)
+ source = os.path.join(self.installdir, contents_installdir[0])
+ # it's one directory but has a wrong name
+ if len(contents_installdir) == 1 and os.path.isdir(source):
+ target = os.path.join(self.installdir, self.openfoamdir)
+ self.log.debug("Renaming %s to %s", source, target)
+ os.rename(source, target)
+ else:
+ mkdir(openfoam_installdir)
+ for fil in contents_installdir:
+ if fil != self.openfoamdir:
+ source = os.path.join(self.installdir, fil)
+ target = os.path.join(openfoam_installdir, fil)
+ self.log.debug("Moving %s to %s", source, target)
+ shutil.move(source, target)
+ os.chdir(openfoam_installdir)
+ except OSError as err:
+ raise EasyBuildError("Failed to move all files to %s: %s", openfoam_installdir, err)
+
+ def patch_step(self, beginpath=None):
+ """Adjust start directory and start path for patching to correct directory."""
+ self.cfg['start_dir'] = os.path.join(self.installdir, self.openfoamdir)
+ super(EB_OpenFOAM, self).patch_step(beginpath=self.cfg['start_dir'])
+
+ def configure_step(self):
+ """Configure OpenFOAM build by setting appropriate environment variables."""
+ # compiler & compiler flags
+ comp_fam = self.toolchain.comp_family()
+
+ extra_flags = ''
+ if comp_fam == toolchain.GCC: # @UndefinedVariable
+ if get_software_version('GCC') >= LooseVersion('4.8'):
+ # make sure non-gold version of ld is used, since OpenFOAM requires it
+ # see http://www.openfoam.org/mantisbt/view.php?id=685
+ extra_flags = '-fuse-ld=bfd'
+
+ # older versions of OpenFOAM-Extend require -fpermissive
+ if self.is_extend and self.looseversion < LooseVersion('2.0'):
+ extra_flags += ' -fpermissive'
+
+ if self.looseversion < LooseVersion('3.0'):
+ extra_flags += ' -fno-delete-null-pointer-checks'
+
+ elif comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
+ # make sure -no-prec-div is used with Intel compilers
+ extra_flags = '-no-prec-div'
+
+ for env_var in ['CFLAGS', 'CXXFLAGS']:
+ env.setvar(env_var, "%s %s" % (os.environ.get(env_var, ''), extra_flags))
+
+ # patch out hardcoding of WM_* environment variables
+ # for example, replace 'export WM_COMPILER=Gcc' with ': ${WM_COMPILER:=Gcc}; export WM_COMPILER'
+ for script in [os.path.join(self.builddir, self.openfoamdir, x) for x in ['etc/bashrc', 'etc/cshrc']]:
+ self.log.debug("Patching out hardcoded $WM_* env vars in %s", script)
+ # disable any third party stuff, we use EB controlled builds
+ regex_subs = [(r"^(setenv|export) WM_THIRD_PARTY_USE_.*[ =].*$", r"# \g<0>")]
+
+ # this does not work for OpenFOAM Extend lower than 2.0
+ if not self.is_extend or self.looseversion >= LooseVersion('2.0'):
+ key = "WM_PROJECT_VERSION"
+ regex_subs += [(r"^(setenv|export) %s=.*$" % key, r"export %s=%s #\g<0>" % (key, self.version))]
+
+ WM_env_var = ['WM_COMPILER', 'WM_COMPILE_OPTION', 'WM_MPLIB', 'WM_THIRD_PARTY_DIR']
+ # OpenFOAM >= 3.0.0 can use 64 bit integers
+ if not self.is_extend and self.looseversion >= LooseVersion('3.0'):
+ WM_env_var.append('WM_LABEL_SIZE')
+ for env_var in WM_env_var:
+ regex_subs.append((r"^(setenv|export) (?P<var>%s)[ =](?P<val>.*)$" % env_var,
+ r": ${\g<var>:=\g<val>}; export \g<var>"))
+ apply_regex_substitutions(script, regex_subs)
+
+ # inject compiler variables into wmake/rules files
+ ldirs = glob.glob(os.path.join(self.builddir, self.openfoamdir, 'wmake', 'rules', 'linux*'))
+ if self.looseversion >= LooseVersion('1906'):
+ ldirs += glob.glob(os.path.join(self.builddir, self.openfoamdir, 'wmake', 'rules', 'General', '*'))
+ langs = ['c', 'c++']
+
+ # NOTE: we do not want to change the Debug rules files becuse
+ # that would change the cOPT/c++OPT values from their empty setting.
+ suffixes = ['', 'Opt']
+ wmake_rules_files = [os.path.join(ldir, lang + suff) for ldir in ldirs for lang in langs for suff in suffixes]
+ wmake_rules_files += [os.path.join(ldir, "general") for ldir in ldirs]
+
+ mpicc = os.environ['MPICC']
+ mpicxx = os.environ['MPICXX']
+ cc_seq = os.environ.get('CC_SEQ', os.environ['CC'])
+ cxx_seq = os.environ.get('CXX_SEQ', os.environ['CXX'])
+
+ if self.toolchain.mpi_family() == toolchain.OPENMPI:
+ # no -cc/-cxx flags supported in OpenMPI compiler wrappers
+ c_comp_cmd = 'OMPI_CC="%s" %s' % (cc_seq, mpicc)
+ cxx_comp_cmd = 'OMPI_CXX="%s" %s' % (cxx_seq, mpicxx)
+ else:
+ # -cc/-cxx should work for all MPICH-based MPIs (including Intel MPI)
+ c_comp_cmd = '%s -cc="%s"' % (mpicc, cc_seq)
+ cxx_comp_cmd = '%s -cxx="%s"' % (mpicxx, cxx_seq)
+
+ comp_vars = {
+ # specify MPI compiler wrappers and compiler commands + sequential compiler that should be used by them
+ 'cc': c_comp_cmd,
+ 'CC': cxx_comp_cmd,
+ 'cOPT': os.environ['CFLAGS'],
+ 'c++OPT': os.environ['CXXFLAGS'],
+ }
+ for wmake_rules_file in wmake_rules_files:
+ # the cOpt and c++Opt files don't exist in the General directories (which are included for recent versions)
+ if not os.path.isfile(wmake_rules_file):
+ continue
+ fullpath = os.path.join(self.builddir, self.openfoamdir, wmake_rules_file)
+ self.log.debug("Patching compiler variables in %s", fullpath)
+ regex_subs = []
+ for comp_var, newval in comp_vars.items():
+ regex_subs.append((r"^(%s\s*=\s*).*$" % re.escape(comp_var), r"\1%s" % newval))
+ # replace /lib/cpp by cpp, but keep the arguments
+ regex_subs.append((r"^(CPP\s*=\s*)/lib/cpp(.*)$", r"\1cpp\2"))
+ apply_regex_substitutions(fullpath, regex_subs)
+
+ # enable verbose build for debug purposes
+ # starting with openfoam-extend 3.2, PS1 also needs to be set
+ env.setvar("FOAM_VERBOSE", '1')
+
+ # installation directory
+ env.setvar("FOAM_INST_DIR", self.installdir)
+
+ # third party directory
+ self.thrdpartydir = "ThirdParty-%s" % self.version
+ # only if third party stuff is actually installed
+ if os.path.exists(self.thrdpartydir):
+ os.symlink(os.path.join("..", self.thrdpartydir), self.thrdpartydir)
+ env.setvar("WM_THIRD_PARTY_DIR", os.path.join(self.installdir, self.thrdpartydir))
+
+ env.setvar("WM_COMPILER", self.wm_compiler)
+ env.setvar("WM_MPLIB", self.wm_mplib)
+
+ # Set Compile options according to build type
+ env.setvar("WM_COMPILE_OPTION", self.build_type)
+
+ # parallel build spec
+ env.setvar("WM_NCOMPPROCS", str(self.cfg['parallel']))
+
+ # OpenFOAM >= 3.0.0 can use 64 bit integers
+ if not self.is_extend and self.looseversion >= LooseVersion('3.0'):
+ if self.toolchain.options['i8']:
+ env.setvar("WM_LABEL_SIZE", '64')
+ else:
+ env.setvar("WM_LABEL_SIZE", '32')
+
+ # make sure lib/include dirs for dependencies are found
+ openfoam_extend_v3 = self.is_extend and self.looseversion >= LooseVersion('3.0')
+ if self.looseversion < LooseVersion("2") or openfoam_extend_v3:
+ self.log.debug("List of deps: %s" % self.cfg.dependencies())
+ for dep in self.cfg.dependencies():
+ dep_name = dep['name'].upper(),
+ dep_root = get_software_root(dep['name'])
+ env.setvar("%s_SYSTEM" % dep_name, "1")
+ dep_vars = {
+ "%s_DIR": "%s",
+ "%s_BIN_DIR": "%s/bin",
+ "%s_LIB_DIR": "%s/lib",
+ "%s_INCLUDE_DIR": "%s/include",
+ }
+ for var, val in dep_vars.items():
+ env.setvar(var % dep_name, val % dep_root)
+ else:
+ for depend in ['SCOTCH', 'METIS', 'CGAL', 'Paraview']:
+ dependloc = get_software_root(depend)
+ if dependloc:
+ if depend == 'CGAL' and get_software_root('Boost'):
+ env.setvar("CGAL_ROOT", dependloc)
+ env.setvar("BOOST_ROOT", get_software_root('Boost'))
+ else:
+ env.setvar("%s_ROOT" % depend.upper(), dependloc)
+
+ def build_step(self):
+ """Build OpenFOAM using make after sourcing script to set environment."""
+
+ # Some parts of OpenFOAM uses CMake to build
+ # make sure the basic environment is correct
+ setup_cmake_env(self.toolchain)
+
+ precmd = "source %s" % os.path.join(self.builddir, self.openfoamdir, "etc", "bashrc")
+ if not self.is_extend and self.looseversion >= LooseVersion('4.0'):
+ if self.looseversion >= LooseVersion('2006'):
+ cleancmd = "cd $WM_PROJECT_DIR && wclean -platform -all && cd -"
+ else:
+ cleancmd = "cd $WM_PROJECT_DIR && wcleanPlatform -all && cd -"
+ else:
+ cleancmd = "wcleanAll"
+
+ # make directly in install directory
+ cmd_tmpl = "%(precmd)s && %(cleancmd)s && %(prebuildopts)s %(makecmd)s" % {
+ 'precmd': precmd,
+ 'cleancmd': cleancmd,
+ 'prebuildopts': self.cfg['prebuildopts'],
+ 'makecmd': os.path.join(self.builddir, self.openfoamdir, '%s'),
+ }
+ if self.is_extend and self.looseversion >= LooseVersion('3.0'):
+ qa = {
+ "Proceed without compiling ParaView [Y/n]": 'Y',
+ "Proceed without compiling cudaSolvers? [Y/n]": 'Y',
+ }
+ noqa = [
+ ".* -o .*",
+ "checking .*",
+ "warning.*",
+ "configure: creating.*",
+ "%s .*" % os.environ['CC'],
+ "wmake .*",
+ "Making dependency list for source file.*",
+ r"\s*\^\s*", # warning indicator
+ "Cleaning .*",
+ ]
+ run_cmd_qa(cmd_tmpl % 'Allwmake.firstInstall', qa, no_qa=noqa, log_all=True, simple=True, maxhits=500)
+ else:
+ cmd = 'Allwmake'
+ if self.looseversion > LooseVersion('1606'):
+ # use Allwmake -log option if possible since this can be useful during builds, but also afterwards
+ cmd += ' -log'
+ run_cmd(cmd_tmpl % cmd, log_all=True, simple=True, log_output=True)
+
+ def det_psubdir(self):
+ """Determine the platform-specific installation directory for OpenFOAM."""
+ # OpenFOAM >= 3.0.0 can use 64 bit integers
+ # same goes for OpenFOAM-Extend >= 4.1
+ if self.is_extend:
+ set_int_size = self.looseversion >= LooseVersion('4.1')
+ else:
+ set_int_size = self.looseversion >= LooseVersion('3.0')
+
+ if set_int_size:
+ if self.toolchain.options['i8']:
+ int_size = 'Int64'
+ else:
+ int_size = 'Int32'
+ else:
+ int_size = ''
+
+ archpart = '64'
+ arch = get_cpu_architecture()
+ if arch == AARCH64:
+ # Variants have different abbreviations for ARM64...
+ if self.is_dot_org:
+ archpart = 'Arm64'
+ else:
+ archpart = 'ARM64'
+ elif arch == POWER:
+ archpart = 'PPC64le'
+
+ psubdir = "linux%s%sDP%s%s" % (archpart, self.wm_compiler, int_size, self.build_type)
+ return psubdir
+
+ def install_step(self):
+ """Building was performed in install dir, so just fix permissions."""
+
+ # fix permissions of OpenFOAM dir
+ fullpath = os.path.join(self.installdir, self.openfoamdir)
+ adjust_permissions(fullpath, stat.S_IROTH, add=True, recursive=True, ignore_errors=True)
+ adjust_permissions(fullpath, stat.S_IXOTH, add=True, recursive=True, onlydirs=True, ignore_errors=True)
+
+ # fix permissions of ThirdParty dir and subdirs (also for 2.x)
+ # if the thirdparty tarball is installed
+ fullpath = os.path.join(self.installdir, self.thrdpartydir)
+ if os.path.exists(fullpath):
+ adjust_permissions(fullpath, stat.S_IROTH, add=True, recursive=True, ignore_errors=True)
+ adjust_permissions(fullpath, stat.S_IXOTH, add=True, recursive=True, onlydirs=True, ignore_errors=True)
+
+ # create symlinks in the lib directory to all libraries in the mpi subdirectory
+ # to make sure they take precedence over the libraries in the dummy subdirectory
+ shlib_ext = get_shared_lib_ext()
+ psubdir = self.det_psubdir()
+ openfoam_extend_v3 = self.is_extend and self.looseversion >= LooseVersion('3.0')
+ if openfoam_extend_v3 or self.looseversion < LooseVersion("2"):
+ libdir = os.path.join(self.installdir, self.openfoamdir, "lib", psubdir)
+ else:
+ libdir = os.path.join(self.installdir, self.openfoamdir, "platforms", psubdir, "lib")
+
+ # OpenFOAM v2012 puts mpi into eb-mpi
+ if self.looseversion >= LooseVersion("2012"):
+ mpilibssubdir = "eb-mpi"
+ else:
+ mpilibssubdir = "mpi"
+ mpilibsdir = os.path.join(libdir, mpilibssubdir)
+
+ if os.path.exists(mpilibsdir):
+ for lib in glob.glob(os.path.join(mpilibsdir, "*.%s" % shlib_ext)):
+ libname = os.path.basename(lib)
+ dst = os.path.join(libdir, libname)
+ os.symlink(os.path.join(mpilibssubdir, libname), dst)
+
+ def sanity_check_step(self):
+ """Custom sanity check for OpenFOAM"""
+ shlib_ext = get_shared_lib_ext()
+ psubdir = self.det_psubdir()
+
+ openfoam_extend_v3 = self.is_extend and self.looseversion >= LooseVersion('3.0')
+ if openfoam_extend_v3 or self.looseversion < LooseVersion("2"):
+ toolsdir = os.path.join(self.openfoamdir, "applications", "bin", psubdir)
+ libsdir = os.path.join(self.openfoamdir, "lib", psubdir)
+ dirs = [toolsdir, libsdir]
+ else:
+ toolsdir = os.path.join(self.openfoamdir, "platforms", psubdir, "bin")
+ libsdir = os.path.join(self.openfoamdir, "platforms", psubdir, "lib")
+ dirs = [toolsdir, libsdir]
+
+ # some randomly selected binaries
+ # if one of these is missing, it's very likely something went wrong
+ tools = ["boundaryFoam", "engineFoam", "buoyantSimpleFoam", "buoyantBoussinesqSimpleFoam", "sonicFoam"]
+ tools += ["surfaceAdd", "surfaceFind", "surfaceSmooth"]
+ tools += ["blockMesh", "checkMesh", "deformedGeom", "engineSwirl", "modifyMesh", "refineMesh"]
+
+ # surfaceSmooth is replaced by surfaceLambdaMuSmooth is OpenFOAM v2.3.0
+ if not self.is_extend and self.looseversion >= LooseVersion("2.3.0"):
+ tools.remove("surfaceSmooth")
+ tools.append("surfaceLambdaMuSmooth")
+ # sonicFoam and buoyantBoussineqSimpleFoam deprecated in version 7+
+ if self.is_dot_org and self.looseversion >= LooseVersion('7'):
+ tools.remove("buoyantBoussinesqSimpleFoam")
+ tools.remove("sonicFoam")
+ # buoyantSimpleFoam replaced by buoyantFoam in versions 10+
+ if self.is_dot_org and self.looseversion >= LooseVersion("10"):
+ tools.remove("buoyantSimpleFoam")
+ tools.append("buoyantFoam")
+ # engineFoam replaced by reactingFoam in versions 10+
+ if self.is_dot_org and self.looseversion >= LooseVersion("10"):
+ tools.remove("engineFoam")
+ tools.append("reactingFoam")
+
+ bins = [os.path.join(self.openfoamdir, "bin", x) for x in ["paraFoam"]] + \
+ [os.path.join(toolsdir, x) for x in tools]
+
+ # test setting up the OpenFOAM environment in bash shell
+ load_openfoam_env = "source $FOAM_BASH"
+ custom_commands = [load_openfoam_env]
+
+ # check for the Pstream and scotchDecomp libraries, there must be a dummy one and an mpi one
+ #if self.is_extend:
+ # libs = [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext),
+ # os.path.join(libsdir, "libmetisDecomp.%s" % shlib_ext)]
+ # if self.looseversion < LooseVersion('3.2'):
+ # # Pstream should have both a dummy and a mpi one
+ # libs.extend([os.path.join(libsdir, x, "libPstream.%s" % shlib_ext) for x in ["dummy"]])
+ # else:
+ # libs.extend([os.path.join(libsdir, "libparMetisDecomp.%s" % shlib_ext)])
+ #else:
+ # # OpenFOAM v2012 puts mpi into eb-mpi
+ # if self.is_dot_com and self.looseversion >= LooseVersion("2012"):
+ # mpilibssubdir = "mpi"
+ # else:
+ # mpilibssubdir = "mpi"
+
+ # # there must be a dummy one and an mpi one for both
+ # libs = [os.path.join(libsdir, x, "libPstream.%s" % shlib_ext) for x in ["dummy", mpilibssubdir]] + \
+ # [os.path.join(libsdir, x, "libptscotchDecomp.%s" % shlib_ext) for x in ["dummy", mpilibssubdir]] +\
+ # [os.path.join(libsdir, "libscotchDecomp.%s" % shlib_ext)] + \
+ # [os.path.join(libsdir, "dummy", "libscotchDecomp.%s" % shlib_ext)]
+
+ if not self.is_extend and self.looseversion >= LooseVersion("2.4.0"):
+ # also check for foamMonitor for OpenFOAM versions other than OpenFOAM-Extend
+ bins.append(os.path.join(self.openfoamdir, 'bin', 'foamMonitor'))
+
+ # test foamMonitor; wrap `foamMonitor -h` to generate exit code 1 if any dependency is missing
+ # the command `foamMonitor -h` does not return correct exit codes on its own in all versions
+ test_foammonitor = "! foamMonitor -h 2>&1 | grep 'not installed'"
+ custom_commands.append(' && '.join([load_openfoam_env, test_foammonitor]))
+
+ custom_paths = {
+ 'files': [os.path.join(self.openfoamdir, 'etc', x) for x in ["bashrc", "cshrc"]] + bins, # + libs,
+ 'dirs': dirs,
+ }
+
+ # run motorBike tutorial case to ensure the installation is functional (if it's available);
+ # only for recent (>= v6.0) versions of openfoam.org variant
+ if self.is_dot_org and self.looseversion >= LooseVersion('6'):
+ openfoamdir_path = os.path.join(self.installdir, self.openfoamdir)
+ motorbike_path = os.path.join(openfoamdir_path, 'tutorials', 'incompressible', 'simpleFoam', 'motorBike')
+ if os.path.exists(motorbike_path):
+ test_dir = tempfile.mkdtemp()
+
+ if self.looseversion >= LooseVersion('9'):
+ geom_target_dir = 'geometry'
+ else:
+ geom_target_dir = 'triSurface'
+
+ cmds = [
+ "cp -a %s %s" % (motorbike_path, test_dir),
+ "cd %s" % os.path.join(test_dir, os.path.basename(motorbike_path)),
+ "source $FOAM_BASH",
+ ". $WM_PROJECT_DIR/bin/tools/RunFunctions",
+ "cp $FOAM_TUTORIALS/resources/geometry/motorBike.obj.gz constant/%s/" % geom_target_dir,
+ "runApplication surfaceFeatures",
+ "runApplication blockMesh",
+ "runApplication decomposePar -copyZero",
+ "runParallel snappyHexMesh -overwrite",
+ "runParallel patchSummary",
+ "runParallel potentialFoam",
+ "runParallel simpleFoam",
+ "runApplication reconstructParMesh -constant",
+ "runApplication reconstructPar -latestTime",
+ "cd %s" % self.builddir,
+ "rm -r %s" % test_dir,
+ ]
+ # all commands need to be run in a single shell command,
+ # because sourcing $FOAM_BASH sets up environment
+ custom_commands.append(' && '.join(cmds))
+
+ super(EB_OpenFOAM, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
+
+ def make_module_extra(self, altroot=None, altversion=None):
+ """Define extra environment variables required by OpenFOAM"""
+
+ txt = super(EB_OpenFOAM, self).make_module_extra()
+
+ env_vars = [
+ # Set WM_COMPILE_OPTION in the module file
+ # $FOAM_BASH will then pick it up correctly.
+ ('WM_COMPILE_OPTION', self.build_type),
+ ('WM_PROJECT_VERSION', self.version),
+ ('FOAM_INST_DIR', self.installdir),
+ ('WM_COMPILER', self.wm_compiler),
+ ('WM_MPLIB', self.wm_mplib),
+ ('FOAM_BASH', os.path.join(self.installdir, self.openfoamdir, 'etc', 'bashrc')),
+ ('FOAM_CSH', os.path.join(self.installdir, self.openfoamdir, 'etc', 'cshrc')),
+ ]
+
+ # OpenFOAM >= 3.0.0 can use 64 bit integers
+ if not self.is_extend and self.looseversion >= LooseVersion('3.0'):
+ if self.toolchain.options['i8']:
+ env_vars += [('WM_LABEL_SIZE', '64')]
+ else:
+ env_vars += [('WM_LABEL_SIZE', '32')]
+
+ for (env_var, val) in env_vars:
+ # check whether value is defined for compatibility with --module-only
+ if val:
+ txt += self.module_generator.set_environment(env_var, val)
+
+ return txt
diff --git a/easyblocks/q/quantumespresso.py b/easyblocks/q/quantumespresso.py
new file mode 100644
index 0000000..ff1edd9
--- /dev/null
+++ b/easyblocks/q/quantumespresso.py
@@ -0,0 +1,526 @@
+##
+# Copyright 2009-2023 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for Quantum ESPRESSO, implemented as an easyblock
+
+@author: Kenneth Hoste (Ghent University)
+@author: Ake Sandgren (HPC2N, Umea University)
+"""
+import fileinput
+import os
+import re
+import shutil
+import sys
+from distutils.version import LooseVersion
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import copy_dir, copy_file
+from easybuild.tools.modules import get_software_root, get_software_version
+
+
+class EB_QuantumESPRESSO(ConfigureMake):
+ """Support for building and installing Quantum ESPRESSO."""
+
+ @staticmethod
+ def extra_options():
+ """Custom easyconfig parameters for Quantum ESPRESSO."""
+ extra_vars = {
+ 'hybrid': [False, "Enable hybrid build (with OpenMP)", CUSTOM],
+ 'with_scalapack': [True, "Enable ScaLAPACK support", CUSTOM],
+ 'with_ace': [False, "Enable Adaptively Compressed Exchange support", CUSTOM],
+ }
+ return ConfigureMake.extra_options(extra_vars)
+
+ def __init__(self, *args, **kwargs):
+ """Add extra config options specific to Quantum ESPRESSO."""
+ super(EB_QuantumESPRESSO, self).__init__(*args, **kwargs)
+
+ if LooseVersion(self.version) >= LooseVersion("6"):
+ self.install_subdir = "qe-%s" % self.version
+ else:
+ self.install_subdir = "espresso-%s" % self.version
+
+ def patch_step(self):
+ """Patch files from build dir (not start dir)."""
+ super(EB_QuantumESPRESSO, self).patch_step(beginpath=self.builddir)
+
+ def configure_step(self):
+ """Custom configuration procedure for Quantum ESPRESSO."""
+
+ # compose list of DFLAGS (flag, value, keep_stuff)
+ # for guidelines, see include/defs.h.README in sources
+ dflags = []
+
+ repls = []
+
+ extra_libs = []
+
+ comp_fam_dflags = {
+ toolchain.INTELCOMP: '-D__INTEL',
+ toolchain.GCC: '-D__GFORTRAN -D__STD_F95',
+ }
+ comp_fam = self.toolchain.comp_family()
+ if comp_fam in comp_fam_dflags:
+ dflags.append(comp_fam_dflags[comp_fam])
+ else:
+ raise EasyBuildError("EasyBuild does not yet have support for QuantumESPRESSO with toolchain %s" % comp_fam)
+
+ if self.toolchain.options.get('openmp', False) or self.cfg['hybrid']:
+ self.cfg.update('configopts', '--enable-openmp')
+ dflags.append(" -D__OPENMP")
+
+ if self.toolchain.options.get('usempi', None):
+ dflags.append('-D__MPI -D__PARA')
+ else:
+ self.cfg.update('configopts', '--disable-parallel')
+
+ if self.cfg['with_scalapack']:
+ dflags.append(" -D__SCALAPACK")
+ if self.toolchain.options.get('usempi', None):
+ if get_software_root("impi") and get_software_root("imkl"):
+ self.cfg.update('configopts', '--with-scalapack=intel')
+ else:
+ self.cfg.update('configopts', '--without-scalapack')
+
+ libxc = get_software_root("libxc")
+ if libxc:
+ libxc_v = get_software_version("libxc")
+ if LooseVersion(libxc_v) < LooseVersion("3.0.1"):
+ raise EasyBuildError("Must use libxc >= 3.0.1")
+ dflags.append(" -D__LIBXC")
+ repls.append(('IFLAGS', '-I%s' % os.path.join(libxc, 'include'), True))
+ if LooseVersion(self.version) < LooseVersion("6.5"):
+ extra_libs.append(" -lxcf90 -lxc")
+ else:
+ extra_libs.append(" -lxcf90 -lxcf03 -lxc")
+
+ hdf5 = get_software_root("HDF5")
+ if hdf5:
+ self.cfg.update('configopts', '--with-hdf5=%s' % hdf5)
+ dflags.append(" -D__HDF5")
+ hdf5_lib_repl = '-L%s/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lsz -lz -ldl -lm' % hdf5
+ repls.append(('HDF5_LIB', hdf5_lib_repl, False))
+
+ elpa = get_software_root("ELPA")
+ if elpa:
+ if not self.cfg['with_scalapack']:
+ raise EasyBuildError("ELPA requires ScaLAPACK but 'with_scalapack' is set to False")
+
+ elpa_v = get_software_version("ELPA")
+ if LooseVersion(self.version) >= LooseVersion("6"):
+
+ # NOTE: Quantum Espresso should use -D__ELPA_<year> for corresponding ELPA version
+ # However for ELPA VERSION >= 2017.11 Quantum Espresso needs to use ELPA_2018
+ # because of outdated bindings. See: https://xconfigure.readthedocs.io/en/latest/elpa/
+ if LooseVersion("2018") > LooseVersion(elpa_v) >= LooseVersion("2017.11"):
+ dflags.append('-D__ELPA_2018')
+ else:
+ # get year from LooseVersion
+ elpa_year_v = elpa_v.split('.')[0]
+ dflags.append('-D__ELPA_%s' % elpa_year_v)
+
+ elpa_min_ver = "2016.11.001.pre"
+ else:
+ elpa_min_ver = "2015"
+ dflags.append('-D__ELPA_2015 -D__ELPA')
+
+ if LooseVersion(elpa_v) < LooseVersion(elpa_min_ver):
+ raise EasyBuildError("QuantumESPRESSO %s needs ELPA to be " +
+ "version %s or newer", self.version, elpa_min_ver)
+
+ if self.toolchain.options.get('openmp', False):
+ elpa_include = 'elpa_openmp-%s' % elpa_v
+ elpa_lib = 'libelpa_openmp.a'
+ else:
+ elpa_include = 'elpa-%s' % elpa_v
+ elpa_lib = 'libelpa.a'
+ elpa_include = os.path.join(elpa, 'include', elpa_include)
+ repls.append(('IFLAGS', '-I%s' % os.path.join(elpa_include, 'modules'), True))
+ self.cfg.update('configopts', '--with-elpa-include=%s' % elpa_include)
+ elpa_lib = os.path.join(elpa, 'lib', elpa_lib)
+ self.cfg.update('configopts', '--with-elpa-lib=%s' % elpa_lib)
+
+ if comp_fam == toolchain.INTELCOMP:
+ # set preprocessor command (-E to stop after preprocessing, -C to preserve comments)
+ cpp = "%s -E -C" % os.getenv('CC')
+ repls.append(('CPP', cpp, False))
+ env.setvar('CPP', cpp)
+
+ # also define $FCCPP, but do *not* include -C (comments should not be preserved when preprocessing Fortran)
+ env.setvar('FCCPP', "%s -E" % os.getenv('CC'))
+
+ if comp_fam == toolchain.INTELCOMP:
+ # Intel compiler must have -assume byterecl (see install/configure)
+ repls.append(('F90FLAGS', '-fpp -assume byterecl', True))
+ repls.append(('FFLAGS', '-assume byterecl', True))
+ elif comp_fam == toolchain.GCC:
+ f90_flags = ['-cpp']
+ if LooseVersion(get_software_version('GCC')) >= LooseVersion('10'):
+ f90_flags.append('-fallow-argument-mismatch')
+ repls.append(('F90FLAGS', ' '.join(f90_flags), True))
+
+ super(EB_QuantumESPRESSO, self).configure_step()
+
+ if self.toolchain.options.get('openmp', False):
+ libfft = os.getenv('LIBFFT_MT')
+ else:
+ libfft = os.getenv('LIBFFT')
+ if libfft:
+ if "fftw3" in libfft:
+ dflags.append('-D__FFTW3')
+ else:
+ dflags.append('-D__FFTW')
+ env.setvar('FFTW_LIBS', libfft)
+
+ if get_software_root('ACML'):
+ dflags.append('-D__ACML')
+
+ if self.cfg['with_ace']:
+ dflags.append(" -D__EXX_ACE")
+
+ # always include -w to supress warnings
+ dflags.append('-w')
+
+ if LooseVersion(self.version) >= LooseVersion("6.6"):
+ dflags.append(" -Duse_beef")
+ libbeef = get_software_root("libbeef")
+ if libbeef:
+ repls.append(('BEEF_LIBS_SWITCH', 'external', False))
+ repls.append(('BEEF_LIBS', '%s/lib/libbeef.a' % libbeef, False))
+
+ repls.append(('DFLAGS', ' '.join(dflags), False))
+
+ # complete C/Fortran compiler and LD flags
+ if self.toolchain.options.get('openmp', False) or self.cfg['hybrid']:
+ repls.append(('LDFLAGS', self.toolchain.get_flag('openmp'), True))
+ repls.append(('(?:C|F90|F)FLAGS', self.toolchain.get_flag('openmp'), True))
+
+ # obtain library settings
+ libs = []
+ num_libs = ['BLAS', 'LAPACK', 'FFT']
+ if self.cfg['with_scalapack']:
+ num_libs.extend(['SCALAPACK'])
+ for lib in num_libs:
+ if self.toolchain.options.get('openmp', False):
+ val = os.getenv('LIB%s_MT' % lib)
+ else:
+ val = os.getenv('LIB%s' % lib)
+ if lib == 'SCALAPACK' and elpa:
+ val = ' '.join([elpa_lib, val])
+ repls.append(('%s_LIBS' % lib, val, False))
+ libs.append(val)
+ libs = ' '.join(libs)
+
+ repls.append(('BLAS_LIBS_SWITCH', 'external', False))
+ repls.append(('LAPACK_LIBS_SWITCH', 'external', False))
+ repls.append(('LD_LIBS', ' '.join(extra_libs + [os.getenv('LIBS')]), False))
+
+ # Do not use external FoX.
+ # FoX starts to be used in 6.2 and they use a patched version that
+ # is newer than FoX 4.1.2 which is the latest release.
+ # Ake Sandgren, 20180712
+ if get_software_root('FoX'):
+ raise EasyBuildError("Found FoX external module, QuantumESPRESSO" +
+ "must use the version they include with the source.")
+
+ self.log.debug("List of replacements to perform: %s" % repls)
+
+ if LooseVersion(self.version) >= LooseVersion("6"):
+ make_ext = '.inc'
+ else:
+ make_ext = '.sys'
+
+ # patch make.sys file
+ fn = os.path.join(self.cfg['start_dir'], 'make' + make_ext)
+ try:
+ for line in fileinput.input(fn, inplace=1, backup='.orig.eb'):
+ for (k, v, keep) in repls:
+ # need to use [ \t]* instead of \s*, because vars may be undefined as empty,
+ # and we don't want to include newlines
+ if keep:
+ line = re.sub(r"^(%s\s*=[ \t]*)(.*)$" % k, r"\1\2 %s" % v, line)
+ else:
+ line = re.sub(r"^(%s\s*=[ \t]*).*$" % k, r"\1%s" % v, line)
+
+ # fix preprocessing directives for .f90 files in make.sys if required
+ if LooseVersion(self.version) < LooseVersion("6.0"):
+ if comp_fam == toolchain.GCC:
+ line = re.sub(r"^\t\$\(MPIF90\) \$\(F90FLAGS\) -c \$<",
+ "\t$(CPP) -C $(CPPFLAGS) $< -o $*.F90\n" +
+ "\t$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o",
+ line)
+
+ if LooseVersion(self.version) >= LooseVersion("6.6"):
+ # fix order of BEEF_LIBS in QE_LIBS
+ line = re.sub(r"^(QELIBS\s*=[ \t]*)(.*) \$\(BEEF_LIBS\) (.*)$",
+ r"QELIBS = $(BEEF_LIBS) \2 \3", line)
+
+ # use FCCPP instead of CPP for Fortran headers
+ line = re.sub(r"\t\$\(CPP\) \$\(CPPFLAGS\) \$< -o \$\*\.fh",
+ "\t$(FCCPP) $(CPPFLAGS) $< -o $*.fh", line)
+
+ sys.stdout.write(line)
+ except IOError as err:
+ raise EasyBuildError("Failed to patch %s: %s", fn, err)
+
+ self.log.debug("Contents of patched %s: %s" % (fn, open(fn, "r").read()))
+
+ # patch default make.sys for wannier
+ if LooseVersion(self.version) >= LooseVersion("5"):
+ fn = os.path.join(self.cfg['start_dir'], 'install', 'make_wannier90' + make_ext)
+ else:
+ fn = os.path.join(self.cfg['start_dir'], 'plugins', 'install', 'make_wannier90.sys')
+ try:
+ for line in fileinput.input(fn, inplace=1, backup='.orig.eb'):
+ line = re.sub(r"^(LIBS\s*=\s*).*", r"\1%s" % libs, line)
+
+ sys.stdout.write(line)
+
+ except IOError as err:
+ raise EasyBuildError("Failed to patch %s: %s", fn, err)
+
+ self.log.debug("Contents of patched %s: %s" % (fn, open(fn, "r").read()))
+
+ # patch Makefile of want plugin
+ wantprefix = 'want-'
+ wantdirs = [d for d in os.listdir(self.builddir) if d.startswith(wantprefix)]
+
+ if len(wantdirs) > 1:
+ raise EasyBuildError("Found more than one directory with %s prefix, help!", wantprefix)
+
+ if len(wantdirs) != 0:
+ wantdir = os.path.join(self.builddir, wantdirs[0])
+ make_sys_in_path = None
+ cand_paths = [os.path.join('conf', 'make.sys.in'), os.path.join('config', 'make.sys.in')]
+ for path in cand_paths:
+ full_path = os.path.join(wantdir, path)
+ if os.path.exists(full_path):
+ make_sys_in_path = full_path
+ break
+ if make_sys_in_path is None:
+ raise EasyBuildError("Failed to find make.sys.in in want directory %s, paths considered: %s",
+ wantdir, ', '.join(cand_paths))
+
+ try:
+ for line in fileinput.input(make_sys_in_path, inplace=1, backup='.orig.eb'):
+ # fix preprocessing directives for .f90 files in make.sys if required
+ if comp_fam == toolchain.GCC:
+ line = re.sub("@f90rule@",
+ "$(CPP) -C $(CPPFLAGS) $< -o $*.F90\n" +
+ "\t$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o",
+ line)
+
+ sys.stdout.write(line)
+ except IOError as err:
+ raise EasyBuildError("Failed to patch %s: %s", fn, err)
+
+ # move non-espresso directories to where they're expected and create symlinks
+ try:
+ dirnames = [d for d in os.listdir(self.builddir) if d not in [self.install_subdir, 'd3q-latest']]
+ targetdir = os.path.join(self.builddir, self.install_subdir)
+ for dirname in dirnames:
+ shutil.move(os.path.join(self.builddir, dirname), os.path.join(targetdir, dirname))
+ self.log.info("Moved %s into %s" % (dirname, targetdir))
+
+ dirname_head = dirname.split('-')[0]
+ # Handle the case where the directory is preceded by 'qe-'
+ if dirname_head == 'qe':
+ dirname_head = dirname.split('-')[1]
+ linkname = None
+ if dirname_head == 'sax':
+ linkname = 'SaX'
+ if dirname_head == 'wannier90':
+ linkname = 'W90'
+ elif dirname_head in ['d3q', 'gipaw', 'plumed', 'want', 'yambo']:
+ linkname = dirname_head.upper()
+ if linkname:
+ os.symlink(os.path.join(targetdir, dirname), os.path.join(targetdir, linkname))
+
+ except OSError as err:
+ raise EasyBuildError("Failed to move non-espresso directories: %s", err)
+
+ def install_step(self):
+ """Custom install step for Quantum ESPRESSO."""
+ raise EasyBuildError("STOP")
+ # extract build targets as list
+ targets = self.cfg['buildopts'].split()
+
+ # Copy all binaries
+ bindir = os.path.join(self.installdir, 'bin')
+ copy_dir(os.path.join(self.cfg['start_dir'], 'bin'), bindir)
+
+ # Pick up files not installed in bin
+ def copy_binaries(path):
+ full_dir = os.path.join(self.cfg['start_dir'], path)
+ self.log.info("Looking for binaries in %s" % full_dir)
+ for filename in os.listdir(full_dir):
+ full_path = os.path.join(full_dir, filename)
+ if os.path.isfile(full_path):
+ if filename.endswith('.x'):
+ copy_file(full_path, bindir)
+
+ if 'upf' in targets or 'all' in targets:
+ if LooseVersion(self.version) < LooseVersion("6.6"):
+ copy_binaries('upftools')
+ else:
+ copy_binaries('upflib')
+ copy_file(os.path.join(self.cfg['start_dir'], 'upflib', 'fixfiles.py'), bindir)
+
+ if 'want' in targets:
+ copy_binaries('WANT')
+
+ if 'w90' in targets:
+ copy_binaries('W90')
+
+ if 'yambo' in targets:
+ copy_binaries('YAMBO')
+
+ def sanity_check_step(self):
+ """Custom sanity check for Quantum ESPRESSO."""
+
+ # extract build targets as list
+ targets = self.cfg['buildopts'].split()
+
+ bins = []
+ if LooseVersion(self.version) < LooseVersion("6.7"):
+ # build list of expected binaries based on make targets
+ bins.extend(["iotk", "iotk.x", "iotk_print_kinds.x"])
+
+ if 'cp' in targets or 'all' in targets:
+ bins.extend(["cp.x", "wfdd.x"])
+ if LooseVersion(self.version) < LooseVersion("6.4"):
+ bins.append("cppp.x")
+
+ # only for v4.x, not in v5.0 anymore, called gwl in 6.1 at least
+ if 'gww' in targets or 'gwl' in targets:
+ bins.extend(["gww_fit.x", "gww.x", "head.x", "pw4gww.x"])
+
+ if 'ld1' in targets or 'all' in targets:
+ bins.extend(["ld1.x"])
+
+ if 'gipaw' in targets:
+ bins.extend(["gipaw.x"])
+
+ if 'neb' in targets or 'pwall' in targets or 'all' in targets:
+ if LooseVersion(self.version) > LooseVersion("5"):
+ bins.extend(["neb.x", "path_interpolation.x"])
+
+ if 'ph' in targets or 'all' in targets:
+ bins.extend(["dynmat.x", "lambda.x", "matdyn.x", "ph.x", "phcg.x", "q2r.x"])
+ if LooseVersion(self.version) < LooseVersion("6"):
+ bins.extend(["d3.x"])
+ if LooseVersion(self.version) > LooseVersion("5"):
+ bins.extend(["fqha.x", "q2qstar.x"])
+
+ if 'pp' in targets or 'pwall' in targets or 'all' in targets:
+ bins.extend(["average.x", "bands.x", "dos.x", "epsilon.x", "initial_state.x",
+ "plan_avg.x", "plotband.x", "plotproj.x", "plotrho.x", "pmw.x", "pp.x",
+ "projwfc.x", "sumpdos.x", "pw2wannier90.x", "pw2gw.x",
+ "wannier_ham.x", "wannier_plot.x"])
+ if LooseVersion(self.version) > LooseVersion("5") and LooseVersion(self.version) < LooseVersion("6.4"):
+ bins.extend(["pw2bgw.x", "bgw2pw.x"])
+ elif LooseVersion(self.version) <= LooseVersion("5"):
+ bins.extend(["pw2casino.x"])
+ if LooseVersion(self.version) < LooseVersion("6.4"):
+ bins.extend(["pw_export.x"])
+
+ if 'pw' in targets or 'all' in targets:
+ bins.extend(["dist.x", "ev.x", "kpoints.x", "pw.x", "pwi2xsf.x"])
+ if LooseVersion(self.version) < LooseVersion("6.5"):
+ if LooseVersion(self.version) >= LooseVersion("5.1"):
+ bins.extend(["generate_rVV10_kernel_table.x"])
+ if LooseVersion(self.version) > LooseVersion("5"):
+ bins.extend(["generate_vdW_kernel_table.x"])
+ if LooseVersion(self.version) <= LooseVersion("5"):
+ bins.extend(["path_int.x"])
+ if LooseVersion(self.version) < LooseVersion("5.3.0"):
+ bins.extend(["band_plot.x", "bands_FS.x", "kvecs_FS.x"])
+
+ if 'pwcond' in targets or 'pwall' in targets or 'all' in targets:
+ bins.extend(["pwcond.x"])
+
+ if 'tddfpt' in targets or 'all' in targets:
+ if LooseVersion(self.version) > LooseVersion("5"):
+ bins.extend(["turbo_lanczos.x", "turbo_spectrum.x"])
+
+ upftools = []
+ if 'upf' in targets or 'all' in targets:
+ if LooseVersion(self.version) < LooseVersion("6.6"):
+ upftools = ["casino2upf.x", "cpmd2upf.x", "fhi2upf.x", "fpmd2upf.x", "ncpp2upf.x",
+ "oldcp2upf.x", "read_upf_tofile.x", "rrkj2upf.x", "uspp2upf.x", "vdb2upf.x"]
+ if LooseVersion(self.version) > LooseVersion("5"):
+ upftools.extend(["interpolate.x", "upf2casino.x"])
+ if LooseVersion(self.version) >= LooseVersion("6.3"):
+ upftools.extend(["fix_upf.x"])
+ if LooseVersion(self.version) < LooseVersion("6.4"):
+ upftools.extend(["virtual.x"])
+ else:
+ upftools.extend(["virtual_v2.x"])
+ else:
+ upftools = ["upfconv.x", "virtual_v2.x", "fixfiles.py"]
+
+ if 'vdw' in targets: # only for v4.x, not in v5.0 anymore
+ bins.extend(["vdw.x"])
+
+ if 'w90' in targets:
+ bins.extend(["wannier90.x"])
+ if LooseVersion(self.version) >= LooseVersion("5.4"):
+ bins.extend(["postw90.x"])
+ if LooseVersion(self.version) < LooseVersion("6.1"):
+ bins.extend(["w90chk2chk.x"])
+
+ want_bins = []
+ if 'want' in targets:
+ want_bins = ["blc2wan.x", "conductor.x", "current.x", "disentangle.x",
+ "dos.x", "gcube2plt.x", "kgrid.x", "midpoint.x", "plot.x", "sumpdos",
+ "wannier.x", "wfk2etsf.x"]
+ if LooseVersion(self.version) > LooseVersion("5"):
+ want_bins.extend(["cmplx_bands.x", "decay.x", "sax2qexml.x", "sum_sgm.x"])
+
+ if 'xspectra' in targets:
+ bins.extend(["xspectra.x"])
+
+ yambo_bins = []
+ if 'yambo' in targets:
+ yambo_bins = ["a2y", "p2y", "yambo", "ypp"]
+
+ d3q_bins = []
+ if 'd3q' in targets:
+ d3q_bins = ['d3_asr3.x', 'd3_lw.x', 'd3_q2r.x',
+ 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
+ 'd3_sparse.x', 'd3_sqom.x', 'd3_tk.x']
+ if LooseVersion(self.version) < LooseVersion("6.4"):
+ d3q_bins.append('d3_import3py.x')
+
+ custom_paths = {
+ 'files': [os.path.join('bin', x) for x in bins + upftools + want_bins + yambo_bins + d3q_bins],
+ 'dirs': []
+ }
+
+ super(EB_QuantumESPRESSO, self).sanity_check_step(custom_paths=custom_paths)
diff --git a/easyblocks/r/relion.py b/easyblocks/r/relion.py
new file mode 100644
index 0000000..6213fb3
--- /dev/null
+++ b/easyblocks/r/relion.py
@@ -0,0 +1,125 @@
+##
+# Copyright 2009-2022 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://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# 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/>.
+##
+"""
+EasyBuild support for building and installing RELION, implemented as an easyblock
+
+@author: Jasper Grimm (University of York)
+"""
+from easybuild.easyblocks.generic.cmakemake import CMakeMake
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.config import build_option
+from easybuild.tools.build_log import EasyBuildError, print_warning
+
+
+class EB_RELION(CMakeMake):
+ """Support for building/installing RELION."""
+
+ @staticmethod
+ def extra_options():
+ extra_vars = CMakeMake.extra_options()
+ extra_vars.update({
+ 'cuda_texture': [False, "Enable cuda texture", CUSTOM],
+ 'default_cuda_capability': [None, "Default CUDA capabilitity for building RELION, e.g. '8.6'", CUSTOM],
+ 'doubleprec_cpu': [True, "Enable double precision (CPU)", CUSTOM],
+ 'doubleprec_gpu': [False, "Enable double precision (GPU)", CUSTOM],
+ 'disable_gui': [False, "Build without GUI", CUSTOM],
+ 'use_mkl': [True, "Use MKL for FFT (if MKL is a depencency)", CUSTOM],
+ })
+ return extra_vars
+
+ def configure_step(self, *args, **kwargs):
+ """Custom configure step for RELION"""
+
+ # configure some default options
+ self.cfg.update('configopts', '-DCMAKE_SHARED_LINKER="$LIBS"')
+ self.cfg.update('configopts', '-DMPI_INCLUDE_PATH="$MPI_INC_DIR"')
+
+ gui_deps = get_software_root('FLTK') and get_software_root('X11')
+ if self.cfg['disable_gui'] or not gui_deps:
+ if not gui_deps:
+ print_warning("Missing dependencies for the GUI (FLTK and X11 are required). Building without GUI.")
+ self.cfg.update('configopts', '-DGUI=OFF')
+
+ if get_software_root('MKL') and self.cfg['use_mkl']:
+ self.cfg.update('configopts', '-DMKLFFT=ON')
+
+ # check if CUDA is present
+ if get_software_root('CUDA'):
+ self.cfg.update('configopts', '-DCUDA=ON')
+
+ # check cuda_compute_capabilities
+ cuda_cc = self.cfg['cuda_compute_capabilities'] or build_option('cuda_compute_capabilities') or []
+ if not cuda_cc:
+ raise EasyBuildError("Can't build RELION with CUDA support without"
+ " specifying 'cuda-compute-capabilities'")
+ self.cfg.update('configopts', '-DCUDA_ARCH="%s"' % ' '.join(cuda_cc))
+
+ # check default_cuda_capability
+ default_cc = self.cfg['default_cuda_capability'] or min(cuda_cc)
+ if not self.cfg['default_cuda_capability']:
+ print_warning("No default CUDA capability defined! "
+ "Using '%s' taken as minimum from 'cuda_compute_capabilities'" % default_cc)
+ self.cfg.update('configopts', '-DDEFAULT_CUDA_ARCH="%s"' % default_cc)
+
+ if self.cfg['cuda_texture']:
+ self.cfg.update('configopts', '-DCUDA_TEXTURE=ON')
+
+ if not self.cfg['doubleprec_cpu']:
+ self.cfg.update('configopts', '-DDoublePrec_CPU=OFF')
+
+ if self.cfg['doubleprec_gpu']:
+ self.log.warning("Enabling GPU double precision is not recommnded")
+ self.cfg.update('configopts', '-DDoublePrec_ACC=ON')
+ else:
+ self.cfg.update('configopts', '-DDoublePrec_ACC=OFF')
+
+ else:
+ # CPU build
+ self.cfg.update('configopts', '-DALTCPU=ON')
+
+ if self.cfg['doubleprec_cpu']:
+ self.cfg.update('configopts', '-DDoublePrec_CPU=ON')
+ else:
+ self.cfg.update('configopts', '-DDoublePrec_CPU=OFF')
+
+ super(EB_RELION, self).configure_step(*args, **kwargs)
+
+ def install_step(self, *args, **kwargs):
+ """Custom install step for RELION"""
+ self.cfg['install_cmd'] = 'make -j %s install' % self.cfg['parallel']
+
+ super(EB_RELION, self).install_step(*args, **kwargs)
+
+ def sanity_check_step(self):
+ """Custom sanity check step for RELION."""
+ custom_paths = {
+ 'files': ['bin/relion%s' % x for x in ['', '_autopick', '_batchrun', '_batchrun_mpi']],
+ 'dirs': [],
+ }
+
+ custom_commands = ['relion --help', 'relion --version']
+
+ super(EB_RELION, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
diff --git a/easyblocks/w/wien2k.py b/easyblocks/w/wien2k.py
index e827691..ce6c4c7 100644
--- a/easyblocks/w/wien2k.py
+++ b/easyblocks/w/wien2k.py
@@ -1,5 +1,5 @@
##
-# Copyright 2009-2019 Ghent University
+# Copyright 2009-2023 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -46,7 +46,8 @@ import easybuild.tools.toolchain as toolchain
from easybuild.framework.easyblock import EasyBlock
from easybuild.framework.easyconfig import CUSTOM
from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import extract_file, mkdir, read_file, rmtree2, write_file
+from easybuild.tools.filetools import apply_regex_substitutions, change_dir, extract_file, mkdir, read_file
+from easybuild.tools.filetools import remove_dir, write_file
from easybuild.tools.modules import get_software_root, get_software_version
from easybuild.tools.run import run_cmd, run_cmd_qa
@@ -73,6 +74,8 @@ class EB_WIEN2k(EasyBlock):
'mpi_remote': [False, "Whether to initiate MPI calls locally or remotely", CUSTOM],
'wien_granularity': [True, "Granularity for parallel execution (see manual)", CUSTOM],
'taskset': [None, "Specifies an optional command for binding a process to a specific core", CUSTOM],
+ 'nmatmax': [19000, "Specifies the maximum matrix size", CUSTOM],
+ 'nume': [6000, "Specifies the number of states to output.", CUSTOM],
}
return EasyBlock.extra_options(extra_vars)
@@ -86,9 +89,9 @@ class EB_WIEN2k(EasyBlock):
cmd = "./expand_lapw"
qanda = {'continue (y/n)': 'y'}
no_qa = [
- 'tar -xf.*',
- '.*copied and linked.*',
- ]
+ 'tar -xf.*',
+ '.*copied and linked.*',
+ ]
run_cmd_qa(cmd, qanda, no_qa=no_qa, log_all=True, simple=True)
@@ -102,7 +105,11 @@ class EB_WIEN2k(EasyBlock):
# toolchain-dependent values
comp_answer = None
if self.toolchain.comp_family() == toolchain.INTELCOMP: # @UndefinedVariable
- if LooseVersion(get_software_version("icc")) >= LooseVersion("2011"):
+ if get_software_root('icc'):
+ intelver = get_software_version('icc')
+ elif get_software_root('intel-compilers'):
+ intelver = get_software_version('intel-compilers')
+ if LooseVersion(intelver) >= LooseVersion("2011"):
if LooseVersion(self.version) < LooseVersion("17"):
comp_answer = 'I' # Linux (Intel ifort 12.0 compiler + mkl )
else:
@@ -159,7 +166,7 @@ class EB_WIEN2k(EasyBlock):
else:
line = regexp.sub('\\1:%s:%s' % (key, val), line)
# avoid exit code > 0 at end of configuration
- line = re.sub('(\s+)exit 1', '\\1exit 0', line)
+ line = re.sub(r'(\s+)exit 1', '\\1exit 0', line)
sys.stdout.write(line)
# set correct compilers
@@ -178,24 +185,32 @@ class EB_WIEN2k(EasyBlock):
dc['cc'] = dc.pop('COMPILERC')
dc['fortran'] = dc.pop('COMPILER')
dc['parallel'] = dc.pop('COMPILERP')
- write_file('WIEN2k_COMPILER', '\n'.join(['%s:%s' % (k, v) for k, v in dc.iteritems()]))
+ write_file('WIEN2k_COMPILER', '\n'.join(['%s:%s' % (k, v) for k, v in dc.items()]))
# configure with patched configure script
self.log.debug('%s part I (configure)' % self.cfgscript)
+ if LooseVersion(self.version) >= LooseVersion('21'):
+ perlroot = get_software_root('Perl')
+ if perlroot is None:
+ raise EasyBuildError("Perl is a required dependency of WIEN2k as of version 21")
+ self.perlbin = os.path.join(perlroot, 'bin', 'perl')
+ else:
+ self.perlbin = ''
+
cmd = "./%s" % self.cfgscript
qanda = {
- 'Press RETURN to continue': '',
- 'Your compiler:': '',
- 'Hit Enter to continue': '',
- 'Remote shell (default is ssh) =': '',
- 'Remote copy (default is scp) =': '',
- 'and you need to know details about your installed mpi ..) (y/n)': 'y',
- 'Q to quit Selection:': 'Q',
- 'A Compile all programs (suggested) Q Quit Selection:': 'Q',
- ' Please enter the full path of the perl program: ': '',
- 'continue or stop (c/s)': 'c',
- '(like taskset -c). Enter N / your_specific_command:': 'N',
+ 'Press RETURN to continue': '',
+ 'Your compiler:': '',
+ 'Hit Enter to continue': '',
+ 'Remote shell (default is ssh) =': '',
+ 'Remote copy (default is scp) =': '',
+ 'and you need to know details about your installed mpi ..) (y/n)': 'y',
+ 'Q to quit Selection:': 'Q',
+ 'A Compile all programs (suggested) Q Quit Selection:': 'Q',
+ 'Please enter the full path of the perl program: ': self.perlbin,
+ 'continue or stop (c/s)': 'c',
+ '(like taskset -c). Enter N / your_specific_command:': 'N',
}
if LooseVersion(self.version) >= LooseVersion("13"):
fftw_root = get_software_root('FFTW')
@@ -205,80 +220,123 @@ class EB_WIEN2k(EasyBlock):
else:
raise EasyBuildError("Required FFTW dependency is missing")
qanda.update({
- ') Selection:': comp_answer,
- 'Shared Memory Architecture? (y/N):': 'N',
- 'Set MPI_REMOTE to 0 / 1:': '0',
- 'You need to KNOW details about your installed MPI and FFTW ) (y/n)': 'y',
- 'Please specify whether you want to use FFTW3 (default) or FFTW2 (FFTW3 / FFTW2):': fftw_spec,
- 'Please specify the ROOT-path of your FFTW installation (like /opt/fftw3):': fftw_root,
- 'is this correct? enter Y (default) or n:': 'Y',
+ ') Selection:': comp_answer,
+ 'Shared Memory Architecture? (y/N):': 'N',
+ 'Set MPI_REMOTE to 0 / 1:': '0',
+ 'You need to KNOW details about your installed MPI and FFTW ) (y/n)': 'y',
+ 'Do you want to use FFTW (recommended, but for sequential code not required)? (Y,n):': 'y',
+ 'Please specify whether you want to use FFTW3 (default) or FFTW2 (FFTW3 / FFTW2):': fftw_spec,
+ 'Please specify the ROOT-path of your FFTW installation (like /opt/fftw3):': fftw_root,
+ 'is this correct? enter Y (default) or n:': 'Y',
})
libxcroot = get_software_root('libxc')
- libxcquestion = 'LIBXC (that you have installed%s)? (y,N):' % \
- (' before' if LooseVersion(self.version) < LooseVersion("17") else '')
+
+ if LooseVersion(self.version) < LooseVersion("17"):
+ libxcstr1 = ' before'
+ libxcstr3 = ''
+ elif LooseVersion(self.version) > LooseVersion("19"):
+ libxcstr1 = ' - usually not needed'
+ libxcstr3 = 'root-'
+ else:
+ libxcstr1 = ''
+ libxcstr3 = ''
+
+ if LooseVersion(self.version) > LooseVersion("23"):
+ libxcquestion1 = 'Would you like to use LIBXC (needed ONLY for self-consistent gKS mGGA calculations, for the stress tensor and experts who want to play with different DFT options. It must have been installed before)? (y,N): '
+ else:
+ libxcquestion1 = 'LIBXC (that you have installed%s)? (y,N):' % libxcstr1
+
+ libxcquestion2 = 'Do you want to automatically search for LIBXC installations? (Y,n):'
+ libxcquestion3 = 'Please enter the %sdirectory of your LIBXC-installation!:' % libxcstr3
+ libxcquestion4 = 'Please enter the lib-directory of your LIBXC-installation (usually lib or lib64)!:'
+ libxcquestion5 = 'LIBXC (usually not needed, ONLY for experts who want to play with different DFT options. '
+ libxcquestion5 += 'It must have been installed before)? (y,N):'
+
if libxcroot:
qanda.update({
- libxcquestion: 'y',
- 'Do you want to automatically search for LIBXC installations? (Y,n):': 'n',
- 'Please enter the root-directory of your LIBXC-installation!:': libxcroot,
- 'Please enter the lib-directory of your LIBXC-installation (usually lib or lib64!:': 'lib',
+ libxcquestion1: 'y',
+ libxcquestion2: 'n',
+ libxcquestion3: libxcroot,
+ libxcquestion4: 'lib',
+ libxcquestion5: 'y',
})
else:
- qanda.update({libxcquestion: ''})
+ qanda.update({
+ libxcquestion1: 'N',
+ libxcquestion5: 'N',
+ })
if LooseVersion(self.version) >= LooseVersion("17"):
scalapack_libs = os.getenv('LIBSCALAPACK').split()
scalapack = next((lib[2:] for lib in scalapack_libs if 'scalapack' in lib), 'scalapack')
blacs = next((lib[2:] for lib in scalapack_libs if 'blacs' in lib), 'openblas')
qanda.update({
- 'You need to KNOW details about your installed MPI, ELPA, and FFTW ) (y/N)': 'y',
- 'Do you want to use a present ScaLAPACK installation? (Y,n):': 'y',
- 'Do you want to use the MKL version of ScaLAPACK? (Y,n):': 'n', # we set it ourselves below
- 'Do you use Intel MPI? (Y,n):': 'y',
- 'Is this correct? (Y,n):': 'y',
- 'Please specify the target architecture of your ScaLAPACK libraries (e.g. intel64)!:': '',
- 'ScaLAPACK root:': os.getenv('MKLROOT') or os.getenv('EBROOTSCALAPACK'),
- 'ScaLAPACK library:': scalapack,
- 'BLACS root:': os.getenv('MKLROOT') or os.getenv('EBROOTOPENBLAS'),
- 'BLACS library:': blacs,
- 'Please enter your choice of additional libraries!:': '',
- 'Do you want to use a present FFTW installation? (Y,n):': 'y',
- 'Please specify the path of your FFTW installation (like /opt/fftw3/) '
- 'or accept present choice (enter):': fftw_root,
- 'Please specify the target achitecture of your FFTW library (e.g. lib64) '
- 'or accept present choice (enter):': '',
- 'Do you want to automatically search for FFTW installations? (Y,n):': 'n',
- 'Please specify the ROOT-path of your FFTW installation (like /opt/fftw3/) '
- 'or accept present choice (enter):': fftw_root,
- 'Is this correct? enter Y (default) or n:': 'Y',
- 'Please specify the name of your FFTW library or accept present choice (enter):': '',
- 'Please specify your parallel compiler options or accept the recommendations '
- '(Enter - default)!:': '',
- 'Please specify your MPIRUN command or accept the recommendations (Enter - default)!:': '',
- # the temporary directory is hardcoded into execution scripts and must exist at runtime
- 'Please enter the full path to your temporary directory:': '/tmp',
- })
+ 'You need to KNOW details about your installed MPI, ELPA, and FFTW ) (y/N)': 'y',
+ 'Do you want to use a present ScaLAPACK installation? (Y,n):': 'y',
+ 'Do you want to use the MKL version of ScaLAPACK? (Y,n):': 'n', # we set it ourselves below
+ 'Do you use Intel MPI? (Y,n):': 'y',
+ 'Is this correct? (Y,n):': 'y',
+ 'Please specify the target architecture of your ScaLAPACK libraries (e.g. intel64)!:': '',
+ 'ScaLAPACK root:': os.getenv('MKLROOT') or os.getenv('EBROOTSCALAPACK'),
+ 'ScaLAPACK library:': scalapack,
+ 'BLACS root:': os.getenv('MKLROOT') or os.getenv('EBROOTOPENBLAS'),
+ 'BLACS library:': blacs,
+ 'Please enter your choice of additional libraries!:': '',
+ 'Do you want to use a present FFTW installation? (Y,n):': 'y',
+ 'Please specify the path of your FFTW installation (like /opt/fftw3/) '
+ 'or accept present choice (enter):': fftw_root,
+ 'Please specify the target achitecture of your FFTW library (e.g. lib64) '
+ 'or accept present choice (enter):': '',
+ 'Do you want to automatically search for FFTW installations? (Y,n):': 'n',
+ 'Please specify the ROOT-path of your FFTW installation (like /opt/fftw3/) '
+ 'or accept present choice (enter):': fftw_root,
+ 'Is this correct? enter Y (default) or n:': 'Y',
+ 'Please specify the name of your FFTW library or accept present choice (enter):': '',
+ 'or accept the recommendations (Enter - default)!:': '',
+ # the temporary directory is hardcoded into execution scripts and must exist at runtime
+ 'Please enter the full path to your temporary directory:': '/tmp',
+ })
+ std_qa = {}
elparoot = get_software_root('ELPA')
if elparoot:
+
+ apply_regex_substitutions(self.cfgscript, [(r'cat elpahelp2$', 'cat -n elpahelp2')])
+
+ elpa_dict = {
+ 'root': elparoot,
+ 'version': get_software_version('ELPA'),
+ 'variant': 'elpa_openmp' if self.toolchain.get_flag('openmp') else 'elpa'}
+
+ elpa_dir = "%(root)s/include/%(variant)s-%(version)s" % elpa_dict
+ std_qa.update({
+ r".*(?P<number>[0-9]+)\t%s\n(.*\n)*" % elpa_dir: "%(number)s",
+ })
+
qanda.update({
'Do you want to use ELPA? (y,N):': 'y',
'Do you want to automatically search for ELPA installations? (Y,n):': 'n',
'Please specify the ROOT-path of your ELPA installation (like /usr/local/elpa/) '
'or accept present path (Enter):': elparoot,
+ 'Please specify the lib-directory of your ELPA installation (e.g. lib or lib64)!:': 'lib',
+ 'Please specify the lib-directory of your ELPA installation (e.g. lib or lib64):': 'lib',
+ 'Please specify the name of your installed ELPA library (e.g. elpa or elpa_openmp)!:':
+ elpa_dict['variant'],
+ 'Please specify the name of your installed ELPA library (e.g. elpa or elpa_openmp):':
+ elpa_dict['variant'],
})
else:
qanda.update({'Do you want to use ELPA? (y,N):': 'n'})
else:
qanda.update({
- 'compiler) Selection:': comp_answer,
- 'Shared Memory Architecture? (y/n):': 'n',
- 'If you are using mpi2 set MPI_REMOTE to 0 Set MPI_REMOTE to 0 / 1:': '0',
- 'Do you have MPI and Scalapack installed and intend to run '
- 'finegrained parallel? (This is usefull only for BIG cases '
- '(50 atoms and more / unit cell) and you need to know details '
- 'about your installed mpi and fftw ) (y/n)': 'y',
+ 'compiler) Selection:': comp_answer,
+ 'Shared Memory Architecture? (y/n):': 'n',
+ 'If you are using mpi2 set MPI_REMOTE to 0 Set MPI_REMOTE to 0 / 1:': '0',
+ 'Do you have MPI and Scalapack installed and intend to run '
+ 'finegrained parallel? (This is usefull only for BIG cases '
+ '(50 atoms and more / unit cell) and you need to know details '
+ 'about your installed mpi and fftw ) (y/n)': 'y',
})
no_qa = [
@@ -287,15 +345,14 @@ class EB_WIEN2k(EasyBlock):
"%s[ \t]*.*" % os.getenv('F90'),
"%s[ \t]*.*" % os.getenv('CC'),
".*SRC_.*",
- "Please enter the full path of the perl program:",
]
- std_qa = {
+ std_qa.update({
r'S\s+Save and Quit[\s\n]+To change an item select option.[\s\n]+Selection:': 'S',
'Recommended setting for parallel f90 compiler: .* Current selection: Your compiler:': os.getenv('MPIF90'),
r'process or you can change single items in "Compiling Options".[\s\n]+Selection:': 'S',
r'A\s+Compile all programs (suggested)[\s\n]+Q\s*Quit[\s\n]+Selection:': 'Q',
- }
+ })
run_cmd_qa(cmd, qanda, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)
@@ -329,6 +386,15 @@ class EB_WIEN2k(EasyBlock):
self.log.debug("Patched file %s: %s", parallel_options_fp, read_file(parallel_options_fp))
+ # Set configurable parameters for size of problems.
+ param_subs = [
+ (r'\s+PARAMETER\s+\(\s*NMATMAX\s*=\s*\d+\)', r' PARAMETER (NMATMAX=%s)' % self.cfg['nmatmax']),
+ (r'\s+PARAMETER\s+\(\s*NUME\s*=\s*\d+\)', r' PARAMETER (NUME=%s)' % self.cfg['nume']),
+ ]
+ self.log.debug("param_subs = %s" % param_subs)
+ apply_regex_substitutions('SRC_lapw1/param.inc', param_subs)
+ self.log.debug("Patched file %s: %s", 'SRC_lapw1/param.inc', read_file('SRC_lapw1/param.inc'))
+
def build_step(self):
"""Build WIEN2k by running siteconfig_lapw script again."""
@@ -338,31 +404,30 @@ class EB_WIEN2k(EasyBlock):
qanda = {
'Press RETURN to continue': '\nQ', # also answer on first qanda pattern with 'Q' to quit
- ' Please enter the full path of the perl program: ': '',
- }
+ 'Please enter the full path of the perl program: ': self.perlbin,
+ }
if LooseVersion(self.version) < LooseVersion("17"):
qanda.update({
- 'L Perl path (if not in /usr/bin/perl) Q Quit Selection:': 'R',
- 'A Compile all programs S Select program Q Quit Selection:': 'A',
+ 'L Perl path (if not in /usr/bin/perl) Q Quit Selection:': 'R',
+ 'A Compile all programs S Select program Q Quit Selection:': 'A',
})
else:
qanda.update({
- 'program Q Quit Selection:': 'A',
- 'Path Q Quit Selection:': 'R',
+ 'program Q Quit Selection:': 'A',
+ 'Path Q Quit Selection:': 'R',
})
no_qa = [
- "%s[ \t]*.*" % os.getenv('MPIF90'),
- "%s[ \t]*.*" % os.getenv('F90'),
- "%s[ \t]*.*" % os.getenv('CC'),
- "mv[ \t]*.*",
- ".*SRC_.*",
- ".*: warning .*",
- ".*Stop.",
- "Compile time errors (if any) were:",
- "Please enter the full path of the perl program:",
- ]
+ "%s[ \t]*.*" % os.getenv('MPIF90'),
+ "%s[ \t]*.*" % os.getenv('F90'),
+ "%s[ \t]*.*" % os.getenv('CC'),
+ "mv[ \t]*.*",
+ ".*SRC_.*",
+ ".*: warning .*",
+ ".*Stop.",
+ "Compile time errors (if any) were:",
+ ]
self.log.debug("no_qa for %s: %s" % (cmd, no_qa))
run_cmd_qa(cmd, qanda, no_qa=no_qa, log_all=True, simple=True)
@@ -376,7 +441,7 @@ class EB_WIEN2k(EasyBlock):
cmd = "x_lapw lapw1 %s" % cmd_arg
(out, _) = run_cmd(cmd, log_all=True, simple=False)
- re_success = re.compile("LAPW1\s+END")
+ re_success = re.compile(r"LAPW1\s+END")
if not re_success.search(out):
raise EasyBuildError("Test '%s' in %s failed (pattern '%s' not found)?",
cmd, os.getcwd(), re_success.pattern)
@@ -413,7 +478,8 @@ class EB_WIEN2k(EasyBlock):
# unpack serial benchmark
serial_test_name = "test_case"
- extract_file(testdata_paths['%s.tar.gz' % serial_test_name], tmpdir)
+ srcdir = extract_file(testdata_paths['%s.tar.gz' % serial_test_name], tmpdir, change_into_dir=False)
+ change_dir(srcdir)
# run serial benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
@@ -421,14 +487,15 @@ class EB_WIEN2k(EasyBlock):
# unpack parallel benchmark (in serial benchmark dir)
parallel_test_name = "mpi-benchmark"
- extract_file(testdata_paths['%s.tar.gz' % parallel_test_name], tmpdir)
+ srcdir = extract_file(testdata_paths['%s.tar.gz' % parallel_test_name], tmpdir, change_into_dir=False)
+ change_dir(srcdir)
# run parallel benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-p")
os.chdir(cwd)
- rmtree2(tmpdir)
+ remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError("Failed to run WIEN2k benchmark tests: %s", err)
@@ -492,7 +559,7 @@ class EB_WIEN2k(EasyBlock):
# cleanup
try:
os.chdir(cwd)
- rmtree2(tmpdir)
+ remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError("Failed to clean up temporary test dir: %s", err)
--
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