Merge branch '2020' of...

Merge branch '2020' of https://gitlab.version.fz-juelich.de/hps-public/easybuild-repository into JAX

Custom_EasyBlocks/README.md

+# Custom EasyBlocks
+
+Overview of the custom EasyBlocks.
+
+
+## Quantum ESPRESSO
+
+- __*added by*__ s.achilles
+- __*needed because*__ Installation with GCC 9.x required a change in the EasyBlock.
+- __*difference compared to upstream*__ Upstream EasyBlocks 4.3.3 reflects this change as well as support for GCC 10.
+- __*can be removed*__ when we upgread EasyBlocks 4.3.3+

Custom_EasyBlocks/nvhpc.py

 ##
 # Copyright 2015-2019 Bart Oldeman
-# Copyright 2016-2020 Forschungszentrum Juelich
+# Copyright 2016-2021 Forschungszentrum Juelich
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
@@ -38,6 +38,7 @@ import fileinput
 import re
 import stat
 import sys
+import platform
 
 from easybuild.easyblocks.generic.packedbinary import PackedBinary
 from easybuild.framework.easyconfig import CUSTOM
@@ -90,12 +91,20 @@ class EB_NVHPC(PackedBinary):
         """Easyblock constructor, define custom class variables specific to NVHPC."""
         super(EB_NVHPC, self).__init__(*args, **kwargs)
 
-        # Potential improvement: get "Linux_x86_64" from easybuild.tools.systemtools' get_cpu_architecture()
-        self.nvhpc_install_subdir = os.path.join('Linux_x86_64', self.version)
+        # 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 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')  # only supported in next EasyBuild release
+
         default_cuda_version = self.cfg['default_cuda_version']
         if default_cuda_version is None:
             module_cuda_version_full = get_software_version('CUDA')

Custom_EasyBlocks/vmd.py

+##
+# Copyright 2009-2020 Ghent University
+# Copyright 2015-2020 Stanford University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for VMD, implemented as an easyblock
+
+@author: Stephane Thiell (Stanford University)
+@author: Kenneth Hoste (HPC-UGent)
+"""
+import os
+
+from distutils.version import LooseVersion
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import change_dir, copy_file, extract_file
+from easybuild.tools.run import run_cmd
+from easybuild.tools.modules import get_software_root, get_software_version
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+
+
+class EB_VMD(ConfigureMake):
+    """Easyblock for building and installing VMD"""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize VMD-specific variables."""
+        super(EB_VMD, self).__init__(*args, **kwargs)
+        # source tarballs contains a 'plugins' and 'vmd-<version>' directory
+        self.vmddir = os.path.join(self.builddir, '%s-%s' % (self.name.lower(), self.version))
+        self.surf_dir = os.path.join(self.vmddir, 'lib', 'surf')
+        self.stride_dir = os.path.join(self.vmddir, 'lib', 'stride')
+
+    def extract_step(self):
+        """Custom extract step for VMD."""
+        super(EB_VMD, self).extract_step()
+
+        if LooseVersion(self.version) >= LooseVersion("1.9.3"):
+            change_dir(self.surf_dir)
+            srcdir = extract_file('surf.tar.Z', os.getcwd(), change_into_dir=False)
+            change_dir(srcdir)
+
+    def configure_step(self):
+        """
+        Configure VMD for building.
+        """
+        # make sure required dependencies are available
+        deps = {}
+        for dep in ['FLTK', 'OpenGL', 'netCDF', 'Python', 'Tcl', 'Tk']:
+            deps[dep] = get_software_root(dep)
+            if deps[dep] is None:
+                raise EasyBuildError("Required dependency %s is missing", dep)
+
+        # optional dependencies
+        for dep in ['ACTC', 'CUDA', 'OptiX']:
+            deps[dep] = get_software_root(dep)
+
+        # specify Tcl/Tk locations & libraries
+        tclinc = os.path.join(deps['Tcl'], 'include')
+        tcllib = os.path.join(deps['Tcl'], 'lib')
+        env.setvar('TCL_INCLUDE_DIR', tclinc)
+        env.setvar('TCL_LIBRARY_DIR', tcllib)
+
+        env.setvar('TK_INCLUDE_DIR', os.path.join(deps['Tk'], 'include'))
+        env.setvar('TK_LIBRARY_DIR', os.path.join(deps['Tk'], 'lib'))
+
+        tclshortver = '.'.join(get_software_version('Tcl').split('.')[:2])
+        self.cfg.update('buildopts', 'TCLLDFLAGS="-ltcl%s"' % tclshortver)
+
+        # Netcdf locations
+        netcdfinc = os.path.join(deps['netCDF'], 'include')
+        netcdflib = os.path.join(deps['netCDF'], 'lib')
+
+        # Python locations
+        pymajver = get_software_version('Python').split('.')[0]
+        out, ec = run_cmd("python -c 'import sysconfig; print(sysconfig.get_path(\"include\"))'", simple=False)
+        if ec:
+            raise EasyBuildError("Failed to determine Python include path: %s", out)
+        else:
+            env.setvar('PYTHON_INCLUDE_DIR', out.strip())
+        pylibdir = det_pylibdir()
+        python_libdir = os.path.join(deps['Python'], os.path.dirname(pylibdir))
+        env.setvar('PYTHON_LIBRARY_DIR', python_libdir)
+        out, ec = run_cmd("python%s-config --libs" % pymajver, simple=False)
+        if ec:
+            raise EasyBuildError("Failed to determine Python library name: %s", out)
+        else:
+            env.setvar('PYTHON_LIBRARIES', out.strip())
+
+        # numpy include location, easiest way to determine it is via numpy.get_include()
+        out, ec = run_cmd("python -c 'import numpy; print(numpy.get_include())'", simple=False)
+        if ec:
+            raise EasyBuildError("Failed to determine numpy include directory: %s", out)
+        else:
+            env.setvar('NUMPY_INCLUDE_DIR', out.strip())
+
+        # compiler commands
+        self.cfg.update('buildopts', 'CC="%s"' % os.getenv('CC'))
+        self.cfg.update('buildopts', 'CCPP="%s"' % os.getenv('CXX'))
+
+        # plugins need to be built first (see http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html)
+        change_dir(os.path.join(self.builddir, 'plugins'))
+        cmd = ' '.join([
+            'make',
+            'LINUXAMD64',
+            "TCLINC='-I%s'" % tclinc,
+            "TCLLIB='-L%s'" % tcllib,
+            "TCLLDFLAGS='-ltcl%s'" % tclshortver,
+            "NETCDFINC='-I%s'" % netcdfinc,
+            "NETCDFLIB='-L%s'" % netcdflib,
+            self.cfg['buildopts'],
+        ])
+        run_cmd(cmd, log_all=True, simple=False)
+
+        # create plugins distribution
+        plugindir = os.path.join(self.vmddir, 'plugins')
+        env.setvar('PLUGINDIR', plugindir)
+        self.log.info("Generating VMD plugins in %s", plugindir)
+        run_cmd("make distrib %s" % self.cfg['buildopts'], log_all=True, simple=False)
+
+        # explicitely mention whether or not we're building with CUDA/OptiX support
+        if deps['CUDA']:
+            self.log.info("Building with CUDA %s support", get_software_version('CUDA'))
+            if deps['OptiX']:
+                self.log.info("Building with Nvidia OptiX %s support", get_software_version('OptiX'))
+            else:
+                self.log.warn("Not building with Nvidia OptiX support!")
+        else:
+            self.log.warn("Not building with CUDA nor OptiX support!")
+
+        # see http://www.ks.uiuc.edu/Research/vmd/doxygen/configure.html
+        # LINUXAMD64: Linux 64-bit
+        # LP64: build VMD as 64-bit binary
+        # IMD: enable support for Interactive Molecular Dynamics (e.g. to connect to NAMD for remote simulations)
+        # PTHREADS: enable support for POSIX threads
+        # COLVARS: enable support for collective variables (related to NAMD/LAMMPS)
+        # NOSILENT: verbose build command
+        # FLTK: enable the standard FLTK GUI
+        # TK: enable TK to support extension GUI elements
+        # OPENGL: enable OpenGL
+        self.cfg.update(
+            'configopts', "LINUXAMD64 LP64 IMD PTHREADS COLVARS NOSILENT FLTK TK OPENGL", allow_duplicate=False)
+
+        # add additional configopts based on available dependencies
+        for key in deps:
+            if deps[key]:
+                if key == 'Mesa' or key == 'OpenGL':
+                    self.cfg.update('configopts', "OPENGL MESA", allow_duplicate=False)
+                elif key == 'OptiX':
+                    self.cfg.update('configopts', "LIBOPTIX", allow_duplicate=False)
+                elif key == 'Python':
+                    self.cfg.update('configopts', "PYTHON NUMPY", allow_duplicate=False)
+                else:
+                    self.cfg.update('configopts', key.upper(), allow_duplicate=False)
+
+        # configure for building with Intel compilers specifically
+        if self.toolchain.comp_family() == toolchain.INTELCOMP:
+            self.cfg.update('configopts', 'ICC', allow_duplicate=False)
+
+        # specify install location using environment variables
+        env.setvar('VMDINSTALLBINDIR', os.path.join(self.installdir, 'bin'))
+        env.setvar('VMDINSTALLLIBRARYDIR', os.path.join(self.installdir, 'lib'))
+
+        # configure in vmd-<version> directory
+        change_dir(self.vmddir)
+        run_cmd("%s ./configure %s" % (self.cfg['preconfigopts'], self.cfg['configopts']))
+
+        # change to 'src' subdirectory, ready for building
+        change_dir(os.path.join(self.vmddir, 'src'))
+
+    def build_step(self):
+        """Custom build step for VMD."""
+        super(EB_VMD, self).build_step()
+
+        self.have_stride = False
+        # Build Surf, which is part of VMD as of VMD version 1.9.3
+        if LooseVersion(self.version) >= LooseVersion("1.9.3"):
+            change_dir(self.surf_dir)
+            surf_build_cmd = 'make CC="%s" OPT="%s"' % (os.environ['CC'], os.environ['CFLAGS'])
+            run_cmd(surf_build_cmd)
+            # Build Stride if it was downloaded
+            if os.path.exists(os.path.join(self.stride_dir, 'Makefile')):
+                change_dir(self.stride_dir)
+                self.have_stride = True
+                stride_build_cmd = 'make CC="%s" CFLAGS="%s"' % (os.environ['CC'], os.environ['CFLAGS'])
+                run_cmd(stride_build_cmd)
+            else:
+                self.log.info("Stride has not been downloaded and/or unpacked.")
+
+    def install_step(self):
+        """Custom build step for VMD."""
+
+        # Install must also be done in 'src' subdir
+        change_dir(os.path.join(self.vmddir, 'src'))
+        super(EB_VMD, self).install_step()
+
+        if LooseVersion(self.version) >= LooseVersion("1.9.3"):
+            surf_bin = os.path.join(self.surf_dir, 'surf')
+            copy_file(surf_bin, os.path.join(self.installdir, 'lib', 'surf_LINUXAMD64'))
+            if self.have_stride:
+                stride_bin = os.path.join(self.stride_dir, 'stride')
+                copy_file(stride_bin, os.path.join(self.installdir, 'lib', 'stride_LINUXAMD64'))
+
+    def sanity_check_step(self):
+        """Custom sanity check for VMD."""
+        custom_paths = {
+            'files': ['bin/vmd'],
+            'dirs': ['lib'],
+        }
+        super(EB_VMD, self).sanity_check_step(custom_paths=custom_paths)

Golden_Repo/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb

+easyblock = 'MakeCp'
+
+name = 'ACTC'
+version = '1.1'
+
+homepage = 'https://sourceforge.net/projects/actc'
+description = "ACTC converts independent triangles into triangle strips or fans."
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d']
+
+builddependencies = [('binutils', '2.34')]
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS"'
+
+files_to_copy = [
+    (['tcsample', 'tctest', 'tctest2'], 'bin'),
+    (['tc.h'], 'include/ac'),
+    (['libactc.a'], 'lib'),
+    'COPYRIGHT', 'manual.html', 'prims.gif', 'README',
+]
+
+sanity_check_paths = {
+    'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a',
+              'COPYRIGHT', 'manual.html', 'prims.gif', 'README'],
+    'dirs': [],
+}
+
+modextrapaths = {'CPATH': 'include/ac'}
+
+moduleclass = 'lib'

Golden_Repo/a/AMBER/AMBER-20-gpsmpi-2020.eb

+easyblock = 'CMakeMake'
+
+name = 'AMBER'
+version = '20'
+
+homepage = 'http://ambermd.org'
+description = """
+AMBER: 'Assisted Model Building with Energy Refinement' is a set of molecular
+mechanics force fields and a package of molecular simulation programs.
+
+Citation:
+D.A. Case, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti,
+T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu,
+M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov,
+K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T.S. Lee, S. LeGrand,
+P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K.M. Merz, Y. Miao,
+O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F.Pan, S. Pantano,
+R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen,
+C. Simmerling, N.R.Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang,
+L. Wilson, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York
+and P.A. Kollman (2020),
+AMBER 2020, University of California, San Francisco.
+"""
+
+site_contacts = 'Sandipan Mohanty <s.mohanty@fz-juelich.de>'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('CMake', '3.18.0'),
+    ('binutils', '2.34',),
+]
+dependencies = [
+    ('CMake', '3.18.0'),
+    ('FFTW', '3.3.8'),
+    ('Python', '3.8.5'),
+    ('flex', '2.6.4', '', True),
+]
+
+sources = [
+    'AmberTools20.tar.bz2',
+    'Amber20.tar.bz2',
+]
+
+separate_build_dir = True
+local_build_mpi_parts = "TRUE"
+local_build_cuda_parts = "TRUE"
+
+preconfigopts = "CC=gcc && CXX=g++ && COMPILER=GNU "
+preconfigopts += " && cd %(builddir)s/amber20_src && "
+preconfigopts += " ./update_amber --update && cd ../easybuild_obj && "
+
+configopts = "-DCOMPILER=GNU -DCHECK_UPDATES=OFF -DAPPLY_UPDATES=OFF "
+configopts += " -DINSTALL_TESTS=TRUE  -DMPI=%s " % local_build_mpi_parts
+configopts += " -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE "
+configopts += " -DCUDA=%s " % local_build_cuda_parts
+
+modextravars = {
+    'AMBERHOME': '%(installdir)s/',
+}
+
+modluafooter = '''
+add_property("arch","gpu")
+'''
+
+group = "amber"
+
+modloadmsg = '''
+The access to this software is restricted to members of the group "amber".
+The JSC has a site licence for academic users. If you would like to get
+access please see:
+"http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/Chemistry/AmberConfirmationOfLicence.html"
+'''
+
+moduleclass = 'bio'

Golden_Repo/b/Boost.Python/Boost.Python-1.74.0-GCCcore-9.3.0-nompi.eb

+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.74.0'
+versionsuffix = '-nompi'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/']
+sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
+patches = ['Boost-1.71.0_fix-Python3.patch']
+
+dependencies = [
+    ('Boost', version, versionsuffix),
+    ('Python', '3.8.5')
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'

Golden_Repo/b/Boost/Boost-1.74.0-GCCcore-9.3.0-nompi.eb

+name = 'Boost'
+version = '1.74.0'
+versionsuffix = '-nompi'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/']
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.11'),
+    ('XZ', '5.2.5'),
+    ('ICU', '67.1'),
+]
+
+configopts = '--without-libraries=python'
+
+# do not build boost_mpi
+boost_mpi = False
+
+moduleclass = 'devel'

Golden_Repo/c/CMake/CMake-3.18.0.eb

+easyblock = 'ConfigureMake'
+
+name = 'CMake'
+version = '3.18.0'
+
+homepage = 'http://www.cmake.org'
+description = """CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software.
+"""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = SYSTEM
+
+source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES'
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('ncurses', '6.2'),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it's nice to have an up to date openssl for security reasons
+    # ('OpenSSL', '1.0.1p'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

Golden_Repo/c/CVXOPT/CVXOPT-1.2.1-fix-setup-py.patch

+# Patches the setup.py to use EB settings for BLAS/LAPACK, FFTW, etc
+# original by wpoely86@gmail.com, ported to v1.2.1 by Kenneth Hoste (HPC-UGent)
+--- cvxopt-1.2.1/setup.py.orig	2018-08-30 19:54:12.000000000 +0200
++++ cvxopt-1.2.1/setup.py	2018-10-02 16:28:57.252340779 +0200
+@@ -91,9 +91,11 @@
+ LAPACK_LIB = os.environ.get("CVXOPT_LAPACK_LIB",LAPACK_LIB)
+ BLAS_LIB_DIR = os.environ.get("CVXOPT_BLAS_LIB_DIR",BLAS_LIB_DIR)
+ BLAS_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_BLAS_EXTRA_LINK_ARGS",BLAS_EXTRA_LINK_ARGS)
++FFTW_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_FFTW_EXTRA_LINK_ARGS",'')
+ if type(BLAS_LIB) is str: BLAS_LIB = BLAS_LIB.strip().split(';')
+ if type(LAPACK_LIB) is str: LAPACK_LIB = LAPACK_LIB.strip().split(';')
+-if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(';')
++if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(' ')
++if type(FFTW_EXTRA_LINK_ARGS) is str: FFTW_EXTRA_LINK_ARGS = FFTW_EXTRA_LINK_ARGS.strip().split(' ')
+ BUILD_GSL = int(os.environ.get("CVXOPT_BUILD_GSL",BUILD_GSL))
+ GSL_LIB_DIR = os.environ.get("CVXOPT_GSL_LIB_DIR",GSL_LIB_DIR)
+ GSL_INC_DIR = os.environ.get("CVXOPT_GSL_INC_DIR",GSL_INC_DIR)
+@@ -126,7 +128,7 @@
+ # optional modules
+ 
+ if BUILD_GSL:
+-    gsl = Extension('gsl', libraries = M_LIB + ['gsl'] + BLAS_LIB,
++    gsl = Extension('gsl', libraries = M_LIB + ['gsl'],
+         include_dirs = [ GSL_INC_DIR ],
+         library_dirs = [ GSL_LIB_DIR, BLAS_LIB_DIR ],
+         define_macros = GSL_MACROS,
+@@ -135,11 +137,11 @@
+     extmods += [gsl];
+ 
+ if BUILD_FFTW:
+-    fftw = Extension('fftw', libraries = ['fftw3'] + BLAS_LIB,
++    fftw = Extension('fftw',
+         include_dirs = [ FFTW_INC_DIR ],
+         library_dirs = [ FFTW_LIB_DIR, BLAS_LIB_DIR ],
+         define_macros = FFTW_MACROS,
+-        extra_link_args = BLAS_EXTRA_LINK_ARGS,
++        extra_link_args = BLAS_EXTRA_LINK_ARGS + FFTW_EXTRA_LINK_ARGS,
+         sources = ['src/C/fftw.c'] )
+     extmods += [fftw];
+ 
+@@ -151,7 +153,7 @@
+     extmods += [glpk];
+ 
+ if BUILD_DSDP:
+-    dsdp = Extension('dsdp', libraries = ['dsdp'] + LAPACK_LIB + BLAS_LIB,
++    dsdp = Extension('dsdp', libraries = ['dsdp'],
+         include_dirs = [ DSDP_INC_DIR ],
+         library_dirs = [ DSDP_LIB_DIR, BLAS_LIB_DIR ],
+         extra_link_args = BLAS_EXTRA_LINK_ARGS,
+@@ -160,19 +162,19 @@
+ 
+ # Required modules
+ 
+-base = Extension('base', libraries = M_LIB + LAPACK_LIB + BLAS_LIB,
++base = Extension('base',
+     library_dirs = [ BLAS_LIB_DIR ],
+     define_macros = MACROS,
+     extra_link_args = BLAS_EXTRA_LINK_ARGS,
+     sources = ['src/C/base.c','src/C/dense.c','src/C/sparse.c'])
+ 
+-blas = Extension('blas', libraries = BLAS_LIB,
++blas = Extension('blas',
+     library_dirs = [ BLAS_LIB_DIR ],
+     define_macros = MACROS,
+     extra_link_args = BLAS_EXTRA_LINK_ARGS,
+     sources = ['src/C/blas.c'] )
+ 
+-lapack = Extension('lapack', libraries = LAPACK_LIB + BLAS_LIB,
++lapack = Extension('lapack',
+     library_dirs = [ BLAS_LIB_DIR ],
+     define_macros = MACROS,
+     extra_link_args = BLAS_EXTRA_LINK_ARGS,
+@@ -180,9 +182,10 @@
+ 
+ if not SUITESPARSE_SRC_DIR:
+     umfpack = Extension('umfpack',
+-        libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB,
++        libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + RT_LIB,
+         include_dirs = [SUITESPARSE_INC_DIR],
+         library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR],
++        extra_link_args = BLAS_EXTRA_LINK_ARGS,
+         sources = ['src/C/umfpack.c'])
+ else:
+     umfpack = Extension('umfpack',
+@@ -193,7 +196,6 @@
+             SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ],
+         library_dirs = [ BLAS_LIB_DIR ],
+         define_macros = MACROS + [('NTIMER', '1'), ('NCHOLMOD', '1')],
+-        libraries = LAPACK_LIB + BLAS_LIB,
+         extra_compile_args = UMFPACK_EXTRA_COMPILE_ARGS,
+         extra_link_args = BLAS_EXTRA_LINK_ARGS,
+         sources = [ 'src/C/umfpack.c',
+@@ -206,14 +208,13 @@
+ 
+ if not SUITESPARSE_SRC_DIR:
+     cholmod = Extension('cholmod',
+-        libraries = ['cholmod','colamd','amd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB,
++        libraries = ['cholmod','colamd','amd','suitesparseconfig'] + RT_LIB,
+         include_dirs = [SUITESPARSE_INC_DIR],
+         library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR],
+         sources = [ 'src/C/cholmod.c' ])
+ else:
+     cholmod = Extension('cholmod',
+         library_dirs = [ BLAS_LIB_DIR ],
+-        libraries = LAPACK_LIB + BLAS_LIB,
+         include_dirs = [ SUITESPARSE_SRC_DIR + '/CHOLMOD/Include',
+             SUITESPARSE_SRC_DIR + '/COLAMD',
+             SUITESPARSE_SRC_DIR + '/AMD/Include',
+@@ -235,17 +236,18 @@
+         libraries = ['amd','suitesparseconfig'] + RT_LIB,
+         include_dirs = [SUITESPARSE_INC_DIR],
+         library_dirs = [SUITESPARSE_LIB_DIR],
++        extra_link_args = BLAS_EXTRA_LINK_ARGS,
+         sources = ['src/C/amd.c'])
+ else:
+     amd = Extension('amd',
+         include_dirs = [SUITESPARSE_SRC_DIR + '/AMD/Include',
+             SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ],
+         define_macros = MACROS + [('NTIMER', '1')],
++        extra_link_args = BLAS_EXTRA_LINK_ARGS,
+         sources = [ 'src/C/amd.c', SUITESPARSE_SRC_DIR + '/SuiteSparse_config/SuiteSparse_config.c'] +
+         glob(SUITESPARSE_SRC_DIR + '/AMD/Source/*.c') )
+ 
+ misc_solvers = Extension('misc_solvers',
+-    libraries = LAPACK_LIB + BLAS_LIB,
+     library_dirs = [ BLAS_LIB_DIR ],
+     define_macros = MACROS,
+     extra_link_args = BLAS_EXTRA_LINK_ARGS,

Golden_Repo/c/CVXOPT/CVXOPT-1.2.5-gpsmkl-2020-Python-3.8.5.eb

+easyblock = 'PythonPackage'
+
+name = 'CVXOPT'
+version = '1.2.5'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://cvxopt.org'
+description = """CVXOPT is a free software package for convex optimization based on the Python programming language.
+ Its main purpose is to make the development of software for convex optimization applications straightforward by
+ building on Python's extensive standard library and on the strengths of Python as a high-level programming language.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gpsmkl', 'version': '2020'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['CVXOPT-1.2.1-fix-setup-py.patch']
+checksums = [
+    '94ec8c36bd6628a11de9014346692daeeef99b3b7bae28cef30c7490bbcb2d72',  # cvxopt-1.2.5.tar.gz
+    '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d',  # CVXOPT-1.2.1-fix-setup-py.patch
+]
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SuiteSparse', '5.7.1', '-CUDA'),
+    ('GSL', '2.6'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" '
+preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE'
+
+installopts = ' --no-binary cvxopt'
+
+sanity_check_commands = ['nosetests']
+
+moduleclass = 'math'

Golden_Repo/c/Cirq/Cirq-0.9.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb

+easyblock = 'PythonBundle'
+
+name = 'Cirq'
+version = '0.9.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/quantumlib/cirq'
+description = """A python framework for creating, editing,
+and invoking Noisy Intermediate Scale Quantum (NISQ) circuits."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SciPy-Stack', '2020', versionsuffix),
+    ('protobuf', '3.12.4'),
+    ('texlive', '20200406'),
+]
+
+local_common_opts = {
+    'req_py_majver': '3',
+    'req_py_minver': '0'
+}
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'use_pip_for_deps': False,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('cachetools', '4.1.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20')]),
+    ])),
+    ('pyasn1-modules', '0.2.8', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e')]),
+    ])),
+    ('rsa', '4.6', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa')]),
+    ])),
+    ('google-auth', '1.23.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '5176db85f1e7e837a646cd9cede72c3c404ccf2e3373d9ee14b2db88febad440')]),
+        ('modulename', 'google.auth'),
+    ])),
+    ('googleapis-common-protos', '1.52.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '560716c807117394da12cecb0a54da5a451b5cf9866f1d37e9a5e2329a665351')]),
+        ('modulename', 'googleapiclient')
+    ])),
+    ('grpcio', '1.33.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '21265511880056d19ce4f809ce3fbe2a3fa98ec1fc7167dbdf30a80d3276202e')]),
+        ('modulename', 'grpc')
+    ])),
+    ('google-api-core', '1.23.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '1bb3c485c38eacded8d685b1759968f6cf47dd9432922d34edb90359eaa391e2')]),
+        ('modulename', 'google'),
+    ])),
+    ('httplib2', '0.18.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '8af66c1c52c7ffe1aa5dc4bcd7c769885254b0756e6e69f953c7f0ab49a70ba3')]),
+    ])),
+    ('uritemplate', '3.0.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '5af8ad10cec94f215e3f48112de2022e1d5a37ed427fbd88652fa908f2ab7cae')]),
+    ])),
+    ('google-auth-httplib2', '0.0.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '8d092cc60fb16517b12057ec0bba9185a96e3b7169d86ae12eae98e645b7bc39')]),
+    ])),
+    ('google-api-python-client', '1.12.5', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '1892cd490d164e5ec2f2168dc3b4fa0af68f36ca15a88b91bca1826b3d4f2829')]),
+        ('modulename', 'googleapiclient'),
+    ])),
+    ('typing_extensions', '3.7.4.3', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c')]),
+    ])),
+    ('sortedcontainers', '2.2.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba')]),
+    ])),
+    ('networkx', '2.5', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602')]),
+    ])),
+    ('freezegun', '0.3.15', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'e2062f2c7f95cc276a834c22f1a17179467176b624cc6f936e8bc3be5535ad1b')]),
+    ])),
+    ('protobuf', '3.12.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'c99e5aea75b6f2b29c8d8da5bdc5f5ed8d9a5b4f15115c8316a3f0a850f94656')]),
+        ('modulename', 'google.protobuf')
+    ])),
+    ('cirq', version, dict(list(local_common_opts.items()) + [
+        ('source_tmpl', 'cirq-%(version)s-py3-none-any.whl'),
+        ('checksums', [('sha256', 'd900b861f2132a673b511b22ec80955cedec34c1bfa95d8f39cdc1eab5309242')]),
+        ('use_pip', True),
+        ('unpack_sources', False),
+    ])),
+]
+
+moduleclass = 'quantum'

Golden_Repo/d/DWave/DWave-3.2.0-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb

+easyblock = 'PythonBundle'
+
+name = 'DWave'
+version = '3.2.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://docs.ocean.dwavesys.com'
+description = """Ocean software is a suite of tools D-Wave Systems for solving hard problems with quantum computers."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SciPy-Stack', '2020', versionsuffix),
+    ('Boost.Python', '1.74.0', '-nompi'),
+    ('protobuf', '3.13.0'),
+]
+
+local_common_opts = {
+    'req_py_majver': '3',
+    'req_py_minver': '0'
+}
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+    'use_pip_for_deps': False,
+}
+
+exts_list = [
+    ('plucky', '0.4.3', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '5bc75d43ae6b40f1b7ba42000b37e4934fa6bd2d6a6cd4e47461f803a404c194')]),
+    ])),
+    ('homebase', '1.0.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '9ee008df4298b420852d815e6df488822229c4bd8d571bcd0a454e04232c635e')]),
+    ])),
+    ('dwave-cloud-client', '0.8.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '5472aa523311380bdb5b4e659d127d4fc7acdef73e03234df23890972be2fca3')]),
+        ('modulename', 'dwave.cloud'),
+    ])),
+    ('dwave_networkx', '0.8.8', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '9d6bb1f93d89511aeaa191319da9970e48134a4dccecff59c972e8f1f3107387')]),
+        ('modulename', 'dwave_networkx'),
+    ])),
+    ('dwave-system', '1.3.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'ec1283592211016b30587c67837b23898a74b809de6d715447ff2822798b26f1')]),
+        ('modulename', 'dwave.system'),
+    ])),
+    ('dwave-qbsolv', '0.3.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'aca74f909748cd02d3e59647ae6c81585dd75afcf53a19fa116580c7c7873782')]),
+        ('modulename', 'dwave_qbsolv'),
+    ])),
+    ('dwave-hybrid', '0.6.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'd8b195dabe9e630c31bb9e3362d1cb6d3fab933b94d175719cd3771e346d5934')]),
+        ('modulename', 'hybrid'),
+    ])),
+    ('dwave-neal', '0.5.7', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '86da2141f81ade1e69d595a9840222a45c47b19577c037ef3d4988b5463c26f8')]),
+        ('modulename', 'neal'),
+    ])),
+    ('dimod', '0.9.13', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'a9ab210a2737199b824191089e71fa669b2760b168d0f7ad5aaa7fddcada933f')]),
+    ])),
+    ('dwavebinarycsp', '0.1.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'bf2000c2738df2b3924470f080e73c42e7246b5137fdedc7a2627d5e08479bdf')]),
+    ])),
+    ('fasteners', '0.16', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'c995d8c26b017c5d6a6de9ad29a0f9cdd57de61ae1113d28fac26622b06a0933')]),
+    ])),
+    ('minorminer', '0.2.5', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '3a521099ec64c99295ae8205b08da29c06aad81d3be74fb27a58d22e220a2a33')]),
+    ])),
+    ('penaltymodel', '0.16.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'e2d9e94154a675b33db59dadb9856ee4c8bc1aee1647c664df1b17bc53b04f2a')]),
+    ])),
+    ('penaltymodel-cache', '0.4.3', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '93b76ba83e9b39bca705c341b5e925f4ff5841c20f3e5fac962304656f1ec66e')]),
+        ('modulename', 'penaltymodel.cache')
+    ])),
+    ('penaltymodel-lp', '0.1.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '044ec3a12f78003b044c05b66e9597131bcbb47d775db03dba2d1dc45d2f0efb')]),
+        ('modulename', 'penaltymodel.lp')
+    ])),
+    ('protobuf', '3.13.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '6a82e0c8bb2bf58f606040cc5814e07715b2094caeba281e2e7d0b0e2e397db5')]),
+        ('modulename', 'google.protobuf')
+    ])),
+    ('ortools', '8.0.8283', dict(list(local_common_opts.items()) + [
+        ('source_tmpl', 'ortools-8.0.8283-cp38-cp38-manylinux1_x86_64.whl'),
+        ('checksums', [('sha256', '31020d0b46c8e4ff7d920803c3bb5cbfc5630d319b9b46f70de8d18f9456e9c9')]),
+        ('unpack_sources', False),
+    ])),
+    ('penaltymodel-mip', '0.2.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'c3471a8f10107b163ab0035125fe861a3c55808e7656db9ed524451667ff1e38')]),
+        ('modulename', 'penaltymodel.mip')
+    ])),
+    ('wrapt', '1.12.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7')]),
+    ])),
+    ('Deprecated', '1.2.10', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74')]),
+    ])),
+    ('pyqubo', '1.0.7', dict(list(local_common_opts.items()) + [
+        ('source_tmpl', 'pyqubo-1.0.7-cp38-cp38-manylinux1_x86_64.whl'),
+        ('checksums', [('sha256', '79dfd9a7f2f75a216838e357959b321d55ced7cdf4559037a4704d2f2927f6ba')]),
+        ('unpack_sources', False),
+    ])),
+    ('importlib_resources', '1.0.2', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'd3279fd0f6f847cced9f7acc19bd3e5df54d34f93a2e7bb5f238f81545787078')]),
+    ])),
+    ('dwave-inspector', '0.2.4', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'b596e3cc0055e373e0955b402e1ee43998e0ceb2968e09eeb8a194c67b080e38')]),
+        ('modulename', 'dwave.inspector'),
+    ])),
+    ('dwave-tabu', '0.3.1', dict(list(local_common_opts.items()) + [
+        ('source_tmpl', 'dwave_tabu-0.3.1-cp38-cp38-manylinux1_x86_64.whl'),
+        ('checksums', [('sha256', '6a57c6e0c6d6dce912d36c2c183a2a841c1f2830fab7434ddb912e5200d7dc2f')]),
+        ('unpack_sources', False),
+        ('modulename', 'tabu'),
+    ])),
+    ('dwave-greedy', '0.1.2', dict(list(local_common_opts.items()) + [
+        ('source_tmpl', 'dwave_greedy-0.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+        ('checksums', [('sha256', '88cdb3897159880d02b6e5880285b2b5a5295c3a725ce7c990ce4e72c21724ac')]),
+        ('unpack_sources', False),
+        ('modulename', 'greedy'),
+    ])),
+    ('dwave-ocean-sdk', version, dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'a8a5e0acbd7483f62f65beb6f2fdb397d5370e20df949434521cae0635d954e9')]),
+        ('skipsteps', ['sanitycheck']),
+        ('modulename', 'dwave.system'),  # just a fake for sanity-check
+    ])),
+]
+
+moduleclass = 'quantum'

Golden_Repo/d/darshan-runtime/darshan-runtime-3.2.1-gpsmpi-2020.eb

@@ -44,7 +44,8 @@ sources = ['ftp://ftp.mcs.anl.gov/pub/darshan/releases/darshan-%s.tar.gz' % vers
 
 local_subpath = 'darshan-runtime'
 preconfigopts = 'cd %s;' % local_subpath
-configopts = '--with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_PATH --with-jobid-env=SLURM_JOBID CC=mpicc'
+configopts = '--with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_PATH '
+configopts += ' --with-jobid-env=SLURM_JOBID CC=mpicc --enable-hdf5-mod=$EBROOTHDF5'
 
 prebuildopts = 'cd %s;' % local_subpath
 
@@ -55,4 +56,9 @@ sanity_check_paths = {
     'dirs': []
 }
 
+dependencies = [
+    ("HDF5", "1.10.6"),
+]
+
+
 moduleclass = 'lib'

Golden_Repo/d/darshan-util/darshan-util-3.2.1-gpsmpi-2020.eb

@@ -47,6 +47,8 @@ prebuildopts = 'cd %s;' % local_subpath
 
 preinstallopts = 'cd %s;' % local_subpath
 
+configopts = '--enable-hdf5-mod=$EBROOTHDF5'
+
 sanity_check_paths = {
     'files': ["bin/darshan-job-summary.pl"],
     'dirs': []
@@ -55,6 +57,7 @@ sanity_check_paths = {
 dependencies = [
     ("gnuplot", "5.2.8"),
     ("Perl", "5.32.0"),
+    ("HDF5", "1.10.6"),
 ]
 
 moduleclass = 'lib'

Golden_Repo/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb

@@ -17,6 +17,7 @@ sources = [SOURCELOWER_TGZ]
 builddependencies = [
     ('binutils', '2.34'),
     ('CMake', '3.18.0'),
+    ('texinfo', '6.7'),
 ]
 
 dependencies = [

Golden_Repo/g/GROMACS/GROMACS-2020.4-plumed-gpsmkl-2020.eb

+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC,
+#                                 Ghent University / The Francis Crick Institute
+# Authors::
+# * Wiktor Jurkowski <wiktor.jurkowski@gmail.com>
+# * Fotis Georgatos <fotis@cern.ch>
+# * George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# * Kenneth Hoste <kenneth.hoste@ugent.be>
+# * Adam Huffman <adam.huffman@crick.ac.uk>
+# License::   MIT/GPL
+##
+
+name = 'GROMACS'
+version = '2020.4'
+versionsuffix = '-plumed'
+
+homepage = 'http://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations
+of motion for systems with hundreds to millions of particles. It is primarily designed for
+biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions,
+but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually
+dominate simulations) many groups are also using it for research on non-biological systems, e.g.
+polymers.
+
+Documentation
+=============
+Use `gmx` to execute GROMACS commands on a single node, for example, to prepare your run. Use
+`gmx_mpi mdrun` in your job scripts with `srun`. The user documentation of GROMACS can be found at
+http://manual.gromacs.org/documentation/current/user-guide/index.html.
+
+"""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = {'name': 'gpsmkl', 'version': '2020'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+    ('CMake', '3.18.0'),
+    ('libxml2', '2.9.10')
+]
+
+
+dependencies = [
+    ('PLUMED', '2.7.0'),
+    ('CUDA', '11.0', '', True),
+]
+
+configopts = '-DCMAKE_PREFIX_PATH=$EBROOTHWLOC -DMPIEXEC_MAX_NUMPROCS="24" '
+configopts += '-DMKL_LIBRARIES="${MKLROOT}/lib/intel64/libmkl_intel_ilp64.so;'
+configopts += '${MKLROOT}/lib/intel64/libmkl_sequential.so;${MKLROOT}/lib/intel64/libmkl_core.so" '
+configopts += '-DGMX_CUDA_TARGET_SM="60;70;80" '
+
+mpiexec = 'srun'
+mpiexec_numproc_flag = '"--gres=gpu:1 -n"'
+mpi_numprocs = '24'
+
+runtest = False
+
+modluafooter = '''
+add_property("arch","gpu")
+'''
+
+moduleclass = 'bio'

Golden_Repo/h/HDF5/HDF5-1.10.6-ipsmpi-2020-mt.eb

+name = 'HDF5'
+version = '1.10.6'
+
+homepage = 'http://www.hdfgroup.org/HDF5/'
+description = """HDF5 is a unique technology suite that makes possible the management of
+ extremely large and complex data collections.
+"""
+
+site_contacts = 's.luehrs@fz-juelich.de'
+
+toolchain = {'name': 'ipsmpi', 'version': '2020-mt'}
+toolchainopts = {'optarch': True, 'pic': True, 'usempi': True}
+
+source_urls = [
+    'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major)s.%(version_minor)s/hdf5-%(version)s/src'
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'

Golden_Repo/h/h5py/h5py-2.10.0-ipsmpi-2020-mt-Python-3.8.5.eb

+easyblock = "PythonPackage"
+
+name = 'h5py'
+version = '2.10.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.h5py.org/'
+description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
+ version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
+ amounts of data.
+"""
+
+site_contacts = 's.luehrs@fz-juelich.de'
+
+toolchain = {'name': 'ipsmpi', 'version': '2020-mt'}
+toolchainopts = {'usempi': True}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+req_py_majver = 3
+req_py_minver = 0
+
+# to really use mpi enabled hdf5 we now seem to need a configure step
+prebuildopts = 'export LDSHARED="$CC -shared" &&  python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
+
+builddependencies = [
+    ('pkgconfig', '1.5.1', versionsuffix),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),  # numpy required
+    ('mpi4py', '3.0.3', versionsuffix),  # required for MPI support
+    ('HDF5', '1.10.6'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
+}
+
+moduleclass = 'data'

Golden_Repo/hdfml_overlay/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5-PyTorch-1.7.0.eb

+easyblock = 'PythonBundle'
+
+name = 'PyTorch-Geometric'
+version = '1.6.3'
+local_pytorch_ver = '1.7.0'
+versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver
+
+homepage = 'https://github.com/rusty1s/pytorch_geometric'
+description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch."
+
+site_contacts = 't.breuer@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+local_pysuff = '-Python-%(pyver)s'
+dependencies = [
+    ('Python', '3.8.5'),
+    ('PyTorch', local_pytorch_ver, local_pysuff),
+    ('numba', '0.51.1', local_pysuff),
+    ('h5py', '2.10.0', '-serial%s' % local_pysuff),
+    ('scikit', '2020', local_pysuff),
+    ('torchvision', '0.8.1', local_pysuff),
+    ('trimesh', '3.8.11', local_pysuff),
+    ('METIS', '5.1.0', '-IDX64'),
+]
+
+use_pip = True
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+exts_download_dep_fail = True
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('gdist', '1.0.3', {
+        'source_urls': ['https://pypi.python.org/packages/source/g/gdist'],
+        'modulename': 'gdist',
+    }),
+    ('rdflib', '5.0.0', {
+        'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'],
+        'modulename': 'rdflib',
+    }),
+    ('googledrivedownloader', '0.4', {
+        'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'],
+        'modulename': 'google_drive_downloader',
+    }),
+    ('plyfile', '0.7.2', {
+        'checksums': ['59a25845d00a51098e6c9147c3c96ce89ad97395e256a4fabb4aed7cf7db5541'],
+    }),
+    ('torch_scatter', '2.0.5', {
+        'patches': ['torch_scatter-2.0.5-sm_70.patch'],
+        'prebuildopts': 'FORCE_CUDA=1',
+        'preinstallopts': 'FORCE_CUDA=1',
+        'source_tmpl': '2.0.5.tar.gz',
+        'source_urls': ['https://github.com/rusty1s/pytorch_scatter/archive/'],
+    }),
+    ('torch_sparse', '0.6.8', {
+        'patches': ['torch_sparse-0.6.8-sm_70.patch'],
+        'prebuildopts': 'FORCE_CUDA=1 WITH_METIS=1',
+        'preinstallopts': 'FORCE_CUDA=1 WITH_METIS=1',
+        'source_tmpl': '0.6.8.tar.gz',
+        'source_urls': ['https://github.com/rusty1s/pytorch_sparse/archive/'],
+    }),
+    ('torch_cluster', '1.5.8', {
+        'patches': ['torch_cluster-1.5.8-sm_70.patch'],
+        'prebuildopts': 'FORCE_CUDA=1',
+        'preinstallopts': 'FORCE_CUDA=1',
+        'source_tmpl': '1.5.8.tar.gz',
+        'source_urls': ['https://github.com/rusty1s/pytorch_cluster/archive/'],
+    }),
+    ('torch_spline_conv', '1.2.0', {
+        'patches': ['torch_spline_conv-1.2.0-sm_70.patch'],
+        'prebuildopts': 'FORCE_CUDA=1',
+        'preinstallopts': 'FORCE_CUDA=1',
+        'source_tmpl': '1.2.0.tar.gz',
+        'source_urls': ['https://github.com/rusty1s/pytorch_spline_conv/archive'],
+    }),
+    ('ase', '3.21.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/a/ase'],
+        'modulename': 'ase',
+    }),
+    ('python-louvain', '0.15', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/python-louvain'],
+        'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'],
+        'modulename': 'community',
+    }),
+    ('tqdm', '4.56.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'],
+        'modulename': 'tqdm',
+    }),
+    ('torch_geometric', version, {
+        'checksums': ['347f693bebcc8a621eda4867dafab91c04db5f596d7ed7ecb89b242f8ab5c6a1'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'devel'

Golden_Repo/hdfml_overlay/p/PyTorch-Geometric/torch_cluster-1.5.8-sm_70.patch

+--- setup_orig.py	2021-01-20 10:10:11.609352000 +0100
++++ setup.py	2021-01-20 10:10:37.525550350 +0100
+@@ -39,7 +39,7 @@
+         define_macros += [('WITH_CUDA', None)]
+         nvcc_flags = os.getenv('NVCC_FLAGS', '')
+         nvcc_flags = [] if nvcc_flags == '' else nvcc_flags.split(' ')
+-        nvcc_flags += ['-arch=sm_35', '--expt-relaxed-constexpr']
++        nvcc_flags += ['-gencode=arch=compute_70,code=sm_70', '--expt-relaxed-constexpr']
+         extra_compile_args['nvcc'] = nvcc_flags
+ 
+     extensions_dir = osp.join(osp.dirname(osp.abspath(__file__)), 'csrc')