Merge branch '2020' of...

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

Custom_Hooks/eb_hooks.py

+import grp
+import os
+
+from easybuild.tools.run import run_cmd
+from easybuild.tools.config import build_option
+from easybuild.tools.config import install_path
+from easybuild.tools.build_log import EasyBuildError, print_warning
+from easybuild.tools.toolchain.toolchain import SYSTEM_TOOLCHAIN_NAME
+from easybuild.toolchains.compiler.systemcompiler import TC_CONSTANT_SYSTEM
+
+SUPPORTED_COMPILERS = ["GCC", "iccifort", "PGI", "GCCcore"]
+SUPPORTED_MPIS = ["impi", "psmpi", "OpenMPI", "MVAPICH2"]
+# Maintain toplevel list for easy use of --try-toolchain
+SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES = [
+    "intel",
+    "intel-para",
+    "iomkl",
+    "gpsmkl",
+    "gomkl",
+    "pmvmklc",
+    "gmvmklc",
+]
+# Could potentially make a dictionary of names and supported versions here but that is
+# probably overkill
+SUPPORTED_TOOLCHAIN_FAMILIES = (
+    SUPPORTED_COMPILERS
+    + ["gcccoremkl", "gpsmpi", "ipsmpi", "iimpi", "iompi", "gmvapich2c", "pmvapich2c"]
+    + SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES
+)
+# Also maintain a list of CUDA enabled compilers
+CUDA_ENABLED_TOOLCHAINS = ["pmvmklc", "gmvmklc", "gmvapich2c", "pmvapich2c"]
+# Use this for a heuristic to see if the easyconfig comes from the Golden Repo
+GOLDEN_REPO = "Golden_Repo"
+
+# Some modules should use modaltsoftname by default
+REQUIRE_MODALTSOFTNAME = {
+    "impi": "IntelMPI",
+    "psmpi": "ParaStationMPI",
+    "iccifort": "Intel",
+}
+
+
+def parse_hook(ec, *args, **kwargs):
+    """Custom parse hook to manage installations intended for JSC systems."""
+
+    ec_dict = ec.asdict()
+    # Compilers are are a family (in the Lmod sense)
+    if ec.name in SUPPORTED_COMPILERS:
+        key = "modluafooter"
+        value = 'family("compiler")'
+        if key in ec_dict:
+            if not value in ec_dict[key]:
+                ec[key] = "\n".join([ec[key], value])
+        else:
+            ec[key] = value
+        ec.log.info("[parse hook] Injecting Lmod compiler family")
+        # Supported compilers should also be recursively unloaded
+        key = "recursive_module_unload"
+        if not key in ec_dict or ec_dict[key] is None:
+            ec[key] = True
+            ec.log.info(
+                "[parse hook] Injecting recursive module unloading for supported compiler"
+            )
+    # MPI are are a family (in the Lmod sense)
+    if ec.name in SUPPORTED_MPIS:
+        key = "modluafooter"
+        value = 'family("mpi")'
+        if key in ec_dict:
+            if not value in ec_dict[key]:
+                ec[key] = "\n".join([ec[key], value])
+        else:
+            ec[key] = value
+        ec.log.info("[parse hook] Injecting Lmod mpi family")
+
+    # Check if we need to use 'modaltsoftname'
+    if ec.name in REQUIRE_MODALTSOFTNAME:
+        key = "modaltsoftname"
+        if not key in ec_dict or ec_dict[key] is None:
+            ec[key] = REQUIRE_MODALTSOFTNAME[ec.name]
+            ec.log.info(
+                "[parse hook] Injecting modaltsoftname '%s' for '%s'",
+                key,
+                REQUIRE_MODALTSOFTNAME[ec.name],
+            )
+
+    # Check if CUDA is in the dependencies, if so add the GPU Lmod tag
+    if (
+        "CUDA" in [dep[0] for dep in iter(ec_dict["dependencies"])]
+        or ec_dict["toolchain"]["name"] in CUDA_ENABLED_TOOLCHAINS
+    ):
+        key = "modluafooter"
+        value = 'add_property("arch","gpu")'
+        if key in ec_dict:
+            if not value in ec_dict[key]:
+                ec[key] = "\n".join([ec_dict[key], value])
+        else:
+            ec[key] = value
+        ec.log.info("[parse hook] Injecting gpu as Lmod arch property")
+
+    # Check where installations are going to go and add appropriate site contact
+    # not sure of a fool-proof way to do this, let's just try a heuristic
+    site_contacts = None
+    if "stages" in install_path().lower():
+        users_groups = [grp.getgrgid(g).gr_name for g in os.getgroups()]
+        if any(group in user_groups for group in ["swmanage", "software"]):
+            site_contacts = "sc@fz-juelich.de"
+    if site_contacts is None:
+        # Inject the user
+        site_contacts = os.getenv("USER")
+        # Tag the build as a user build
+        key = "modluafooter"
+        value = 'add_property("build","user")'
+        if key in ec_dict:
+            if not value in ec_dict[key]:
+                ec[key] = "\n".join([ec_dict[key], value])
+        else:
+            ec[key] = value
+        ec.log.info("[parse hook] Injecting user as Lmod build property")
+    if site_contacts:
+        key = "site_contacts"
+        value = site_contacts
+        if key in ec_dict:
+            if ec_dict[key] is not None and value not in ec_dict[key]:
+                value = ",".join([ec_dict[key], value])
+        ec[key] = value
+        ec.log.info("[parse hook] Injecting contact %s", value)
+
+    # If we are parsing we are not searching, in this case if the easyconfig is
+    # located in the search path, warn that it's dependencies will (most probably)
+    # not be resolved
+    if build_option("robot"):
+        search_paths = build_option("search_paths") or []
+        robot_paths = list(set(build_option("robot_path") + build_option("robot")))
+        if ec.path:
+            ec_dir_path = os.path.dirname(os.path.abspath(ec.path))
+        else:
+            ec_dir_path = ''
+        if any(search_path in ec_dir_path for search_path in search_paths) and not any(
+            robot_path in ec_dir_path for robot_path in robot_paths
+        ):
+            raise EasyBuildError(
+                "\nYou are attempting to install an easyconfig distributed with "
+                "EasyBuild but are not properly configured to resolve dependencies "
+                "for this case. Please add additonal options:\n"
+                "  eb --robot=$EASYBUILD_ROBOT:$EBROOTEASYBUILD/easybuild/easyconfigs --try-update-deps ...."
+            )
+
+
+def pre_ready_hook(self, *args, **kwargs):
+    "When we are building something, do some checks for bad behaviour"
+    ec = self.cfg
+    # Grab name, path, toolchain, install path and check if we are installing
+    # GCCcore/MPI
+    name = ec["name"]
+    path_to_ec = os.path.abspath(ec.path)
+    toolchain = ec["toolchain"]
+    is_gcccore = ec["name"] == "GCCcore"
+    is_mpi = ec["moduleclass"] == "mpi" or name in SUPPORTED_MPIS
+
+    # Don't let people use unsupported toolchains (by default)
+    override_toolchain_check = os.getenv("JSC_OVERRIDE_TOOLCHAIN_CHECK")
+    if not override_toolchain_check:
+        toolchain_name = toolchain["name"]
+        if not toolchain_name in SUPPORTED_TOOLCHAIN_FAMILIES:
+            stage = os.getenv("STAGE", default=None)
+            if stage:
+                # Clean things up if it is a Devel stage
+                stage = stage.replace("Devel-", "")
+            else:
+                stage = "<TOOLCHAIN_VERSION>"
+            print_warning(
+                "\nYou are attempting to install software with an unsupported "
+                "toolchain (%s), please use additional arguments to map this to a supported"
+                " toolchain:\n"
+                " eb --try-toolchain=<SUPPORTED_TOOLCHAIN>,%s --try-update-deps ...\n"
+                "where <SUPPORTED_TOOLCHAIN> comes from the list %s\n"
+                "(if you really know what you are doing, you can override this "
+                "behaviour by setting the %s environment variable)\n\n"
+                "...exiting",
+                toolchain_name,
+                stage,
+                SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES,
+                "JSC_OVERRIDE_TOOLCHAIN_CHECK",
+            )
+            exit(1)
+
+    # Don't let people install GCCcore since this probably won't work and will lead them
+    # to reinstall most of our stack. Don't advertise that this can be overridden, only
+    # experts should know that.
+    override_gcccore_check = os.getenv("JSC_OVERRIDE_GCCCORE_CHECK")
+    if not override_gcccore_check:
+        if is_gcccore and not "stages" in install_path().lower():
+            print_warning(
+                "\nYou are attempting to install GCCcore (%s) into a non-system "
+                "location (%s), this won't work as expected without additional effort "
+                "and is likely to lead to building a whole stack of dependencies even "
+                "for simple software. Please contact sc@fz-juelich.de if you wish to "
+                "discuss this further.\n\n"
+                "...exiting",
+                path_to_ec,
+                install_path(),
+            )
+            exit(1)
+
+    # Don't let people install a non-JSC MPI (and don't advertise that this can be
+    # overridden, only experts should know that)
+    override_mpi_check = os.getenv("JSC_OVERRIDE_MPI_CHECK")
+    if not override_mpi_check:
+        if is_mpi and GOLDEN_REPO not in path_to_ec:
+            print_warning(
+                "\nYou are attempting to install a non-system MPI implementation (%s), "
+                "this is very likely to lead to severe performance degradation. Please "
+                "contact sc@fz-juelich.de if you wish to discuss this further.\n\n"
+                "...exiting",
+                path_to_ec,
+            )
+            exit(1)
+
+
+def end_hook(*args, **kwargs):
+    # If the user is part of the development group and the installation is systemwide, 
+    # rebuild the system cache
+    "Refresh Lmod's cache"
+
+    if "stages" in install_path().lower():
+        user = os.getenv("USER")
+        if user == "swmanage":
+            cmd = (
+                "/gpfs/software/juwels/configs/update_system_module_cache.sh"
+            )  # Need to make this generic
+            if os.path.isfile(cmd):
+                print("== Refreshing Lmod's cache...")
+                run_cmd(cmd, log_all=True)
+    else:
+        # Otherwise do nothing, no need to build a user cache, it's very unlikely they 
+        # will have loads of modules
+        pass
+

Golden_Repo/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Python-3.8.5.eb

@@ -25,7 +25,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('Java', '1.8', '', True),
+    ('Java', '1.8', '', SYSTEM),
     ('Python', '3.8.5'),
 ]
 

Golden_Repo/a/ARPACK-NG/ARPACK-NG-3.7.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb

+easyblock = 'ConfigureMake'
+
+name = 'ARPACK-NG'
+version = '3.7.0'
+versionsuffix = '-nompi'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
+
+libarpack.a and libparpack.a have been installed in $EBROOTARPACKMINNG.
+
+In addition the variables ARPACK_ROOT, ARPACK_LIB, PARPACK_ROOT, and PARPACK_LIB are set.
+"""
+
+examples = 'Examples can be found in $ARPACK_ROOT/EXAMPLES'
+
+site_contacts = 'I. Gutheil (i.gutheil@fz-juelich.de)'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ["%(version)s.tar.gz"]
+checksums = ['972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6']
+
+patches = [
+    'ARPACK-NG-%(version)s-install-arpack-examples_gpsmkl.patch'
+]
+
+builddependencies = [
+    ('binutils', '2.34'),
+    ('Autotools', '20200321'),
+    ('pkg-config', '0.29.2')
+]
+
+# We hide it since this should be used just for Jupyter and the MPI version should be preferred for normal cases
+hidden = True
+
+preconfigopts = 'sh bootstrap &&'
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+postinstallcmds = [
+    "cp -r EXAMPLES %(installdir)s/EXAMPLES",
+]
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, ],
+    'dirs': []
+}
+
+modextravars = {
+    'ARPACK_ROOT': '%(installdir)s',
+    'ARPACK_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'

Golden_Repo/a/ant/ant-1.10.9-Java-15.eb

+easyblock = 'PackedBinary'
+
+name = 'ant'
+version = '1.10.9'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in
+ build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of
+ Java applications."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = SYSTEM
+
+source_urls = ['https://archive.apache.org/dist/ant/binaries/']
+sources = ['apache-%(name)s-%(version)s-bin.tar.gz']
+checksums = ['5f8a85ddee6effe79163aa54c7bef6b60305e37200dedc1986437fb5c072a9f3']
+
+dependencies = [('Java', '15')]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

Golden_Repo/b/basemap/basemap-1.2.2-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb

+easyblock = 'Bundle'
+
+name = 'basemap'
+version = '1.2.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://matplotlib.org/basemap/'
+description = """Basemap is a Python matplotlib toolkit for plotting data on maps.
+
+This is the last version of Basemap. Please move development efforts over to Cartopy!
+"""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SciPy-Stack', '2020', versionsuffix),
+    ('GEOS', '3.8.1', versionsuffix),
+    ('PROJ', '7.1.0'),
+]
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_download_dep_fail = True
+
+exts_list = [
+    ('pyshp', '2.1.2', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'],
+        'modulename': 'shapefile',
+    }),
+    ('pyproj', '2.6.1.post1', {  # PyProj 3 needs PROJ 7.2.0, which was released after PROJ went into production
+        'source_urls': ['https://pypi.python.org/packages/source/p/pyproj'],
+        'prebuildopts': 'PROJ_DIR="$EBROOTPROJ" ',
+        'preinstallopts': 'PROJ_DIR="$EBROOTPROJ" ',
+    }),
+    ('basemap', '1.2.2', {
+        'source_urls': ['https://github.com/matplotlib/basemap/archive/'],
+        'source_tmpl': 'v%(version)srel.tar.gz',
+        'prebuildopts': 'GEOS_DIR="$EBROOTGEOS" ',
+        'preinstallopts': 'GEOS_DIR="$EBROOTGEOS" ',
+        'modulename': 'mpl_toolkits.basemap',
+    }),
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'vis'

Golden_Repo/c/Cartopy/Cartopy-0.18.0-gpsmpi-2020-Python-3.8.5.eb

+easyblock = 'PythonBundle'
+
+name = 'Cartopy'
+version = '0.18.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://scitools.org.uk/cartopy/docs/latest/'
+description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Fiona', '1.8.16', versionsuffix),
+    ('GDAL', '3.1.2', versionsuffix),
+    ('GEOS', '3.8.1', versionsuffix),
+    ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+    ('pyproj', '2.6.1.post1', versionsuffix),
+    ('Shapely', '1.7.1', versionsuffix),
+    ('PROJ', '7.1.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('OWSLib', '0.20.0', {
+        'checksums': ['334988857b260c8cdf1f6698d07eab61839c51acb52ee10eed1275439200a40e'],
+    }),
+    ('pyepsg', '0.4.0', {
+        'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'],
+    }),
+    ('pykdtree', '1.3.1', {
+        'checksums': ['0d49d3bbfa0366dbe29176754ec86df75114a25525b530dcbbb75d3ac4c263e9'],
+    }),
+    ('pyshp', '2.1.0', {
+        'modulename': 'shapefile',
+        'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'],
+    }),
+    (name, version, {
+        'checksums': ['7ffa317e8f8011e0d965a3ef1179e57a049f77019867ed677d49dcc5c0744434'],
+    }),
+]
+
+moduleclass = 'geo'

Golden_Repo/c/cppcheck/cppcheck-2.2-GCCcore-9.3.0.eb

+easyblock = 'CMakeMake'
+name = 'cppcheck'
+version = '2.2'
+
+homepage = 'http://cppcheck.sourceforge.net/'
+description = """Cppcheck is a static analysis tool for C/C++ code"""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s-%(version)s.tar.bz2']
+
+dependencies = [
+    ('binutils', '2.34'),
+    ('Qt5', '5.14.2'),
+    ('PCRE', '8.44'),
+    ('CMake', '3.18.0'),
+]
+
+configopts = '-DUSE_Z3:BOOL=OFF'
+
+sanity_check_paths = {
+    'files': ['bin/cppcheck'],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

Golden_Repo/d/distributed/distributed-2.30.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb

+easyblock = 'Bundle'
+
+name = 'distributed'
+version = '2.30.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://distributed.readthedocs.io/'
+description = """Dask.distributed is a lightweight library for distributed computing in Python.
+ It extends both the concurrent.futures and dask APIs to moderate sized clusters."""
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('dask', '2.22.0', versionsuffix),
+    ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+]
+
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('zict', '2.0.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/z/zict'],
+        'source_tmpl': 'zict-%(version)s.tar.gz',
+    }),
+    ('HeapDict', '1.0.1', {
+        'modulename': 'heapdict',
+        'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'],
+    }),
+    ('tornado', '5.0.2', {
+        'source_urls': ['https://pypi.python.org/packages/source/t/tornado'],
+    }),
+    ('tblib', '1.7.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/t/tblib'],
+    }),
+    ('msgpack', '1.0.0', {
+        'modulename': 'msgpack',
+        'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'],
+    }),
+    ('sortedcontainers', '2.3.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'],
+    }),
+    (name, version, {
+        'source_urls': ['https://pypi.python.org/packages/source/d/distributed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-worker'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'tools'

Golden_Repo/f/FFTW/FFTW-3.3.8-GCCcore-9.3.0-nompi.eb

+name = 'FFTW'
+version = '3.3.8'
+versionsuffix = '-nompi'
+
+homepage = 'http://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete
+Fourier transform (DFT) in one or more dimensions, of arbitrary input size,
+and of both real and complex data."""
+
+site_contacts = 'i.gutheil@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303']
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+# We hide it since this should be used just for Jupyter and the MPI version should be preferred for normal cases
+hidden = True
+
+# no quad precision, requires GCC v4.6 or higher
+# see also
+# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html
+with_quad_prec = True
+
+# compilation fails on AMD systems when configuring with --enable-avx-128-fma,
+# because Intel compilers do not support FMA4 instructions
+use_fma4 = True
+
+# can't find mpirun/mpiexec and fails
+# runtest = 'check'
+
+modextravars = {
+    'FFTW_ROOT': '%(installdir)s',
+    'FFTW_INCLUDE': '%(installdir)s/include',
+    'FFTW_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'

Golden_Repo/f/FFTW/FFTW-3.3.8-ipsmpi-2020-mt.eb

+name = 'FFTW'
+version = '3.3.8'
+
+homepage = 'http://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete
+Fourier transform (DFT) in one or more dimensions, of arbitrary input size,
+and of both real and complex data."""
+
+site_contacts = 'i.gutheil@fz-juelich.de'
+
+toolchain = {'name': 'ipsmpi', 'version': '2020-mt'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+
+# See https://github.com/FFTW/fftw3/commit/10e2040af822a08ed49d2f6a1db45a7a3ad50582
+patches = ['fftw_no-gcc-intel_2020.patch']
+
+checksums = [
+    '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303',
+    'f226cc6dbdc9d11d4340567ef3227d78284c4dc44b8e63c3901a079aa9527da6'
+]
+
+# no quad precision, requires GCC v4.6 or higher
+# see also
+# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html
+with_quad_prec = False
+
+# Intel compilers do not support FMA4 instructions
+use_fma4 = False
+
+# can't find mpirun/mpiexec and fails
+# runtest = 'check'
+
+modextravars = {
+    'FFTW_ROOT': '%(installdir)s',
+    'FFTW_INCLUDE': '%(installdir)s/include',
+    'FFTW_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'

Golden_Repo/f/Fiona/Fiona-1.8.16-gpsmpi-2020-Python-3.8.5.eb

+easyblock = 'PythonBundle'
+
+name = 'Fiona'
+version = '1.8.16'
+versionsuffix = "-Python-%(pyver)s"
+
+homepage = 'https://github.com/Toblerity/Fiona'
+description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data
+in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries,
+mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using
+multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS
+packages such as pyproj, Rtree, and Shapely."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('GDAL', '3.1.2', versionsuffix),
+    ('Shapely', '1.7.1', versionsuffix),  # optional
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+    ('cligj', '0.5.0', {
+        'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'],
+    }),
+    ('click-plugins', '1.1.1', {
+        'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'],
+    }),
+    ('munch', '2.5.0', {
+        'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'],
+    }),
+    (name, version, {
+        'checksums': ['fd6dfb65959becc916e9f6928618bfd59c16cdbc413ece0fbac61489cd11255f'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/fio'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'data'

Golden_Repo/g/GPAW/GPAW-20.1.0-gpsmkl-2020-Python-3.8.5.eb

@@ -35,7 +35,7 @@ dependencies = [
     ('HDF5', '1.10.6'),
     ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
     ('libvdwxc', '0.4.0'),
-    ('GPAW-setups', '0.9.20000', '', True),
+    ('GPAW-setups', '0.9.20000', '', SYSTEM),
 ]
 
 preconfigopts = 'export MKL_ROOT=$MKLROOT && '

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

@@ -48,7 +48,7 @@ builddependencies = [
 
 # Removed ('hwloc', '2.0.3') from dependencies due to runtime failures.
 dependencies = [
-    ('CUDA', '11.0', '', True),
+    ('CUDA', '11.0', '', SYSTEM),
 ]
 
 configopts = '-DCMAKE_PREFIX_PATH=$EBROOTHWLOC -DMPIEXEC_MAX_NUMPROCS="24" '

Golden_Repo/g/GROMACS/GROMACS-2020.4-intel-para-2020.eb

@@ -47,7 +47,7 @@ builddependencies = [
 
 # Removed ('hwloc', '2.0.3') from dependencies due to runtime failures.
 dependencies = [
-    ('CUDA', '11.0', '', True),
+    ('CUDA', '11.0', '', SYSTEM),
 ]
 
 configopts = '-DCMAKE_PREFIX_PATH=$EBROOTHWLOC -DMPIEXEC_MAX_NUMPROCS="24"'

Golden_Repo/g/GSL/GSL-2.6-GCCcore-9.3.0.eb

+easyblock = 'ConfigureMake'
+
+name = 'GSL'
+version = '2.6'
+
+homepage = 'http://www.gnu.org/software/gsl/'
+description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
+ The library provides a wide range of mathematical routines such as random number generators, special functions
+ and least-squares fitting.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True}
+
+builddependencies = [('binutils', '2.34')]
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = "--with-pic"
+
+moduleclass = 'numlib'

Golden_Repo/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0.eb

@@ -37,7 +37,7 @@ dependencies = [
     ('Ghostscript', '9.52'),
     ('GLib', '2.64.4'),
     ('GTS', '0.7.6'),
-    ('Java', '1.8', '', True),
+    ('Java', '1.8', '', SYSTEM),
     ('libpng', '1.6.37'),
     ('librsvg', '2.48.8'),
     ('Pango', '1.44.7'),

Golden_Repo/g/gcccoremkl/gcccoremkl-9.3.0-2020.2.254.eb

@@ -19,9 +19,9 @@ local_comp = (local_comp_name, local_comp_version)
 dependencies = [
     local_comp,
     ('binutils', '2.34', '', local_comp),
-    ('imkl', local_mklver, '', True),
+    ('imkl', local_mklver, '', SYSTEM),
 ]
 
-hiddendependencies = [('imkl', local_mklver, '', True)]
+hiddendependencies = [('imkl', local_mklver, '', SYSTEM)]
 
 moduleclass = 'toolchain'

Golden_Repo/h/HDF/HDF-4.2.15-GCC-9.3.0.eb

@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
 builddependencies = [
     ('flex', '2.6.4'),
     ('Bison', '3.6.4'),
+    ('Java', '15', '', SYSTEM),
 ]
 
 dependencies = [
@@ -30,7 +31,8 @@ source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.s
 
 preconfigopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
 preconfigopts += 'export LIBS="-ltirpc $LIBS" && '
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
 
 prebuildopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
 

Golden_Repo/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb

@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
 builddependencies = [
     ('flex', '2.6.4'),
     ('Bison', '3.6.4'),
+    ('Java', '15', '', SYSTEM),
 ]
 
 dependencies = [
@@ -30,7 +31,8 @@ source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.s
 
 preconfigopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
 preconfigopts += 'export LIBS="-ltirpc $LIBS" && '
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
 
 prebuildopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
 

Golden_Repo/h/HDF5/HDF5-1.10.6-GCCcore-9.3.0-serial.eb

@@ -20,6 +20,7 @@ checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa']
 
 builddependencies = [
     ('binutils', '2.34'),
+    ('Java', '15', '', SYSTEM)
 ]
 
 dependencies = [
@@ -27,4 +28,6 @@ dependencies = [
     ('Szip', '2.1.1'),
 ]
 
+configopts = '--enable-java'
+
 moduleclass = 'data'