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Custom_EasyBlocks/README.md

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+# Custom EasyBlocks
+
+Overview of the custom EasyBlocks.
+
+## allinea
+
+- __*added by*__ s.achilles
+- __*needed because*__ we need to allow multiple license files
+- __*difference compared to upstream*__ the aforementioned parameter
+- __*can not be removed*__ at least until that option is merged upstream
+
+## CUDA
+
+- __*added by*__ s.achilles
+- __*needed because*__ the new easyblocks removes the stubs
+- __*difference compared to upstream*__ the aforementioned parameter
+- __*can not be removed*__ until we update to EB 4.8.1 which contains [PR #2793](https://github.com/easybuilders/easybuild-easyblocks/pull/2793)
+
+## MPICH
+
+- __*added by*__ d.alvarez
+- __*needed because*__ optional `check_static_libs` parameter in the sanity check (used with `psmpi.py`)
+- __*difference compared to upstream*__ the aforementioned parameter
+- __*can not be removed*__ at least until that option (needed just for `psmpi.py`) is merged upstream (PR: #2787)
+
+## PSMPI
+
+- __*added by*__ d.alvarez
+- __*needed because*__ CUDA support
+- __*difference compared to upstream*__ the supporting code to enable CUDA support
+- __*can not be removed*__ until the CUDA options are pushed upstream (PR: #2787)
+
+## OPENMPI
+
+- __*added by*__ d.alvarez
+- __*needed because*__ the check for `mpirun` should be optional
+- __*difference compared to upstream*__ making that check optional
+- __*can not be removed*__ until the check is made optional upstream (PR: #2788)
+
+## CODE_SATURNE
+
+- __*added by*__ m.cakircali
+- __*needed because*__ there is no support to install `code_saturn` upstream
+- __*can not be removed*__ at least until the easyblock is added upstream
+
+## NVIDIA_DRIVER
+
+- __*added by*__ d.alvarez
+- __*needed because*__ we custom-install the NVIDIA driver libraries in the EB stack
+- __*can not be removed*__ at least until the easyblock is added upstream
+
+## generic/SYSTEM_BUNDLE
+
+- __*added by*__ d.alvarez
+- __*needed because*__ it is the basic support for the MPI settings modules
+- __*can not be removed*__
+
+## SUITESPARSE
+
+- __*added by*__ d.alvarez
+- __*needed because*__ added CUDA-related tweaks not present in upstream
+- __*difference compared to upstream*__ the aforementioned
+- __*can not be removed*__ Once the PR is merged upstream. Hopefully with the next release
+
+## JULIA
+
+- __*added by*__ j.goebbert
+- __*needed because*__ we offer more functionality compared to upstream
+- __*difference compared to upstream*__ upstream has not yet an EasyBlock for julia, juliabundle and juliapackage
+- __*can not be removed*__ once merged with upstream
+
+## VMD
+- __*added by*__ j.goebbert
+- __*needed because*__ we replaced the Mesa module by our own OpenGL module compared to upstream
+- __*difference compared to upstream*__ upstream checks for Mesa inside the easyblock
+- __*can not be removed*__ once upstream uses our OpenGL module
+
+## GROMACS
+- __*added_by*__ j.meinke
+- __*needed because*__ want to use easyconfig parameters to determine CUDA capability.
+- __*difference compared to upstream*__ upstream doesn't have such a feature
+- __*can not be removed*__ until merged upstream
+
+## LAMMPS
+- __*added_by*__ d.alvarez
+- __*needed because*__ upstream does not include the changes that we used in the latest stage
+- __*difference compared to upstream*__ various, done by Alan
+- __*can not be removed*__ until merged upstream or the changes here are deprecated (need to be assesed by an expert)
+
+## NAMD
+- __*added_by*__ d.alvarez
+- __*needed because*__ need to disable CUDA support even if CUDA comes as a dependency
+- __*difference compared to upstream*__ upstream doesn't have such a feature
+- __*can not be removed*__ until merged upstream
+
+## ELPA
+- __*added_by*__ d.alvarez
+- __*needed because*__ to autodetect CUDA and support CUDA compute capabilities
+- __*difference compared to upstream*__ upstream doesn't have such a feature
+- __*can not be removed*__ until merged upstream (https://github.com/easybuilders/easybuild-easyblocks/pull/2673)
+
+## CP2K
+- __*added_by*__ th.mueller
+- __*needed because*__  support for libvori; alternative versions of dbcsr; contains loads of widely obsolete stuff; is  essentially a highly non-portable easyblock working only with intel and gnu (which I am not going to change!); running the tests will not work within an eb environment - at least not sensibly. 
+- __*difference compared to upstream*__ no support for libvori 
+- __*can not be removed*__

Custom_EasyBlocks/allinea.py

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+# This file is part of JSC's public easybuild repository (https://github.com/easybuilders/jsc)
+##
+# Copyright 2013-2021 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 Allinea tools, implemented as an easyblock
+
+@author: Kenneth Hoste (Ghent University)
+@author: Sebastian Achilles (Forschungszentrum Juelich GmbH)
+"""
+import os
+import shutil
+import stat
+
+from easybuild.easyblocks.generic.binary import Binary
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions, copy_file
+from easybuild.tools.py2vs3 import string_type
+
+
+class EB_Allinea(Binary):
+    """Support for building/installing Allinea."""
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Define extra easyconfig parameters specific to Allinea."""
+        extra = Binary.extra_options(extra_vars)
+        extra.update({
+            'templates': [[], "List of templates.", CUSTOM],
+            'sysconfig': [None, "system.config file to install.", CUSTOM],
+        })
+        return extra
+
+    def extract_step(self):
+        """Extract Allinea installation files."""
+        EasyBlock.extract_step(self)
+
+    def configure_step(self):
+        """No configuration for Allinea."""
+        # ensure a license file is specified
+        if self.cfg['license_file'] is None:
+            raise EasyBuildError("No license file specified.")
+
+    def build_step(self):
+        """No build step for Allinea."""
+        pass
+
+    def install_step(self):
+        """Install Allinea using install script."""
+
+        if self.cfg['install_cmd'] is None:
+            self.cfg['install_cmd'] = "./textinstall.sh --accept-licence %s" % self.installdir
+
+        super(EB_Allinea, self).install_step()
+
+        # copy license file
+        # allow to copy multiple licenses
+        lic_path = os.path.join(self.installdir, 'licences')
+        licenses = self.cfg['license_file']
+        if isinstance(licenses, string_type):
+            licenses = [licenses]
+        try:
+            for license in licenses:
+                shutil.copy2(license, lic_path)
+        except OSError as err:
+            raise EasyBuildError(
+                "Failed to copy license file to %s: %s", lic_path, err)
+
+        # copy templates
+        templ_path = os.path.join(self.installdir, 'templates')
+        for templ in self.cfg['templates']:
+            path = self.obtain_file(templ, extension='qtf')
+            if path:
+                self.log.debug('Template file %s found' % path)
+            else:
+                raise EasyBuildError('No template file named %s found', templ)
+
+            try:
+                # use shutil.copy (not copy2) so that permissions of copied file match with rest of installation
+                shutil.copy(path, templ_path)
+            except OSError as err:
+                raise EasyBuildError(
+                    "Failed to copy template %s to %s: %s", templ, templ_path, err)
+
+        # copy system.config if requested
+        sysconf_path = os.path.join(self.installdir, 'system.config')
+        if self.cfg['sysconfig'] is not None:
+            path = self.obtain_file(self.cfg['sysconfig'], extension=False)
+            if path:
+                self.log.debug('system.config file %s found' % path)
+            else:
+                raise EasyBuildError(
+                    'No system.config file named %s found', sysconf_path)
+
+            copy_file(path, sysconf_path)
+            adjust_permissions(sysconf_path, stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH,
+                               recursive=False, relative=False)
+
+    def sanity_check_step(self):
+        """Custom sanity check for Allinea."""
+        custom_paths = {
+            'files': ['bin/ddt', 'bin/map'],
+            'dirs': [],
+        }
+        super(EB_Allinea, self).sanity_check_step(custom_paths=custom_paths)