Merge branch '2020' of...

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

Golden_Repo/j/Jupyter/notebook-6.0.3_jsc.patch

+diff
+--- notebook-6.0.3.orig/notebook/services/contents/filecheckpoints.py   2020-04-28 06:26:51.384296390 +0200
++++ notebook-6.0.3/notebook/services/contents/filecheckpoints.py        2020-04-28 06:30:55.139342947 +0200
+@@ -14,7 +14,7 @@
+ 
+ from jupyter_core.utils import ensure_dir_exists
+ from ipython_genutils.py3compat import getcwd
+-from traitlets import Unicode
++from traitlets import Unicode, Integer
+ 
+ from notebook import _tz as tz
+ 
+@@ -28,6 +28,35 @@
+     you want file-based checkpoints with another ContentsManager.
+     """
+ 
++    checkpoint_permissions = Integer(
++        0o644,
++        config=True,
++        help="""The permission of your checkpoint files.
++
++        By default, it is 0o644
++        """,
++    )
++
++    restore_permissions = Integer(
++        0o644,
++        config=True,
++        help="""The permission of a restored checkpoint.
++
++        By default, it is 0o644
++        """,
++    )
++
++    checkpoint_dir_umask = Integer(
++        0o022,
++        config=True,
++        help="""The umask for the checkpoint directory.
++
++        Keep in mind that it depends on your system umask, too.
++
++        By default, it is 0o022
++        """,
++    )
++
+     checkpoint_dir = Unicode(
+         '.ipynb_checkpoints',
+         config=True,
+@@ -50,21 +79,29 @@
+     # ContentsManager-dependent checkpoint API
+     def create_checkpoint(self, contents_mgr, path):
+         """Create a checkpoint."""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         checkpoint_id = u'checkpoint'
+         src_path = contents_mgr._get_os_path(path)
+         dest_path = self.checkpoint_path(checkpoint_id, path)
+         self._copy(src_path, dest_path)
+-        return self.checkpoint_model(checkpoint_id, dest_path)
++        os.chmod(dest_path, self.checkpoint_permissions)
++        ret = self.checkpoint_model(checkpoint_id, dest_path)
++        os.umask(original_umask)
++        return ret
+ 
+     def restore_checkpoint(self, contents_mgr, checkpoint_id, path):
+         """Restore a checkpoint."""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         src_path = self.checkpoint_path(checkpoint_id, path)
+         dest_path = contents_mgr._get_os_path(path)
+         self._copy(src_path, dest_path)
++        os.chmod(dest_path, self.restore_permissions)
++        os.umask(original_umask)
+ 
+     # ContentsManager-independent checkpoint API
+     def rename_checkpoint(self, checkpoint_id, old_path, new_path):
+         """Rename a checkpoint from old_path to new_path."""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         old_cp_path = self.checkpoint_path(checkpoint_id, old_path)
+         new_cp_path = self.checkpoint_path(checkpoint_id, new_path)
+         if os.path.isfile(old_cp_path):
+@@ -75,9 +112,11 @@
+             )
+             with self.perm_to_403():
+                 shutil.move(old_cp_path, new_cp_path)
++        os.umask(original_umask)
+ 
+     def delete_checkpoint(self, checkpoint_id, path):
+         """delete a file's checkpoint"""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         path = path.strip('/')
+         cp_path = self.checkpoint_path(checkpoint_id, path)
+         if not os.path.isfile(cp_path):
+@@ -86,23 +125,29 @@
+         self.log.debug("unlinking %s", cp_path)
+         with self.perm_to_403():
+             os.unlink(cp_path)
++        os.umask(original_umask)
+ 
+     def list_checkpoints(self, path):
+         """list the checkpoints for a given file
+ 
+         This contents manager currently only supports one checkpoint per file.
+         """
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         path = path.strip('/')
+         checkpoint_id = "checkpoint"
+         os_path = self.checkpoint_path(checkpoint_id, path)
+         if not os.path.isfile(os_path):
++            os.umask(original_umask)
+             return []
+         else:
+-            return [self.checkpoint_model(checkpoint_id, os_path)]
++            ret = self.checkpoint_model(checkpoint_id, os_path)
++            os.umask(original_umask)
++            return [ret]
+ 
+     # Checkpoint-related utilities
+     def checkpoint_path(self, checkpoint_id, path):
+         """find the path to a checkpoint"""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         path = path.strip('/')
+         parent, name = ('/' + path).rsplit('/', 1)
+         parent = parent.strip('/')
+@@ -117,16 +162,19 @@
+         with self.perm_to_403():
+             ensure_dir_exists(cp_dir)
+         cp_path = os.path.join(cp_dir, filename)
++        os.umask(original_umask)
+         return cp_path
+ 
+     def checkpoint_model(self, checkpoint_id, os_path):
+         """construct the info dict for a given checkpoint"""
++        original_umask = os.umask(self.checkpoint_dir_umask)
+         stats = os.stat(os_path)
+         last_modified = tz.utcfromtimestamp(stats.st_mtime)
+         info = dict(
+             id=checkpoint_id,
+             last_modified=last_modified,
+         )
++        os.umask(original_umask)
+         return info
+ 
+     # Error Handling
+

Golden_Repo/j/JupyterCollection/JupyterCollection-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterCollection'
+version = '2020.2.5'
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'http://www.jupyter.org'
+description = """
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+dependencies = [
+    ('JupyterKernel-Bash',       '0.7.1', '-' + version),
+    ('JupyterKernel-Cling',      '0.7',   '-' + version),
+    ('JupyterKernel-JavaScript', '5.2.0', '-' + version),
+    ('JupyterKernel-Julia',      '1.5.2', '-' + version),
+    ('JupyterKernel-Octave',     '6.1.0', '-' + version),
+    ('JupyterKernel-PyParaView', '5.8.1', '-' + version),
+    # ('JupyterKernel-PyQuantum',  '1.1',   '-' + version),
+    ('JupyterKernel-R',          '4.0.2', '-' + version),
+    ('JupyterKernel-Ruby',       '2.7.1', '-' + version),
+    ('JupyterProxy-XpraHTML5',   '0.3.0', '-' + version),
+    ('Jupyter', version, local_pysuffix),
+]
+
+skipsteps = ['configure', 'build', 'install', 'sanity_check']
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-Bash/JupyterKernel-Bash-0.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Bash'
+version = '0.7.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/takluyver/bash_kernel'
+description = """
+Native Bash kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_common_opts = {
+    'req_py_majver': '3',
+    'req_py_minver': '0'
+}
+
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_default_options = {
+    'download_dep_fail': True,
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+}
+
+exts_list = [
+    # 0.7.2 fails with BackendUnavailable. Might be fixable --no-use-pep517
+    ('bash_kernel', '0.7.1', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '29f895819e076e3f225e37034b70b5265a559e2964e020c942024f51ea6153e8')]),
+        ('use_pip',  True),
+    ])),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    # Create virtual environment to ensure we install in the correct directory !!!
+    'python3 -m venv %(installdir)s --system-site-packages',
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'source %%(installdir)s/bin/activate\n'
+        'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+        'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+        'EOF'
+    ) % (local_jupyter_path),
+
+    # Jupyter Kernel: Bash - https://github.com/takluyver/bash_kernel
+    # installs bash_kernel in $JUPYTER_DATA_DIR/kernels
+    'source %(builddir)s/env.sh && ${EBROOTPYTHON}/bin/python3 -m bash_kernel.install --user',
+    'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+    # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+    'rm %(installdir)s/pyvenv.cfg',
+    'rm -r %(installdir)s/bin',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/bash/kernel.json',
+    ],
+    'dirs': [
+        'lib/python%(pyshortver)s/site-packages',
+        'share/jupyter/kernels/bash/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-Cling/JupyterKernel-Cling-0.7-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Cling'
+version = '0.7'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/root-project/cling'
+description = """
+Native C kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+    ('Cling', version),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    # Create virtual environment to ensure we install in the correct directory !!!
+    'python3 -m venv %(installdir)s --system-site-packages',
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'source %%(installdir)s/bin/activate\n'
+        'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+        'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+        'EOF'
+    ) % (local_jupyter_path),
+
+    # Jupyter Kernel: Cling (C++)
+    'source %(builddir)s/env.sh && pip3 install ${EBROOTCLING}/share/cling/Jupyter/kernel',
+    (
+        'source %(builddir)s/env.sh && '
+        '    jupyter-kernelspec install --prefix=%(installdir)s ${EBROOTCLING}/share/cling/Jupyter/kernel/cling-cpp17'
+    ),
+
+    # correct shebang to correct python binary
+    (
+        'source %(builddir)s/env.sh && '
+        '    abs2python="#! ${EBROOTPYTHON}/bin/python" && '
+        '    sed "1s@^.*@$abs2python@g" -i %(installdir)s/bin/jupyter-cling-kernel'
+    ),
+    'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+    # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+    'rm %(installdir)s/pyvenv.cfg',
+    'rm %(installdir)s/bin/python',
+    'rm %(installdir)s/bin/python3',
+    'rm %(installdir)s/bin/activate',
+    'rm %(installdir)s/bin/activate*',
+    'rm %(installdir)s/bin/easy_install*',
+    'rm %(installdir)s/bin/pip*',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/cling-cpp17/kernel.json',
+    ],
+    'dirs': [
+        # 'lib/python%(pyshortver)s/site-packages',
+        'share/jupyter/kernels/cling-cpp17/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-JavaScript/JupyterKernel-JavaScript-5.2.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-JavaScript'
+version = '5.2.0'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://www.npmjs.com/package/ijavascript'
+description = """
+Native JavaScript kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+    'PATH': ['bin'],
+    'NODE_PATH': ['lib/node_modules'],  # npm´s search path to extra modules
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'export PATH=%%(installdir)s/bin:${PATH}\n'
+        'export NODE_PATH=%%(installdir)s/lib/node_modules\n'
+        'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+        'EOF'
+    ) % (local_jupyter_path),
+
+    'source %(builddir)s/env.sh && npm install ijavascript@5.2.0 -g --prefix %(installdir)s',
+    # installs ijavascript in $JUPYTER_DATA_DIR/kernels
+    'source %(builddir)s/env.sh && ijsinstall --install=local',
+    'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/javascript/kernel.json',
+    ],
+    'dirs': [
+        'lib/node_modules/',
+        'share/jupyter/kernels/javascript/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-Julia/JupyterKernel-Julia-1.5.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Julia'
+version = '1.5.2'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/IRkernel/IRkernel'
+description = """
+Native R kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+    ('Julia', version),
+]
+
+local_common_opts = {
+    'req_py_majver': '3',
+    'req_py_minver': '0'
+}
+
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_default_options = {
+    'download_dep_fail': True,
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+}
+
+exts_list = [
+    ('julia', '0.5.3', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'b13207125709fdba069a25c4e54ff366f0bc308807b2aa0f3b66924101799c58')]),
+        ('use_pip',  True),
+    ])),
+]
+
+local_jupyter_path = 'share/jupyter'
+local_julia_depot_path = "%(installdir)s/share/julia/site/"  # for Julia packages needed for Jupyter
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+modextravars = {
+    'JULIA_DEPOT_PATH': local_julia_depot_path,
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    # Create virtual environment to ensure we install in the correct directory !!!
+    'python3 -m venv %(installdir)s --system-site-packages',
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'source %%(installdir)s/bin/activate\n'
+        'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+        ''
+        'export JULIA_DEPOT_PATH=%s\n'
+        'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+        'EOF'
+    ) % (local_julia_depot_path, local_jupyter_path),
+
+    # installs ijulia in JULIA_DEPOT_PATH and kernel in $JUPYTER_DATA_DIR/kernels
+    'source %(builddir)s/env.sh && julia -e \'using Pkg; Pkg.add("IJulia"); Pkg.build("IJulia")\'',
+
+    # to trigger the precompilation
+    'source %(builddir)s/env.sh && julia -e \'using IJulia\'',
+
+    # adjust permissions of precompiled files
+    'for i in $(find %s); do chmod +r $i; done' % local_julia_depot_path,
+
+    # configure Python<->Julia bridge (of python package julia)
+    'source %(builddir)s/env.sh && python -c "import julia; julia.install()"',
+
+    # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+    'rm %(installdir)s/pyvenv.cfg',
+    'rm %(installdir)s/bin/python',
+    'rm %(installdir)s/bin/python3',
+    'rm %(installdir)s/bin/activate',
+    'rm %(installdir)s/bin/activate*',
+    'rm %(installdir)s/bin/easy_install*',
+    'rm %(installdir)s/bin/pip*',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/julia-%(version_major_minor)s/kernel.json',
+    ],
+    'dirs': [
+        'lib/python%(pyshortver)s/site-packages',
+        'share/jupyter/kernels/julia-%(version_major_minor)s/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-Octave/JupyterKernel-Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Octave'
+version = '6.1.0'
+local_octavever = '6.1.0'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/Calysto/octave_kernel'
+description = """
+Native Octave kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+    ('Octave', local_octavever, '-nompi'),  # ensure it is available
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+    # no dependency to Octave as it is loaded in kernel.sh
+]
+
+local_jupyter_path = 'share/jupyter'
+local_kernel_dir = 'octave'
+local_kernel_name = 'Octave-%s' % local_octavever
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    # Create virtual environment to ensure we install in the correct directory !!!
+    'python3 -m venv %(installdir)s --system-site-packages',
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'source %%(installdir)s/bin/activate\n'
+        'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+        'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+        'EOF'
+    ) % (local_jupyter_path),
+
+    # enable use of Octave from production stage Stages/2020
+    'source %(builddir)s/env.sh && pip3 install ipykernel ',
+    'rm -rf %(installdir)s/share/jupyter/kernels/',  # remove any kernel installed by ipykernel
+    'source %(builddir)s/env.sh && pip3 install ipyparallel ',
+
+    # install Python package octave_kernel
+    'source %(builddir)s/env.sh && pip3 install octave_kernel==0.32.0 ',
+
+    # write kernel.sh
+    (
+        '{ cat >> %%(builddir)s/env.sh; } << \'EOF\'\n'
+        'export KERNEL_DIR=%s\n'
+        'export KERNEL_NAME=%s\n'
+        'EOF'
+    ) % (local_kernel_dir, local_kernel_name),
+    (
+        '{ source %%(builddir)s/env.sh && '
+        '  cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.sh; } << \'EOF\'\n'
+        '#!/bin/bash \n'
+        '\n'
+        '# Load required modules \n'
+        'module purge \n'
+        'module load Stages/2020 \n'
+        'module load GCC/9.3.0 \n'
+        '\n' \
+        'module load Python/%%(pyver)s \n'
+        'module load Jupyter/%s%s \n'
+        'module load Octave/%s-nompi \n'
+        '\n'
+        'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH} \n'
+        '\n'
+        'exec python $@\n'
+        'EOF'
+    ) % (local_kernel_dir, local_jupyterver, local_pysuffix, local_octavever),
+    'source %(builddir)s/env.sh && chmod +x %(installdir)s/share/jupyter/kernels/${KERNEL_DIR}/kernel.sh',
+
+    # write kernel.json
+    (
+        '{ source %%(builddir)s/env.sh && '
+        '  cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.json; } << \'EOF\'\n'
+        '{ \n'
+        '  "argv": [ \n'
+        '    "%%(installdir)s/share/jupyter/kernels/%s/kernel.sh", \n'
+        '    "-m", \n'
+        '    "octave_kernel", \n'
+        '    "-f", \n'
+        '    "{connection_file}" \n'
+        '  ], \n'
+        '  "display_name": "%s", \n'
+        '  "mimetype": "text/x-octave", \n'
+        '  "language": "python", \n'
+        '  "name": "%s" \n'
+        '}\n'
+        'EOF'
+    ) % (local_kernel_dir, local_kernel_dir, local_kernel_name, local_kernel_name),
+
+    # ensure correct permissions
+    'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+    # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+    'rm %(installdir)s/pyvenv.cfg',
+    'rm -r %(installdir)s/bin',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/%s/kernel.sh' % local_kernel_dir,
+        'share/jupyter/kernels/%s/kernel.json' % local_kernel_dir,
+    ],
+    'dirs': [
+        'lib/python%(pyshortver)s/site-packages',
+        'share/jupyter/kernels/octave/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-PyParaView/JupyterKernel-PyParaView-5.8.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Binary'
+
+name = 'JupyterKernel-PyParaView'
+version = '5.8.1'
+local_paraviewver = '5.8.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.paraview.org'
+description = """
+Special ParaView kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+sources = [
+    ('logo-128x128.png'),
+    ('logo-32x32.png'),
+    ('logo-64x64.png'),
+]
+
+builddependencies = [
+    ('binutils', '2.34'),
+    # ('ParaView', local_paraviewver, '-EGL' + local_pysuffix, ('gpsmkl', '2020')),  # ensure it is available
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_kernel_dir = 'pyparaview'
+local_kernel_name = 'PyParaView-%s' % local_paraviewver
+
+modextrapaths = {
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    (
+        '{ cat >> %%(builddir)s/env.sh; } << \'EOF\'\n'
+        'export KERNEL_DIR=%s\n'
+        'export KERNEL_NAME=%s\n'
+        'EOF'
+    ) % (local_kernel_dir, local_kernel_name),
+    'source %%(builddir)s/env.sh && python -m ipykernel install --name=%s --prefix=%%(installdir)s' % local_kernel_dir,
+
+    # write logo image
+    (
+        'source %%(builddir)s/env.sh && '
+        '    cp %%(builddir)s/logo-32x32.png %%(installdir)s/share/jupyter/kernels/%s/logo-32x32.png'
+    ) % (local_kernel_dir),
+    (
+        'source %%(builddir)s/env.sh && '
+        '    cp %%(builddir)s/logo-64x64.png %%(installdir)s/share/jupyter/kernels/%s/logo-64x64.png'
+    ) % (local_kernel_dir),
+    (
+        'source %%(builddir)s/env.sh && '
+        '    cp %%(builddir)s/logo-128x128.png %%(installdir)s/share/jupyter/kernels/%s/logo-128x128.png'
+    ) % (local_kernel_dir),
+
+    # write kernel.sh
+    (
+        '{ source %%(builddir)s/env.sh && '
+        '  cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.sh; } << \'EOF\'\n'
+        '#!/bin/bash \n'
+        '\n'
+        '# Load required modules \n'
+        'module purge \n'
+        'module use $OTHERSTAGES \n'
+        'module load Stages/2020 \n'
+        'module load GCC/9.3.0 \n'
+        'module load ParaStationMPI \n'
+        'module load Python/%%(pyver)s \n'
+        'module load Jupyter/%s%s \n'
+        '\n'
+        'module load ParaView/%s-EGL%s \n'
+        'module unload VTK \n'
+        '\n'
+        'exec python -m ipykernel $@\n'
+        'EOF'
+    ) % (local_kernel_dir,
+         local_jupyterver, local_pysuffix,
+         local_paraviewver, local_pysuffix),
+    'source %(builddir)s/env.sh && chmod +x %(installdir)s/share/jupyter/kernels/${KERNEL_DIR}/kernel.sh',
+
+    # write kernel.json
+    (
+        '{ source %%(builddir)s/env.sh && '
+        '  cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.json; } << \'EOF\'\n'
+        '{ \n'
+        '  "argv": [ \n'
+        '    "%%(installdir)s/share/jupyter/kernels/%s/kernel.sh", \n'
+        '    "-m", \n'
+        '    "ipykernel_launcher", \n'
+        '    "-f", \n'
+        '    "{connection_file}" \n'
+        '  ], \n'
+        '  "display_name": "%s", \n'
+        '  "language": "python", \n'
+        '  "name": "%s" \n'
+        '}\n'
+        'EOF'
+    ) % (local_kernel_dir, local_kernel_dir, local_kernel_name, local_kernel_name),
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/%s/kernel.sh' % local_kernel_dir,
+        'share/jupyter/kernels/%s/kernel.json' % local_kernel_dir,
+    ],
+    'dirs': [
+        'share/jupyter/kernels/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-R/JupyterKernel-R-4.0.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-R'
+version = '4.0.2'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://github.com/IRkernel/IRkernel'
+description = """
+Native R kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Jupyter', local_jupyterver, local_pysuffix),
+    ('R', '4.0.2', '-nompi'),
+]
+
+modextrapaths = {
+    'JUPYTER_PATH': 'share/jupyter',  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    # Jupyter Kernel: R - https://github.com/IRkernel/IRkernel
+    # installs R kernel in $EBROOTJUPYTER/share/jupyter/kernels
+    'R -e \'IRkernel::installspec(name="ir40", displayname="R 4.0", prefix="%(installdir)s")\'',
+
+    # force options(bitmapType='cairo') -> https://github.com/IRkernel/IRkernel/issues/388
+    (
+        'sed -i "s#IRkernel::main()#options(bitmapType=\'cairo\') ; IRkernel::main()#g" '
+        '       %(installdir)s/share/jupyter/kernels/ir40/kernel.json'
+    ),
+]
+
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/ir40/kernel.json',
+    ],
+    'dirs': [
+        'share/jupyter/kernels/ir40/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterKernel-Ruby/JupyterKernel-Ruby-2.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Ruby'
+version = '2.7.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://github.com/SciRuby/iruby'
+description = """
+Native Ruby kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python',  '3.8.5'),
+    ('Jupyter', local_jupyterver, local_pysuffix),
+    ('Ruby',    '2.7.1'),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+    'JUPYTER_PATH': ['share/jupyter'],  # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+    'echo "#!/bin/bash" > %(builddir)s/env.sh',
+    'echo "export JUPYTER_DATA_DIR=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyter_path,
+
+    # install Ruby kernel in $JUPYTHER_PATH
+    'source %(builddir)s/env.sh && iruby register --force ',
+
+    # ensure correct permissions
+    'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+    'files': [
+        'share/jupyter/kernels/ruby/kernel.json',
+    ],
+    'dirs': [
+        'share/jupyter/kernels/ruby/',
+    ],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterProxy-XpraHTML5/JupyterProxy-XpraHTML5-0.3.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb

+easyblock = 'PythonBundle'
+
+name = 'JupyterProxy-XpraHTML5'
+version = '0.3.0'
+
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+homepage = 'https://xpra.org'
+description = """
+Jupyter proxy for Xpra HTML5 sessions.
+Xpra is an open-source multi-platform persistent remote display server and client
+for forwarding applications and desktop screens.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.34'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('Jupyter', local_jupyterver, '-Python-%(pyver)s'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+}
+
+local_common_opts = {
+    'req_py_majver': '3',
+    'req_py_minver': '0'
+}
+
+exts_list = [
+    ('jupyter-xprahtml5-proxy', '0.3.0', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', 'db852682e8e366091e6a3984b60ac3d2e6b3197be2ef074440c11cb09e23b80b')]),
+        ('source_urls', ['https://github.com/FZJ-JSC/jupyter-xprahtml5-proxy/archive/']),
+        ('source_tmpl', 'v0.3.0_devel.tar.gz'),
+        ('patches', ['jupyter_xprahtml5_proxy-launch_xpra.patch']),
+        ('modulename', 'jupyter_xprahtml5_proxy'),
+    ])),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterProxy-XpraHTML5/jupyter_xprahtml5_proxy-launch_xpra.patch

+diff -Naur jupyter-xprahtml5-proxy.orig/jupyter_xprahtml5_proxy/share/launch_xpra.sh jupyter-xprahtml5-proxy/jupyter_xprahtml5_proxy/share/launch_xpra.sh
+--- jupyter-xprahtml5-proxy.orig/jupyter_xprahtml5_proxy/share/launch_xpra.sh   2020-11-19 00:13:39.000000000 +0100
++++ jupyter-xprahtml5-proxy/jupyter_xprahtml5_proxy/share/launch_xpra.sh        2020-11-20 18:49:09.557792000 +0100
+@@ -5,10 +5,17 @@
+ # Do it here.
+
+ # example
+-# module purge > /dev/null
+-# module use $OTHERSTAGES > /dev/null
+-# module load Stages/2020 > /dev/null
+-# module load GCCcore/.9.3.0 > /dev/null
+-# module load xpra/4.0.4-Python-3.8.5 > /dev/null
++module purge
++module use $OTHERSTAGES
++module load Stages/2020
++module load GCCcore/.9.3.0
++module load xpra/4.0.4-Python-3.8.5
++module load jsc-xdg-menu/.2020.3
++
++if ! command -v xterm &> /dev/null
++then
++    echo "xterm not found - trying to load the xterm-module"
++    module load xterm
++fi
+
+ xpra "$@"
+

Golden_Repo/jurecadc_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb

@@ -36,7 +36,7 @@ builddependencies = [
     ('archspec', '0.1.0', '-Python-%(pyver)s'),
 ]
 dependencies = [
-    ('CUDA', '11.0', '', True),
+    ('CUDA', '11.0', '', SYSTEM),
     ('Python', '3.8.5'),
     ('libpng', '1.6.37'),
     ('libjpeg-turbo', '2.0.5'),

Golden_Repo/jurecadc_overlay/v/Vampir/Vampir-9.9.0.eb

+# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild
+# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany
+# Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
+# License::   New BSD
+#
+# This work is based from experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+##
+easyblock = 'Binary'
+
+name = "Vampir"
+version = "9.9.0"
+local_archsuffix = "-linux-x86_64"
+
+homepage = 'http://www.vampir.eu'
+description = """The VAMPIR software tool provides an easy-to-use framework that enables
+developers to quickly display and analyze arbitrary program behavior at any level of detail.
+The tool suite implements optimized event analysis algorithms and customizable displays that
+enable fast and interactive rendering of very complex performance monitoring data.
+
+"""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = SYSTEM
+
+sources = ['vampir-%s%s-setup.sh' % (version, local_archsuffix)]
+
+install_cmd = './vampir-%(version)s-linux-x86_64-setup.sh --silent --instdir=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ["bin/vampir", "doc/vampir-manual.pdf"],
+    'dirs': []
+}
+
+modextravars = {
+    'VAMPIR_LICENSE': '/p/software/jurecadc/licenses/vampir/vampir.license',
+}
+
+moduleclass = 'tools'

Golden_Repo/jurecadc_overlay/v/VampirServer/VampirServer-9.9.0-gpsmpi-2020.eb

+# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild
+# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany
+# Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
+# License::   New BSD
+#
+# This work is based from experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+##
+easyblock = 'Binary'
+
+name = "VampirServer"
+version = "9.9.0"
+
+homepage = 'http://www.vampir.eu'
+description = """The VAMPIR software tool provides an easy-to-use framework that enables
+developers to quickly display and analyze arbitrary program behavior at any level of detail.
+The tool suite implements optimized event analysis algorithms and customizable displays that
+enable fast and interactive rendering of very complex performance monitoring data.
+"""
+
+usage = """
+To start VampirServer
+module load Vampir VampirServer
+vampir &
+BATCH_OPT="--account=<budget> --partition=<partition>" vampirserver start -n 4 mpi
+(note server + port + server_id)
+- Use it
+Vampir GUI-> open other -> remote file -> server + port
+- To stop VampirServer
+vampirserver stop <server_id>
+"""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+toolchainopts = {"usempi": True}
+
+sources = ['vampirserver-%s-linux-x86_64-setup.sh' % (version)]
+
+install_cmd = ('./vampirserver-%(version)s-linux-x86_64-setup.sh --silent --instdir=%(installdir)s '
+               '&& %(installdir)s/bin/vampirserver config --silent')
+
+sanity_check_paths = {
+    'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"],
+    'dirs': []
+}
+
+# Remove Cray-specific 'ap' launcher,
+# use SLURM launcher as MPI launcher and default
+postinstallcmds = [
+    'rm %(installdir)s/etc/server/launcher/ap',
+    '''sed -i s/'BATCH_OPT=""'/'#BATCH_OPT=""'/g %(installdir)s/etc/server/launcher/custom/slurm''',
+    'cp %(installdir)s/etc/server/launcher/custom/slurm %(installdir)s/etc/server/launcher/mpi',
+]
+
+modextravars = {
+    'VAMPIR_LICENSE': '/p/software/jurecadc/licenses/vampir/vampir.license',
+}
+
+moduleclass = 'perf'

Golden_Repo/jusuf_overlay/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 = [
@@ -28,7 +29,8 @@ dependencies = [
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
 
-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 '
 
 sanity_check_paths = {
     'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],

Golden_Repo/jusuf_overlay/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 = [
@@ -28,7 +29,8 @@ dependencies = [
 sources = [SOURCELOWER_TAR_GZ]
 source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
 
-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 '
 
 sanity_check_paths = {
     'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],

Golden_Repo/juwelsbooster_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb

@@ -36,7 +36,7 @@ builddependencies = [
     ('archspec', '0.1.0', '-Python-%(pyver)s'),
 ]
 dependencies = [
-    ('CUDA', '11.0', '', True),
+    ('CUDA', '11.0', '', SYSTEM),
     ('Python', '3.8.5'),
     ('libpng', '1.6.37'),
     ('libjpeg-turbo', '2.0.5'),

Golden_Repo/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb

@@ -36,7 +36,7 @@ builddependencies = [
     ('archspec', '0.1.0', '-Python-%(pyver)s'),
 ]
 dependencies = [
-    ('CUDA', '11.0', '', True),
+    ('CUDA', '11.0', '', SYSTEM),
     ('Python', '3.8.5'),
     ('libpng', '1.6.37'),
     ('libjpeg-turbo', '2.0.5'),

Golden_Repo/l/libxc/README.md

+# libxc
+
+The default version of `libxc` in the stage `2020` is `4.3.4`. We decided against the newer version `libxc/5.0.0`, as some applications would need to be patched. However, also not every application is working with version `4.3.4`, as the API changed between version 3 and 4. This lead to the fact that we need two different version:
+
+- `libxc/3.0.1`
+- `libxc/4.3.4`
+
+Both versions are installed for the following toolchains:
+
+- `GCC/9.3.0`
+- `iccifort-2020.2.254-GCC-9.3.0`
+
+## ABINIT
+
+`ABINIT/8.X` is only working with `libxc/3.0.1` due to changes in the API. Starting with `ABINIT/9.X` version 4.3.0 or later is supported.
+
+## Quantum ESPRESSO
+
+While Quantum ESPRESSO 6.6 would work with `libxc/5.0.0`, QE would require a patch. From the Quantum ESPRESSO User Guide (https://www.quantum-espresso.org/Doc/user_guide.pdf):
+
+**Note  for  version  5.0.0:** the `f03` interfaces  are  no  longer  available  in `libxc` 5.0.0. They have been reintroduced in the current develop version.  Version 5.0.0 is still usable, but, before compiling Quantum ESPRESSO, a string replacement is necessary, namely `‘xcf03’` must berepalced with `‘xcf90’` everywhere in the following files: `funct.f90, xcldalsdadrivers.f90, xcggadrivers.f90, xcmggadrivers.f90, dmxcdrivers.f90` and `dgcxcdrivers.f90` in `Modules` folder and `xctestqelibxc.f90` in `PP/src` folder.
+
+## Note for future Stage 2021
+
+Check if all application can work with the newest version of `libxc`, e.g. 5.0.0. One common version would be desirable.