diff --git a/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.8.0-GCCcore-11.3.0-2023.3.6.eb b/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.8.0-GCCcore-11.3.0-2023.3.6.eb
index 638aa5740164cdf4ac2ebdbcea580333ab723f2c..cfacda0030863ab03bdd9fc8b75fb0e0f6a45fea 100644
--- a/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.8.0-GCCcore-11.3.0-2023.3.6.eb
+++ b/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.8.0-GCCcore-11.3.0-2023.3.6.eb
@@ -59,21 +59,23 @@ exts_list = [
('matlab-proxy', '0.8.0', {
'patches': [
'noVersionCheck.patch',
+ 'matlabproxy_timeout.patch',
],
'checksums': [
('sha256', '965b0b7cfa6314638435089f211106c114b838e8f4945cb5f5dacb15c0cdf71f'),
('sha256', 'c21ba8969da77c88a266c97dc73dc64dc7a8f4fc20391f311bb4a6992d6e812c'),
+ ('sha256', '4f7d9f67566496223f01156f168e02af61b6b0a441afcaf7258b08f6ec79762d'),
],
}),
('jupyter-matlab-proxy', '0.8.0', {
'source_urls': ['https://github.com/mathworks/jupyter-matlab-proxy/archive/'],
'source_tmpl': 'v%(version)s.tar.gz',
'patches': [
- 'timeout.patch',
+ 'jupytermatlabproxy_timeout.patch',
],
'checksums': [
('sha256', 'b1785c8bed32d187c2fa15d921d047dd7483ec20442cdc5f34c0aad1ca06bac5'),
- ('sha256', 'f44b7eee2d73b492a885c6b051b755330ff973e083d341933d28172156f0ff16'),
+ ('sha256', '4d15cc52352dc0cdeb03cc01285cf01cfe01393f3eee77fe1c2e205d691a5b8d'),
],
}),
]
diff --git a/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.9.0-GCCcore-11.3.0-2023.3.6.eb b/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.9.0-GCCcore-11.3.0-2023.3.6.eb
new file mode 100644
index 0000000000000000000000000000000000000000..a9163da038dd08343e9cfde7c9b0ca95df97ff52
--- /dev/null
+++ b/Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.9.0-GCCcore-11.3.0-2023.3.6.eb
@@ -0,0 +1,136 @@
+easyblock = 'PythonBundle'
+
+name = 'JupyterProxy-Matlab'
+version = '0.9.0'
+local_jupyterver = '2023.3.6'
+versionsuffix = '-' + local_jupyterver
+
+# only users of the UNIX-group 'matlab' must have access
+# group = 'matlab'
+
+homepage = 'https://github.com/mathworks/jupyter-matlab-proxy'
+description = """The MATLAB integration for Jupyter enables you to open a MATLAB desktop
+in a web browser tab, directly from your Jupyter environment.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.38'),
+ # check for existance
+ # ('MATLAB', '2023a'),
+ # ('XServer', '21.1.6'),
+]
+
+dependencies = [
+ ('Python', '3.10.4'),
+ ('JupyterLab', local_jupyterver),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+ 'filter': ('python -c "import %(ext_name)s"', ''),
+ 'download_dep_fail': True,
+ 'source_urls': [PYPI_SOURCE],
+ 'use_pip': True,
+ 'sanity_pip_check': True,
+ 'use_pip_for_deps': False,
+}
+
+exts_list = [
+ # enable classic jupyter ####
+ ('jupyter_contrib_core', '0.4.2', {
+ 'checksums': [('sha256', '1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb')],
+ }),
+ ('jupyter_highlight_selected_word', '0.2.0', {
+ 'checksums': [('sha256', '9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b')],
+ }),
+ ('jupyter_nbextensions_configurator', '0.6.1', {
+ 'checksums': [('sha256', '4b9e1270ccc1f8e0a421efb8979a737f586813023a4855b9453f61c3ca599b82')],
+ }),
+ ('jupyter_contrib_nbextensions', '0.7.0', {
+ 'checksums': [('sha256', '06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca')],
+ }),
+ # core-packages ####
+ ('aiohttp-session', '2.12.0', {
+ 'checksums': [('sha256', '0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950')],
+ }),
+ ('matlab-proxy', '0.9.0', {
+ 'checksums': [
+ ('sha256', 'd8e76ef8c5d89aab286ad5bad65ecbdde1dca8803e2101f7d13e6f3ee3cb5cb5'),
+ ],
+ }),
+ ('jupyter-matlab-proxy', '0.8.0', {
+ 'source_urls': ['https://github.com/mathworks/jupyter-matlab-proxy/archive/'],
+ 'source_tmpl': 'v%(version)s.tar.gz',
+ 'patches': [
+ 'jupytermatlabproxy_timeout.patch',
+ ],
+ 'checksums': [
+ ('sha256', 'b1785c8bed32d187c2fa15d921d047dd7483ec20442cdc5f34c0aad1ca06bac5'),
+ ('sha256', '4d15cc52352dc0cdeb03cc01285cf01cfe01393f3eee77fe1c2e205d691a5b8d'),
+ ],
+ }),
+]
+
+postinstallcmds = [
+ (
+ '{ cat > %(installdir)s/bin/matlab; } << EOF \n'
+ '#!/bin/bash \n'
+ '\n'
+ '# Load required modules \n'
+ 'module purge \n'
+ 'module load Stages/${STAGE} \n'
+ 'module load GCCcore/.11.3.0 \n'
+ 'module load MATLAB \n'
+ 'module load XServer/21.1.6 \n'
+ '\n'
+ 'matlab "\$@" \n'
+ '\n'
+ 'EOF'
+ ),
+ 'chmod +x %(installdir)s/bin/matlab',
+ (
+ '{ cat > %(installdir)s/bin/Xvfb; } << EOF \n'
+ '#!/bin/bash \n'
+ '\n'
+ '# Load required modules \n'
+ '# and ensure stderr stays empty as matlab-proxy seems to fail if not \n'
+ 'module purge 2>&1 \n'
+ 'module load Stages/${STAGE} 2>&1 \n'
+ 'module load GCCcore/.11.3.0 2>&1 \n'
+ 'module load MATLAB 2>&1 \n'
+ 'module load XServer/21.1.6 2>&1 \n'
+ '\n'
+ 'Xvfb "\$@" 2>&1\n'
+ '\n'
+ 'EOF'
+ ),
+ 'chmod +x %(installdir)s/bin/Xvfb'
+]
+
+
+modextravars = {
+ 'MWI_USE_EXISTING_LICENSE': 'True',
+ 'MWI_PROCESS_START_TIMEOUT': '600',
+}
+
+# Jupyter-matlab-kernel DISABLED:
+# https://github.com/mathworks/jupyter-matlab-proxy/issues/62
+modextrapaths = {
+ # 'MWI_CUSTOM_MATLAB_ROOT': 'lib/python%(pyshortver)s/site-packages/jupyter_matlab_proxy/',
+ # '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"))
+# """
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterProxy-Matlab/jupytermatlabproxy_timeout.patch b/Golden_Repo/j/JupyterProxy-Matlab/jupytermatlabproxy_timeout.patch
new file mode 100644
index 0000000000000000000000000000000000000000..bd1e4cf7e819450ec9c34aecb1524698c8fc4926
--- /dev/null
+++ b/Golden_Repo/j/JupyterProxy-Matlab/jupytermatlabproxy_timeout.patch
@@ -0,0 +1,12 @@
+diff -Naur 0.8.0.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py 0.8.0/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py
+--- 0.8.0.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py 2023-10-16 13:08:25.138590609 +0200
++++ 0.8.0/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py 2023-10-16 12:55:47.863830331 +0200
+@@ -93,7 +93,7 @@
+ "--config",
+ config["extension_name"],
+ ],
+- "timeout": 100,
++ "timeout": 1800,
+ "environment": _get_env,
+ "absolute_url": True,
+ "launcher_entry": {"title": "Open MATLAB", "icon_path": icon_path},
diff --git a/Golden_Repo/j/JupyterProxy-Matlab/matlabproxy_timeout.patch b/Golden_Repo/j/JupyterProxy-Matlab/matlabproxy_timeout.patch
new file mode 100644
index 0000000000000000000000000000000000000000..a3fdc0a6ad20357ef3b83d70d8fef5663ba3bb31
--- /dev/null
+++ b/Golden_Repo/j/JupyterProxy-Matlab/matlabproxy_timeout.patch
@@ -0,0 +1,12 @@
+diff -Naur 0.8.0.orig/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py 0.8.0/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py
+--- 0.8.0.orig/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py 2023-10-16 13:09:23.368725542 +0200
++++ 0.8.0/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py 2023-10-16 12:57:02.458981541 +0200
+@@ -36,7 +36,7 @@
+ MATLAB_PORT_CHECK_DELAY_IN_SECONDS = 1
+ # The maximum amount of time in seconds the Embedded Connector can take
+ # for launching, before the matlab-proxy server concludes that something is wrong.
+- EMBEDDED_CONNECTOR_MAX_STARTUP_DURATION_IN_SECONDS = 120
++ EMBEDDED_CONNECTOR_MAX_STARTUP_DURATION_IN_SECONDS = 600
+
+ def __init__(self, settings):
+ """Parameterized constructor for the AppState class.
diff --git a/Golden_Repo/j/JupyterProxy-Matlab/timeout.patch b/Golden_Repo/j/JupyterProxy-Matlab/timeout.patch
deleted file mode 100644
index 11a1e821789ab3712ee650566bd4a2b27a90a3a8..0000000000000000000000000000000000000000
--- a/Golden_Repo/j/JupyterProxy-Matlab/timeout.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur 0.7.1.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py 0.7.1/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py
---- 0.7.1.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py 2023-08-21 14:27:12.000000000 +0200
-+++ 0.7.1/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py 2023-08-29 22:16:29.568376240 +0200
-@@ -48,7 +48,7 @@
- "--config",
- config["extension_name"],
- ],
-- "timeout": 100,
-+ "timeout": 1800,
- "environment": _get_env,
- "absolute_url": True,
- "launcher_entry": {"title": "Open MATLAB", "icon_path": icon_path},
diff --git a/Golden_Repo/m/MATLAB/MATLAB-2023b-GCCcore-11.3.0.eb b/Golden_Repo/m/MATLAB/MATLAB-2023b-GCCcore-11.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..ff2500d5bda552cd123ecdb9745a89d3cc9fba48
--- /dev/null
+++ b/Golden_Repo/m/MATLAB/MATLAB-2023b-GCCcore-11.3.0.eb
@@ -0,0 +1,72 @@
+# Attention: before calling 'eb':
+# export EB_MATLAB_KEY as fileInstallationKey
+# or export EB_MATLAB_LICFILE as license file
+
+name = 'MATLAB'
+version = '2023b'
+
+# only users of the UNIX-group 'matlab' must have access
+group = 'matlab'
+
+homepage = 'https://www.mathworks.com/products/matlab.html'
+description = """MATLAB is a high-level language and interactive environment
+that enables you to perform computationally intensive tasks faster than with
+traditional programming languages such as C, C++, and Fortran.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d96b9b3b36fad31a68061b7e64f6e0c7c3c072f85881290877cc5fc675ccb06f']
+
+dependencies = [
+ ('X11', '20220504'), # mlab req. libXt.so which is not on the computes
+ ('Java', '11', '', SYSTEM)
+]
+
+java_options = '-Xmx2048m'
+
+# if we remove
+# ```
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "runtime/glnxa64"))
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "bin/glnxa64"))
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "sys/os/glnxa64"))
+# ```
+# from the lua-Script. (needs a modification of eb-block-matlab)
+# postinstallcmds = [
+# # create a wrapper script to ensure we do not mess up the environment
+# # because MATLAB comes with its own libstdc++ and other system libs
+# # in $EBROOTMATLAB/sys/os/glnxa64/
+# 'mv %(installdir)s/bin/matlab %(installdir)s/bin/matlab.bin ',
+# (
+# '{ cat > %(installdir)s/bin/matlab; } << EOF\n'
+# '#!/bin/bash\n'
+# '\n'
+# 'MYPATH=\$(readlink -f \$0)\n'
+# 'export MATLAB_PATH=\$(realpath \$(dirname "\$MYPATH")/..)\n'
+# '\n'
+# 'export LD_LIBRARY_PATH=\$MATLAB_PATH/runtime/glnxa64:\$LD_LIBRARY_PATH\n'
+# 'export LD_LIBRARY_PATH=\$MATLAB_PATH/bin/glnxa64:\$LD_LIBRARY_PATH\n'
+# 'export LD_LIBRARY_PATH=\$MATLAB_PATH/sys/os/glnxa64:\$LD_LIBRARY_PATH\n'
+# '\n'
+# '"\$MATLAB_PATH/bin/matlab.bin" "\$@"\n'
+# 'EOF'
+# ),
+# 'chmod +x %(installdir)s/bin/matlab',
+# ]
+
+modloadmsg = """
+Attention: This software is RESTRICTED to ACADEMIC users who are members of the group matlab\n.
+"""
+
+modextravars = {
+ 'MATLAB_ROOT': '%(installdir)s',
+ 'MLM_LICENSE_FILE': '27000@zam2076.zam.kfa-juelich.de',
+}
+
+sanity_check_paths = {
+ 'files': ['bin/matlab', 'bin/glnxa64/MATLAB'],
+ 'dirs': [],
+}
+
+moduleclass = 'math'