- Add more server URLs with updated ones in neurodesk.ardc.edu.au.conf

- Modify test-cvmfs.yml and test_cvmfs.sh for better server probing
- Add static strace executable to Docker image for debugging purposes and remove packaged strace
- Adjust jupyter environment variables for Docker compatibility on Apple silicon
- Fix user-mapping.xml for VNC connection and remove obsolete configuration file

.github/workflows/test-cvmfs.yml

@@ -38,8 +38,7 @@ jobs:
                         "s1bnl-cvmfs.openhtc.io",
                         "s1osggoc-cvmfs.openhtc.io:8080",
                         "s1brisbane-cvmfs.openhtc.io",
-                        "cvmfs-brisbane.neurodesk.org", 
-                        "cvmfs-perth.neurodesk.org",
+                        "s1perth-cvmfs.openhtc.io",
                         "s1nikhef-cvmfs.openhtc.io",
                         "cvmfs-frankfurt.neurodesk.org",
                         "cvmfs-geoproximity.neurodesk.org",
@@ -63,69 +62,4 @@ jobs:
       with:
         filename: .github/job_failure_issue_template.md
         update_existing: true
-        search_existing: open
-
-
-
-# # currently not yet working:
-  # cvmfs-egi.gridpp.rl.ac.uk:8000
-#   "s1ral-cvmfs.openhtc.io:8080",
-
-#   "cvmfs-s1.hpc.swin.edu.au:8080",
-# s1swinburne-cvmfs.openhtc.io:8080,
-
-#   "cvmfs-stratum-one.ihep.ac.cn:8080",
-# s1ihep-cvmfs.openhtc.io:8080,
-
-# vmfs-s1bnl.opensciencegrid.org, 
-#   "s1bnl-cvmfs.openhtc.io:8080",
-
-# cvmfs01.nikhef.nl, 
-#   "s1nikhef-cvmfs.openhtc.io:8080",
-
-
-# working
-# cvmfs-s1fnal.opensciencegrid.org:8000
-# s1fnal-cvmfs.openhtc.io:8080",
-# Illinois, USA
-
-# sampacs01.if.usp.br:8000
-# "s1sampa-cvmfs.openhtc.io:8080",
-# Sao Paulo, Brazil
-
-# cvmfs-s1goc.opensciencegrid.org:8000
-# "s1osggoc-cvmfs.openhtc.io:8080",
-# Lincoln, Nebraska, USA
-
-# cvmfs-brisbane.neurodesk.org
-# "s1brisbane-cvmfs.openhtc.io",
-# Brisbane, Australia
-
-# cdn:
-# s1ral-cvmfs.openhtc.io
-# s1nikhef-cvmfs.openhtc.io
-# s1bnl-cvmfs.openhtc.io
-# s1fnal-cvmfs.openhtc.io:8080
-# s1ihep-cvmfs.openhtc.io:8080
-# s1swinburne-cvmfs.openhtc.io:8080
-# s1sampa-cvmfs.openhtc.io:8080
-# s1osggoc-cvmfs.openhtc.io:8080
-# s1brisbane-cvmfs.openhtc.io
-
-
-# stratum1:
-# cvmfs-egi.gridpp.rl.ac.uk:8000
-# cvmfs01.nikhef.nl:8000
-# cvmfs-s1bnl.opensciencegrid.org:8000
-# cvmfs-s1fnal.opensciencegrid.org:8000
-# cvmfs-stratum-one.ihep.ac.cn:8000
-# cvmfs-s1.hpc.swin.edu.au:8000
-# sampacs01.if.usp.br:8000
-# cvmfs-s1goc.opensciencegrid.org:8000
-# cvmfs-brisbane.neurodesk.org
-
-
-
-
-# DNS setup:
-
+        search_existing: open

.github/workflows/test_cvmfs.sh

@@ -51,12 +51,9 @@ curl --head http://cvmfs-geoproximity.neurodesk.org/cvmfs/neurodesk.ardc.edu.au/
 echo "[DEBUG]: Test download from cvmfs.neurodesk.org"
 curl --head http://cvmfs.neurodesk.org/cvmfs/neurodesk.ardc.edu.au/.cvmfspublished
 
-cvmfs_config probe neurodesk.ardc.edu.au
-
 cvmfs_config stat -v neurodesk.ardc.edu.au
 
 
-
 ## Test if containers are on CVMFS:
 wget https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/cvmfs/log.txt
 echo "debug logfile:"

Dockerfile

@@ -12,6 +12,7 @@ USER root
 #========================================#
 # Core services
 #========================================#
+
 
 # Install base image dependencies
 RUN apt-get update --yes \
@@ -34,7 +35,6 @@ RUN apt-get update --yes \
         libssl-dev \
         libwebp-dev \
         libssh2-1-dev \
-        strace \
         # SSH (Optional)
         libpango1.0-dev \
         ## VNC
@@ -57,8 +57,13 @@ RUN apt-get update --yes \
         apt-transport-https \
         && apt-get clean && rm -rf /var/lib/apt/lists/* 
 
+# add a static strace executable to /opt which we can copy to containers for debugging:
+RUN mkdir -p /opt/strace \
+    && wget -qO- https://github.com/JuliaBinaryWrappers/strace_jll.jl/releases/download/strace-v6.7.0%2B1/strace.v6.7.0.x86_64-linux-gnu.tar.gz | tar xz -C /opt/strace --strip-components=1 \
+    && chmod +x /opt/strace
+
 ARG TOMCAT_REL="9"
-ARG TOMCAT_VERSION="9.0.87"
+ARG TOMCAT_VERSION="9.0.97"
 ARG GUACAMOLE_VERSION="1.5.5"
 
 ENV LANG ""
@@ -205,9 +210,10 @@ RUN /opt/conda/bin/pip install nipype matplotlib datalad-container datalad-osf o
 # Install jupyter-server-proxy and disable announcements
 # Deprecated: jupyter labextension install ..
 # jupyter_server_proxy needs to be at least 4.2.0 to fix CVE-2024-35225
+# jupyterlmod==4.0.3 needs to be pinned for now because they broken the API after that and have not fixed it yet in  5.2.1: https://github.com/cmd-ntrf/jupyter-lmod/issues/79
 RUN /opt/conda/bin/pip install jupyter-server-proxy \
     && /opt/conda/bin/jupyter labextension disable @jupyterlab/apputils-extension:announcements \ 
-    && /opt/conda/bin/pip install jupyterlmod \ 
+    && /opt/conda/bin/pip install jupyterlmod==4.0.3 \ 
     && /opt/conda/bin/pip install jupyterlab-git \
     && /opt/conda/bin/pip install jupyterlab_rise \
     && /opt/conda/bin/pip install ipycanvas \
@@ -391,5 +397,6 @@ RUN rm /home/${NB_USER}/skipcache \
 # Set SINGULARITY_BINDPATH and MODULEPATH here so it's available within a notebook (the startup scripts set these things too late):
 ENV APPTAINER_BINDPATH=/data,/mnt,/neurodesktop-storage,/tmp,/cvmfs
 ENV MODULEPATH=/cvmfs/neurodesk.ardc.edu.au/containers/modules/
+# This workaround is currently needed for Docker on Apple silicone - they broke normal mounting of /cvmfs in the custom docker kernel. Mounting as writable works around it.
 ENV neurodesk_singularity_opts=" -w "
 

config/cvmfs/neurodesk.ardc.edu.au.conf

@@ -1,3 +1,3 @@
-CVMFS_USE_GEOAPI=no
-CVMFS_SERVER_URL="http://cvmfs.neurodesk.org/cvmfs/@fqrn@;http://cvmfs-geoproximity.neurodesk.org/cvmfs/@fqrn@"
+CVMFS_USE_GEOAPI=yes
+CVMFS_SERVER_URL="http://s1perth-cvmfs.openhtc.io/cvmfs/@fqrn@;http://s1fnal-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1sampa-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1osggoc-cvmfs.openhtc.io:8080/cvmfs/@fqrn@;http://s1brisbane-cvmfs.openhtc.io/cvmfs/@fqrn@;http://s1nikhef-cvmfs.openhtc.io/cvmfs/@fqrn@;http://cvmfs.neurodesk.org/cvmfs/@fqrn@;http://s1bnl-cvmfs.openhtc.io/cvmfs/@fqrn@"
 CVMFS_KEYS_DIR="/etc/cvmfs/keys/ardc.edu.au/"

config/guacamole/user-mapping.xml

@@ -1,16 +1,30 @@
 <user-mapping>
     <authorize username="jovyan" password="password">
-        <connection name="Desktop Dynamic-Resolution (RDP)">
+        <connection name="Desktop RDP - changes resolution by resizing window and waiting for refresh">
             <protocol>rdp</protocol>
             <param name="hostname">localhost</param>
             <param name="username">jovyan</param>
             <param name="password">password</param>
             <param name="port">3389</param>
-            <param name="security\">any</param>
+            <param name="security">any</param>
             <param name="ignore-cert">true</param>
-            <param name="resize-method\">reconnect</param>
+            <param name="resize-method">reconnect</param>
             <param name="enable-drive">true</param>
             <param name="drive-path">/home/jovyan/Desktop</param>
         </connection>
+        <connection name="Desktop VNC - changes resolution by running lxrandr on a terminal">
+            <protocol>vnc</protocol>
+            <param name="hostname">localhost</param>
+            <param name="username">jovyan</param>
+            <param name="password">password</param>
+            <param name="port">5901</param>
+            <param name="enable-sftp">true</param>
+            <param name="sftp-hostname">localhost</param>
+            <param name="sftp-username">jovyan</param>
+            <param name="sftp-port">2222</param>
+            <param name="sftp-directory">/home/jovyan/Desktop</param>
+            <param name="sftp-private-key">
+            </param>
+        </connection>
     </authorize>
 </user-mapping>

config/jupyter/before_notebook.sh

@@ -32,8 +32,7 @@ if [ ! -d "/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/" ]; then
 
                 echo "\
                 ==================================================================
-                Testing which CVMFS server is fastest"
-                cvmfs_talk -i neurodesk.ardc.edu.au host probe
+                CVMFS servers:"
                 cvmfs_talk -i neurodesk.ardc.edu.au host info
             fi
         fi

config/jupyter/environment_variables.sh

@@ -37,14 +37,11 @@ export MPLCONFIGDIR=/home/${NB_USER}/.config/matplotlib-mpldir
 export PATH=$PATH:/home/${NB_USER}/.local/bin:/opt/conda/bin:/opt/conda/condabin
 
 # this adds --nv to the singularity calls -> but only if a GPU is present
-if [ "`lspci | grep -i nvidia`" ]
+if [ "$(lspci | grep -i nvidia)" ]
 then
         export neurodesk_singularity_opts="${neurodesk_singularity_opts} --nv "
 fi
 
-# fix for kernel bug in docker on arm64 when using a read-only bindmount from a fuse mount. The -w flag makes the container writable instead of read-only which works around the issue
-export neurodesk_singularity_opts="${neurodesk_singularity_opts} -w "
-
 export PS1='\u@neurodesktop-$NEURODESKTOP_VERSION:\w$ '
 
 alias ll='ls -la'