apply singularity -w workaround only on macos with apple silicon (and…

… in jupyter notebooks)

Dockerfile

@@ -51,9 +51,9 @@ ARG TOMCAT_REL="9"
 ARG TOMCAT_VERSION="9.0.97"
 ARG GUACAMOLE_VERSION="1.5.5"
 
-ENV LANG ""
-ENV LANGUAGE ""
-ENV LC_ALL ""
+ENV LANG=""
+ENV LANGUAGE=""
+ENV LC_ALL=""
 
 # Install apptainer
 RUN add-apt-repository -y ppa:apptainer/ppa \
@@ -337,7 +337,7 @@ COPY --chown=${NB_UID}:${NB_GID} ./config/lxde/libfm.conf /home/${NB_USER}/.conf
 RUN touch /home/${NB_USER}/.sudo_as_admin_successful
 
 ENV DONT_PROMPT_WSL_INSTALL=1
-ENV LMOD_CMD /usr/share/lmod/lmod/libexec/lmod
+ENV LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod
 
 # Add startup and config files for neurodesktop, jupyter, guacamole, vnc
 RUN mkdir /home/${NB_USER}/.vnc \
@@ -388,8 +388,10 @@ ADD "https://api.github.com/repos/neurodesk/example-notebooks/git/refs/heads/mai
 RUN rm /home/${NB_USER}/skipcache \
     && git clone --depth 1 https://github.com/NeuroDesk/example-notebooks
 
-# Set SINGULARITY_BINDPATH and MODULEPATH here so it's available within a notebook (the startup scripts set these things too late):
+# 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 "
+ENV neurodesk_singularity_opts=" -w "
+# It would be better not to have to set any of these variables here, but I don't know how to get them into the jupyter notebooks otherwise

config/jupyter/environment_variables.sh

@@ -38,9 +38,18 @@ export PATH=$PATH:/home/${NB_USER}/.local/bin:/opt/conda/bin:/opt/conda/condabin
 
 # workaround for docker on MacOS - this -w flag should only be done when needed, because it prevents apptainer overlay bind mounts from working if they do not yet exist inside the container
 # check if the user is running on MacOS with Apple Silicon through our CPU Frequency hack file /home/${NB_USER}/.local/cpuinfo_with_ARM_MHz_fix
+# echo "[INFO] Checking if our CPU Frequency hack file is present to determine if we are running on MacOS with Apple Silicon to then set the -w workaround."
 if [ -f ~/.local/cpuinfo_with_ARM_MHz_fix ]; then
+        # echo "[INFO] Detected MacOS with Apple Silicon, setting -w workaround for singularity."
         export neurodesk_singularity_opts=" -w "
 fi
+# Test this in jupyter terminal, desktop terminal and a notebook:
+# !echo $neurodesk_singularity_opts
+# test if the workaround is still needed: ml fsl; fslmaths or 
+# import lmod
+# await lmod.load('fsl/6.0.4')
+# await lmod.list()
+# !fslmaths
 
 # # this adds --nv to the singularity calls -> but only if a GPU is present
 # if [ "$(lspci | grep -i nvidia)" ]

config/jupyter/jupyterlab_startup.sh

@@ -104,22 +104,23 @@ if [ ! -L "/neurocommand/local/containers" ]; then
 fi
 
 # Create a cpufino file with a valid CPU Mhz entry for ARM cpus
+echo "[INFO] Checking for ARM CPU and adding a CPU Mhz entry in /proc/cpuinfo to work around a bug in Matlab that expects this value to be present."
 if ! grep -iq 'cpu.*hz' /proc/cpuinfo; then
+    mkdir -p /home/${NB_USER}/.local
     cpuinfo_file=/home/${NB_USER}/.local/cpuinfo_with_ARM_MHz_fix
     cp /proc/cpuinfo $cpuinfo_file
     chmod u+rw $cpuinfo_file
     sed -i '/^$/c\cpu MHz         : 2245.778\n' $cpuinfo_file
     sudo mount --bind $cpuinfo_file /proc/cpuinfo
+    echo "[INFO] Added CPU Mhz entry in /proc/cpuinfo to work around a bug in Matlab that expects this value to be present."
 fi
 
 # Start and stop SSH server to initialize host
 sudo service ssh restart
 sudo service ssh stop
 
-
 source /opt/neurodesktop/environment_variables.sh
 
-
 conda init bash
 mamba init bash