[Bug]: mne with vscode permissions error on Nectar Desktop

[air2310]

Version

Neurodesk through Nectar research cloud virtual desktop service (not sure what version is running)

What platform are you seeing the problem on?

Nectar

What happened

Opening any of the mne/vscode containers results in the following error from vscode:

""Unable to write program user data. A system error occurred. Please make sure the following directories are writable:
~/.confic/Code
/opt/vscode-extensions
/neurodesktop-storage"

It seems as though the opt directory is indeed not writable, so that might be the route of the issue.

Screenshot of error attached:

How to reproduce

Open up any of the mne/code containers through the virtual desktop service.

Relevant log output or screenshot

No response

[stebo85]

Dear @air2310,

yes, that's indeed a bug. The problem comes from a missing /neurodesktop-storage bind mount.

The problem exists in the cloud version of neurodesk and on nectar

To fix it in nectar:

vi ~/.bashrc

Then add this at the end of the file:

export neurodesk_singularity_opts="${neurodesk_singularity_opts} --bind /neurodesktop-storage "

I will fix this now in nectar.

To fix it in the cloud version:

vi ~/.bashrc

Then change this:

export neurodesk_singularity_opts="${neurodesk_singularity_opts} --bind /home/jovyan:/home/matlab/.matlab/R2022a_licenses,/home/jovyan:/opt/matlab/R2022a/licenses "

To:

export neurodesk_singularity_opts="${neurodesk_singularity_opts} --bind /neurodesktop-storage,/home/jovyan:/home/matlab/.matlab/R2022a_licenses,/home/jovyan:/opt/matlab/R2022a/licenses "

This will be fixed with the new cloud image that @aswinnarayanan is working on and should be ready in a few days.

Thank you for finding this problem :)
Steffen

[stebo85]

There is also another little bug in the mne container that tries to execute module load inside the container when opening a terminal. For this the fix is:

replace:

if [ -d /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules ]; then
        # export MODULEPATH="/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules"
        module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*
else
        export MODULEPATH="/neurodesktop-storage/containers/modules"              
        module use $MODULEPATH
        export CVMFS_DISABLE=true
fi


if [ -f '/usr/share/module.sh' ]; then
        echo 'Run "ml av" to see which tools are available - use "ml <tool>" to use them in this shell.'
        if [ -v "$CVMFS_DISABLE" ]; then
                if [ ! -d $MODULEPATH ]; then
                        echo 'Neurodesk tools not yet downloaded. Choose tools to install from the Application menu.'
                fi
        fi
fi

with

if [ -f '/usr/share/module.sh' ]; then
        if [ -d /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules ]; then
                module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*
        else
                export MODULEPATH="/neurodesktop-storage/containers/modules"
                module use $MODULEPATH
                export CVMFS_DISABLE=true
        fi

        echo 'Run "ml av" to see which tools are available - use "ml <tool>" to use them in this shell.'
        if [ -v "$CVMFS_DISABLE" ]; then
                if [ ! -d $MODULEPATH ]; then
                        echo 'Neurodesk tools not yet downloaded. Choose tools to install from the Application menu.'
                fi
        fi
fi

[air2310]

Thanks @stebo85! I somehow didn't see the github notification about your response to this, so only just found it, but it will still be super helpful to me in the coming days :) If the new cloud image is up and running, I can let you know if there's any further issues with it soon.