Bunya

Neurodesk is installed at the University of Queensland’s supercomputer “Bunya”. To access Neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open OnDemand) or run:

salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --mem=5G --job-name=TinyInteractive --time=01:00:00 --partition=debug --account=REPLACE_THIS_WITH_YOUR_AccountString srun --export=PATH,TERM,HOME,LANG --pty /bin/bash -l

Then load the neurodesk modules:

module use /sw/local/rocky8/noarch/neuro/software/neurocommand/local/containers/modules/
export APPTAINER_BINDPATH=/scratch,/QRISdata

Now you can list all modules (Neurodesk modules are the first ones in the list):

ml av

Or you can module load any tool you need:

ml qsmxt/6.4.1

If you want to use GUI applications (fsleyes, afni, suma, matlab, etc.) you need to overwrite the temporary directory to be /tmp (otherwise you get an error that it cannot connect to the DISPLAY):

export TMPDIR=/tmp

For matlab you also need to create a network license file in your ~/Downloads/network.lic:

cat <<EOF > ~/Downloads/network.lic
SERVER uq-matlab.research.dc.uq.edu.au ANY 27000
USE_SERVER
EOF

Note

If you are using AFNI on Bunya then the default detach behaviour will cause SIGBUS errors and a crash. To fix this run AFNI with:

afni -no_detach

Note

MRIQC has its $HOME variable hardcoded to be /home/mriqc. This leads to problems on Bunya. A workaround is to run this before mriqc:

export neurodesk_singularity_opts="--home $HOME:/home"

If you are missing an application, please contact mail.neurodesk@gmail.com and ask for the neurodesk installation to be updated on Bunya.

Using this inside a jupyter notebook

You need to install this in addition:

pip install jupyterlab_niivue ipyniivue jupyterlmod jupyterlab_slurm

Then start a notebook and run these commands:

import module
await module.load('niimath')