Installation Examples on Neurodesk

Ubuntu 24.04

Mon, 01 Jan 0001 00:00:00 +0000

On this page we show specific examples of the different ways of how Neurodesk can be installed on a local computer. We start from the highest level using the Neurodesk app, then go lower level via docker, neurocommand and down to the lowest level using neurocontainers. We also show on each level how containers can be streamed via CVMFS or downloaded locally.

Running Neurodesk on a Ubuntu 24.04 computer

On a linux machine you have mutliple options to use Neurodesk:

Bunya

Mon, 01 Jan 0001 00:00:00 +0000

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 On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) 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):

Greatlakes

Mon, 01 Jan 0001 00:00:00 +0000

Setup on a desktop

module load singularity
# now change to a directory with enough storage, e.g. /nfs/turbo/username
git clone https://github.com/neurodesk/neurocommand.git 
cd neurocommand 
pip3 install -r neurodesk/requirements.txt --user 
bash build.sh --cli
bash containers.sh
export SINGULARITY_BINDPATH=`pwd -P`
bash containers.sh itksnap
# now select a version of itksnap to install. For this copy and paste the installation
echo "module load singularity" >> ~/.bashrc
echo "module use $PWD/local/containers/modules/" >> ~/.bashrc
echo "export SINGULARITY_BINDPATH=/nfs/,/scratch/" >> ~/.bashrc

Setup on with a jupyter notebook

Start new Jupyter notebook by entering “load singularity” in the Module Commands field:

Sherlock

Mon, 01 Jan 0001 00:00:00 +0000

Neurodesk runs on Stanfords supercomputer “Sherlock” and below are different ways of accessing it.

Using Neurodesk on Sherlock via ssh

Using Neurodesk containers

Setup your ~/.ssh/config

Nectar Virtual Desktop Service

Mon, 01 Jan 0001 00:00:00 +0000

Note

Link to Nectar Virtual Desktop Service: **https://desktop.rc.nectar.org.au**

This option is only available to Australian researchers. See [here](https://desktop.rc.nectar.org.au/about/) for more information

There are a few differences between the open-source version of Neurodesk and what’s hosted on Nectar VDI:

There is no /neurodesktop-storage folder (the folder on the Desktop does not lead anywhere).
Files uploaded via drag and drop do not get stored on the desktop but in /home/vdiuser/thinclient_drives/GUACFS

Instructions for use

Go to https://desktop.rc.nectar.org.au/