Greatlakes

Use Neurodesk on Greatlakes - the HPC at University of Michigan

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:

image

Then run these commands:

!pip install jupyterlmod

# Restart the kernel by clicking Kernel -> Restart Kernel

import module
await module.load('niimath')