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Windows 11 and Windows Subsystem for Linux

1. Install WSL

Follow the instructions to enable Windows Subsystem for Linux 2 in Windows 11: Microsoft WSL install guide.

2. Configure CVMFS, Singularity, and Lmod (only needs to be done once)

Install build tools

sudo apt update
sudo apt install make gcc

Install Singularity

export SINGULARITY_VERSION=3.9.3 VERSION=1.17.2 OS=linux ARCH=amd64
wget -q https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz
sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz
rm go$VERSION.$OS-$ARCH.tar.gz
export GOPATH=${HOME}/go
export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin
mkdir -p $GOPATH/src/github.com/sylabs
cd $GOPATH/src/github.com/sylabs
wget -q https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
tar -xzvf singularity-ce-${SINGULARITY_VERSION}.tar.gz
cd singularity-ce-${SINGULARITY_VERSION}
./mconfig --prefix=/usr/local/singularity
make -C builddir
sudo make -C builddir install
cd ..
sudo rm -rf singularity-ce-${SINGULARITY_VERSION}
sudo rm -rf /usr/local/go $GOPATH

Set up bindpaths for Singularity (e.g. in `.bashrc`)

export PATH="/usr/local/singularity/bin:${PATH}"
export SINGULARITY_BINDPATH='/cvmfs,/mnt,/home'

CVMFS

Follow the instructions in the CVMFS setup guide.

Lmod

sudo apt install lmod

3. Use Neurodesk containers

Initialise the Neurodesk modules:

module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*

Example usage of fsleyes:

ml fsl
fsleyes

List the available programs:

ml av