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Using Singularity on Our Clusters§

Singularity is installed on all our clusters. You can use containers you have downloaded in your space.

Run singularity --version to see which version we currently have installed.

Set up cache locations and bind directories§

The cache directories should be set to somewhere in your space so they don't fill up /tmp on the login nodes.

The bindpath specifies what directories are made available inside the container - only your home is bound by default so you need to add Scratch.

# Create a .singularity directory in your Scratch
mkdir $HOME/Scratch/.singularity

# Set all the Singularity cache dirs to Scratch
export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity/
export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull

# Bind your Scratch directory so it is accessible from inside the container
export SINGULARITY_BINDPATH=/scratch/scratch/$USER

Different subdirectories are being set for each cache so you can tell which files came from where.

You probably want to add those export statements to your .bashrc under # User specific aliases and functions so those environment variables are always set when you log in.

For more information on these options, have a look at the Singularity documentation: