Biocluster Singularity
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Module[edit]
- Load Singularity Module to run any singularity commands
module load singularity/3.4.1
Creating Containers[edit]
- This can not be done on the Biocluster. It has to be done on your local machine. This is a security risk to allow users to create or edit containers.
Download Containers[edit]
- You need to use the biologin nodes (biologin-0 and biologin-1) to download containers
- This will not work from the compute nodes as they do not have access to the internet
- Download a pre-existing container from Singularity Hub - https://singularity-hub.org/. singularity-r is an example R container
singularity pull --name singularity-r.simg shub://nickjer/singularity-r
- Download a pre-existing container from Docker - https://hub.docker.com/. r-base is an example R container
singularity pull docker://r-base
Running Containers[edit]
- Do not use the biologin nodes (biologin-0 and biologin-1) to run containers. The login nodes are only allowed to be used to download containers
- From a compute node or a SLURM job script, run the following. r-base_latest.sif is name of the container. R is the program to run in the container. This can be bash to get a command line.
singularity exec r-base_latest.sif R
