Biocluster Singularity

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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  • Containers contain applications in a way that keep them isolated from the host system that they run on. Containers allow a developer to package up an application with all of the parts it needs, such as libraries and other dependencies, and ship it all out as one package.
  • Singularity is a program that can launch containers securely in a HPC environment. Other similar programs are Docker, LXD, and Kubernetes.


  • Load Singularity Module to run any singularity commands
module load singularity/3.8.1

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 on a HPC resource

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 - singularity-r is an example R container
singularity pull --name r-base_latest.sif shub://nickjer/singularity-r
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


  • Your home folder is automatically mounted
  • You should have access to any group folders in /home/groups, /home/labs, and /private_stores
  • The local /scratch space is accessible.


  • If the container does run properly or can't find the command it is trying to run, its possible that the program exists in the /home folder within the singularity container. Since we automatically mount the biocluster's /home folder in the container, it then can't find the command. To get around this, you can remount the biocluster's /home folder in a new directory
singularity exec --no-mount hostfs --bind /home:/newhome container.sif