Difference between revisions of "Biocluster Singularity"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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(Running Containers)
(Creating Containers)
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== Creating Containers ==
 
== Creating Containers ==
* 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.
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* 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 ==
 
== Download Containers ==

Revision as of 10:51, 3 February 2020

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 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 - https://singularity-hub.org/. singularity-r is an example R container
singularity pull --name singularity-r.simg 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
  • You should have access to any group folders in /home/groups, /home/labs, and /private_stores
  • /scratch space is accessible.

Mounting Storage[edit]

  • By default singularity will only have your home folder mounted.
  • To mount /home/group, /home/lab, or /private_stores folder, please use the -B parameter to bind the folder into singularity
  • The format is -B source_dir:container_dir where source_dir is the location on the compute node and container_dir is the directory in the container you want the folder to bind to. We recommend to always keep them the same.
singularity exec -B /private_stores/mirrors:/private_stores/mirrors r-base_latest.sif R