Difference between revisions of "Biocluster Singularity"

Revision as of 09:52, 3 February 2020

module load singularity/3.4.1

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

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

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.

@@ Line 26: / Line 26: @@
 </pre>
-== Mounting Storage ==
+== Storage ==
-* By default singularity will only have your home folder mounted.
+* Your home folder is automatically mounted
-* To mount /home/group, /home/lab, or /private_stores folder, please use the -B parameter to bind the folder into singularity
+* You should have access to any group folders in /home/groups, /home/labs, and /private_stores
-* 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.
+* The local /scratch space is accessible.
-<pre>
-singularity exec -B /private_stores/mirrors:/private_stores/mirrors r-base_latest.sif R