Versions Compared

Old Version 7

changes.mady.by.user davidls

Saved on

compared with

New Version Current

changes.mady.by.user davidls

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Building a Container from a pre-built on dockerhub

Info

Due to the security settings on the cluster, when building a singularity container using the default settings it is possible that it will fail.  To work around this. user can try two things:

  1. Set the SINGULARITY_CACHEDIR to something other than one of your user/group/lab storage

  2. Build the container is a directory that is not one of your user/group/lab storage locations

A recommendation for this is to use /tmp on the compute node for both.  Please make sure when creating your interactive sessions to request enough memory for your container  as /tmp uses memory on the computing node as no physical hard drives exist in the computing nodes.

When building a container for singularity from dockerhub, 

Code Block
languagebash
themeMidnight
[user@login001 ~]$ srun -p sandbox -c4 --mem=24G -t 60 --pty /bin/bash
[user@node-0005 ~]$ module load tools/Singularity
[user@node-0005 ~]$ singularity pull docker://godlovedc/lolcow
NFO: Converting OCI blobs to SIF format
WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process
INFO: Starting build...
INFO: Creating SIF file...
[user@node-0005 ~]$ singularity exec lolcow_latest.sif sinfo
FATAL: "sinfo": executable file not found in $PATH
[user@node-0005 ~]$

...