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module load tools/Singularity



Table of Contents

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Building a Container from a pre-built on dockerhub


Info

Due to the security settings on Mana, when building a singularity container on Mana with the default settings it is possible that it will fail.  This is due to restrictions placed on a user home directory as far as who is granted access.  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.

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[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 $PATH
[user@node-0005 ~]$

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External Links

Intro to Singularity : Presentation material from a 2021 workshop from the UH CI team

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