How to run the job script on the Singularity container_?

STa

Hi all, I deployed PBS pro(free demo) cluster with 2 host.

• node138: altair license manager, server host, execution host
• node139: execution host

And installed Singularity on both node and I have confirmed it worked.

[pbsdata@node139 ~]$ singularity exec /home/pbsdata/singularity_img/lolcow.sif cowsay moo
 _____
< moo >
 -----
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

 

My goal is that job script command run on the singularity container without singularity command like "singularity exec ***.sif command" in order to entrust container management to PBS.

In the Administrator's Guide, there is Singularity sample command;

qsub -v CONTAINER_IMAGE=pbsuser/test-image 

Then I prepared Singularity image file and job script.

#!/bin/sh
#PBS -N lolcowJob
#PBS -l select=1:ncpus=1:host=node139:container_engine=singularity,walltime=00:01:00
#PBS -o output.txt
#PBS -e error.txt
#PBS -v CONTAINER_IMAGE="/home/pbsdata/singularity_img/lolcow.sif"
cowsay moo

But it seems that the container does not start and the command in the container not found.

/var/spool/pbs/mom_priv/jobs/554.node138.SC: line 1: cowsay: command not found

Could you tell me where is my misunderstanding?

Thank you.

STa

I would like to add some information of my environment.

• OS is Rocky Linux 9.3.
• pbs_version = 2022.1.4.20231010124201
• singularity-ce version 4.1.0
• Singularity image I am using for test is created by following.

singularity build lolcow.sif library://sylabs-jms/testing/lolcow

If there is a lack of information, please let me know.

Thank you.