[slurm-users] [External] Re: Using "Environment Modules" in a SLURM script

Prentice Bisbal pbisbal at pppl.gov
Mon Jan 25 17:15:26 UTC 2021

I run into this problem occasionally. In my organization, most accounts 
are created with tcsh as the default shell, and then users copy my bash 
submission script example from my online documentation, or copy someone 
else's submission script written in bash. And then when the job runs, it 
fails with an error about the module command not being found.

The problem you are describing is because the module command is defined 
differently in bash and tcsh. In bash it's a function, but in tcsh it is 
an alias. Slurm jobs inherit the environment of the shell submitting the 
script, but when one of those shells is tcsh and the other is bash, or 
vice-versa, the definition of the command 'module' doesn't survive.

On RHEL-based systems, if your using the environment modules RPM,  the 
module command itself is defined in the the files 

One easy fix to this problem is that if someone is using tcsh but is 
using a bash submission script, they can make the interpreter of their 
bash submission script a login shell, which will process 
/etc/profile.d/*.sh by adding a -l to the interpreter line of their script:

#!/bin/bash -l

I imagine that this will work with someone using bash as their login 
shell, but writing their sbatch script in tcsh, but I've never come 
across that scenario.


On 1/22/21 9:34 AM, Thomas M. Payerle wrote:
> On our clusters, we typically find that an explicit source of the 
> initialization dot files is need IF the default shell of
> the user submitting the job does _not_ match the shell being used to 
> run the script.  I.e., for sundry historical and other reasons,
> the "default" login shell for users on our cluster is tcsh, so if an 
> user with login shell of tcsh submits a bash job script, they generally
> need to do an explicit "source ~/.profile".
> On Fri, Jan 22, 2021 at 5:42 AM Gestió Servidors 
> <sysadmin.caos at uab.cat <mailto:sysadmin.caos at uab.cat>> wrote:
>     Hello,
>     I use “Environment Modules” (http://modules.sourceforge.net/
>     <http://modules.sourceforge.net/>) in my SLURM cluster. In my
>     scripts I do need to add an explicit “source
>     /soft/modules-3.2.10/Modules/3.2.10/init/bash”. However, in
>     several examples I have read about SLURM scripts, nobody comments
>     that. So, have I forgotten a parameter in SLURM to “capture”
>     environment variables into the script or is it a problem due to my
>     distribution (CentOS-7)???
>     Thanks.
> -- 
> Tom Payerle
> DIT-ACIGS/Mid-Atlantic Crossroads payerle at umd.edu <mailto:payerle at umd.edu>
> 5825 University Research Park               (301) 405-6135
> University of Maryland
> College Park, MD 20740-3831

Prentice Bisbal
Lead Software Engineer
Research Computing
Princeton Plasma Physics Laboratory

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