Giving your group members access to OpenPBS job output and error files

If you are working with a group of people on a cluster and use OpenPBS, the default permissions of the output and error log files are annoying because the person who started the job (maybe some days) is the only one allowed to read them — and maybe he’s not at work when the job finished.

So you need to tell PBS to set the proper permissions. The first idea may be to simply set your umask properly, e.g., to 0007 if the unix group of the team is your primary group. But this won’t work because it gets ignored by PBS by default (and also the project group most likely is NOT your primary group, usually this is users or a group named after your user account that only has a single member: you).

The solution is to adapt your PBS Batch Submission Script and add the following line to the header:

#PBS -W umask=0007

This is enough if the unix group used by the project is your primary group, but this is often not the case. Therefore, you also need this line (assuming the unix group is named project01):

#PBS -W group_list=project01

Note that the this does NOT affect output files written by the programs you start in the job script, it only affects the PBS output and error files (i.e., the STDOUT and STDERR logs of these programs).

Sources:
https://marylou.byu.edu/documentation/system-access/groups
https://twiki.cern.ch/twiki/bin/view/Main/OpenPBS
Verfied to work for OpenPBS version 2.5.9.

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About dfspspirit

PhD student in bioinformatics, interested in photography, level design, digital image manipulation, architecture and, of course, bioinformatics.
This entry was posted in Bioinformatics, supercomputing and tagged , , , . Bookmark the permalink.

One Response to Giving your group members access to OpenPBS job output and error files

  1. web site says:

    “Giving your group members access to OpenPBS job output and error files | spirit’s spinney” ended up being a wonderful blog post. However, if it possessed much more images it might be perhaps even even better. Thank u ,Arron

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