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HPC Trouble Shooting

The following outlines some of the potential issues with using CQUni's HPC Systems and provides some potential solutions or work arounds.

My PBS Job finishes almost immediately with an error

Indicator: 

The job is submitted and accepted, but the job finishes almost immediately.  The error file contains:

command not found /var/spool/PBS/mom_priv/jobs/#######.pbsserver.SC

and/or

No such file or directory

Cause:

The PBS script file which is used to submit the job contains ^M (control M's), which is the dos version of a "end of line" character.  These ^M's cause the HPS Scheduler to not read the submission script file correctly.  This might occur if you cut and paste script code directly from a website site, or if the file was created or edited from a "Windows System".

If you execute the command cat –vet <PBS submission script filename> and you see ^M's in your file, this will be the cause of your issues.

Solution:

To remove the ^M's in your script file, issue the following command:

dos2unix <filename>

This command will convert your file into a unix file format.