you didn't specify what clustering method u r using. Are u using drmaa
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Fax: +64(0)3 479 7866
On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi <pa...@uab.edu> wrote:
> We experienced an issue where some of the galaxy jobs were sitting in the
> 'new' state for a quite long time. They were not waiting for cluster
> resources to become available, but haven't been even queued up through
> DRMAA. We are currently using non-debug mode and following were my
> * No indication of new jobs in paster.log file
> * database/pbs script didn't contain any associated job scripts
> * in backend database - job table contained their galaxy job id but no
> command_line input was recorded
> Also, not all the jobs are waiting in the 'new' state. Many jobs submitted
> after above waiting jobs got completed successfully on the cluster. Is there
> any job submission logic within galaxy which is being used for submitting
> jobs? Any clues on how to debug this issue will be really helpful.
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