job_conf.xml is outside of my knowledge. Better wait to see what the others can tell us. -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu On Thu, Jun 12, 2014 at 8:31 AM, Shrum, Donald C <DCShrum@admin.fsu.edu> wrote:
It's set to 600 seconds so I don't think that is the issue... Is there some sort of wait time to set in job_conf.xml
-----Original Message----- From: Evan Bollig [mailto:boll0107@umn.edu] Sent: Thursday, June 12, 2014 9:27 AM To: Shrum, Donald C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] jobs submitted to a cluster
Hey Donny,
What is the value of keep_completed on your queue (from qmgr -c 'p s')? Could it be that your spool is flushing completed jobs immediately? I ran into issues the other day with libdrmaa requiring at least keep_complete = 60 seconds to properly detect completed jobs and clean up after itself.
Cheers,
-E
-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu
On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <DCShrum@admin.fsu.edu> wrote:
I've setup galaxy to submit jobs to our HPC cluster as the logged in user. I used the drama python module to submit the jobs to our moab server.
It appears that the working directory for a submitted job is being removed by galaxy prior to the job completing on the cluster.
I can see a working directory is created in the logs: galaxy.jobs DEBUG 2014-06-12 08:21:03,786 (15) Working directory for job is: /panfs/storage.local/software/galaxy-dist/database/job_working_directo ry/000/15
I've confirmed the directory is created by watching on the file system and within about two seconds of the folder being created it is deleted. [root@admin 000]# watch -d ls -lR Every 2.0s: ls -lR Thu Jun 12 08:21:06 2014 total 64 drwxrwxrwx 2 dcshrum dcshrum 4096 Jun 12 08:21 15
I see the job sent via DRMAA: galaxy.jobs.handler DEBUG 2014-06-12 08:21:03,795 (15) Dispatching to drmaa runner galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) submitting file /panfs/storage.local/software/galaxy-dist/database/job_working_directo ry/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,566 (15) native specification is: -N galaxyjob -l nodes=1,walltime=2:00 -q genacc_q galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:05,892 (15) submitting with credentials: dcshrum [uid: 232706] galaxy.jobs.runners.drmaa INFO 2014-06-12 08:21:06,196 (15) queued as 7570705.moab.local
The job fails: galaxy.jobs.runners.drmaa DEBUG 2014-06-12 08:21:06,698 (15/7570705.moab.local) state change: job finished, but failed galaxy.jobs.runners DEBUG 2014-06-12 08:21:07,124 (15/7570705.moab.local) Unable to cleanup /panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh: [Errno 2] No such file or directory: '/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/15/galaxy_15.sh'
I can see the same error in my moab log: *** error from copy /bin/cp: cannot create regular file `/panfs/storage.local/software/galaxy-dist/database/job_working_direct ory/000/15/galaxy_15.o': No such file or directory *** end error output
Any idea as to why galaxy removes the working directory? Is there a setting in the job_conf.xml that would resolve this?
Thanks for any pointers.
Donny FSU Research Computing Center
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