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:boll0...@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
e...@msi.umn.edu
boll0...@umn.edu


On Thu, Jun 12, 2014 at 7:36 AM, Shrum, Donald C <dcsh...@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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