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


On Thu, Jun 12, 2014 at 8:31 AM, Shrum, Donald C <dcsh...@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: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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>
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