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_directory/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_directory/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_directory/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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
