On Wed, Aug 17, 2011 at 2:59 AM, Roman Valls <brainst...@nopcode.org> wrote:

> On 2011-08-16 23:49, Luobin Yang wrote:
> > Hi, Nate,
> >
> > On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor <n...@bx.psu.edu
> > <mailto:n...@bx.psu.edu>> wrote:
> >
> >     Hi Luobin,
> >
> >     Sorry for the delay in response.  I would suggest moving this
> discussion
> >     to the galaxy-dev mailing list since it does not contain any private
> >     data.  The wide audience on galaxy-dev may be able to come up with
> >     additional ideas than what we on the Galaxy Team come up with.
> >
> >     Please see my responses inline below.
> >
> >     Luobin Yang wrote:
> >     > Hi,
> >     >
> >     > Thanks for Martin Dahlo's excellent blog (
> >     > http://mdahlo.blogspot.com/2011/06/galaxy-on-uppmax.html)  on
> >     making SLURM
> >     > work with GALAXY, I am able to run galaxy jobs on a cluster, but
> >     I've got a
> >     > couple of issues:
> >     >
> >     > 1. Sometimes a job is in waiting state and it won't start to run
> >     until I
> >     > restart galaxy.
> >
> >     When this happens, is the job stuck in Galaxy or in the queueing
> system
> >     (PBS, SGE, something else?)?
> >
> >
> > When this happens, the job is stuck in Galaxy, it doesn't submit the job
> > to SLURM queueing system.
>
>
>
>
>
> Could you send the output of "squeue -u youruser" and (if possible) the
> logs from SLURM ? You can ask for them to your sysadmins, tell them the
> exact timestamp so that they can look it up easily.
>
> Perhaps the most useful logs are the ones you get when galaxy is running
> (out of ./run.sh output), paste them as well.
>

Hi, Roman, I already switched from SLURM to Torque PBS for our cluster for a
while because I had to get a working system in a limited time. It turned out
the PBS job runner in Galaxy doesn't have any such issues working with
Torque PBS.  Even though Torque PBS doesn't have some features that are
available in SLURM, it works fine for our cluster at the moment. Thanks
anyway!


>
>
>
>
>
> >
> >     In your config file (universe_wsgi.ini), is track_jobs_in_database =
> >     True or False?  Are you using SQLite or another database?  If you
> watch
> >
> >
> > I am using PostgreSQL database system.
> >
> > track_jobs_in_database is False in my config file. Which option is
> > better when I have a queueing system?
> >
> >
> >     the Galaxy log, are any exceptions or other errors logged when a job
> >     becomes stuck?
> >
> >
> > Galaxy log doesn't show any exception or errors.
> >
> >
> >     > 2. Sometimes a job is in running state even though it is already
> >     finished
> >     > and restarting galaxy can make the job's state change from running
> to
> >     > finished.
> >
> >     Most likely, Galaxy is setting metadata on the job's outputs.  You
> can
> >     probably speed up this process by setting:
> >
> >        set_metadata_externally = True
> >
> >     in the config file.
> >
> >     Thanks,
> >     --nate
> >
> >     >
> >     > I am wondering what's causing those issues and how they can be
> fixed.
> >     >
> >     > Thanks,
> >     > Luobin
> >
> >     >
> >
> >
> >
> >
> > ___________________________________________________________
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>
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