Hi, Nate,

On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor <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
> > 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.

> 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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