I did a merge of galaxy-central that included the patch you posted
today. The scheduling problem seems to have gone away. Although I'm still
getting back 'Job output not returned from cluster' for errors. This seems
odd, as the system previously would output stderr correctly.

Kyle


On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor <n...@bx.psu.edu> wrote:

> On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote:
>
> > I'm running a test Galaxy system on a cluster (merged galaxy-dist on
> Janurary 4th). And I've noticed some odd behavior from the DRMAA job runner.
> > I'm running a multithread system, one web server, one job_manager, and
> three job_handlers. DRMAA is the default job runner (the command for
> tophat2 is drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being the
> engine underneath.
> >
> > My test involves trying to run three different Tophat2 jobs. The first
> two seem to start up (and get put on the SGE queue), but the third stays
> grey, with the job manager listing it in state 'new' with command line
> 'None'. It doesn't seem to leave this state. Both of the jobs that actually
> got onto the queue die (reasons unknown, but much to early, probably some
> tophat/bowtie problem), but one job is listed in error state with stderr as
> 'Job output not returned from cluster', while the other job (which is no
> longer in the SGE queue) is still listed as running.
>
> Hi Kyle,
>
> It sounds like there are bunch of issues here.  Do you have any limits set
> as to the number of concurrent jobs allowed?  If not, you may need to add a
> bit of debugging information to the manager or handler code to figure out
> why the 'new' job is not being dispatched for execution.
>
> For the 'error' job, more information about output collection should be
> available from the Galaxy server log.  If you have general SGE problems
> this may not be Galaxy's fault.  You do need to make sure that the
> stdout/stderr files are able to be properly copied back to the Galaxy
> server upon job completion.
>
> For the 'running' job, make sure you've got 'set_metadata_externally =
> True' in your Galaxy config.
>
> --nate
>
> >
> > Any ideas?
> >
> >
> > Kyle
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