In our case someone had installed and started a second development
instance of galaxy but used the same database as the first development
instance. So the ids were mixed up and and causing some jobs to crash.
Yuck!
Thanks,
Liisa
From: Nate Coraor <n...@bx.psu.edu>
To: Liisa Koski <liisa.ko...@basf.com>
Cc: kellr...@soe.ucsc.edu, "galaxy-dev@lists.bx.psu.edu"
<galaxy-dev@lists.bx.psu.edu>, galaxy-dev-boun...@lists.bx.psu.edu
Date: 14/01/2013 10:48 AM
Subject: Re: [galaxy-dev] DRMAA runner weirdness
On Jan 11, 2013, at 9:32 AM, Liisa Koski wrote:
> Hello,
> Can you please post the link to this patch? I do not see it in the mail
thread and I too have noticed some issues with the DRMAA job running since
updating to the Oct. 23rd distribution. I don't know if it is related yet
but I'd like to try the patch to see. I have two local instances of Galaxy
(prod and dev). On my dev instance (which is fully up to date), when I run
the same job multiple times, sometimes it finishes and sometimes it dies,
this is independent of which node it runs on. My prod instance is still at
the Oct. 03 distribution and does not experience this problem. So I am
afraid to update our production instance.
>
> Thanks in advance,
> Liisa
Hi Liisa,
Here's the one that Kyle is referring to:
https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944f967e2c859d5552c00e3e38a2da0
However, this patch should only fix the problem of the server segfaulting
when deleting certain jobs (ones that have not yet been dispatched to the
cluster).
--nate
>
>
>
>
> From: Kyle Ellrott <kellr...@soe.ucsc.edu>
> To: Nate Coraor <n...@bx.psu.edu>
> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> Date: 10/01/2013 07:44 PM
> Subject: Re: [galaxy-dev] DRMAA runner weirdness
> Sent by: galaxy-dev-boun...@lists.bx.psu.edu
>
>
>
> 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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>
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