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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