My theory of about what was happening...
As Nate suggested there were multiple issues.
First, the patch he posted (
was to stop "attempt to stop jobs that have no external ID set". So
maybe I was running into some sort of occurrences issue, perhaps by running
multiple job runners. That may have been causing the jobs with null
commands lines or the ones that never returned, despite not being on the
queue (at least those issues disappeared after his patch)
Second, something seems to have changed in our cluster setup since the last
time I ran Tophat2. SGE's behavior in regards to the 'ulimit -v' setting
got a lot more stringent (maybe the admins changed some settings...). So
previously I could set 'ulimit -v unlimited' in my profile and just be done
with it. But SGE started blocking that so ulimit operations started
returning 'cannot modify limit: Operation not permitted'. So when bowtie
(under tophat) used up too much memory, the whole job was unceremoniously
killed, without even letting the runner script dump the log files to
stderr. The work around for this is to use the resource flag to allocate
'v_mem' (ie drmaa://-l v_mem=10G/).
On Fri, Jan 11, 2013 at 6:32 AM, Liisa Koski <liisa.ko...@basf.com> wrote:
> 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,
> From: Kyle Ellrott <kellr...@soe.ucsc.edu>
> To: Nate Coraor <n...@bx.psu.edu>
> Cc: "firstname.lastname@example.org" <email@example.com>
> 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.
> On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor
> 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.
> > Any ideas?
> > Kyle
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