Hey Peter, Sorry about that. Nate and I talked about this and we believe the following pull request should likely fix the problem.
https://bitbucket.org/galaxy/galaxy-central/pull-request/390 -John On Mon, May 12, 2014 at 8:53 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Thu, Jun 27, 2013 at 11:09 PM, Robert Baertsch > <robert.baert...@gmail.com> wrote: >> I submitted a workflow that in turn submits a drm job to sun grid engine. >> >> The queue had an error (probably due to a problem with automount). >> >> Traceback (most recent call last): >> File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py", line 60, >> in run_next >> method(arg) >> File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 169, >> in queue_job >> external_job_id = self.ds.runJob(jt) >> File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py", >> line 331, in runJob >> _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) >> File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py", >> line 213, in c >> return f(*(args + (error_buffer, sizeof(error_buffer)))) >> File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py", >> line 90, in error_check >> raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) >> DeniedByDrmException: code 17: error: no suitable queues >> >> When the sysadmin cleared the error, the job started running normally after >> being in an error state for 10 minutes. >> >> The cool thing is that galaxy kept running without a problem. >> >> galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) >> state change: job is running >> galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) >> state change: job is queued and active >> galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) >> state change: job is running >> >> >> However in the history panel, the job shows as queued but not running, even >> if I refresh the history panel. >> >> Is this normal or should the status change to running? >> >> I'm using this version of straight galaxy: >> >> changeset: 10162:f295092476c7 >> branch: stable >> parent: 10160:2efb1083676b >> user: Dannon Baker <dannonba...@me.com> >> date: Sat Jun 15 09:08:09 2013 -0400 >> summary: Fix reports import issue reported by Lance, >> https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e4b3/943 >> >> >> -Robert Baertsch >> UC Santa Cruz > > Good question - I've just have a job "fail" like this, with the > following in my log: > > 014-05-12T14:24:28.366979+01:00 ppserver galaxy.jobs.runners ERROR > 2014-05-12 14:24:28,261 (10622) Unhandled exception calling > queue_job#012Traceback (most recent call last):#012 File > "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line > 62, in run_next#012 method(arg)#012 File > "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 154, > in queue_job#012 external_job_id = self.ds.runJob(jt)#012 File > "/mnt/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", > line 331, in runJob#012 _h.c(_w.drmaa_run_job, jid, > _ct.sizeof(jid), jobTemplate)#012 File > "/mnt/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", > line 213, in c#012 return f(*(args + (error_buffer, > sizeof(error_buffer))))#012 File > "/mnt/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", > line 90, in error_check#012 raise _ERRORS[code-1]("code %s: %s" % > (code, error_buffer.value))#012DeniedByDrmException: code 17: error: > no suitable queues > > (Apologies there are no line breaks, we send our logging to syslog) > > i.e. DeniedByDrmException: code 17: error: no suitable queues > > >From the user's perspective the job is still say in the "grey" pending state. > Is that the correct behaviour? It sounds like (from Robert's email) the > job is pending and if the cluster administrator attended to it, the job > might run. > > We're using Univa Grid Engine, and perhaps I am looking in the wrong > place, but the job seems to have been rejected rather than held. If so, > then Galaxy should treat this as a failed job (red). > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/