1:53 p.m.
On Thu, Jun 27, 2013 at 11:09 PM, Robert Baertsch
<robert.baertsch(a)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 <dannonbaker(a)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/506338ce32ae458f6d1...
-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