On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock <p.j.a.c...@googlemail.com> 
> wrote:
>> Hi all,
>>
>> Something has changed in the job handling, and in a bad way. On my
>> development machine submitting jobs to the cluster didn't seem to be
>> working anymore (never sent to SGE). I killed Galaxy and restarted:
>> ...
>> (segmentation fault)
>
> Looking into the problem with submitting the jobs, there seems to be
> a problem with task splitting somehow recursing - the same file is
> split four times, the filename getting longer and longer:

Turning off task splitting I could run the same job OK on SGE.

So, the good news is the problems seem to be specific to the
task splitting code. Also I have reproduced the segmentation
fault when restarting Galaxy (after stopping Galaxy with one
of these broken jobs).

Starting server in PID 17996.
serving on http://127.0.0.1:8081
galaxy.jobs.runners.drmaa ERROR 2012-11-15 11:07:27,762 (327/None)
Unable to check job status
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
line 296, in check_watched_items
    state = self.ds.jobStatus( job_id )
  File 
"/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py",
line 522, in jobStatus
    _h.c(_w.drmaa_job_ps, jobName, _ct.byref(status))
  File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/helpers.py",
line 213, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
  File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py",
line 90, in error_check
    raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InvalidArgumentException: code 4: Job id, "None", is not a valid job id
galaxy.jobs.runners.drmaa WARNING 2012-11-15 11:07:27,764 (327/None)
job will now be errored
./run.sh: line 86: 17996 Segmentation fault      (core dumped) python
./scripts/paster.py serve universe_wsgi.ini $@

The problem is the job_id variable is "None" (note this is a string,
not the Python special object None) in check_watched_items().

Peter
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