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:
Starting server in PID 12180. serving on http://127.0.0.1:8081 galaxy.jobs.runners.drmaa ERROR 2012-11-15 09:56:28,192 (320/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 09:56:28,193 (320/None) job will now be errored ./run.sh: line 86: 12180 Segmentation fault (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@
I restarted and it happened again, third time lucky. I presume this was one segmentation fault for each orphaned/zombie job (since I'd tried two cluster jobs which got stuck).
I was running with revision 340438c62171, https://bitbucket.org/galaxy/galaxy-central/changeset/340438c62171578078323d... as merged into my tools branch, https://bitbucket.org/peterjc/galaxy-central/changeset/d49200df0707579f41fc4...
Any thoughts?
Thanks,
Peter