I had a close look at the code in

galaxy-dist / lib / galaxy / jobs / handler.py
galaxy-dist / lib / galaxy / jobs / runners / drmaa.py

and found that stopping "deleted" and "deleted_new" seems to be normal
routine for the job handler. Could not find any exception that caused the

I do notice in the galaxy-dist on bitbucket, there is one commit with
comment "Fix shutdown on python >= 2.6.2 by calling setDaemon when creating
threads (these are still...", it seems to be relevant?

I will do the update to 11 Jan release and see if it fixes the issue.


On Fri, Jan 18, 2013 at 4:03 PM, Derrick Lin <klin...@gmail.com> wrote:

> Hi guys,
> We have updated our galaxy to 20 Dec 2012 release. Recently we found that
> some submitted jobs could not start (stay gray forever).
> We found that it was caused by the job manager sent jobs to a handler
> (handler0) whose python process crashed and died.
> From the handler log we found the last messages right before the crash:
> galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 Stopping job 3032:
> galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 stopping job 3032 in
> drmaa runner
> We restarted the galaxy, handler0 is up for few seconds then died again
> with the same error messages except the job number moved to the next one.
> We observed that the jobs it was trying to stop are all previous jobs
> whose status is either "deleted" or "deleted_new".
> We have never seen this in the past, so wondering if there is bugs in the
> new release?
> Cheers,
> Derrick
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