On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:

> Hello all,
> 
> I've noticed we have about a dozen stalled upload jobs on our server
> from several users. e.g.
> 
> Job ID        User    Last Update     Tool    State   Command Line    Job 
> Runner      PID/Cluster ID
> 2352  xxxx    21 hours ago    upload1         upload  None    None    None
> ...
> 2339  yyyy    19 hours ago    upload1         upload  None    None    None
> 
> The job numbers are consecutive (2339 to 2352) and reflect a problem
> for a couple of hours yesterday morning. I believe this was due to the
> underlying file system being unmounted (without restarting Galaxy),
> and at the time restarting Galaxy fixed uploading files. Test jobs
> since then have completed normally - but these zombie jobs remain.
> 
> Using the "Stop jobs" option does not clear these dead upload jobs.
> 
> Restarting the Galaxy server does not clear them either.
> 
> This is our production server and was running galaxy-dist, changeset
> 5743:720455407d1c - which I have now updated to the current release,
> 6621:26920e20157f - which makes no difference to these stalled jobs.
> 
> Does anyone have any insight into what might be wrong, and how to get
> rid of these zombie tasks?

Hi Peter,

Are you using the nginx upload module?

There's no way to fix these from within Galaxy, unfortunately.  You'll have to 
update them in the database.

--nate

> 
> Thanks,
> 
> Peter
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