On Fri, Mar 16, 2012 at 11:00 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> 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
>
> Hi Nate,
>
> Sorry for the delay - I must have missed your reply.
>
> No, we're not using nginx here.
>
> What should I edit in the database? Presumably rather than deleting
> these jobs I should set the state to finished with error?
>
> (Is there any documentation about the Galaxy database schema,
> and the values of fields in it - or is that all considered to be an
> internal detail?)

Sorry to nag - my zombie jobs are still there and I'd like a little
guidance about how to delete them (e.g. which tables and what
status should I change them to).

Thanks,

Peter

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