For what it is worth, I think the right way to handle this is to add a new
table that tracks job state changes. Whenever the state of a job changes a
row would be written with the job id, new state, and timestamp.
(You could then try to populate it for existing jobs in exactly the way you
propose as part of a migration).
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, May 8, 2013 at 11:38 AM, Geert Vandeweyer <
geert.vandewey...@ua.ac.be> wrote:
> Hi all,
>
> I'm fiddling with this, and I have a proof of principle working for PBS
> jobs using very ugly sql-alchemy hack.
>
> Idea is:
> - if job goes from queued to running : store seconds since epoch in
> 'runtime'
> - if job goes from running to finished : compare time, store difference as
> runtime.
>
> I've created an extra field 'runtime' for holding this info, using seconds
> since epoch.
> When querying afterwards, one should filter for 'OK' jobs, and discard
> jobs that are still running.
>
> right now, i have these statements to add timestamps to the database
> (somewhere in the check_watched_items function in pbs.py) :
>
> self.sa_session.execute('**UPDATE job SET runtime = :runtime WHERE id =
> :id',{'runtime':runtime,'id':**galaxy_job_id})
>
> Does anybody know how to translate this to a proper sqlalchemy statement
> such as (which does not work):
>
> self.sa_session.query(self.**model.Job).filter_by(id=**
> galaxy_job_id).update({"**runtime":runtime},synchronize_**session=False)
> or
> sa_session.execute(self.sa_**session.Table('job').update().**
> values(runtime=runtime).where(**id=galaxy_job_id))
>
> If I can figure this out, I'll try to polish it and create a pull request.
>
>
> Best,
>
> Geert
>
>
> On 05/08/2013 03:58 PM, Bossers, Alex wrote:
>
>> +1 for me!
>> Alex
>>
>>
>> ______________________________**__________
>> Van:
>> galaxy-dev-boun...@lists.bx.**psu.edu<galaxy-dev-boun...@lists.bx.psu.edu>[
>> galaxy-dev-boun...@lists.bx.**psu.edu<galaxy-dev-boun...@lists.bx.psu.edu>]
>> namens Peter Cock [p.j.a.c...@googlemail.com]
>> Verzonden: woensdag 8 mei 2013 12:06
>> To: Geert Vandeweyer
>> Cc: galaxy-dev@lists.bx.psu.edu
>> Onderwerp: Re: [galaxy-dev] Track Job Runtime
>>
>> On Wed, May 8, 2013 at 10:08 AM, Geert Vandeweyer
>> <geert.vandewey...@ua.ac.be> wrote:
>>
>>> Hi,
>>>
>>> Are there options available to track the actual runtime of jobs on a
>>> cluster
>>> and store them in the database?
>>>
>> Not yet, but I'd really like to have that information too.
>>
>> Peter
>> ______________________________**_____________________________
>> Please keep all replies on the list by using "reply all"
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>>
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>>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/**cognitivegenetics <http://ua.ac.be/cognitivegenetics>
> http://www.linkedin.com/pub/**geert-vandeweyer/26/457/726<http://www.linkedin.com/pub/geert-vandeweyer/26/457/726>
>
> ______________________________**_____________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
> http://galaxyproject.org/**search/mailinglists/<http://galaxyproject.org/search/mailinglists/>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
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