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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter Cock [p.j.a.cock@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.vandeweyer2@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
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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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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