If you refer to using one machine as master AND host simultaneously, which
you never tried: let me tell you it does work well with SGE/OGE. I have it
running, and it just works out great. It enhances the load control on that
machine, due to the great configuration possibilities on queue level (max.
cores, queue ranking, user restrictions etc.).
I did not connect it to Galaxy yet (which is also installed on the same
machine), but I do not see a reason why that should not work out. Indeed,
the reason for acting like this was the need to set up a modularized
system, using defined interfaces. Currently everything is physically in on
one machine, but that will change. Galaxy for example does not care, where
and how a cluster is set up physically, it just connects to a given
ressource.

Regarding the initial question: at least jobs in the cluster queue will
indeed finish, because after submission those jobs are decoupled from
Galaxy, by definition; it's like submitting from a desktop machine, which
can be switched off afterwards. Additionally, I would wonder if Galaxy
(which has really great fail safe mechanisms) would not be able to
reconnect to the cluster, asking for jobs, which were submitted before
restart and not noted as "finished" or "picked up" after restart (noted
internally within the DB). I would say test it and get back to the mailing
list :).

Best,
Sebastian


Langhorst, Brad schrieb:
> Unless something has recently changed, you will need to set up a cluster
> to get jobs to persist across galaxy restarts.
>
> You can do this with just a single node acting as both queue master and
> job runner using sun grid engine (i think, I have not tried this myself)
>
> Brad
> On Aug 27, 2012, at 12:51 PM,
> kauerb...@comcast.net<mailto:kauerb...@comcast.net> wrote:
>
> Hello,
>
>
>
> If I were to stop and re-start the Galaxy server with the run.sh script
> would jobs that are aleady running or are in the queue be lost when the
> server is re-started?  If so, is there another method to use which would
> not lose the running or queued jobs?
>
>
>
> Thank you.
>
>
>
>
> ___________________________________________________________
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> --
> Brad Langhorst
> langho...@neb.com<mailto:langho...@neb.com>
> 978-380-7564
>
>
>
>
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-- 
Sebastian Schaaf, M.Sc. Bioinformatics
Chair of Biometry and Bioinformatics
Department of Medical Information Sciences, Biometry and Epidemiology
University of Munich
Marchioninistr. 15, K U1 (postal)
Marchioninistr. 17, U 006 (office)
D-81377 Munich (Germany)
Tel: +49 89 2180-78178

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