[Beowulf] slow jobs when run through queue
cap at nsc.liu.se
Wed Dec 6 04:53:55 PST 2017
On Wed, 06 Dec 2017 21:39:20 +1100
Chris Samuel <chris at csamuel.org> wrote:
> On Wednesday, 6 December 2017 8:09:20 PM AEDT Peter Kjellström wrote:
> > If you got only a 4x performance reduction when running a 48x over
> > subscribe on 1/48 the amount of cores then something is wrong with
> > your base line. That is, the "run without queue system" case seems
> > suspicsious.
> If this is, as I suspect is likely, bioinformatics code it could well
> be that it is a pipeline type application and only part of the
> application may be able to make use of parallelism (and then might
> not be very good at it).
Even more reason not to give it 48x more resource to waste then :-)
Probably wise to go back to a smaller set of resources and no over
subscribe and evaluate behavior.
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