[GE users] Specify the number of nodes when you submit job array

reuti reuti at staff.uni-marburg.de
Wed Oct 20 09:54:12 BST 2010


Am 20.10.2010 um 01:16 schrieb aali:

> >> Then don't use a job array. Either submit a single job that runs the computations serially or a submit the first job and let it submit
> >> the other tasks to the same queue instance.
> > This is one option, besides my initial suggestion to submit with a hard node request.
> 
> I agree that these are 'potential' solutions, but not very efficient in terms of making use of the resources- I may end up using any of them if I can't use job array.
>  
> >But you can use this to submit an advance reservation with an attached PE which you already have with "allocation_rule $pe_slots". 
> Into this granted AR you submit the job array then.
> 
> I tried with orte_fillup, but it didn't work for me, I will do more exp. tomorrow.

No, with $fill_up you might get different machines, you must use the initially one used "threaded" with "allocation_rule $pe_slots" and request maybe a range of slots:

$ qrsub -pe threaded 1-8 ...

to get any of the available machines. Then you submit into this AR the array job (here without any PE request). Just to note, that the number of slots which are granted will be fixed over the lifetime of the AR, even when some of the other serial jobs outside of this AR on this node left it already.

The value for "slots" in the PE definition is the value for all jobs using this PE, so often it's set to the number of cores in the cluster or an arbitrary high value. With "8" you would allow only 8 slots using this PE at any time.

-- Reuti


> Thanks for your help!
> Ahmed
>  
> -- Reuti
> 
> 
> > --
> >                                Michael van Elst
> > Internet: mlelstv at serpens.de
> >                                "A potential Snark may lurk in every tree."
> >
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