[Beowulf] slow jobs when run through queue

Tim Cutts tjrc at sanger.ac.uk
Wed Dec 6 10:35:11 PST 2017

Of course, if you charge for your cluster time, that hurts them in the wallet, since they pay for all the allocated unused time.  If you don’t charge (which is the case for us) it’s hard to incentivise them not to do this.  Shame works, a bit.  We publish cluster analytics showing CPU efficiency and memory efficiency league tables for the users, and that has had some good effects in the past...


> On 6 Dec 2017, at 18:20, David Mathog <mathog at caltech.edu> wrote:
> on Wed, 06 Dec 2017 21:39:20 +1100 Chris Samuel wrote:
>> 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).
> Exactly.  Super frustrating to set something like '--cpus=40' and then watch the resulting heap of programs sit for long periods of time (hours, not seconds) running only on a single CPU.
> Regards,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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