[Beowulf] slow jobs when run through queue

[David Mathog]

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