[gmx-developers] thread cannibalism

Sander Pronk pronk at cbr.su.se
Wed Jul 7 12:28:00 CEST 2010

You can set the number of threads with -nt <number>; the default is 0, which means as many threads as there are cores/hardware threads.

On Jul 7, 2010, at 12:18 , David van der Spoel wrote:

> Hi,
> I'm now enjoying the automatic thread parallellization which works wonders on my Mac Pro with eight cores, and I assume on other multi-core boxes too.
> Is there an option to limit the number of threads per node for mdrun?
> I'm asking because we are using a queue system where we allow multiple independent (single core) jobs per node. If each of these were to start 4 or 8 cores the overall efficiency would be lower, but if the other jobs are not mdrun it might mean that these get pushed away.
> Note that the same could happen with other programs, e.g. Gaussian uses shared memory as well.
> Is there any solution other than disallowing multiple jobs per node?
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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