[gmx-developers] thread cannibalism

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 7 12:18:27 CEST 2010


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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