[gmx-developers] thread cannibalism

[David van der Spoel]

On 2010-07-07 12.28, Sander Pronk wrote:
> 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.
>
Strangely this option does not show up when I do

mdrun -hidden -h |& grep thread


> 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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>


-- 
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