[gmx-users] About the -npme option of mdrun and domain decomposition

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 23 21:16:14 CET 2008

Nicolas wrote:
> Hello,
> I'm trying to use Gromacs 4 mdrun with the Slurm scheduler and I'm a bit 
> confused by the Slurm nomenclature. The cluster has 4 cpu/node. I want 
> to run a job on 8 tasks with 1 cpu/task and 4 task/node. So, my job will 
> run on 2 nodes. If I set the -npme option to 1, the PME calculation will 
> run on 1 nodes, which means 4 cpu, is that right?
No, mdrun counts in cores, so this means a 7/1 split which will not be 
efficient. 6/2 or 5/3 should be better depending on the system.

> Another thing: according to the manual and the mailing list, domain 
> decomposition starts to be more efficient above ~12 nodes. If I run my 
> job on 4 nodes (so, 2 task/node) with domain decomposition (let say 1 
> node dedicated to the PME), will I limit the loss of efficiency anyway 
> (even by few percent)?
No, DD is almost always more efficient.

> Thanks
> Nicolas
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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