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

Nicolas nsapay at ucalgary.ca
Tue Dec 23 17:23:28 CET 2008


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?
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)?


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