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?
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)?
Thanks
Nicolas
begin:vcard
fn:Nicolas Sapay
n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[email protected]
title:Post-doctoral fellow
tel;work:403-220-6869
x-mozilla-html:TRUE
url:http://moose.bio.ucalgary.ca/
version:2.1
end:vcard
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