[gmx-users] Best performace with 0 core for PME calcuation

Carsten Kutzner ckutzne at gwdg.de
Mon Jan 12 10:41:26 CET 2009

On Jan 10, 2009, at 8:32 PM, Nicolas wrote:

> Berk Hess a écrit :
>> Hi,
>> Setting -npme 2 is ridicolous.
>> mdrun estimates the number of PME nodes by itself when you do not  
>> specify -npme.
>> In most cases you need 1/3 or 1/4 of the nodes doing pme.
>> The default -npme guess of mdrun is usually not bad,
>> but might need to tuned a bit.
>> At the end of the md.log file you find the relative PP/PME load
>> so you can see in which direction you might need to change -npme,
>> if necessary.
> Actually, I have tested npme ranging from 0 to 5, but 2 is well  
> representative of what happens. For example with 5 cores for the  
> PME, the perfs reach a plateau at 14-15 cores. So, setting npme to 0  
> systematically gives the best results. I have also tested -1. With,  
> npme set to -1, the performances are the same than for 0 until 8  
> cores. Above that, the guess is not so efficient.

Hi Nicolas,

as Berk mentioned, you should expect a different optimal number of PME  
nodes for
each number of total nodes you test on. So the way to go is to fix the  
number of total
nodes and vary the number of PME nodes until you find the best  
performance for that
number of nodes. Then move on to another number of total nodes. I have  
a small tool that does a part of this job for you by finding out the  
optimum number
of PME nodes for a given number of total nodes. If you want to give it  
a try, I can
send it to you. Typically the optimum number of PME nodes should not  
be too far
off the mdrun estimate. If it is far off, this could point out some  
network or MPI
problem. Note that separate PME nodes can only work if the MPI ranks  
are not scattered
among the nodes, i.e. on 4-core nodes the ranks 0-3 should be on the  
same node
as well as ranks 4-7 and so on. This is printed at the very start of a  


Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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