[gmx-users] PME nodes

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 6 13:08:53 CEST 2009

XAvier Periole wrote:
> Dears,
> I am having troubles finding the better balance between the PME CPUs and 
> the rest.
> I played with the rdd, rcon and -npme options but nothing really appears 
> very
> straightforwardly best.
> I'd appreciate if some of you could post their experience in that 
> matter. I mean the
> number of pme nodes as compared the total number of CPUs used.
> I think this info as been discussed recently on the list but the archive 
> is not accessible.
> It may matter that I have a system containing about 70000 atoms, a 
> protein in a bilayer.

Some advice that I got from Berk long ago has worked beautifully for me.  You 
want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the 
relative PME load as 25% if your parameters create such a balance), 2:1 for an 
octahedron.  My scaling has been great using this information, without having to 
alter -rdd, -rcon, etc.


> Best,
> XAvier.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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