[gmx-users] About PP/PME

[Justin Lemkul]

On Fri, Apr 5, 2013 at 10:03 PM, 陈照云 <chenzhaoyun06 at gmail.com> wrote:

> I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw
> to reduce the load imbalance and improve the performance?
> The PME-node is 16 and the PP-node is 80.How to divide?
>

Generally, if you're losing a lot of performance, mdrun writes this
information near the end of the .log file and tells you how to improve it.
 What you're using is a rather significant imbalance between PP and PME.
 Are you setting -npme manually or letting mdrun decide?  Normally, mdrun
guesses pretty well.  The ratio of PP/PME it decides depends on your .mdp
settings and how much work the PME part is supposed to do.  For triclinic
unit cells, a 3:1 PP/PME ratio is usually best.  For dodecahedral or
octahedral unit cells, 2:1 PP/PME.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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