[gmx-users] g_tune_pme for multiple nodes

Carsten Kutzner ckutzne at gwdg.de
Mon Sep 3 12:01:43 CEST 2012

Hi Chandan,

g_tune_pme also finds the optimal number of PME cores if the cores
are distributed on multiple nodes. Simply pass the total number of
cores to the -np option. Depending on the MPI and queue environment
that you use, the distribution of the cores over the nodes may have
to be specified in a hostfile / machinefile. Check g_tune_pme -h
on how to set that.


On Aug 28, 2012, at 8:33 PM, Chandan Choudhury <iitdckc at gmail.com> wrote:

> Dear gmx users,
> I am using 4.5.5 of gromacs.
> I was trying to use g_tune_pme for a simulation. I intend to execute
> mdrun at multiple nodes with 12 cores each. Therefore, I would like to
> optimize the number of pme nodes. I could execute g_tune_pme -np 12
> md.tpr. But this will only find the optimal PME nodes for single nodes
> run. How do I find the optimal PME nodes for multiple nodes.
> Any suggestion would be helpful.
> Chandan
> --
> Chandan kumar Choudhury
> NCL, Pune
> -- 
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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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