[gmx-users] Regarding g_tune_pme optimization

Carsten Kutzner ckutzne at gwdg.de
Thu Nov 1 16:55:24 CET 2012


On Nov 1, 2012, at 4:13 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Dear all Gromacs users,
> I have *two *questions:
> 1) I have been doing my simulation on a computer having 24
>     processors. I issued *g_tune_pme -s *.tpr ........ -launch *command to
> directly launch my *mdrun *with the optimized settings. At the end of
> optimization, g_tune_pme has given -npme as *'0'*. My doubt is, how could
> it be possible to get best performance without dedicated PME nodes?
This is normal, it just means that 24 PME nodes are optimal and thus no
*separate* PME nodes are needed.


> 2) What could be the optimum value for *-rcom *to get the best performance
> on a super cluster (*i.e., 256 nodes*)?
> Thanks in advance
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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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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