Re: Cube vs. Truncated Octahedron Performance

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Oct 21 2010 - 18:02:20 CDT

On Thu, 2010-10-21 at 18:04 -0400, Alexander Predeus wrote:
> Dear all,
>
> I am studying a large protein-DNA complex. The size of the system
> solvated in cubic box was ~460k atoms. I have decided to use truncated
> octahedron, which turned out to be only 360k atoms. But to my
> disappointment, when I ran the (truncated octahedron) system on TACC
> Ranger using 512 cores, it actually performed WORSE then the cube!
>
> Is it because the system is smaller and scales worse now (due to
> number of patches etc), or am I overlooking something important? I
> have turned "wrapNearest" option on, so the cell looks like a proper
> truncated octahedron; all the energies look reasonable too. Are there
> any other options to play with to improve the performance?

please check out:

http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdPerformanceTuning

axel.

>
> All the best,
>
> -- Alex Predeus,
> Michigan State University
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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