[gmx-users] High speed performance

[Kutzner, Carsten]

Hi Asma,

whether your performance is good/expected depends on some other
parameters you have not mentioned. What time step length do you
use? What electrostatics method? What do you mean by “CPU with
5 nodes?”, I assume you are using 5 MPI ranks on a 40 core CPU?

http://arxiv.org/abs/1507.00898 is a benchmark study with larger
MD systems, however you might find your CPU configuration in one
of the tables and could at least estimate the performance for
your smaller system.

Best,
  Carsten


> On 03 Aug 2015, at 15:03, Asmaa El khodary <asma.moh_990 at aucegypt.edu> wrote:
> 
> Hi,
> I'm currently simulating a protein consists of 2776 atoms with 173 residues
> using CPU with 5 nodes, 40 core processors. The performance of the
> simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is
> this realistic or not?
> Thanks in Advance
> Asma
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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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa