optimal CPU number for parallel MD of a small system

From: Isaure Chauvot de Beauchêne (ichauvot_at_lbpa.ens-cachan.fr)
Date: Fri Oct 19 2012 - 08:32:57 CDT


   I plane to run a parallel MD simulation of a 6500 aas protein in gb
implicite solvant on the cluster describe below**. I need to compute
an estimation of the CPU time necessary before I get access to the
cluster where it will run.

I did a benchmark on 8 CPU, but I couln't find anywhere benchmarks
about the paralleling efficiency of NAMD for such a small system.
How could I get an estimation of the optimal number of 8-CPU nodes to
use (other than tests, since I don't have access to any cluster now)?
I only need a rough approximation.

**The Cluster:
1536 compute nodes i.e. 12288 cores of Harpertown processor and 1344
compute nodes of nehalem processor : 10 752 cores. The network is an
Infiniband (IB 4x DDR) double plane network for the Harpertown section
of the machine. On the Nehalem section of the machine, 4 InfiniBand 4X
QDR drivers provide 72 IB 4X QDR ports on output of each IRU (576 Go/s).

Many thanks in advance,

Dr Isaure Chauvot de Beauchêne
Ph.D student
Team: "Bioinformatics, Modelisation and Molecular Dynamics" (BiMoDyM),  
Dir L. Tchertanov.
Laboratory of Biology and Applied Pharmacology (LBPA)
CNRS UMR 8113 - ENS Cachan
Bâtiment d'Alembert, 3e étage
61, avenue du Président Wilson
94235 Cachan cedex
Phone: +33 1 47 40 68 76
Fax:   +33 1 47 40 76 71

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