[gmx-users] Running Gromacs in Clusters

[Erik Marklund]

Hi,

Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms on 192 cores at ~45 ns a day. with half the number of processors I get ~27 ns a day. It will of course depend on the hardware, particular algorithms, run parameters, and on the system details.

Erik

7 nov 2012 kl. 16.51 skrev Marcelo Depolo:

> Good afternoon,
> 
> 
> I wonder if anyone has experience running Gromacs in MPI. I'm paralleling the
> processes and want to know how many processors reduces the computation time to
> the minimum. I am currently using 24 processors for a system of 170 000
> atoms and obtaining a simulation of 50ns in 15 days. There's a way to
> reduce more this computational time?
> 
> Thanks in advance!
> -- 
> Marcelo Depólo Polêto
> Departamento de Bioquímica e Biologia Molecular
> Universidade Federal de Viçosa - UFV
> *Website: http://opensourcebioinformatics.com/site/*
> --
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html