[gmx-users] Running Gromacs in Clusters

[Szilárd Páll]

Hi,

With a fast network like Cray's you can easily get to 400-500 atoms/core
core with 4.5 (that's 400+ cores for your system), perhaps even further.
With 4.6 this improves quite a bit (up to 2-3x).

--
Szilárd


On Wed, Nov 7, 2012 at 5:19 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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
>
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