[gmx-users] Running Gromacs in Clusters

[Erik Marklund]

Hi,

I see degrading scaling when going from 96 to 192 cores on a cray for my system. I have periodic molecules and do umbrella sampling (with small deviations from the reference) which might affect the performance. My code is based on 4.5.5 without performance-critical modifications.

Erik

9 nov 2012 kl. 03.06 skrev 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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-----------------------------------------------
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