[gmx-users] best price/performance for GMX?

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Mon Sep 24 19:31:30 CEST 2001

Hi All!

That's a good question.  I'm using a 100 Mb/s ethernet with Lam too and
dind't find gromacs performace in parallel so spectacular.  Does it depend
on network speed? My molecular system?

As soon as I install gromacs in SGI Origin 4 proc. I'll take new
tests.  For the moment we are running simulations on GNU/linux cluster. 

On Mon, 24 Sep 2001, Bert de Groot wrote:

> Hi all,
> We're about to extend our linux cluster and are interested to hear if there's any specific hardware that you, fellow gromacs-ers, recommend.
> So far we have a cluster consisting of 40 dual PII/PIII using standard
> fast ethernet (100 Mb/s) and our experience is that with a typical system size of about 100.000 atoms using PME, the scaling with LAM-MPI and also MPICH is not very spectacular. So in practice, most jobs are running on a single, two-processor node, which
> is not too bad with the speed that gromacs offers, but still for some jobs it would be nice to be able tu use more than two processors.  Would a gigabit ethernet or Myrinet help?
> And if yes, how much?
> cheers,
> Bert
> ____________________________________________________________________________
> Dr. Bert de Groot
> Max Planck Institute for Biophysical Chemistry
> Theoretical molecular biophysics group
> Am Fassberg 11 
> 37077 Goettingen, Germany
> tel: +49-551-2011306, fax: +49-551-2011089
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
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Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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