[gmx-users] paralel scaleing
spoel at xray.bmc.uu.se
Thu Aug 7 21:18:00 CEST 2003
> > > Here I found that the calculations of LJ parts which consuming lots of
> > > cpus are not paralleled at all. Maybe this is the reasons why scaling
> > > factor is not increaded greatly from 2 cpus to 4 cpus.
> > > DO you agree with me ?
> > > How to improve ?
> > > I use gromacs 3.1.4.
> > PME scaling is poor, but it depends on your system size too.
> on the other hand, with myrinet scaling should be considerably better.
> Are you sure that you're actually making full use of the hardware?
> (ie is the scaling at least better (for that system) than for fast ethernet?)
That's true, and I've found that with Scali I do get some speedup up to
8 processors for a 80000 atom system. However, it is strongly system
> 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
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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