[gmx-users] paralel scaleing

[David]

O> >
> > > 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
dependent. 

> 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
> ____________________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++