[gmx-users] How to buy a new cluster?

[David van der Spoel]

On Thu, 2004-12-02 at 14:55 -0500, Ran Friedman wrote:
> David van der Spoel wrote:
> > On Thu, 2004-12-02 at 13:05 -0500, Ran Friedman wrote:
> >   
> > > Relating to the same topic - are 64bit processors really superior when
> > > running GMX, especially considering their higher price and slower
> > > clock speed relative to the conventional 32bit processors?
> > >     
> > check the benchmarks
> > www.gromacs.org/benchmarks/single.php
> > 
> > the athlon64/opteron chips are 50% faster per clock as the Xeons. 
> >   
> I've run a few tests, including the benchmark, and the opterons were a
> little bit slower. 
> Following your input (and some discussions on the mailing list), I
> suspect that this was due to the compilation of gmx, fft or both -
> I've compiled gmx using gcc. 
> 
> Can any of the GMX users/developers comment on it?
yes, recompile with the Intel compiler for optimal performance.

> > Especially to answer this question I have updated the table above with a
> > column "rate" giving a processor speed per clock cycle.
> > 
> > 
> >   
> 
> -- 
> ------------------------------------------------------
> Ran Friedman
> Laser Laboratory for Fast Reactions in Biology
> Department of Biochemistry
> Faculty of Life Sciences
> Tel-Aviv University
> Tel. +972-3-6409824
> Fax. +972-3-6409875
> ------------------------------------------------------
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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