[gmx-developers] benchmark Lys errors?

David spoel at xray.bmc.uu.se
Tue Mar 30 07:40:48 CEST 2004

On Tue, 2004-03-30 at 04:06, Josh Hursey wrote:

> >>>Yes, your protein has now more atoms than what fits on one processor.
> >>>Although it maybe shouldn't crash, you are already way beyond the
> >>>maximum performancewise. More than 4 processors is not worthwhile for
> >>>such small systems...
> >>
> >>Is there a rough metric for determing when one has allocated too many processors for a given system?
> >>'
> > 
> > Depends on the communication speed. For cut-off sims you need a few
> > thousand atoms per processor, for PME sims more than that.
> So when looking at a General Protein, what determines the scaling limit? I assume it involves an evaluation of the number of 
> atoms in the system and the type of calculation involved.
In the end it's merely the system size, but it depends on your
network/CPU combination as well. For typical systems, such as the Lys
benchmark it can easily be measured. Just run the cut-off and the PME
benchmarks on 1,2,4,6,8 processors and make an informed decision.

I have run a 200,000 atom system on 16 processors (with PME) but in the
end I moved it to 8 processors, which was somewaht slower but gave me
more throughput since I had a limited CPU time on that cluster.

As soon as there are more jobs that CPUs it is worthwhile to reduce the
number of CPUs per job.
David van der Spoel, PhD, Assist. 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

More information about the gromacs.org_gmx-developers mailing list