[gmx-developers] benchmark Lys errors?
spoel at xray.bmc.uu.se
Sun Mar 28 20:32:05 CEST 2004
On Sun, 2004-03-28 at 19:03, Josh Hursey wrote:
> > Subject: Re: [gmx-developers] benchmark Lys errors?
> > From: David <spoel at xray.bmc.uu.se>
> > To: gmx-developers at gromacs.org
> > Date: Sat, 27 Mar 2004 23:28:23 +0100
> > Reply-To: gmx-developers at gromacs.org
> >>There are 7429 total borders
> >>Division over nodes in atoms:
> >> 1453 1451 1449 1450 1450 1450 1450 1450 1450
> >>1450 1450 1452 1452 1449 1452 1449
> >>Fatal error: Shake block crossing node boundaries
> >>constraint between atoms (1446,1453)
> >>Could anyone help me for this question?
> > 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.
> >>Thanks in advance!
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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
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