[gmx-developers] benchmark Lys errors?

[David]

On Sun, 2004-03-28 at 00:09, MailList wrote:
> Hi, there,
> 
> When I tried the Lys/Cutoff and Lys/Pme in the benchmark with 16 processors,
> it failed in the GROMPP with the following the error message(it happens in
> both GROMACS 3.1.4 and 3.2.1, but no errors for 2 or 4 processors):
> 
> .......
> Checking consistency between energy and charge groups...
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 7882 charge group borders and 7846 shake borders
> 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...
> 
> Thanks in advance!
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++