[gmx-users] Fatal error: Shake block crossing node boundaries

[David van der Spoel]

Jianwei Wang wrote:
> Hello, I got an error message while using 8 processors becuase of Shake
> block crossing node boundaries. Everything was fine when I used a single
> processor. Any idea how to ease this problem? Thanks! JW
> 

use max 3 or 4 processors

> The error message:
> ============
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 1470 charge group borders and 1470 shake borders
> There are 1470 total borders
> Division over nodes in atoms:
>      321     321     320     321     321     321     324     321
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: splitter.c, line: 121
>                                                                           
>      
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (0,680)
> ==============
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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://folding.bmc.uu.se
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