[gmx-users] problem with Shake block crossing node boundaries

[David van der Spoel]

Siavoush Dastmalchi wrote:
> Hi,
> 
> I don't know why I get the following error message when I use more than one node when I run grompp (e.g., grompp -np 32 .....). From previous emails, I gathered that I need to reduce the number of nodes. But for me it just works when I use a single node.
> 
upgrade to newer version 3.3.2, or reduce the number of nodes, maybe 16. 
Alternatively use constraints = all-bonds iso constraints = h-bonds.
With so few atoms per processor it will be very slow by the way.
> Any suggestions?  Cheers, Siavoush 
> 
> Here is the error:
> 
> Walking down the molecule graph to make shake-blocks
> There are 556 charge group borders and 1 shake borders
> There are 556 total borders
> Division over nodes in atoms:
>       41      41      42      40      42      42      44      41      42      41      42      42      42      41      42      40      43      42      41      41      41      42      40      41      42      40      41      37      42      43      41      42
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: splitter.c, line: 121
> 
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (1270,1283)
> -------------------------------------------------------
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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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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