[gmx-users] Shake block crossing node boundaries

[David van der Spoel]

Suman Chakrabarty wrote:
> Hi,
> 
> I am trying brownian dynamics simulation of a single polymer chain
> consisting of 100 atoms in vacuum. All bonds are constrained by LINCS.
> I am trying to use the particle decomposition scheme for parallel run
> since for a molecule in vacuum domain decomposition seems to be a
> waste. I am using the 4.0.4 version.
> 
> But for whatever number of nodes I choose (> 1), I am getting the
> following error (in this case the number of nodes was 4):
> 
> =================================================================================
> The number of constraints is 99
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest
> There are: 100 Atoms
> splitting topology...
> There are 100 charge group borders and 1 shake borders
> There are 100 total borders
> Division over nodes in atoms:
>       25      25      25      25
> Walking down the molecule graph to make constraint-blocks
> 
> -------------------------------------------------------
> Program mdrun_mpi_d, VERSION 4.0.4
> Source code file: splitter.c, line: 130
> 
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (75,76)
> -------------------------------------------------------
> ==================================================================

Parallel lincs does not work with particle decomposition unfortunately. 
Try DD.

> 
> 
> So is there any way to avoid such an error and still have a particle
> decomposed parallel run or I am forced to use single processor always?
> Thanks.
> 
> 
> Regards,
> Suman.
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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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