[gmx-developers] Little bug in particle decomposition due to PME nodes

[David van der Spoel]

Jochen Hub wrote:
> Hi,
> 
> when running the CVS mdrun (Version 3.3.99_development_20080718) on 4 
> nodes with particle decompostion, I get the following error:
> 
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.99_development_20080718
> Source code file: partdec.c, line: 235
> 
> Fatal error:
> Atomid 86858 is larger than number of atoms (69496)
> -------------------------------------------------------
> 
> The error is due to cr->npmenodes which is set to -1 by default. This 
> way split_top (in partdec.c) tries to split the sytesm into 5 
> (=nnodes-npmenodes) parts. When trying to circumvent that with -npme 0 I 
> get I segmentation fault.
> 
> Has this bug already been corrected during the last month (our 
> CVS-Version is from June 18th)?
> 
> Cheers, Jochen
> 
> 
yes it has (by someone in your corridor :)).

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se