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

Jochen Hub jhub at gwdg.de
Wed Aug 27 19:32:00 CEST 2008


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

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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