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

Jianhui Tian jianhuitian at gmail.com
Wed Sep 27 17:01:49 CEST 2006

Hi GMX-Users,

I got an error message when using gromacs on 2 processors on the same computer.
The error message is like this:
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 24390 charge group borders and 26054 shake borders
There are 24390 total borders
Division over nodes in atoms:
   21234   21234
Program grompp_d, VERSION 3.3
Source code file: splitter.c, line: 121

Fatal error:
Shake block crossing node boundaries
constraint between atoms (21226,21234)
I saw one people had similiar problems before with 8 processors, one
suggestion for him was to use at most 3 or 4 processors.  I tried not
to use shake and the system can be ran on 2 processors well.

Thanks a lot in advance.

Best Regards,

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