[gmx-users] Shake block errors with d.lzm

Ganesh CN ganesh.mailinglist at gmail.com
Thu Jan 24 13:56:52 CET 2008


I am novice GROMACS user and I am trying to use the d.lzm benchmark of
GROMACS for a parallel MPI run.  Its working fine for the 8 processor case,
but from 16 processors onwards (tried until 256 processors), running grompp
is giving me errors for "Shake block crossing node boundaries".  ( I am not
a MD person at all, so I have no idea what this means.).  The version I am
using is 3.3.1 and the command line I used is

$ grompp -f cutoff.mdp -np 16

The exact error I am getting is :

Checking consistency between energy and charge groups...
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 7882 charge group borders and 7846 shake borders
There are 7429 total borders
Division over nodes in atoms:
    1453    1451    1449    1449    1449    1452    1449    1452    1449
1452    1449    1452    1449    1452    1449    1451
Program grompp, VERSION 3.3.1
Source code file: splitter.c, line: 121

Fatal error:
Shake block crossing node boundaries
constraint between atoms (1447,1454)

I saw that there were a couple of other threads which talked about this:


But none of them had any solutions provided.  The second one said I tried
looking up the bugzilla and documentation for any bugs and found this :
http://bugzilla.gromacs.org/show_bug.cgi?id=110.  It seems to suggest that
there is something wrong with the topology file, but I am using the standard
topology file shipped with d.lzm.

Does anybody faced this problem before and has a solution ? Or is this a
known issue ?

Thanks in advance,
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