Ganesh CN wrote:
Hi,
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:
http://www.gromacs.org/pipermail/gmx-users/2005-January/013680.html
http://www.gromacs.org/pipermail/gmx-developers/2004-January/000733.html
<http://www.gromacs.org/pipermail/gmx-developers/2004-January/000733.html>
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
<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 ?
you can not use so many processors for such a small system in 3.3. In
4.0 you will be able to do it.
Thanks in advance,
Ganesh
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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