[gmx-users] Shake block errors with d.lzm
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 24 14:25:43 CET 2008
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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