[gmx-developers] restarting from cpt with different #nodes - genborn code fixed

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 9 23:16:43 CEST 2010

On 2010-07-09 21.47, David van der Spoel wrote:
> Hi,
> when I restart a run from a checkpoint file made on 8 processors, it
> runs on 8 or 2 or 1 processors, but when I run it on 4 processors it
> crashes at step zero with this message:
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.99-dev-20100708-f7f0d52
> Source code file: /home/spoel/GG/gromacs/src/gmxlib/pbc.c, line: 860
> Fatal error:
> Internal error in pbc_dx_aiuc, set_pbc_dd or set_pbc has not been called
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Any clues?
This was caused by the pbc structure not being initialized when calling 
calc_gb_forces. With the fixes the code does not crash with this warning 
anymore. Now I am testing whether this also fixes other crashes.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

More information about the gromacs.org_gmx-developers mailing list