[gmx-developers] GB Dom Decomp problem

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 6 19:29:40 CEST 2010


I'm running a long GV simulation on 8 cores, and after tens of 
nanoseconds it crashes with this error:

Program mdrun, VERSION 4.5-beta1-20100730-f9ac35b
Source code file: /scratch/spoel/GG/gromacs/src/mdlib/domdec.c, line: 2629

Fatal error:
Step 83099555: The domain decomposition grid has shifted too much in the 
Y-direction around cell 1 0 0

Original output is:

Making 3D domain decomposition 2 x 2 x 2
starting mdrun 'Generated by trjconv : MPRA t= 2000.00000'
100000000 steps, 200000.0 ps (continuing from step 82508605, 165017.2 ps).
step 82508605, will finish Tue Aug 10 16:01:41 2010

Simulations run with angular comm removed, so the protein should not 
move away from the center of the box.

Can this be prevented?

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