[gmx-users] domain decomposition error

[Fabio Affinito]

Hi,
I'm trying to run a simulation with 4.5.3 (double precision) on bluegene.
I get this error:


> NOTE: Turning on dynamic load balancing
> 
> vol 0.35! imb F 54% pme/F 2.06 step 100, remaining runtime:     3 s
> vol 0.33! imb F 48% pme/F 2.09 step 200, remaining runtime:     2 s
> vol 0.35! imb F 28% pme/F 2.42 step 300, remaining runtime:     1 s
> vol 0.34! imb F 26% pme/F 2.46 step 400, remaining runtime:     0 s
> 
> -------------------------------------------------------
> Program mdrun_mpi_bg_d, VERSION 4.5.3
> Source code file: domdec.c, line: 3581
> 
> Fatal error:
> Step 490: The X-size (0.799998) times the triclinic skew factor (1.000000) is smaller than the smallest allowed cell size (0.800000) for domain decomposition grid cell 4 2 2
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> "Everything's formed from particles" (Van der Graaf Generator)
> 
> Error on node 188, will try to stop all the nodes
> Halting parallel program mdrun_mpi_bg_d on CPU 188 out of 256
> 

Can anybody give me some hint about that?

Thanks in advance,

Fabio
-- 
*********************************************
Fabio Affinito, PhD
CINECA
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)