[gmx-users] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU

Andreas Kring akring at fys.ku.dk
Tue Nov 4 13:36:59 CET 2008

Hi all.

I have just installed GROMACS 4.0. My system consists of one hydroxide 
ion and 999 polarizable water molecules. When the system is minimized 
(using only one CPU) with a steepest descent minimizer, there are no 
problems. But when I try to minimize exactly the same system using 4 or 
8 CPUs, I get the following error:

Reading file topol.tpr, VERSION 4.0 (double precision)
Making 1D domain decomposition 4 x 1 x 1
Steepest Descents:
    Tolerance (Fmax)   =  1.00000e+01
    Number of steps    =       100000

A list of missing interactions:
           exclusions of  14987 missing     -1

Program mdrun4_d, VERSION 4.0
Source code file: domdec_top.c, line: 337

Software inconsistency error:
One or more interactions were multiple assigned in the domain decompostion

"Microsecond Here I Come" (P.J. Van Maaren)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun4_d on CPU 0 out of 4

gcq#161: "Microsecond Here I Come" (P.J. Van Maaren)

Any ideas why this could be?


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