[gmx-developers] MPI issues with Gromacs 4

Mark Abraham Mark.Abraham at anu.edu.au
Mon Aug 3 06:46:10 CEST 2009

rainy908 at yahoo.com wrote:
> Hi,
> Hi,
> I'm having MPI compatibility issues while running Gromacs v4.0.4.  I've
> tried using openmpi/bin/mpirun, openmpi-1.2.7-intel-mx2g/bin/mpirun, and
> openmpi-intel-mx2g/bin/mpirun, but none of them seem to be compatible - they
> caused my simulation to crash due to the error:
> "Program mdrun_mpi, VERSION 3.3.1
> Source code file: init.c, line: 69
> Fatal error:
> run input file md3_2.tpr was made for 4 nodes,
>              while mdrun_mpi expected it to be for 1 nodes."
> Does anyone have insight on this problem?  Thanks.

Yep. You're running GROMACS version 3.3.1, like it says, not version 
4.0.4, like you claim.

In 3.x, grompp needed to know how many parallel nodes you intended to 
use so that it could do the spatial decomposition. Then the number of 
processors supplied for the subsequent mdrun needed to match the input 
file. You're mismatching within your calls to 3.3.1 programs, and so 
it's complaining.

In 4.x this is all done automagically by mdrun, and grompp will not 
accept this input.

This problem has nothing whatsoever to do with the MPI library.


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