[gmx-developers] MPI issues with Gromacs 4

rainy908 at yahoo.com rainy908 at yahoo.com
Mon Aug 3 06:12:12 CEST 2009



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.

2009/8/2 Mark Abraham <Mark.Abraham at anu.edu.au>

> rainy908 at yahoo.com wrote:
>> So I've been able to get access to Gromacs v4.0.4 on another supercomputer
>> cluster.  However, I've been told that there are compatibility issues
>> regarding the MPI with Gromacs v4.  Also, I'm using the MARTINI force
>> field
>> with Gromacs, but I'm not sure how well it is tested with v4?
> Please start a new email with a new subject when you change topics. You
> should also try to search the archives for clues on these topics. I'm not
> aware of general problems with modern MPI libraries and GROMACS 4. The use
> GROMACS makes of MPI functionality is quite undemanding.
> Mark\
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