[gmx-users] problem with openmpi and gromacs4.0

Daniel Larsson larsson at xray.bmc.uu.se
Thu Nov 6 17:56:28 CET 2008

On Nov 6, 2008, at 15:04 , hui sun wrote:

> Dear all,
> Recently, we installed the gromacs4.0 with openmpi parallel program.  
> When we started a simulation with np=1, the simulation was finished  
> normally. But when the same tpr file was run with np=n (n>1), I  
> obtained the following error message:
> MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with  
> errorcode -1
> My used command is & mpirun -np 32 -hostfile mpd.hosts mdrun_mpi -s  
> large.tpr -o large.trr -c large.gro -g large.log
> The content of the mpd.hosts file is following,
>                            node1  slots=8
> .
> .
> .
> nodex  slots=8
> It must be noted that my tpr file is produced via the gromacs 3.3.3.  
> Is this related to the error?

Most probably you need to run the same version of grompp as mdrun.

(Another tip is to use the option "-deffnm large" instead of -s -o -c - 
g with large names.)

> I don't know what to do now and how can I overcome this. Could you  
> help me?
> Thanks in advance!
> Hui Sun
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