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

Mike Hanby mhanby at uab.edu
Thu Nov 6 17:30:34 CET 2008

I would suggest that you test OpenMPI first using a simple hello world
on 32 processors to see if it can run successfully:


$ mkdir -p ~/jobs/helloworld && cd ~/jobs/helloworld

$ vi ./helloworld-mpi.c



#include <stdio.h>

#include <mpi.h>


main(argc, argv)


int   argc;

char  *argv[];


  int  rank, size, len;


  MPI_Init(&argc, &argv);

  MPI_Comm_rank(MPI_COMM_WORLD, &rank);

  MPI_Comm_size(MPI_COMM_WORLD, &size);


  MPI_Get_processor_name(name, &len);

  printf ("Hellow world! I'm %d of %d on %s\n", rank, size, name);





/*---------------------end code------------------------*/


$ rm helloworld*.o && /path/to/openmpi/bin/mpicc -o helloworld-openmpi

$ mpirun -np 32 -hostfile mpd.hosts helloworld-openmpi


See if that works properly first.




From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of hui sun
Sent: Thursday, November 06, 2008 8:04 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] problem with openmpi and gromacs4.0 


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?

I don't know what to do now and how can I overcome this. Could you help


Thanks in advance!


Hui Sun



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