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

[Mike Hanby]

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

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

 

#include <stdio.h>

#include <mpi.h>

int

main(argc, argv)

 

int   argc;

char  *argv[];

{

  int  rank, size, len;

  char name[MPI_MAX_PROCESSOR_NAME];

  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);

 

  MPI_Finalize();

  exit(0);

}

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

 

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

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

 

See if that works properly first.

 

Mike

 

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
me?

 

Thanks in advance!

 

Hui Sun

  

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