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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of hui sun
Sent: Thursday, November 06, 2008 8:04 AM
To: [email protected]
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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