Users,
Thanks for the response. To further clarify I am running rhel5 on a
single quad machine. I tried Chandan Choudhury's suggestion and that
hello world program doesnt output anything on my machine. Here is what
i did:
1. mpicc mpitest.c -o test
2. mpirun -np 2 test
I made a slight change to the hello world program: (mpitest2.c now)
####################################################
#include <stdio.h>
#include <mpi.h>
int main(int argc, char *argv[] )
{
int rank, size;
MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &size );
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
printf( "Hello world from process %d of %d\n", rank, size );
MPI_Finalize();
return 0;
}
####################################################
Then ran:
1. mpicc mpitest2.c -o test2
2. mpirun -np 2 test2
Error message:
test2: symbol lookup error: /usr/local/lib/libmpi.so.0: undefined
symbol: orte_help_want_aggregate
test2: symbol lookup error: /usr/local/lib/libmpi.so.0: undefined
symbol: orte_help_want_aggregate
I tried searching the openmpi list but nothing stood out to me as a
solution. I am not overly familiar with openmpi either so this is a bit
past my expertise. Any other thoughts or suggestions would be great!
-Matt-
Chandan Choudhury wrote:
I had also had trouble installing gmx (paralley). But now, its solved.
I would suggest you to see that the mpi is running or not.
Here is a sample mpi C program:
####################################################
#include <stdio.h>
#include "mpi.h"
int main( argc, argv )
int argc;
char **argv;
{
int rank, size;
MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &size );
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
printf( "Hello world from process %d of %d\n", rank, size );
MPI_Finalize();
return 0;
}
########################################################
save as mpitest.c
compile mpitest.c
mpirun -np 2 -machilefile mac a.out
If every thing is ok. Then the output will be :
Hello world from process
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Feb 6, 2010 at 5:47 AM, Jussi Lehtola
<jussi.leht...@helsinki.fi <mailto:jussi.leht...@helsinki.fi>> wrote:
On Fri, 2010-02-05 at 15:29 -0500, Matthew L. Danielson wrote:
> Compiling fftw and openmpi seems to finish successfully. The serial
> version of gromacs installed correctly, just when i issue
--enable-mpi i
> am seeing this error message (i can attached the config.log if
it would
> help):
> "checking size of int... configure: error: cannot compute sizeof
(int)"
>
> From what i can get out of the mail-archive, I think this is
problem
> with the mpi installation or not finding the correct files etc.
I have
> tried re-installing openmpi (always removing the old version)
using yum
> (installed version 1.3.2) and installing openmpi from their website
> (1.4.1). Both seem to install correctly, yet the same error message
> arises when i do ./configure --enable-mpi for gromacs.
What distribution are you using? If you are running Fedora 12, you
need
to load the MPI environment module with e.g.
$ module load openmpi-x86_64
Furthermore, you should have the fftw-devel and openmpi-devel packages
installed on your system.
--
------------------------------------------------------
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi <mailto:jussi.leht...@helsinki.fi>, p.
191 50632
------------------------------------------------------
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi <mailto:jussi.leht...@helsinki.fi>
------------------------------------------------------
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Matthew L. Danielson
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College of Pharmacy, Nursing, and Health Sciences
Purdue University
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