[gmx-users] Compiling 4.0.7 parallel fails

[Matthew L. Danielson]

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.lehtola at helsinki.fi <mailto:jussi.lehtola at 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.lehtola at helsinki.fi <mailto:jussi.lehtola at helsinki.fi>, p.
>     191 50632
>     ------------------------------------------------------
>     Mr. Jussi Lehtola, M. Sc., Doctoral Student
>     Department of Physics, University of Helsinki, Finland
>     jussi.lehtola at helsinki.fi <mailto:jussi.lehtola at helsinki.fi>
>     ------------------------------------------------------
>
>
>     --
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>

-- 

Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
MCMP RHPH 504c
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West Lafayette, IN 47907-2091

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