FYI attached here OpenMPI install details

On Wed, Oct 8, 2008 at 7:56 PM, Sangamesh B <forum.san@gmail.com> wrote:


On Wed, Oct 8, 2008 at 7:16 PM, Jeff Squyres <jsquyres@cisco.com> wrote:
On Oct 8, 2008, at 9:10 AM, Sangamesh B wrote:

      I wanted to switch from mpich2/mvapich2 to OpenMPI, as OpenMPI supports both ethernet and infiniband. Before doing that I tested an application 'GROMACS' to compare the performance of MPICH2 & OpenMPI. Both have been compiled with GNU compilers.

After this benchmark, I came to know that OpenMPI is slower than MPICH2.

This benchmark is run on a AMD dual core, dual opteron processor. Both have compiled with default configurations.

The job is run on 2 nodes - 8 cores.

OpenMPI - 25 m 39 s.
MPICH2  -  15 m 53 s.


A few things:

- What version of Open MPI are you using?  Please send the information listed here:
1.2.7

   http://www.open-mpi.org/community/help/

- Did you specify to use mpi_leave_pinned?  
No
Use "--mca mpi_leave_pinned 1" on your mpirun command line (I don't know if leave pinned behavior benefits Gromacs or not, but it likely won't hurt) 

- Did you enable processor affinity?
No
 Use "--mca mpi_paffinity_alone 1" on your mpirun command line.
Will use these options in the next benchmark

- Are you sure that Open MPI didn't fall back to ethernet (and not use IB)?  Use "--mca btl openib,self" on your mpirun command line.
I'm using TCP. There is no infiniband support. But eventhough the results can be compared?

- Have you tried compiling Open MPI with something other than GCC?
No.
 Just this week, we've gotten some reports from an OMPI member that they are sometimes seeing *huge* performance differences with OMPI compiled with GCC vs. any other compiler (Intel, PGI, Pathscale).  We are working to figure out why; no root cause has been identified yet.
I'll try for other than gcc and comeback to you

--
Jeff Squyres
Cisco Systems


_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users


*****************************************************************************
**                                                                         **
** WARNING:  This email contains an attachment of a very suspicious type.  **
** You are urged NOT to open this attachment unless you are absolutely     **
** sure it is legitimate.  Opening this attachment may cause irreparable   **
** damage to your computer and your files.  If you have any questions      **
** about the validity of this message, PLEASE SEEK HELP BEFORE OPENING IT. **
**                                                                         **
** This warning was added by the IU Computer Science Dept. mail scanner.   **
*****************************************************************************