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:
http://www.open-mpi.org/community/help/
- Did you specify to use mpi_leave_pinned? 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? Use "--mca mpi_paffinity_alone
1" on your mpirun command line.
- 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.
- Have you tried compiling Open MPI with something other than GCC?
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.
--
Jeff Squyres
Cisco Systems
