On Fri, Oct 10, 2008 at 10:40 PM, Brian Dobbins <bdobbins@gmail.com> wrote:

Hi guys,

On Fri, Oct 10, 2008 at 12:57 PM, Brock Palen <brockp@umich.edu> wrote:

Actually I had a much differnt results,

gromacs-3.3.1 one node dual core dual socket opt2218 openmpi-1.2.7 pgi/7.2
mpich2 gcc

For some reason, the difference in minutes didn't come through, it seems, but I would guess that if it's a medium-large difference, then it has its roots in PGI7.2 vs. GCC rather than MPICH2 vs. OpenMPI. Though, to be fair, I find GCC vs. PGI (for C code) is often a toss-up - one may beat the other handily on one code, and then lose just as badly on another.

I think my install of mpich2 may be bad, I have never installed it before, only mpich1, OpenMPI and LAM. So take my mpich2 numbers with salt, Lots of salt.

I think the biggest difference in performance with various MPICH2 install comes from differences in the 'channel' used.. I tend to make sure that I use the 'nemesis' channel, which may or may not be the default these days. If not, though, most people would probably want it. I think it has issues with threading (or did ages ago?), but I seem to recall it being considerably faster than even the 'ssm' channel.

Sangamesh: My advice to you would be to recompile Gromacs and specify, in the Gromacs compile / configure, to use the same CFLAGS you used with MPICH2. Eg, "-O2 -m64", whatever. If you do that, I bet the times between MPICH2 and OpenMPI will be pretty comparable for your benchmark case - especially when run on a single processor.

I reinstalled all softwares with -O3 optimization. Following are the performance numbers for a 4 process job on a single node:

MPICH2:     26 m 54 s
OpenMPI:   24 m 39 s

More details:

$ /home/san/PERF_TEST/mpich2/bin/mpich2version
MPICH2 Version:         1.0.7
MPICH2 Release date:    Unknown, built on Mon Oct 13 18:02:13 IST 2008
MPICH2 Device:          ch3:sock
MPICH2 configure:       --prefix=/home/san/PERF_TEST/mpich2
MPICH2 CC:      /usr/bin/gcc -O3 -O2
MPICH2 CXX:     /usr/bin/g++ -O2
MPICH2 F77:     /usr/bin/gfortran -O3 -O2
MPICH2 F90:     /usr/bin/gfortran -O2

$ /home/san/PERF_TEST/openmpi/bin/ompi_info
                Open MPI: 1.2.7
   Open MPI SVN revision: r19401
                Open RTE: 1.2.7
   Open RTE SVN revision: r19401
                    OPAL: 1.2.7
       OPAL SVN revision: r19401
                  Prefix: /home/san/PERF_TEST/openmpi
Configured architecture: x86_64-unknown-linux-gnu
           Configured by: san
           Configured on: Mon Oct 13 19:10:13 IST 2008
          Configure host: locuzcluster.org
                Built by: san
                Built on: Mon Oct 13 19:18:25 IST 2008
              Built host: locuzcluster.org
              C bindings: yes
            C++ bindings: yes
      Fortran77 bindings: yes (all)
      Fortran90 bindings: yes
Fortran90 bindings size: small
              C compiler: /usr/bin/gcc
     C compiler absolute: /usr/bin/gcc
            C++ compiler: /usr/bin/g++
   C++ compiler absolute: /usr/bin/g++
      Fortran77 compiler: /usr/bin/gfortran
Fortran77 compiler abs: /usr/bin/gfortran
      Fortran90 compiler: /usr/bin/gfortran
Fortran90 compiler abs: /usr/bin/gfortran
             C profiling: yes
           C++ profiling: yes
     Fortran77 profiling: yes
     Fortran90 profiling: yes
          C++ exceptions: no
          Thread support: posix (mpi: no, progress: no)
Internal debug support: no
     MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
         libltdl support: yes
   Heterogeneous support: yes
mpirun default --prefix: no

Thanks,
Sangamesh

Cheers,
- Brian

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