On Fri, Oct 10, 2008 at 10:40 PM, Brian Dobbins <bdobb...@gmail.com> wrote:
>
> Hi guys,
>
> On Fri, Oct 10, 2008 at 12:57 PM, Brock Palen <bro...@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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MPICH2
[san@locuzcluster mpich2-1.0.7]$ ./configure --help
[san@locuzcluster mpich2-1.0.7]$ export CC=`which gcc`
[san@locuzcluster mpich2-1.0.7]$ export CXX=`which g++`
[san@locuzcluster mpich2-1.0.7]$ export F77=`which gfortarn`
[san@locuzcluster mpich2-1.0.7]$ export F90=`which gfortran`
[san@locuzcluster mpich2-1.0.7]$ export CFLAGS=-O3
[san@locuzcluster mpich2-1.0.7]$ export FFLAGS=-O3
[san@locuzcluster mpich2-1.0.7]$ ./configure
--prefix=/home/san/PERF_TEST/mpich2 | tee config_out
[san@locuzcluster mpich2-1.0.7]$ make | tee make_out
OPENMPI
[san@locuzcluster openmpi-1.2.7]$ export FC=`which gfortran`
[san@locuzcluster openmpi-1.2.7]$ ./configure
--prefix=/home/san/PERF_TEST/openmpi | tee config_out
[san@locuzcluster openmpi-1.2.7]$ make | tee make_out
[san@locuzcluster openmpi-1.2.7]$ make install | tee install_out
FFTW
$ export CC=`which gcc`
$ export CXX=`which g++`
$ export F77=`which gfortran`
$ export CFLAGS=-O3
$ export FFLAGS=-O3
GROMACS
With MPICH2
$ export CC=`which gcc`
$ export CXX=`which g++`
$ export F77=`which gfortran`
$ export CFLAGS="-I/home/san/PERF_TEST/fftw/include -O3"
$ export LDFLAGS="-L/home/san/PERF_TEST/fftw/lib"
$ export MPICC=/home/san/PERF_TEST/mpich2/bin/mpicc
With OPENMPI
$ export CC=`which gcc`
$ export CXX=`which g++`
$ export F77=`which gfortran`
$ export CFLAGS="-I/home/san/PERF_TEST/fftw/include -O3"
$ export LDFLAGS="-L/home/san/PERF_TEST/fftw/lib"
