[gmx-users] SMP vs Infiniband
spoel at xray.bmc.uu.se
Thu Feb 26 22:10:01 CET 2004
On Thu, 2004-02-26 at 20:09, Tranchemontagne, Denis wrote:
> I just got done running the gmxbench mark on a small cluster and am
> noticing some odd results. I am currently only running d.villin
> I am using a version of mpich provided by our infiniband supplier, not
> sure how it was built. fftw is 2.1.5 with --enable-mpi and
> --enable-float options.
> gromacs 3.2 compiled with --enable-mpi and --program-suffix=_mpi.
> The systems are dual 2.4 GHz Xeons running rh 7.3 linux with
> 2.4.18-27.7.xsmp as the kernel.
> When I run on as 2 processes on the smp machine I see a about 75%
> improvement, however if I run as 2 processes each on a different
> machine over infiniband I see 85% improvement.
> This seems counter intuitive.
This means you have very good communication between machines... It also
means that the SMP communication is not optimal. For serious benchmarks
you'll have to use a larger system...
> My typical run is grompp -np 2 -v ; mpirun -np -hostfile host
> mdrun_mpi -v
> I also tried mdrun_mpi -v -shuffle.
> Any help or suggestions would be appreciated.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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