[gmx-users] GROMACS parallel performance(sorry to post again)

[Zhong Wenyu]

Hi,everyone.
    I'm sorry to post this mail again, but it really disturbed me and I haven't found a solution in the previous post.
    I am a newbie to gromacs and have used NAMD for some time. I think maybe Gromacs can do something NAMD can't, So I came into your area.
    I have compiled single precision versions of fftw and gromacs with icc. The Cflags used were "-O3 ¨Cip ¨Cunroll -xN". Now the first problem bothered me was the parallel performance of Gromacs. It was unreasonable on a Xeon 2.4 cluster made by myself. The OS was Rocks 3.2.0 based on RedHat 3.0EL, network was 1000Mbit ethernet. Hyperthreading was on and it was about 10%-20% faster than off while running namd.
    The option used like this:
    grompp -f grompp.mdp -c conf.gro -p topol.top -po mdout.mdp -np $NSLOTS -shuffle -sort
    mpirun -np $NSLOTS -machinefile $nodefile mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
benchmarks:
    Villin:
           CPUs   (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
            1:     45.429      1.424    345.125      2.897
            4:     46.467      1.458    352.941      2.833
            8:     29.621    929.329    225.000      4.444
    DPPC:
           CPUs    (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
            1:     18.722    675.081      5.781    172.968
            8:     33.108      1.195     10.221     97.833
           16:     42.312      1.528     13.072     76.500
    Considering Hyperthreading was on, while CPUs was 4, actually it was 2.
    The performance was far away from the benchmark on website of Gromacs, and almost as same as a previous post describing:  http://www.gromacs.org/pipermail/gmx-users/2004-June/011028.html. but I haven't seen his solution.
    What's the problem? How cloud I do? Maybe I should close hyperthreading or recompile Gromacs or other thing?
    Please help me. 
    Thanks a lot.
Wenyu Zhong
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