[gmx-users] GROMACS parallel performance

Zhong Wenyu wyzhong78 at 163.com
Fri Nov 26 11:32:29 CET 2004

    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 the 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
           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
           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?
    Thanks a lot.
Wenyu Zhong
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20041126/cda45390/attachment.html>

More information about the gromacs.org_gmx-users mailing list