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

[David van der Spoel]

On Tue, 2004-11-30 at 20:24 +0800, Zhong Wenyu wrote:
> 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?

turn off hyperthreading. compare performance in ps/day to NAMD.

parallel scaling will be improved in v 4.0

>     Please help me. 
>     Thanks a lot.
> Wenyu Zhong
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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