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<DIV><FONT size=2>Hi,everyone.</FONT></DIV>
<DIV><FONT size=2> 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.</FONT></DIV>
<DIV><FONT size=2> I have compiled single precision versions
of fftw and gromacs with icc. The Cflags used were "<SPAN lang=EN-US
style="FONT-SIZE: 12pt; COLOR: red; FONT-FAMILY: ËÎÌå; mso-bidi-font-family: ËÎÌå; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA">-O3
¨Cip ¨Cunroll -xN</SPAN>". 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.</FONT></DIV>
<DIV><FONT size=2> The option used like
this:</FONT></DIV>
<DIV><FONT size=2> grompp -f grompp.mdp -c conf.gro -p
topol.top -po mdout.mdp -np $NSLOTS -shuffle -sort<BR> mpirun
-np $NSLOTS -machinefile $nodefile mdrun -s topol.tpr -o traj.trr -c confout.gro
-e ener.edr -g md.log</FONT></DIV>
<DIV><FONT size=2>benchmarks:</FONT></DIV>
<DIV><FONT size=2> Villin:</FONT><FONT
size=2><BR> CPUs
(Mnbf/s) (GFlops) (ps/NODE hour) (NODE
hour/ns)<BR>
1: 45.429
1.424 345.125 2.897</FONT></DIV>
<DIV><FONT size=2>
4: 46.467
1.458 352.941 2.833</FONT></DIV>
<DIV><FONT size=2>
8: 29.621 929.329
225.000 4.444</FONT></DIV>
<DIV><FONT size=2> DPPC:</FONT><FONT
size=2><BR> CPUs
(Mnbf/s) (GFlops) (ps/NODE hour) (NODE hour/ns)</FONT></DIV>
<DIV><FONT
size=2> 1:
18.722 675.081
5.781
172.968<BR>
8: 33.108
1.195 10.221 97.833</FONT></DIV>
<DIV><FONT
size=2> 16:
42.312 1.528
13.072 76.500<BR> Considering
Hyperthreading was on, while CPUs was 4, actually it was 2.</FONT></DIV>
<DIV><FONT size=2> The performance was far away from the
benchmark on website of Gromacs, and almost as same as a previous post
describing: <A
href="http://www.gromacs.org/pipermail/gmx-users/2004-June/011028.html">http://www.gromacs.org/pipermail/gmx-users/2004-June/011028.html</A>.
but I haven't seen his solution.</FONT></DIV>
<DIV><FONT size=2> What's the problem?</FONT></DIV>
<DIV><FONT size=2> Thanks a lot.</FONT></DIV>
<DIV><FONT size=2>Wenyu Zhong</DIV></FONT></BODY></HTML>