Yiannis Nicolis wrote:
Le 29 mai 06 à 20:46, David van der Spoel a écrit :
Yiannis wrote:
Hello,
Has anybody tried to use gromacs in parallel with the Intel Core
Duo macintoshes?
I installed gromacs and lam on some iMac with intel core duo
2x1.83GHz running the latest OSX with all updates.
I have everything working OK but the scaling is very inefficient.
Here are the results of the dppc benchmark:
1 process: 1 CPU on 1 Mac 216 ps/day
2 process: 2 CPU on 1 Mac 437 ps/day
2 process: 1 CPU on each of 2 Mac 275 ps/day
4 process: 2 CPU on each of 2 Mac 499 ps/day
6 process: 2 CPU on each of 3 Mac 471 ps/day
this is normal. you can buy inifiniband or similar communication
hardware or wait for GROMACS 4.0. This won't be this year most likely.
Thanks for the reply,
Is that meaning that our 100Mbs ethernet is not fast enough for a good
scaling and we'll have similar scalings with dual xeons or is this
specific Mac/Intel issue?
has nothing to do with Mac.
I looked at the archives of the list but I did not found any reference
on the subject.
search for scaling and ethernet
Thank you,
Ioannis
Clearly, I have a great gain when I use both processors on the same
computer but a very small gain when I use different computers. This
is a 100 Mbs ethernet (I tested a transfer rate of 88Mbs with scp)
so it's not a network problem.
All runs with:
grompp -shuffle -sort -np #
mpirun -np # mdrun_mpi
I compiled fftw3 with
./configure --enable-float --with-gcc-arch=prescott
and lam 7.1.2 with
./configure --with-trillium --with-fc=gfortran --with-rpi=usysv --
with-tcp-short=524288 --with-rsh=ssh --with-shm-short=524288
and gromacs is 3.3.1 compiled just with
./configure --enable-mpi --program-suffix=_mpi
Is there something I can do to improve scaling?
Have you any scaling experience with such hardware to compare with
my benchmarks?
Should I try another program than lam? Openmpi? Any experience with
xgrid? Is gromacs parallelisation working with xgrid?
What is the meaning of the messages in the md#.log such as :
"Load imbalance reduced performance to 600% of max" (that's for the
6 jobs run)
and what is the meaning of the following table on md0.log).
It reports "Total Scaling: 99% of max performance" but in reality
its speed is 471ps/day for 6 processors compared to 216 for one,
that gives 471/216/6=36%. (in other words on 1 processor it takes
4006 s and in 6 it takes 1833 s).
That's for the 6 jobs run:
Detailed load balancing info in percentage of average
Type NODE: 0 1 2 3 4 5 Scaling
-----------------------------------------------
LJ:100 99 100 99 97 101 98%
Coulomb:103 87 95 101 103 107 93%
Coulomb [W3]:141 126 97 89 71 73 70%
Coulomb [W3-W3]: 92 105 99 100 105 96 94%
Coulomb + LJ:105 91 96 100 101 105 94%
Coulomb + LJ [W3]:168 134 100 83 57 55 59%
Coulomb + LJ [W3-W3]: 94 103 99 99 103 98 96%
Outer nonbonded loop:111 94 92 93 91 116 85%
1,4 nonbonded interactions:100 100 100 100 99 99 99%
NS-Pairs:100 100 99 99 99 100 99%
Reset In Box:100 100 100 100 99 99 99%
Shift-X:100 100 100 100 99 99 99%
CG-CoM:100 100 100 100 99 99 99%
Sum Forces:100 100 99 99 99 100 99%
Angles:100 100 100 100 99 99 99%
Propers:100 100 100 100 99 99 99%
Impropers:100 100 100 100 99 99 99%
RB-Dihedrals:100 100 100 100 99 99 99%
Virial:100 100 100 100 99 99 99%
Update:100 100 100 100 99 99 99%
Stop-CM:100 100 100 100 99 99 99%
Calc-Ekin:100 100 100 100 99 99 99%
Lincs:100 100 100 100 99 99 99%
Lincs-Mat:100 100 100 100 99 99 99%
Constraint-V:100 100 100 100 99 99 99%
Constraint-Vir:100 100 100 100 99 99 99%
Settle: 99 99 99 99 100 100 99%
Total Force:100 100 98 99 100 99 99%
Total Shake: 99 99 99 99 100 100 99%
Total Scaling: 99% of max performance
Thanks for any help,
Ioannis
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______________________________________________________________________ __
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
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________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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