[gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 30 15:05:26 CEST 2006
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.
>> ______________________________________________________________________ __
>> 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://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++
>> _______________________________________________
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>
> _______________________________________________
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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://folding.bmc.uu.se
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