[gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

[Yiannis Nicolis]

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?
I looked at the archives of the list but I did not found any  
reference on the subject.
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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