[gmx-developers] FMM in GMX-5.x

[Yorquant Wang]

Hi,
     So, if the size of the simulation is big enough, FMM can be faster
than PME.  Even though I heard that FMM is very hard to be coded into
program, I just want to know the state of implement of FMM to GMX5.x .
     It seems that FMM probabily can behave better than PME in massively
parallelled architecture hardware, for example the mutliple GPU or CPU or
MIC nodes clusters.  I quite look forword that.


2014-08-15 4:42 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:

>
>
>
> On Thu, Aug 14, 2014 at 1:42 PM, Smart Eagle <wangykoo at gmail.com> wrote:
>
>> Hi,
>>     I just notice that GMX have plan to implement FMM in to GMX to
>> calculate long-term forces for MD. You know PME will suffer FFT NxN all
>> communactiom problems and FMM seemly can scale much better than FME. Indeed
>> there have been a progrom called MODYLAS which have implement FMM to MD (J.
>> Chem. Theory Comput. 2013, 9, 3201−3209‍).
>>     I just want to know therotically, which is larger between FMM and PME
>> for the time cost of long-term forces calculation in one MD steps in one
>> nodes ? (means the basic calculation load for each method without
>> consideration of communications between nodes). ‍‍‍
>>
>
> Theoretically - it depends on the size of the simulation (which fixes N)
> and the quality of the implementations (which fix the prefactors in the
> asymptotic analysis of O(N) vs O(N log N)).
>
> Practically - you could analyze the total flops on a given problem, but it
> would tell you little about the performance on a single node, because how
> well the implementation handles data flow is what dominates performance
> (now, and more so in the future). Adding inter-node parallelism makes that
> worse.
>
> Mark
>
>
>> cheers up
>>
>>
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-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
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