[gmx-developers] FMM in GMX-5.x
wangykoo at gmail.com
Sat Aug 16 15:00:20 CEST 2014
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:
>> 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
>> cheers up
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