[gmx-developers] gromacs software development

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 2 08:07:46 CEST 2007

Erik Lindahl wrote:
> Hi,
> "I'm back", as certain governators would say :-)
> First, I think we should separate the issue of domain decomposition from 
> FFT, so the first task would be to create a truly parallel 3D FFT.
> Currently, the algorithm I implemented is essentially the same as used 
> in FFTW2, where the grid is only decomposed along the x-axis. This is 
> bad for two reasons: (i) it limits the number of nodes we can use for 
> PME, and (ii) even when the direct-space system has beautiful balanced 
> domain decomposition they have to send coordinates to a more or less 
> orthogonal x-axis decomposition in fourier space.
> What we'd like is simply an algorithm that decomposed FFTs in 1D/2D/3D. 
> This is not rocket science in terms of mathematics, but requires a bit 
> of juggling with data and communication to make sure things end up in 
> the right place. There is a pretty good but superficial paper by 
> Eleftheriou that describes the high-level approach, but essentially it's 
> a matter of:
> 1. Starting with a 3D domain decomposed grid
> 2. Communicate so each node has whole arrays e.g. along the z axis
> 3. Do 1D FFTs
> 4. Communicate/transponse so each node has arrays e.g. along the y axis
> 3. Do 1D FFTs
> 4. Communicate/transponse so each node has arrays along the last axis
> 5. Don't communicate more, do the convolution in transposed coordinates
> 6. Repeat everything backwards.
> I do think the "2 weeks" estimate is very optimistic, though - I'd guess 
> a month for the basic implementation, and a bit more time for tweaking 
> to minimize communication!
> Cheers,
> Erik

I've put your comments in http://wiki.gromacs.org/index.php/FFTW-3D and 
updated the time limit. The time limits I  estimated for all projects re 
relatively wild guesses, but it is meant for a full time developer, not 
someone with a job on the side :).

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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