[gmx-developers] Current status FFTW-3D

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 28 08:37:12 CEST 2007

Roland Schulz wrote:
> Hi David, Carsten and Erik,
> I'd like to go ahead and start to implement the 3d FFT part.
> Do you prefer or recommend a new implemantation or is adapting an existing 
> implemantation as good? I think the 3d FFT from Steve Plimpton 
> (http://www.sandia.gov/~sjplimp/docs/fft/README.html) which is used in LAMMPS 
> could be used and is fulfilling the requirements. I wouldn't recommend to use 
> the library as shared library (compile time dependences) but to simply take 
> the code into the Gromacs CVS. This is also the way it was done for LAMMPS.
> I quickly introduce myself: I studied Physics at the University of
> Heidelberg and I'm now a UTK graduate student in the Genome Science and
> Technology program and work in Prof. Jeremy C. Smith's group Center for
> Molecular Biophysics at the ORNL.
> Roland Schulz (and Jeremy Smith)

Hi Roland,

I've added a line with this info to the wiki at:

Are you aware of any benchmarks of this code? Part of new versus 
existing code will depend on performance, even though the algorithm that 
Erik laid out on the wiki is probably very similar to this implementation.

Some practical issues:
- The library need not be shared to be separate from GROMACS, the 
default is to link statically anyway. In other words it would be good if 
it were implemented in a separate subdirectory etc, with a clear interface.
- The gromacs code (optionally) uses a subset of processors for PME. The 
new algorithm needs to be able to handle this (not difficult, but you 
can not use MPI_COMM_WORLD for instance).
- In the end we would like to have the copyright of new code, but that 
is not of immediate concern, I guess we first need a working code.

Thanks for this initiative.
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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