[gmx-developers] Regd. Electrostatic calc. time

[David]

On Fri, 2003-08-08 at 04:30, Anjan Raghunathan wrote:
> Hi,
>    I'd like to know if there are any particular optimizing flags or code that were involved in calculating the electrostatic code, particularly PME in gromacs.
>    The reason I as k this is because I have written a patch that could use Fast Multipole Method to calculate the electrostatic interaction. Though theoretically is supposed to calculate the interaction(electrostatic) faster(than PME), it seems top be nearly 15 times slower than PME(for approx. 10^4 particles). Any suggestions on how to optimize this for gromacs; while compiling(some flags) or even using some optimised code from gromacs?
> 
> thanks,
> Anjan
this is great news! I've been meaning to look at it for a long while.
There is however some indication that the turning point lies a bit
higher (100,000 atoms, see:
@Article{Petersen95,
  author = 	 {H. G. Petersen},
  title = 	 {Accuracy and efficiency of the particle mesh {E}wald
method},
  journal = 	 {J. Chem. Phys.},
  year = 	 1995,
  volume =	 103,
  pages =	 {3668-3679}
}
)


As far as I know there is nothing special in PME, except a few assembly
tricks for truncating a real to an integer. Furthermore the FFT is
important.

However, FMM is also supposed to scale much better in parallel, so do
you have a parallel implementation and have you tested that?



> _______________________________________
> 
> Anjan V. Raghunathan
> Graduate Research Assistant
> Computational Electronics Group
> 3213 Beckman Institute,
> Univ. of Illinois at Urbana-Champaign.
> 
> E-mail:araghuna at uiuc.edu 
> Off: 217-244-1964
> Res: 217-355-5418
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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