Re: Intel Kernel Math Library

From: case <>
Date: Thu 6 Jun 2002 08:02:25 -0700

On Thu, Jun 06, 2002, Joffre Heredia wrote:
> We then started looking for an alternative to the SANDER FFT functions
> and found the Intel Kernel Math Library
> ( It seems
> they have, as SGI, a fast solution to FFT calculations.
> As SANDER 7 is using the ewald method by default, I was wondering if
> there would be any compiler option for using the Intel MKL instead of
> the SANDER built-in FFT functions. In the case this is not possible, I
> would like to know if the AMBER developers are thinking about the
> possibility of using the Intel MKL in a next release.

I don't know of any efforts along these lines by the "core" Amber developers,
but we are always happy to take suggestions.

Note, however, that slowness in FFT's is often not a serious problem. For
example, on the "jac" benchmark (150 residue protein in water), about 5%
of the time is spent in the FFT routines (on a 1.2 GHz Athlon processor).
And that benchmark doesn't use the RESPA multiple-time-step algorithm, which
could cut the FFT percentage about in half. So it's not clear that there is
much to be gained by speeding up the FFT libraries.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Thu Jun 06 2002 - 08:02:25 PDT
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