[Bioperl-l] Help with testing of parallel Smith-Waterman code on x86 workstations

[Aaron J Mackey]

You should get in touch with Arpith Jacob <jarpith at acm.org>; he has
already done this as you've described (with both diagonal and horizontal
vector implementations), and has benchmarks available.  It seems a popular
thing to do these days ;)

-Aaron

On Tue, 8 Jul 2003, Nemo Physche wrote:

>
> Hello all,
>
> I'm writing a parallel version of the Smith-Waterman local alignment
> algorithm
> using SIMD technology (MMX/SSE/SSE2) on Intel x86 platforms. The
> implementations are based on two published papers in "Bioinformatics."
> Speeds
> vary according to a wide variety of factors, but is considerably faster than
> the normal integer implementation of the algorithm.
>
> I need help testing the code on a wide variety of platforms including Intel
> 486/Pentium without MMX, Pentium MMX, Pentium 2/3 and Pentium 4 for a wide
> variety of clock speeds. The code is written using MMX/SSE/SSE2 instructions
> and as such does not use AMD specific 3DNow instructions, however the code
> should run unchanged on AMD processors. Anyone with AMD machines are also
> welcome.
>
> The programs are written in C and assembly and should be compilable in Linux
> or
> Windows (Djgpp) with GCC 3.2.3. The code will be probably be released under
> the MIT or Apache license.
>
> Please contact me if you are interested in helping.
>
> Thanks,
> ~nemo
>
>
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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu