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

Nemo Physche nemo at palaydium.net
Wed Jul 9 00:13:14 EDT 2003

Hello all,

I'm writing a parallel version of the Smith-Waterman local alignment
using SIMD technology (MMX/SSE/SSE2) on Intel x86 platforms. The
implementations are based on two published papers in "Bioinformatics."
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

The programs are written in C and assembly and should be compilable in Linux
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.


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