Help with testing of parallel Smith-Waterman code on x86 workstations

Nemo Physche nemo at palaydium.net
Thu Jul 10 20:50:52 EST 2003


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 + 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.

Thanks,
~nemo




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