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

[Nemo Physche]

Just to clear things up a little, I'm not looking for a cluster of
workstations, just single workstations. The program achieves parallelism on
a single machine, by simultaneously calculating multiple rows of the
comparison matrix using multimedia extensions (termed MMX/SSE/SSE2 by
intel). So if anyone has a Pentium 2/3/4 or AMD machine and some time to
spare, please send me a line.

Thanks,
-nemo

> >> 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
> >>