[EMBOSS] Parallelizing Emboss

praneet praneet at Sun.COM
Fri Nov 3 11:59:06 UTC 2006

Hello Everyone,

We at Sun Microsystems just got started with Emboss. So, apologies if 
you don't find the questions asked below as particularly bright.
We are evaluating Emboss and trying to figure out if it can be parallelized.
Eventually, Emboss* may be* available on Sun Grid 
(http://www.sun.com/service/sungrid/overview.jsp and 

I've a few  questions

   1. What do you think is the best way to parallelize Emboss? best here
      means we are ready for a cost performance trade-off. Our options are
         1. Input partioning or
         2. Writing mpi constructs
   2. Are there any existing guidelines/ reference implementation/ docs
      or any relevant material pertaining to parallelizing Emboss?
   3. Out of the 160 applications, which ones do you think should be
      parallelized? We don't have time to parallelize all applications
      if we go the mpi route. A starting list of 5 applications would
      serve our purpose. From what I could find on the net, palindrome
      and einverted seem to be slow. Are these two good candidates to
      get us started?

Anything else that you think may enlighten us would be heartily welcome.

Thanks in advance


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