Subject: [EMBOSS] Parallelizing Emboss
From: "praneet" <praneet@Sun.COM>
Date: Fri, November 3, 2006 11:59 am
To: emboss@lists.open-bio.org
Priority: Normal
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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
http://www.network.com/\).
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
--praneet
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Subject: Re: [EMBOSS] Parallelizing Emboss
From: "Guermonprez, Paul" <paul.guermonprez@intel.com>
Date: Fri, November 3, 2006 1:55 pm
To: emboss@lists.open-bio.org
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hello,
Glad to hear it, a good target may be "water",
a smith waterman implementation.
We had a similar topic on [emboss-dev] lately.
Of course before parallelizing an algo the first step is
to optimize it in serial mode, you may find information
about emboss-water optimization done at intel
a few months ago here :
please find the pdf of the slides here :
http://www.guermonprez.net/projects/emboss/emboss-EBI_06_06.pdf
and the sources here (need emboss 3.0.0 to work) :
http://www.guermonprez.net/projects/emboss/emboss-runsh.tar.gz
the software speed gain ( x11 ) was measured on intel
architecture
but you can get more or less the same on different
hardware too.
regards, paul.
Paul Guermonprez - Intel
Sr. Software Engineer - Digital Health EMEA
email : paul.guermonprez@intel.com
phone : +33 1 58 87 72 41
mobile : +33 6 26 23 67 62
