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 : [EMAIL PROTECTED] phone : +33 1 58 87 72 41 mobile : +33 6 26 23 67 62 -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of praneet Sent: Friday, November 03, 2006 12:59 PM To: [email protected] Subject: [EMBOSS] Parallelizing Emboss 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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
