[Bioclusters] question: what is your rate limiting computational step?

Joe Landman landman at scalableinformatics.com
Sun Feb 15 20:22:08 EST 2009

Hi folks:

   (purely non-commercial purpose question)

   We are looking to get feedback from informatics users and researchers 
where your computational bottlenecks are.   Basically, we are trying to 
understand which programs or algorithms are the most time/resource 
consuming.  The groups we speak to frequently often have their own 
particular needs, so I would like to make sure we are addressing the 
larger community of informatics users and researchers.

   The goal of this effort is to explore whether or not acceleration of 
some of these codes is possible or beneficial on GPU based systems.

   Part of my reason for asking is that I see a number of dynamic 
programming algorithms have been accelerated on FPGAs and other 
platforms, but I am not seeing large usage of these accelerators.  This 
suggests that the barriers to obtaining/using these accelerators may be 
larger than the benefit of using them ... either because the costs are 
too high, or the wrong thing is being accelerated, and bottlenecks are 
elsewhere.  The GPU-HMMer work recently announced does seem to have good 
uptake, and we want to see what else we should be looking at.

   We would like to know where the computational rate limiting steps are 
today, and what you need to run faster, and what the benefit of 
additional speed would be (as well as how much additional speed is 
needed to positively impact your research).

   Please feel free to email me offline, if there is interest, we will 
summarize.  Again, strictly non-commercial in nature.



Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423 x121
fax  : +1 866 888 3112
cell : +1 734 612 4615

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