[Bioclusters] cluster computing options

[chris dagdigian]

Hi Amit,

You will find that most life science applications are not parallel 
aware. The majority are standalone binaries or algorithims that are run 
serially or in "embarassingly parallel" mode.

There are starting to be exceptions, especially for those researchers 
who are doing chemistry, structural and molecular modelling work. The 
problem is that lots of those programs are commercial (supplied by 
companies like MSI and Accelrys) and others are made available under all 
sorts of license clauses.  An example of this is AMBER 
(http://www.amber.ucsf.edu/amber/amber.html) which happens to be MPI 
aware but is available to academics under license that apparently costs 
$400 USD...

-chris


Amit Murthy wrote:

> Hi,
> 
> I am approaching biocomputing with only a computer engineering
> background. I intend to set up a Globus grid locally in order to learn
> more about grid computing. In this context I would like to run a sample
> bio computing related problem and benchmark the grid with different
> numbers of nodes. The focus will be more on learning about grid
> computing. I need to identify a biocomputing problem to act as an
> application on top of the cluster.
> 
> I am looking for suggestions from people as to what problems I should
> select  for the benchmarking. It will be helpful if the code for the bio
> computing part is available open source and has already been
> parallelized.
> 
> Any suggestions/pointers will be helpful.
> 
> Thanks and regards,
> 
> Amit
> 
> 
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bioclusters
> 


-- 
Chris Dagdigian, <dag@sonsorol.org>
Life Science IT & Research Computing Freelancer
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
Yahoo IM: craffi