[Biojava-dev] Parallel Programming

[Andreas Prlic]

Hi,

I am all for good support of parallelism. Many (all?) of the algorithms
that are in BioJava are building blocks that already now can easily run in
multi threaded environments. The multiple sequence aligner especially is
written so it can leverage multi CPUs.

In your experience, did you have any problems running BioJava in a multi
CPU context? What is needed to improve support? Documentation?

Andreas




On Thursday, May 29, 2014, Daniel Asarnow <dasarnow at gmail.com> wrote:

> Udaya,
> I've developed code local parallelism in structure alignments, outside of
> the BioJava tree, and there's some support already in BioJava for
> client-server distributed structure alignments as well. I'm not aware of
> other parallel execution support in BioJava (although there may be).g
>
> This is all to say that I am also interested in working on parallelism in
> BioJava. To be clear, I'm not a BioJava developer myself, just a small time
> contributor (CATH parser), so of course we need to hear the opinions of the
> committers.
>
> Andreas et al., what do you think of greater internal parallelism in
> BioJava? If it should be supported, how do you think it should be done?
> Different algorithms in BioJava have different prospects for parallelism,
> but presumably the approach should be as uniform as possible within each of
> the two general cases: algorithms which are suitable for direct parallelism
> (e.g. within the algorithm itself), and algorithms which are serial, but
> can be run in parallel on multiple inputs.
>
> Regards,
> -da
>
>
> On Thu, May 29, 2014 at 10:46 AM, Udaya Tejwani <udayatejwani at hotmail.com
> <javascript:;>>
> wrote:
>
> > Hi,
> >
> >
> >
> > I would like to update source code of BioJava to leverage use of multiple
> > processors to facilitate parallel code execution.  Can anybody point me
> in
> > the direction of how I can go about doing that?  What is the process
> > involved?
> >
> >
> >
> > Thanks,
> >
> > Udaya
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org <javascript:;>
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org <javascript:;>
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
-----------------------------------------------------------------------