[Biojava-dev] Parallel Programming

[Daniel Asarnow]

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).

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>
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
>
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