[Beowulf] Maker2 genomic software license experience?

James Lowey jlowey at gmail.com
Thu Nov 8 21:32:16 PST 2012


Bingo, the code changes so fast that parallelism is best left to the scheduler, for now...


James Lowey
Director, NCS
TGen


On Nov 8, 2012, at 6:52 AM, Skylar Thompson <skylar.thompson at gmail.com> wrote:

> On 11/08/12 02:35, Tim Cutts wrote:
>> On 8 Nov 2012, at 10:10, Andrew Holway <andrew.holway at gmail.com> wrote:
>> 
>> 
>>> It's all a bit academic now (ahem) as the MPI component is a Perl
>>> program, and Perl isn't supported on BlueGene/Q. :-(
>>> 
>>> huh? perl mpi?
>>> 
>>> Interpreted language? High performance message passing interface?
>>> 
>>> confused.
>> Welcome to the wonderful world of bioinformatics and genomics "high performance" computing.  Didn't  you know that perl, python, ruby and java are all much faster than C and FORTRAN?  Apparently it's a well-known fact, and what would I, a mere system administrator, know otherwise?
>> 
>> Sarcasm mode off now.
>> 
>> Tim
> I guess if your development time is sufficiently shorter than the
> equivalent compiled code, it could make sense. In Genome Sciences here
> at University of Washington, the grad students are taught Python and R,
> and there's a number of people who love the Python MPI bindings. We also
> have some C MPI users, but it's not as popular as Python.
> 
> I supposed what you can say is, for the right application, Python MPI
> certainly is faster than serial Python.
> 
> Skylar
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