[Beowulf] Maker2 genomic software license experience?

Skylar Thompson skylar.thompson at gmail.com
Thu Nov 8 05:52:50 PST 2012


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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