[Beowulf] Maker2 genomic software license experience?

Lux, Jim (337C) james.p.lux at jpl.nasa.gov
Fri Nov 9 05:06:46 PST 2012


Maybe that's why you need a cluster...
Rather than spend labor time making the code faster, just buy a faster
machine  (assuming Amdahl's law doesn't bite you).  Especially for some
specialized domain areas, there may not be more labor time available to
buy, at any price.

I don't know how sophisticated they are, but python does do some sort of
compilation, just like matlab and octave do, it's just done on the fly.
So it's not like you're going to interpret the inside of the loop over and
over again.

On 11/8/12 5:52 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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