python in parallel for pattern discovery in genome data

[sismex01 at hebmex.com]

> From: BalyanM [mailto:manojbalyan at ccmb.res.in] 
> Sent: Miércoles, 30 de Julio de 2003 06:19 a.m.
> To: python-list at python.org
> Subject: python in parallel for pattern discovery in genome data
> 
> 
> Hi,
> 
> I am new to python.I am using it on redhat linux 9.
> I am interested to run python on a sun machine(SunE420R,os=solaris)
> with 4 cpu's for a pattern discovery/search program on biological
> sequence(genomic sequence).I want to write the python code so that it
> utilizes all the 4 cpu's.Moreover do i need some other libraries.
> Kindly advice.
> 
> Thanks
> 
> Sincerely,
> 
> Manoj
>

Well, when designing and writing your code, take into account that
Python has a single central interpreter lock, so if you use
multiple threads, only one will be running in any given instant,
even if you have four processors.

What you'd need to do is write your utilities in two parts, one that
does "all the work", and another one a front end.  The front end
dispatches jobs to the backends, keeping a pool of back end
active backend processes, and since each backend is an independant
process, you can use as many processors as you have.

Good luck, hope this helps.

-gustavo


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