[Numpy-discussion] std(axis=1) memory footprint issues + moving avg / stddev

Torgil Svensson torgil.svensson at gmail.com
Mon Aug 28 19:30:58 CDT 2006


> The C-code is basically a directy "translation" of the original Python
> code.
...
> If I had to do it over again, I would place the std implementation there where
> it could be appropriately optimized.

Isn't C-code a good place for optimizations?

//Torgil


On 8/27/06, Travis Oliphant <oliphant.travis at ieee.org> wrote:
> Torgil Svensson wrote:
> > Hi
> >
> > ndarray.std(axis=1) seems to have memory issues on large 2D-arrays. I
> > first thought I had a performance issue but discovered that std() used
> > lots of memory and therefore caused lots of swapping.
> >
> There are certainly lots of intermediate arrays created as the
> calculation proceeds.  The calculation is not particularly "smart."  It
> just does the basic averaging and multiplication needed.
>
> > I want to get an array where element i is the stadard deviation of row
> > i in the 2D array. Using valgrind on the std() function...
> >
> > $ valgrind --tool=massif python -c "from numpy import *;
> > a=reshape(arange(100000*100),(100000,100)).std(axis=1)"
> >
> > ... showed me a peak of 200Mb memory while iterating line by line...
> >
> >
> The C-code is basically a directy "translation" of the original Python
> code.  There are lots of temporaries created (apparently 5 at one point
> :-).  I did this before I had the _internal.py code in place where I
> place Python functions that need to be accessed from C.  If I had to do
> it over again, I would place the std implementation there where it could
> be appropriately optimized.
>
>
>
> -Travis
>
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