Why is numpy c extension slow?

Posted by Bitwise on Stack Overflow See other posts from Stack Overflow or by Bitwise
Published on 2012-12-13T16:53:13Z Indexed on 2012/12/13 17:03 UTC
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numpy

I am working on large numpy arrays, and some native numpy operations are too slow for my needs (for example simple operations such as "bitwise" A&B).

I started looking into writing C extensions to try and improve performance. As a test case, I tried the example given here, implementing a simple trace calculation. I was able to get it to work, but was surprised by the performance: for a (1000,1000) numpy array, numpy.trace() was about 1000 times faster than the C extension!

This happens whether I run it once or many times. Is this expected? Is the C extension overhead that bad? Any ideas how to speed things up?

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