[Numpy-discussion] Best way to insert C code in numpy code

Sturla Molden sturla@molden...
Tue Sep 22 09:45:31 CDT 2009


Xavier Gnata skrev:
> I have a large 2D numpy array as input and a 1D array as output.
> In between, I would like to use C code.
> C is requirement because it has to be fast and because the algorithm 
> cannot be written in a numpy oriented way :( (no way...really).
>   
There are certain algorithms that cannot be vectorized, particularly 
those that are recursive/iterative. One example is MCMC methods such as 
the Gibbs sampler. You can get around it by running multiple Markov 
chains in parallel, and vectorizing this parallelism with NumPy. But you 
cannot vectorize one long chain. Vectorizing with NumPy only applies to 
data parallel problems.

But then there is a nice tool you should not about: Cython in pure 
Python mode. You just add some annotations to the Python code, and the 
.py file can be compiled to efficient C.

http://wiki.cython.org/pure

This is quite similar in spirit to the optional static typing that makes 
certain implementations of Common Lisp (CMUCL, SBCL, Franz) so insanely 
fast.



 












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