[Numpy-discussion] my cython is slow

Eric Firing efiring@hawaii....
Thu Jan 8 12:34:14 CST 2009

John Hunter wrote:
> On Wed, Jan 7, 2009 at 5:37 PM, Eric Firing <efiring@hawaii.edu> wrote:
>> A couple small changes speed it up quite a bit:
>> efiring@manini:~/temp/nnbf$   python test_nnbf.py
>> loading data... this could take a while
>> testing nnbf...
>>    10 trials: mean=0.0150, min=0.0100
>> testing numpy...
>>    10 trials: mean=0.0660, min=0.0600
>> It is all a matter of keeping Python objects and function calls out of inner
>> loops.  I suspect there is quite a bit more that could be done in that
>> regard, but I haven't looked.
> Much  faster, but no longer correct, as you'll see if you uncomment
> out the nose test test_neighbors that compare actual vs desired.
> Is the pointer arithmetic correct:
>   dataptr + i
> I would have thought perhaps:
>   dataptr + i*n
> but this is segfaulting.  Do we need to use a stride?

Sorry, I was too hasty.  Yes, it seems like i*n should be correct, but 
it isn't; we are missing something simple and fundamental here.  I don't 
see it immediately, and won't be able to look at it for a while.


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