[Numpy-discussion] distance matrix speed (original) (raw)

Sebastian Beca sebastian.beca at gmail.com
Thu Jun 15 19:08:21 EDT 2006

Hi, I'm working with NumPy/SciPy on some algorithms and i've run into some important speed differences wrt Matlab 7. I've narrowed the main speed problem down to the operation of finding the euclidean distance between two matrices that share one dimension rank (dist in Matlab):

Python: def dtest(): A = random( [4,2]) B = random( [1000,2])

d = zeros([4, 1000], dtype='f')
for i in range(4):
    for j in range(1000):
        d[i, j] = sqrt( sum( (A[i] - B[j])**2 ) )
return d

Matlab: A = rand( [4,2]) B = rand( [1000,2]) d = dist(A, B')

Running both of these 100 times, I've found the python version to run between 10-20 times slower. My question is if there is a faster way to do this? Perhaps I'm not using the correct functions/structures? Or this is as good as it gets?

Thanks on beforehand,

Sebastian Beca Department of Computer Science Engineering University of Chile

PD: I'm using NumPy 0.9.8, SciPy 0.4.8. I also understand I have ATLAS, BLAS and LAPACK all installed, but I havn't confirmed that.

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