quickly summing numpy arrays element-wise

Question

Let's say I want to do an element-wise sum of a list of numpy arrays:

tosum = [rand(100,100) for n in range(10)]

I've been looking for the best way to do this. It seems like numpy.sum is awful:

timeit.timeit('sum(array(tosum), axis=0)',
              setup='from numpy import sum; from __main__ import tosum, array',
              number=10000)
75.02289700508118
timeit.timeit('sum(tosum, axis=0)',
              setup='from numpy import sum; from __main__ import tosum',
              number=10000)
78.99106407165527

Reduce is much faster (to the tune of nearly two orders of magnitude):

timeit.timeit('reduce(add,tosum)',
              setup='from numpy import add; from __main__ import tosum',
              number=10000)
1.131795883178711

It looks like reduce even has a meaningful lead over the non-numpy sum (note that these are for 1e6 runs rather than 1e4 for the above times):

timeit.timeit('reduce(add,tosum)',
              setup='from numpy import add; from __main__ import tosum',
              number=1000000)
109.98814797401428

timeit.timeit('sum(tosum)',
              setup='from __main__ import tosum',
              number=1000000)
125.52461504936218

Are there other methods I should try? Can anyone explain the rankings?

Edit

numpy.sum is definitely faster if the list is turned into a numpy array first:

tosum2 = array(tosum)
timeit.timeit('sum(tosum2, axis=0)',
              setup='from numpy import sum; from __main__ import tosum2',
              number=10000)
1.1545608043670654

However, I'm only interested in doing a sum once, so turning the array into a numpy array would still incur a real performance penalty.

user_6701520 · Answer

Numpy sum is not awful, you are simply using numpy in the wrong way. You won't be able to make use of numpy's speed advantage if you combine normal python, functions (including reduce!), loops and lists with numpy arrays. If you want your code to be fast, you must only use numpy.

Since you did not specify any imports in your code snippet, I am not sure what the function randn is doing or where it comes from, so I just assumed that tosum should just represent a list of 10 matrices of some random numbers. The following code snippet shows that numpy is definitely not as slow as you claim it to be:

import numpy as np
import timeit

def test_np_sum(n=10):
    # n represents the numbers of matrices to sum up element wise
    tosum = np.random.randint(0, 100, size=(n, 10, 10)) # n 10x10 matrices, shape = (n, 10, 10)
    summed = np.sum(tosum, axis=0) # shape = (10, 10)

And then testing it:

timeit.timeit('test_np_sum()', number=10000, setup='from __main__ import test_np_sum')

0.8418250999999941

quickly summing numpy arrays element-wise

2 Answers