Optimizing access on numpy arrays for numba


I recently stumbled upon numba and thought about replacing some homemade C extensions with more elegant autojitted python code. Unfortunately I wasn’t happy, when I tried a first, quick benchmark. It seems like numba is not doing much better than ordinary python here, though I would have expected nearly C-like performance:

from numba import jit, autojit, uint, double
import numpy as np
import imp
import logging

def sum_accum(accmap, a):
    res = np.zeros(np.max(accmap) + 1, dtype=a.dtype)
    for i in xrange(len(accmap)):
        res[accmap[i]] += a[i]
    return res

autonumba_sum_accum = autojit(sum_accum)
numba_sum_accum = jit(double[:](int_[:], double[:]), 

accmap = np.repeat(np.arange(1000), 2)
accmap = np.repeat(accmap, 10)
a = np.random.randn(accmap.size)

ref = sum_accum(accmap, a)
assert np.all(ref == numba_sum_accum(accmap, a))
assert np.all(ref == autonumba_sum_accum(accmap, a))

%timeit sum_accum(accmap, a)
%timeit autonumba_sum_accum(accmap, a)
%timeit numba_sum_accum(accmap, a)

accumarray = imp.load_source('accumarray', '/path/to/accumarray.py')
assert np.all(ref == accumarray.accum(accmap, a))

%timeit accumarray.accum(accmap, a)

This gives on my machine:

10 loops, best of 3: 52 ms per loop
10 loops, best of 3: 42.2 ms per loop
10 loops, best of 3: 43.5 ms per loop
1000 loops, best of 3: 321 us per loop

I’m running the latest numba version from pypi, 0.11.0. Any suggestions, how to fix the code, so it runs reasonably fast with numba?


def numbaMax(arr):
    MAX = arr[0]
    for i in arr:
        if i > MAX:
            MAX = i
    return MAX

def autonumba_sum_accum2(accmap, a):
    res = np.zeros(numbaMax(accmap) + 1)
    for i in xrange(len(accmap)):
        res[accmap[i]] += a[i]
    return res

10 loops, best of 3: 26.5 ms per loop <- original
100 loops, best of 3: 15.1 ms per loop <- with numba but the slow numpy max
10000 loops, best of 3: 47.9 ┬Ás per loop <- with numbamax

Answered By – M4rtini

This Answer collected from stackoverflow, is licensed under cc by-sa 2.5 , cc by-sa 3.0 and cc by-sa 4.0

Leave a Reply

(*) Required, Your email will not be published