Numba 3x slower than numpy

Question

We have a vectorial numpy get_pos_neg_bitwise function that use a mask=[132 20 192] and a df.shape of (500e3, 4) that we want to accelerate with numba.

from numba import jit
import numpy as np
from time import time

def get_pos_neg_bitwise(df, mask):
    """
    In [1]: print mask
    [132  20 192]

    In [1]: print df
    [[  1 162  97  41]
     [  0 136 135 171]
     ...,
     [  0 245  30  73]]

    """
    check = (np.bitwise_and(mask, df[:, 1:]) == mask).all(axis=1)
    pos = (df[:, 0] == 1) & check
    neg = (df[:, 0] == 0) & check
    pos = np.nonzero(pos)[0]
    neg = np.nonzero(neg)[0]
    return (pos, neg)

Using tips from @morningsun we made this numba version:

@jit(nopython=True)
def numba_get_pos_neg_bitwise(df, mask):
    posneg = np.zeros((df.shape[0], 2))
    for idx in range(df.shape[0]):
        vandmask = np.bitwise_and(df[idx, 1:], mask)

        # numba fail with # if np.all(vandmask == mask):
        vandm_equal_m = 1
        for i, val in enumerate(vandmask):
            if val != mask[i]:
                vandm_equal_m = 0
                break
        if vandm_equal_m == 1:
            if df[idx, 0] == 1:
                posneg[idx, 0] = 1
            else:
                posneg[idx, 1] = 1
    pos = list(np.nonzero(posneg[:, 0])[0])
    neg = list(np.nonzero(posneg[:, 1])[0])
    return (pos, neg)

But it still 3 times slower than the numpy one (~0.06s Vs ~0,02s).

if __name__ == '__main__':

    df = np.array(np.random.randint(256, size=(int(500e3), 4)))
    df[:, 0] = np.random.randint(2, size=(1, df.shape[0]))  # set target to 0 or 1
    mask = np.array([132,  20, 192])

    start = time()
    pos, neg = get_pos_neg_bitwise(df, mask)
    msg = '==> pos, neg made; p={}, n={} in [{:.4} s] numpy'
    print msg.format(len(pos), len(neg), time() - start)

    start = time()
    msg = '==> pos, neg made; p={}, n={} in [{:.4} s] numba'
    pos, neg = numba_get_pos_neg_bitwise(df, mask)
    print msg.format(len(pos), len(neg), time() - start)
    start = time()
    pos, neg = numba_get_pos_neg_bitwise(df, mask)
    print msg.format(len(pos), len(neg), time() - start)

Am I missing something ?

In [1]: %run numba_test2.py
==> pos, neg made; p=3852, n=3957 in [0.02306 s] numpy
==> pos, neg made; p=3852, n=3957 in [0.3492 s] numba
==> pos, neg made; p=3852, n=3957 in [0.06425 s] numba
In [1]:

JoshAdel JoshAdel · Accepted Answer · 2015-12-31T13:40:11

Try moving the call to np.bitwise_and outside of the loop since numba can't do anything to speed it up:

@jit(nopython=True)
def numba_get_pos_neg_bitwise(df, mask):
    posneg = np.zeros((df.shape[0], 2))
    vandmask = np.bitwise_and(df[:, 1:], mask)

    for idx in range(df.shape[0]):

        # numba fail with # if np.all(vandmask == mask):
        vandm_equal_m = 1
        for i, val in enumerate(vandmask[idx]):
            if val != mask[i]:
                vandm_equal_m = 0
                break
        if vandm_equal_m == 1:
            if df[idx, 0] == 1:
                posneg[idx, 0] = 1
            else:
                posneg[idx, 1] = 1
    pos = np.nonzero(posneg[:, 0])[0]
    neg = np.nonzero(posneg[:, 1])[0]
    return (pos, neg)

Then I get timings of:

==> pos, neg made; p=3920, n=4023 in [0.02352 s] numpy
==> pos, neg made; p=3920, n=4023 in [0.2896 s] numba
==> pos, neg made; p=3920, n=4023 in [0.01539 s] numba

So now numba is a bit faster than numpy.

Also, it didn't make a huge difference, but in your original function you return numpy arrays, while in the numba version you were converting pos and neg to lists.

In general though, I would guess that the function calls are dominated by numpy functions, which numba can't speed up, and the numpy version of the code is already using fast vectorization routines.

Update:

You can make it faster by removing the enumerate call and index directly into the array instead of grabbing a slice. Also splitting pos and neg into separate arrays helps to avoid slicing along a non-contiguous axis in memory:

@jit(nopython=True)
def numba_get_pos_neg_bitwise(df, mask):
    pos = np.zeros(df.shape[0])
    neg = np.zeros(df.shape[0])
    vandmask = np.bitwise_and(df[:, 1:], mask)

    for idx in range(df.shape[0]):

        # numba fail with # if np.all(vandmask == mask):
        vandm_equal_m = 1
        for i in xrange(vandmask.shape[1]):
            if vandmask[idx,i] != mask[i]:
                vandm_equal_m = 0
                break
        if vandm_equal_m == 1:
            if df[idx, 0] == 1:
                pos[idx] = 1
            else:
                neg[idx] = 1
    pos = np.nonzero(pos)[0]
    neg = np.nonzero(neg)[0]
    return pos, neg

And timings in an ipython notebook:

    %timeit pos1, neg1 = get_pos_neg_bitwise(df, mask)
    %timeit pos2, neg2 = numba_get_pos_neg_bitwise(df, mask)

    100 loops, best of 3: 18.2 ms per loop
    100 loops, best of 3: 7.89 ms per loop

Numba 3x slower than numpy

1 Answers