simple test

Recently I moved my main PC from MBA mid 2011 to MBP mid 2014.
This machine has GPU.
There are some libraries to use GPU from python. i.e. PyCuda, PyOpenGL, Theano, etc…
I used theano and write very simple test.
Compare the time for calculate dot product of two arrays of numpy and theano.

import numpy as np
import theano
import theano.tensor as T
tm1 = T.matrix()
tm2 = T.matrix()
matd =,tm2)

1st round 2×2.

m1 = np.matrix([[1,2],[3,4]])
m2 = np.matrix([[3,4],[5,6]])
CPU times: user 19 µs, sys: 2 µs, total: 21 µs
Wall time: 22.9 µs
matrix([[13, 16],
         [29, 36]])

time f([[1,2],[3,4]],[[3,4],[5,6]])
CPU times: user 168 µs, sys: 25 µs, total: 193 µs
Wall time: 171 µs
array([[ 13.,  16.],
       [ 29.,  36.]])

Hmm, numpy was faster than theano.

2nd round 1000×1000

a = [range(1000) for i in range(1000)]
b = [range(1000) for i in range(1000)]
CPU times: user 1.84 s, sys: 5.33 ms, total: 1.85 s
Wall time: 1.85 s

time tc = f(a,b)
CPU times: user 256 ms, sys: 12.1 ms, total: 268 ms
Wall time: 174 ms

Theano was faster than numpy.

3rd round 10000×10000

a = [range(10000) for i in range(10000)]
b = [range(10000) for i in range(10000)]
time c=f(a,b)
CPU times: user 2min 16s, sys: 1.4 s, total: 2min 18s
Wall time: 31.9 s

I don’t have enough knowledge about GPU coding, but I think theano is powerful tool.


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: