[Numpy-discussion] Slicing slower than matrix multiplication?

Jasper van de Gronde th.v.d.gronde@hccnet...
Fri Dec 11 07:55:57 CST 2009


Dag Sverre Seljebotn wrote:
> Jasper van de Gronde wrote:
>> I've attached a test file which shows the problem. It also tries adding
>> columns instead of rows (in case the memory layout is playing tricks),
>> but this seems to make no difference. This is the output I got:
>>
>>     Dot product: 5.188786
>>     Add a row: 8.032767
>>     Add a column: 8.070953
>>
>> Any ideas on why adding a row (or column) of a matrix is slower than
>> computing a matrix product with a similarly sized matrix... (Xi has less
>> columns than Xi2, but just as many rows.)
>>   
> I think we need some numbers to put this into context -- how big are the 
> vectors/matrices? How many iterations was the loop run? If the vectors 
> are small and the loop is run many times, how fast the operation "ought" 
> to be is irrelevant as it would drown in Python overhead.

Originally I had attached a Python file demonstrating the problem, but 
apparently this wasn't accepted by the list. In any case, the matrices 
and vectors weren't too big (60x20), so I tried making them bigger and 
indeed the "fast" version was now considerably faster.

But still, this seems like a very odd difference. I know Python is an 
interpreted language and has a lot of overhead, but still, selecting a 
row/column shouldn't be THAT slow, should it? To be clear, this is the 
code I used for testing:
--------------------------------------------------------------------
import timeit

setupCode = """
import numpy as np

P = 60
N = 20

Xi = np.random.standard_normal((P,N))
w = np.random.standard_normal((N))
Xi2 = np.dot(Xi,Xi.T)
E = np.dot(Xi,w)
"""

N = 10000

dotProduct = timeit.Timer('E = np.dot(Xi,w)',setupCode)
additionRow = timeit.Timer('E += Xi2[P/2,:]',setupCode)
additionCol = timeit.Timer('E += Xi2[:,P/2]',setupCode)
print "Dot product: %f" % dotProduct.timeit(N)
print "Add a row: %f" % additionRow.timeit(N)
print "Add a column: %f" % additionCol.timeit(N)
--------------------------------------------------------------------


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