[SciPy-user] Getting the right numerical libraries for scipy

William K. Coulter wcoulter@berkeley....
Thu Apr 2 15:35:42 CDT 2009


I wanted to optimize my python code to use the scipy.sparse library; 
however, benchmarking reveals that multiplying a sparse and dense matrix 
takes over 100 times as long as multiplying the equivalent two dense 
matrices.

This suggests that I have at least one of the numerical libraries linked 
with python, but that the sparse ones aren't.

I understand that numpy/distutils/system_info.py should contain some 
helpful information, but I can't read the output and don't know how to 
ensure that the libraries are there in a clean install.

How could I check for the libraries and what would I do to install them 
if they are not there?  I'm on a redhat system.

Thanks much,

-- Will

PS: Here's an example of what I'm comparing (b is the dense
representation of a sparse matrix; c is dense).  counter2 > 100*counter1 
for many iterations:

bsp = sparse.csc_matrix(b)
t1 = time.time()
for i in range(n):
     np.dot(b,c)
t2 = time.time()
counter1 += t2-t1

t1 = time.time()
for i in range(n):
     bsp.matmat(c)
t2 = time.time()
counter2 += t2-t1



-- 
  William K. Coulter
  Graduate Student, Helen Wills Neuroscience Institute, UC Berkeley



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