[SciPy-dev] sparse matrix support status

[Ed Schofield]

Hi Jonathan,

Thanks very much for the benchmarks and detailed comments.  Your  
conclusions also ring true for me, especially that matrix  
construction is currently slow and that we need better documentation.

I have only one question for now.  Could you please explain the comment

 > dok_matrix.setdiag() appears to change the matrix shape if you're not
 > careful, rendering it pretty useless for building the matrices for  
this
 > problem

in more detail?  The code for setdiag() is:

     def setdiag(self, values, k=0):
         N = len(values)
         for n in range(N):
             self[n, n+k] = values[n]
         return

which grows the matrix only if it's currently smaller than len 
(values) x len(values).  What's the problem this behaviour caused?   
Would you prefer to fix the size of a dok_matrix in advance and have  
a run-time check on the len(values)?  Or was the problem with the  
second argument?

-- Ed



On 22/11/2005, at 8:05 PM, Jonathan Guyer wrote:

>
> On Oct 7, 2005, at 4:00 PM, I wrote:
>
>>  regardless, pysparse is BSD
>> licensed, so it's perfectly legal to use his code to improve
>> scipy.sparse (assuming that rigorous benchmarking determines that  
>> there
>> are, in fact, improvements to be made). We'll do some tests and, if a
>> merge is warranted, we'll run it by Roman out of courtesy.
>
> I've finally done some benchmarking of scipy.sparse and PySparse and
> posted my results and comments on plone[*]:
>
>      <http://www.scipy.org/wikis/featurerequests/SparseSolvers>
>
> Bottom line is that, with a couple of exceptions, PySparse is both
> faster and less memory intensive than SciPy. I don't know whether
> anything can be lifted from PySparse to improve SciPy's  
> implementation.
>
> [*] Not that this comes as a surprise to anybody here, but the SciPy
> plone wiki is scary slow. I also couldn't get it to accept reST, even
> though I've seen other people using it there.
> -- 
> Jonathan E. Guyer, PhD
> Metallurgy Division
> National Institute of Standards and Technology
> <http://www.metallurgy.nist.gov/>
>
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