[SciPy-user] Converting dense into sparse matrices is slow

Nils Wagner nwagner at mecha.uni-stuttgart.de
Mon Mar 20 05:53:36 CST 2006


Robert Cimrman wrote:
> Nils Wagner wrote:
>   
>> Hi all,
>>
>> AFAIK linalg.kron only works with dense matrices.
>> It would be nice if kron can handle sparse matrices as well.
>> The example (bao.py) takes a lot of time
>>
>> Kronecker product (sec): 6.28
>> Dense to sparse (sec): 70.09
>> Number of nonzero elements 16129
>> If one uses a dense matrix there are 16777216 entries.
>>
>>  Anyway, is it possible to accelerate some operations (especially
>> csr_matrix()) in bao.py ?
>>
>> Nils
>>     
>
> Hi Nils,
>
> the actual conversion is done by *fulltocsc() function of sparsetools, 
> which IMHO allocates space for the whole dense matrix which is very 
> large in your case. Maybe a two-pass approach would be faster - 1. count 
> the actual nonzeros, 2. build the matrix. I cannot try it right now, 
> though...
>
> r.
>
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>   
Hi Robert,

Thank you for your short note.

BTW, a fix for

http://projects.scipy.org/scipy/scipy/ticket/40

would be awesome.

Cheers,

                Nils



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