[SciPy-Dev] scipy.sparse versus pysparse

[nicky van foreest]

Hi Pauli,

Thanks for your clarifications.

NIcky


On 23 July 2014 23:09, Pauli Virtanen <pav at iki.fi> wrote:

> 23.07.2014, 23:08, nicky van foreest kirjoitti:
> > Sure. Please see below.   I included an extra time stamp to analyse
> > the results in slightly more detail. It turns out that the
> > matrix-vector multiplications are roughly the same in scipy.stats
> > and pysparse, but that building the matrices in pysparse is way
> > faster.
>
> The benchmark is mainly measuring the speed of dok_matrix.__setitem__
> for scalars (dok_matrix.setdiag is naive and justs sets items in a for
> loop).
>
> Neither dok_matrix or lil_matrix is very fast. This is largely limited
> by the fact that they use Python dict and Python lists as data
> structures, which have non-negligible overheads.
>
> lil_matrix was optimized in Scipy 0.14.0, so you may get better
> results using it (for those Scipy versions). Additionally, vectorized
> assignment into sparse matrices is now supported, so further
> performance improvement can be obtained by replacing the for loops in
> fillOffDiagonal.
>
> There may be some room for optimization in dok_matrix for scalar
> assignment, but this is probably not more than 2x. The remaining 10x
> factor vs. pysparse requires pretty much not using Python data
> structures for storing the numbers.
>
> csr, csr, bsr, and dia are OK, but the data structures are not
> well-suited for matrix assembly.
>
> --
> Pauli Virtanen
>
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