[SciPy-dev] slow setitem

Benny Malengier benny.malengier@gmail....
Mon Nov 30 08:02:20 CST 2009


A question about the sparse matrix and suggestion for speed improvement.

I have a code of 1000*1000 sparse matrix of 11 full diagonals. Using csr.
Assigning the matrix via setdiags takes 14 seconds, of which 13
seconds is in the check_format function of sparse/base.py.

This is due to setdiag doing:

     self[i, i + k] = v

while setitem in compressed.py always does a

     self.check_format(full_check=True)

Removing the check_format reduces assignment of the matrix to 1 second.
Is it really needed that the assignmentof setdiag is again checked via
check_format?
Allowing for a setitem that does not call check_format would be usefull.

One could set a dirty flag on a setitem call, and do a check_format
only when a computation is performed and the flag is dirty. On the
other hand, I'm not making errors, and to have a flag like
NOCHECKS=TRUE would be handy as it would speed up the code a lot.
I could create a solution that is acceptable for scipy, but then I'd
need to know how such a solution should look like.

Note that there are quite some zeroes in my diagonals now too, that
are now set to 0., if setitem would be fast, I could drop setdiag
call, and do a fast setitem call. Or are sparse matrixes supposed to
be used differently?

Benny


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