[SciPy-dev] Ideas for scipy.sparse?
Fri Apr 11 16:35:19 CDT 2008
> > 1) I need N-dimensional sparse arrays. Some of the storage formats in
> > scipy.sparse (dok, coo, maybe lil) could be generalized to
> > N-dimensions, but some work would have to be done.
> To make this efficient, you'd probably need a lower-level
> implementation of a hash-based container like DOK.
> BTW, which applications use sparse N-dimensional arrays?
The big place that I need them right now is for handling so called
ghost cells. If you are not familiar with this idea, ghost cells are
parts of a distributed array that are not on your local processor
(they are on another one). When we fetch the ghost cells we need a
structure to store them in and a sparse N-dim array is the best
In terms of true applications for N-dim sparse arrays, I am not sure.
But, the higher-dimension an array is the more important sparsity is.
Sure numpy can handle 6 dimensional arrays, but if they are dense,
they will likely be too big. So I guess a better question is: what
are the applications for N-dimensional dense arrays -> if you find an
application for N>3, then you should probably consider using sparse
> > 2) I need these things to be in numpy. I hate to start another
> > "should this go into numpy or scipy" thread, but I actually do think
> > there is a decent case for moving the core sparse arrays into numpy
> > (not the solvers though). Please hear me out:
> I don't see the need for or utility of sparse arrays in numpy. Numpy
> does low-level manipulation of dense arrays/memory buffers.
True, well sort of. That is what Numpy does today. But, I think
there are good reasons to extend that reach more broadly to other
types of arrays. My understanding of the scope of numpy is that it is
the "base layer." I feel that sparse arrays are (conceptually) a part
of that base layer.
> > 3) I need sparse arrays that are implemented more in C. What do I
> > mean by this. I am using cython for the performance critical parts of
> > my package and there are certain things (indexing in tight loops for
> > example) that I need to do in c. Because the current sparse array
> > classes are written in pure python (with a few c++ routines underneath
> > for format conversions), this is difficult. So...
> All of the costly operations on CSR/CSC/COO matrices are done in C++.
> Only lil_matrix and dok_matrix are pure-Python implementations.
Yes, but to use the fast c++ code, I have to go through a slow python
layer - the actual csr/csc/coo classes and slow+fast = slow in my
book. Also, the dok/lil formats are some of the most important and
they should be optimized.
> Indexing sparse arrays inside a Python loop *is* slow, but there's not
> much that can be done about it.
I will write a simple dok format sparse matrix using cython and we can
compare the performance.
> > I think it would be a very good idea to begin moving the sparse array
> > classes to cython code. This would be a very nice approach because it
> > could be done gradually, without breaking any of the API. The benefit
> > is that we could improve the performance of the sparse array classes
> > drammatically, while keeping things very maintainable.
> I'm not aware of any performance problems with the existing backend to
> scipy.sparse. What would you implement in cython that's not already
> implemented in scipy.sparse.sparsetools?
This is absolutely true. Don't misunderstand me. I think that the
c++ backend in sparsetools in _really_ nice and I am not suggesting
changing that to anything else. The only think I would implement in
cython is the higher-level sparse classes. These are the slow part
(they are pure python) and cython would help a lot there. Again, I
_really_ like the current design and interfaces of these classes and I
am not suggesting changing that (other than to support N-dim arrays
for certain formats).
> > 3) That we begin to move their implementation to using Cython (as an
> > aside, cython does play very well with templated C++ code). This
> > could provide a much nicer way of tying into the c++ code than using
> > swig.
> In the context of scipy.sparse, what's wrong with SWIG and C++? What
> would be improved by using Cython?
Think of it in terms of layers (I will use the csr format as an example):
sparse/csr.py => top level python class that wraps the lower layers.
sparsetools/csr.py => thin swig generated python wrapper that
sparsetools/csr.h => fast c++ code
Using swig forces me to deal with two layers of python code before I
can talk to the fast c++ code. The problem with this is that I want
to call the top level layer from C! This would be like NumPy not
having a C API!
The cython stack would look like this
sparse/csr.pyx => top level python class that is a C extension
type and can be called from C or python
sparsetools/csr.h => fast c++ code
In that case, I could write my extension code in C and talk directly
to the C interface without any overhead of multiple layers of Python.
To me that is a huge difference. But again, the existing c++ code
could be used with probably no modifications.
> > Alright, fire away :)
> Nathan Bell firstname.lastname@example.org
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