[Numpy-discussion] Scipy dot

Nicolas SCHEFFER scheffer.nicolas@gmail....
Wed Nov 7 16:41:37 CST 2012


Hi,

I've written a snippet of code that we could call scipy.dot, a drop-in
replacement for numpy.dot.
It's dead easy, and just answer the need of calling the right blas
function depending on the type of arrays, C or F order (aka slowness
of np.dot(A, A.T))

While this is not the scipy mailing list, I was wondering if this
snippet would relevant and/or useful to others, numpy folks, scipy
folks or could be integrated directly in numpy (so that we keep the
nice A.dot(B) syntax)
This bottleneck of temporary copies has been a problem for lots of
users and it seems everybody has their own snippets.
This code is probably not written as it should, I hope the community
can help improving it! ;)
First FIXME is to make it work for arrays of dimensions other than 2.

Suggestions highly appreciated!

Thanks!

===
Code (also on http://pastebin.com/QrRk0kEf)

def dot(A, B, out=None):
    """ A drop in replaement for numpy.dot
    Computes A.B optimized using fblas call
    note: unlike in numpy the returned array is in F order"""
    import scipy.linalg as sp
    gemm = sp.get_blas_funcs('gemm', arrays=(A,B))

    if out is None:
        lda, x, y, ldb = A.shape + B.shape
        if x != y:
            raise ValueError("matrices are not aligned")
        dtype = np.max([x.dtype for x in (A, B)])
        out = np.empty((lda, ldb), dtype, order='F')

    if A.flags.c_contiguous and B.flags.c_contiguous:
        gemm(alpha=1., a=A.T, b=B.T, trans_a=True, trans_b=True,
c=out, overwrite_c=True)
    if A.flags.c_contiguous and B.flags.f_contiguous:
        gemm(alpha=1., a=A.T, b=B, trans_a=True, c=out, overwrite_c=True)
    if A.flags.f_contiguous and B.flags.c_contiguous:
        gemm(alpha=1., a=A, b=B.T, trans_b=True, c=out, overwrite_c=True)
    if A.flags.f_contiguous and B.flags.f_contiguous:
        gemm(alpha=1., a=A, b=B, c=out, overwrite_c=True)
    return out
==


Timing (EPD, MKL):

In [15]: A = np.array(np.random.randn(1000, 1000), 'f')

In [16]: %timeit np.dot(A, A)
100 loops, best of 3: 7.19 ms per loop

In [17]: %timeit np.dot(A.T, A.T)
10 loops, best of 3: 27.7 ms per loop

In [18]: %timeit np.dot(A, A.T)
100 loops, best of 3: 18.3 ms per loop

In [19]: %timeit np.dot(A.T, A)
100 loops, best of 3: 18.7 ms per loop

In [20]: %timeit dot(A, A)
100 loops, best of 3: 7.16 ms per loop

In [21]: %timeit dot(A.T, A.T)
100 loops, best of 3: 6.67 ms per loop

In [22]: %timeit dot(A, A.T)
100 loops, best of 3: 6.79 ms per loop

In [23]: %timeit dot(A.T, A)
100 loops, best of 3: 7.02 ms per loop


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