[Numpy-discussion] MemoryError with dot(A, A.T) where A is 800MB on 32-bit Vista

greg whittier gregwh@gmail....
Wed Jun 9 11:49:34 CDT 2010


When I run

import numpy as np

a = np.ones((400, 500000), dtype=np.float32)
c = np.dot(a, a.T)

produces a "MemoryError" on the 32-bit Enthought Python Distribution
on 32-bit Vista.  I understand this has to do with the 2GB limit with
32-bit python and the fact numpy wants a contiguous chunk of memory
for an array.  When I look at the memory use in the task manager
though, it looks like it's trying to allocate enough for two
400x500000 arrays.  I guess it's explicitly forming a.T.  Is there a
way to avoid this?  I tried

c = scipy.lib.blas.fblas.dgemm(1.0, a, a, trans_b=1)

but I get the same result.  It appears to be using a lot of extra
memory.  Isn't this just a wrapper to the blas library that passes a
pointer to the memory location of a?  Why does it seem to be
generating the transpose?  Is there a way to do A*A.T without two
copies of A?

Thanks,
Greg


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