Building a huge numpy array using pytables

Question

How can I create a huge numpy array using pytables. I tried this but gives me the \"ValueError: array is too big.\" error:

import numpy as np
import tables a         


        

Answer 1

You could try to use tables.CArray class as it supports compression but...

I think questions is more about numpy than pytables because you are creating array using numpy before storing it with pytables.

In that way you need a lot of ram to execute np.zeros((ndim,ndim) - and this is probably the place where exception: "ValueError: array is too big." is raised.

If matrix/array is not dense then you could use sparse matrix representation available in scipy: http://docs.scipy.org/doc/scipy/reference/sparse.html

Another solution is to try to access your array via chunks if it you don't need whole array at once - check out this thread: Very large matrices using Python and NumPy