How to create a huge sparse matrix in scipy
You are using an older version of SciPy. In the original implementation of sparse matrices, indices where stored in an int32 variable, even on 64 bit systems. Even if you define them to be uint32, as you did, they get casted. So whenever your matrix has more than 2^31 - 1 nonzero entries, as is your case, the indexing overflows and lots of bad things happen. Note that in your case the weird negative number of elements is explained by:
>>> np.int32(np.int64(3289288566))-1005678730The good news is that this has already been figured out. I think this is the relevant PR, although there were some more fixes after that one. In any case, if you use the latest release candidate for SciPy 0.14, your problem should be gone.