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    I want to be able to perform, for example, pairwise distance between all points in a 200.000 x 1000 matrix in python without having enough ram to keep the whole distance matrix in memory. I am looking for information on how to do that :) so more concrete answers then a vague "look into two whole sub fields of computer science" would be helpfull! Commented Apr 22, 2013 at 15:26
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    You probably want to take a look at numpy's memmap and possibly PyTables as a starting point. Commented Apr 22, 2013 at 15:42
  • From the first related question below the user @cronos suggested to use h5py, and I believe it can be used for your problem too. 1-Is it possible to np.concatenate memory-mapped files? 2-Concatenate Numpy arrays without copying Commented May 2, 2013 at 17:03