best way to preserve numpy arrays on disk

I am looking for a fast way to preserve large numpy arrays. I want to save them to the disk in a binary format, then read them back into memory relatively fastly. cPickle is not fast enough, unfortunately.

I found numpy.savez and numpy.load. But the weird thing is, numpy.load loads a npy file into “memory-map”. That means regular manipulating of arrays really slow. For example, something like this would be really slow:

#!/usr/bin/python
import numpy as np;
import time; 
from tempfile import TemporaryFile

n = 10000000;

a = np.arange(n)
b = np.arange(n) * 10
c = np.arange(n) * -0.5

file = TemporaryFile()
np.savez(file,a = a, b = b, c = c);

file.seek(0)
t = time.time()
z = np.load(file)
print "loading time = ", time.time() - t

t = time.time()
aa = z['a']
bb = z['b']
cc = z['c']
print "assigning time = ", time.time() - t;

more precisely, the first line will be really fast, but the remaining lines that assign the arrays to obj are ridiculously slow:

loading time =  0.000220775604248
assining time =  2.72940087318

Is there any better way of preserving numpy arrays? Ideally, I want to be able to store multiple arrays in one file.

Answer

I’m a big fan of hdf5 for storing large numpy arrays. There are two options for dealing with hdf5 in python:

http://www.pytables.org/

http://www.h5py.org/

Both are designed to work with numpy arrays efficiently.