scipy-spatial

I would take a look at scipy.spatial.distance.cdist: http://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.cdist.html import numpy as np import scipy a = np.random.normal(size=(10,3)) b = np.random.normal(size=(1,3)) dist = scipy.spatial.distance.cdist(a,b) # pick the appropriate distance metric dist for the default distant metric is equivalent to: np.sqrt(np.sum((a-b)**2,axis=1)) although cdist is much more efficient for large arrays (on my machine for your size problem, … Read more