Function vdot is used in a couple of places to find the dot product of a matrix of shape [n, 1]. This caused an exception for a version of numpy I was using (or perhaps it is the underlying lapack or something?). I am a bit confused as it worked on my laptop running numpy-1.5.0 but not on another machine running the same version of numpy. Anyway, I dump the numpy.matrix with spae (n,1) into a numpy array with shape (n) and it fixed it.