Eigenvectors computed with numpy's eigh and svd do not match

Just play with small numbers to debug your problem.

Start with A=np.random.randn(3,2) instead of your much larger matrix with size (50,20)

In my random case, I find that

v1 = array([[-0.33872745,  0.94088454],   [-0.94088454, -0.33872745]])

and for v2:

v2 = array([[ 0.33872745, -0.94088454],   [ 0.94088454,  0.33872745]])

they only differ for a sign, and obviously, even if normalized to have unit module, the vector can differ for a sign.

Now if you try the trick

assert np.all(np.isclose(V1,-1*V2))

for your original big matrix, it fails... again, this is OK. What happens is that some vectors have been multiplied by -1, some others haven't.

A correct way to check for equality between the vectors is:

assert allclose(abs((V1*V2).sum(0)),1.)

and indeed, to get a feeling of how this works you can print this quantity:

(V1*V2).sum(0)

that indeed is either +1 or -1 depending on the vector:

array([ 1., -1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,    1., -1.,  1.,  1.,  1., -1., -1.])

EDIT: This will happen in most cases, especially if starting from a random matrix. Notice however that this test will likely fail if one or more eigenvalues has an eigenspace of dimension larger than 1, as pointed out by @Sven Marnach in his comment below:

There might be other differences than just vectors multiplied by -1. If any of the eigenvalues has a multi-dimensional eigenspace, you might get an arbitrary orthonormal basis of that eigenspace, and to such bases might be rotated against each other by an arbitraty unitarian matrix