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There is no simple fix. For an ill-conditioned matrix $A$, the harm (loss of precision) is already done the moment you wrote those numbers in a numpy array, because that tiny $10^{-16}$ perturbation from the exact non-representable values is already harmful. You could increase your working precision; but at that point the question is if your matrix entries $... 3 Yes, the eigenvectors found with this method may depend on$x$and$y$, but no, it doesn't matter in practice. If$A$and$B$share a basis of common eigenvectors, then $$A = V\operatorname{diag}(\alpha_1,\dots,\alpha_n)V^{-1}, \quad B = V\operatorname{diag}(\beta_1,\dots,\beta_n)V^{-1}.$$ If$A$has all distinct eigenvalues, then$V$is unique, up to ... 2 This problem is known as joint diagonalization, and it has two variants: orthogonal, in which the basis vectors are orthonormal, and non-orthogonal, which is harder to solve, but which may be more appropriate to your application. The simplest method I know of seeks a unitary matrix$U$that minimizes the sum of squares of the off-diagonal elements of$U^HAU$... 2 As its documentation suggests in multiple places, rref is "mainly of academic interest" (read: "used only to explain Gaussian elimination to undergrads"), and is not a serious competitor of SVD-based algorithms in terms of stability. I recommend against it. 2 We can do some transformations to your problem to show that it's easily solvable via a linear program: Given a matrix$M$with non-negative real entries and a vector$vyou wish to solve the problem: \begin{align} \min_v \quad & \lVert Mv \rVert_\infty \\ s.t. \quad & v_i\ge0 \\ & \sum_i v_i = 1 \end{align} Now, note that\lVert Mv \...