Thanks so much for writing back! The full error message is:
ValueError: Mass matrix contains zeros on the diagonal.
The derivative of RV ind .ravel()[0] is zero.
The derivative of RV flu .ravel()[0] is zero.
(on and on with all the indices where the derivative is zero).
The model is a stochastic block model. NUTS takes four variables and two of them have these derivate equals zero errors.
Can the problem is ‘derivative being too small’ be solved by changing the numerical resolution of Python? The prior works on the subset of data, but when I increase the data used, it does not work? (The prior should not be very uninformative I thought from this)