"Divide by zero encountered in log" when not dividing by zero

That's the warning you get when you try to evaluate log with 0:

>>> import numpy as np
>>> np.log(0)
__main__:1: RuntimeWarning: divide by zero encountered in log

I agree it's not very clear.

So in your case, I would check why your input to log is 0.

PS: this is on numpy 1.10.4

I had this same problem. It looks like you're trying to do logistic regression. I was doing MULTI-CLASS Classification with logistic regression. But you need to solve this problem using the ONE VS ALL approach (google for details).

If you don't set your yval variable so that only has '1' and '0' instead of yval = [1,2,3,4,...] etc., then you will get negative costs which lead to runaway theta and then lead to you reaching the limit of log(y) where y is close to zero.

The fix should be to pre-treat your yval variable so that it only has '1' and '0' for positive and negative examples.