How to test program that takes a long time to run?

Part of testing is using a variety of inputs, including large values. If the algorithm is not exactly fast (e.g. O(n^2) or greater) what options exist to accelerate the testing process or at least make it more bearable?

As a specific example if someone has an implementation of matrix multiplication that should run in O(n^3) and they test on 100 digit matrix, is there anything that can be done to at least see where the program is currently at, or if it has just hung?

I'm using Netbeans and was wondering if there's anyway to at least see how long the program has been executing for?