Comparing large arrays

I have two arrays, generated from even larger text source files (one is ~50K elements and the other is about 90K elements). I need to compare the two, and produce a result array that contains only the elements of array 1 that are not also in array 2. It seems like array_diff() is exactly the tool needed, but it times out. So my questions are - 1. Should I be getting a time out with this size job (I don't have a good feel for this - although 5x10^9 comparisons certainly sounds like lots!)? 2. Is there a better way to do this? Thanks, -- Murray