Have you checked memory usage near the time of the crash? Does it start disk swapping sometime before the crash?

If it's a memory issue, you'll have to decide if you need everything "available" memory at the same time. There are a number of ways to use disk as an extension, all of them slower. For instance, use files instead of the large arrays, and read/write them as needed, with some care. Or tie them. Or something like DBM::Deep.