OK, so I am writing a program that unfortunately needs to use a huge data structure to complete its work, but it is failing with a "out of memory error" during its initialization. While I understand entirely what that means and why it is a problem, I am having trouble overcoming it, since my program needs to use this large structure and I don't know any other way to store it.

The program first indexes a large corpus of text files that I provide. This works fine.

Then it uses this index to initialize a large 2D array. This array will have nXn entries, where "n" is the number of unique words in the corpus of text. For the relatively small chunk I am testing it on(about 60 files) it needs to make approximately 30,000x30,000 entries. this will probably be bigger once I run it on my full intended corpus too.

It consistently fails every time, after it indexes, while it is initializing the data structure(to be worked on later).

Things I have done include:
revamp my code to use a primitive "int[]" instead of a "TreeMap"
eliminate redundant structures, etc...
Also, I have run eclipse with "eclipse -vmargs -Xmx2g" to max out my allocated memory

I am fairly confident this is not going to be a simple line of code solution, but is most likely going to require a very new approach. I am looking for what that approach is, any ideas?

Thanks, B.