OP solved it, closing

Multithreading will not help when you use inefficient algorithm, because multithreading can make your code only two- or four- or eight- times faster or so, and this will not help if your algorithm is 1000 times too slow for large arrays.

You most probably need to think of a better idea. But it's difficult to give any specific hints without knowing what is your current approach.

I've checked the multithreading code for this one,and still got the timeout error!
Any suggestion for optimizing that better?