If you're still running out of memory, you'll have to find out where you are storing your data and maybe not store all the data in RAM. If you are storing the bulk of your data in a hash, an easy way of trading time for space is to use DB_File or some other key/value store that can be tied to a hash. Update: Also see Tie::DBI, which just had a new release out.

Often it also helps to output progress through your file so that you get an idea where in your program you run out of memory.