You have been advised in the chatterbox already to show the Perl code that relates to this problem. From your snippet you showed in the CB, I see you're not checking the error while opening the file. Maybe that is a problem. Or maybe your machine does not have enough RAM to read the file as a whole into memory. Or maybe your algorithm is just bad and takes a very long time for more lines. You don't show any code, so we can't help you further.