Write some Software

I have working code written in perl. It runs thousands, sometimes billions of combinations, but it is "slow". It's hard to describe "slow", but it runs at about 1000 combinations per second (not calculations per second, there are many calculations within each combination). But I am told by the perl programmer that created it that it could be re-written in C++ to be made 100 times faster. He also thought that re-writing the perl code might make it faster too, but no idea how much faster. (The 1000 combinations per second is based on running on a VPS server. It may be faster on your computer locally. As long as it is 100x or more faster, that is the goal.) I want the attached script to be re-written to be made at least 100x faster. It can be re-written in perl if that could do it, but I suspect we need to re-write it in C++. The script is part of an online process where a CSV gets uploaded, the algorithm runs, and then the web page displays a bunch of the output and hosts other output files for download/review. It is a PHP server, although I don't know if that matters. It would also be nice if there was a way for the algorithm to tell the webpage how long it's going to take so that we can have a progress bar (not sure how that works). I have attached the script and some example input files so you can see what happens when you run it and for benchmarking.