I have a rather ponderous script that aligns DNA sequences and assigns penalties for interactions generating a list of low penalty DNA sequences for PCR (polymerase chain reaction) ... the program takes about 5 min to select primers from several thousand bases of DNA ... when i run this script on a windows computer with 16 gByte of RAM it is not any faster than another computer with < 2 gByte of RAM ... both show 98 MB CPU usage ... is there a way to increase the RAM usage for perl scripts?
oversimplifying here: perl tends to use what it needs for memory so it sounds like you are not memory constrained. i would suggest you investigate whether your application is suitable for multi-threading and if so start researching "multiprocessor kernel threads".
you can generally use threading (and increase performance!) if you can get work done in parallel, e.g. if you just work through log files and you don't need the results of all the earlier files, you could just run your script multiple times or use threading, where threading gives you a much nicer way to communicate.