Basically, I using an algorithm called 'miranda' to look at miRNA targets and it only runs on a single thread. It compares everything in one file against everything in another file, produces a file as an output and runs off of the command line in terminal. The process took roughly 20 hours to create the output file.
I was advised by my supervisor that if i split one of the files up into say 4 equally sized parts, and ran them in four separate terminal windows this would decrease the overall time it took for the process to be completed.
I found that when I was using a single terminal window, the process would take up about 100-120% of the CPU. However, when running four terminal windows, each individual process only takes between 30-40% of the CPU.
How much effect does splitting the file up like this have in the overall time it takes to run the process? Although I split it across four threads, will the effect only be an increase in speed of about 1.5 times?