doing more faster...

What is the best way to run a program in parallel?

Just run two copies of it at the same time. :)

But that works.

And more often than not it is the easiest and most useful form of doing twice the work for the least cost. If you wrote your program that it takes input from a file or from the command line then running it twice will only cost you the time to write the bash script that runs it that way.