This all assumes a linux machine. Sorry.

To run

$ make

$ ./main INPUT_FILE_NAME OUTPUT_FILE_NAME

To profile

$ make clean

$ make profile

Because we don't want output to count in our profile, we always write to /dev/null when profiling:

$ ./main INPUT_FILE_NAME /dev/null

$ gprof main > gprof.out

The output of gprof is a bit inscrutable, but it's very helpful to pinpoint places where the code is slow. It's what I've used to optimize things.