I have this program which prints the time difference between 2 different instances, but it prints in accuracy of seconds. I want to print it in milliseconds and another in n
Read first the time(7) man page.
Then, you can use clock_gettime(2) syscall (you may need to link -lrt to get it).
So you could try
struct timespec tstart={0,0}, tend={0,0};
clock_gettime(CLOCK_MONOTONIC, &tstart);
some_long_computation();
clock_gettime(CLOCK_MONOTONIC, &tend);
printf("some_long_computation took about %.5f seconds\n",
((double)tend.tv_sec + 1.0e-9*tend.tv_nsec) -
((double)tstart.tv_sec + 1.0e-9*tstart.tv_nsec));
Don't expect the hardware timers to have a nanosecond accuracy, even if they give a nanosecond resolution. And don't try to measure time durations less than several milliseconds: the hardware is not faithful enough. You may also want to use clock_getres to query the resolution of some clock.