How to count CPU Usage of multiprocess application in Linux
I suggest keeping the data for each process separately.
When you have a new sample, each process may fall in one of three categories:
1. Existed both before and after - subtract old from new.
2. Exists now, but not before - just take the new values.
3. Existed before, but not now - ignore it. You're missing something here, because it may have used CPU during 90% of your sample period, but I hope you don't need perfect accuracy.
It makes you keep more data between samples, and requires using a more complicated data structure, but it should give reasonable results.
If you need accurate result or if life time of processes are short, then you must read time usage of a process when it is terminated.
There is atleast two ways:
1) Use wait4(2) or wait3(2) functions to wait process termination. Those functions will return utime and stime of the process.
2) Keep terminated processes in zombie state until reading of /prox/<pid>/stat.