I am working on a project and I'm paid by hours. The majority of my work is computational programming and I need to run not-very-light computational jobs each day multiple times. Quite often the programs take more than a few minutes to run and although I try to do something else while they're running, sometimes I really have nothing relevant to do before getting the results. If I add up the time I wait for the jobs to run and have nothing else to do, it could be more than an hour per day.
So my first question is: Should I count this waiting time when I report my hours or should I exclude it?
If I exclude it, there would be two subsequent problems:
Firstly, given that I have a limited amount of work to do in each phase, and transition to the next phase is dependent on meeting with my supervisor and aggregating the results, which happens only once a week, I can't fill in 40 hours per week (which is expected of me, given that I'm a full-time employee). Secondly, my wage would be lower, even though I'm actually fully satisfying all the expectations of my supervisor and reaching the phase goals on time.