Like so many simple questions, the answer has to start with 'It depends....' It depends on how quickly you want the clouds to move, and of course on how fast the clouds themselves are moving - their apparent speed - as clouds crossing the frame appear to move faster than clouds coming towards camera or away (well of course, that's true of anything moving).
I find I use 1 frame per 8 sec to per 15 sec most often. 1 frame per 30 sec usually results in to much speeding up, and smaller intervals than 8 sec are usually too slow except for fast-moving storm clouds.
....I did this at 2 fps.... I let the HVX roll for about 2 hours.... worked out to about 2 minutes... of course I was using my FS100.... I think you have to hack the HVX to get 2 fps....