The CPU Fan is controlled according to the CPU Temperatures. If the CPU Temp should spike to a high temperature long enough, then the CPU Fan will automatically increase also and then decrease when the CPU temps lowers.
The CPU fan should never stop entirely. At idle with low CPU Temps it should run fairly slow while under heavy loads and high temps it should run at Maximum RPM Speed.
If the CPU Fan is constantly speeding up and slowing down in a rhythmic way (cycling), then it could be software related.