I have one doubt.what is the difference between System timer module and Periodic interrupt timer in MPC5644A?in which places,have we used?
Main difference between PIT and STM is that PIT contains RTI which can be used for wake up from STOP mode and PIT can be used to trigger DMA. Another difference is that PIT decrements from set value to zero and STM increments from zero to set value.
You can use it anywhere you want. There is no rule about usage.
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