Selecting the core will determine which core's startup code will initialize the peripheral. Either core can do initialization, just need to make sure:
- Initialization is done before use.
- Software state machine is accurate.
- Cores don't access the peripheral at the same time.
Generally, the second point is tricky as the initialization initializes the state machine. But you can set this manually.
The third point is also tricky unless you use a hardware semaphore or other mechanism to ensure exclusive access.
It's going to be a lot more straightforward to dedicate FDCAN to a single core if you can.
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