Q: How to choose the I/O pins for self diagnose routines, such as JTAG interface? What's the software tools for micro-controller to browse through stack info? again what pins are involved?
A: The MCU manufacturers designate pins for the JTAG connections, but often they share functions with other devices, such as general-purpose I/O, analog-to-digital converter input, and so on. So, you might not have the pins available for JTAG in a real design. While using a development board or prototype, you want those pins free for the JTAG connections. For self diagnostics you use the MCU to check its connections, write a test message on any attached display, let someone test a keypad, and so on. There's more to it, of course, but the idea is to ensure the MCU and the attached devices operate properly before you go into the actual application code.
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