Can you use Atmel studio IDE with the M2? Over USB port? or using the JTAG?
thanks
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Over USB it would be easy to do. The SAM3X has native USB so there shouldn’t be a problem uploading firmware from Atmel Studio using the built-in SAM-BA bootloader on the chip. JTAG pins I think are exposed but only via little pads and not in an industry standard pinout so it won’t be as easy.
Having said that, the issue you could easily run into is that the normal method for getting serial text is out the USB port. The Arduino core has a USB driver. Without that you’d need to provide one in order to get serial output. Or, you can use one of the normal TTL serial ports (at least one of which exposed externally) and then use a 3.3v TTL serial to USB dongle to communicate.