Just powered up the due board, with no inputs connected and the blink LED example, the temperature over the SAM3X8e is almost around 50 deg C. When the example is verified, uploaded, and LED blinks, the temp is around 50 deg C. Used the erase and Reset button as guided in the forums, but the SAM chip is too hot.
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What is your power supply voltage?
Is the SAM3X8e the device getting hot or is it something else on the board.
What board do you have? Did you have to solder the headers to the board?