After creating the port link: sudo ln –sf /dev/ttymxc3 /dev/ttyS0 The Arduino Due IDE worked smoothly. Naturally I immediately ran the blink sample which works as expected but leaves several questions. 1. Uploading a program resets the Arduino SAM3X, but how I do that in software.? For example, from a C++ or Python program on the Udoo. (I found the Arduino hardware reset which works just fine.) 2. When Ubuntu is shutdown the SAM3X is still running the blink program since the board is still powered. How would I shutdown the Arduino at the same time? 3. No blinky lights!! The blink program requires me to add my own LED. What dummkopf forgot the blinky lights! I want an immediate refund 4. The Arduino IDE defines two 'boards': a)Arduino Due (Programming Port) and b)Arduino Due (Native USB Port) Both worked OK, but I am not sure of the meaning or pratical uses.