Electrical – Unique Serial Number for Atmel SAM Series

You don't need an external EEPROM for this. Get a microcontroller with EEPROM instead, that's smaller and easier to use, because you don't need an SPI or I²C module anymore. Also, you can easily program the EEPROM from the computer.

So, basically, you want a PIC or other microcontroller with:

• (E)U(S)ART connection
• EEPROM
• 3 GPIO pins for the LEDs

Most microcontroller manufacturers have a part selection tool. For microchip, that's MAPS. That's how you can lookup which chip you need.

For these (very minimalistic) requirements, a very small chip enough. Have a look at the PIC12F1822: 8 pins, XLP if you need that, 256 bytes EEPROM, etc. This chip has just enough I/O pins for your three LEDs.

However, from your question it looks like you're a beginner in PIC, and then perhaps a somewhat bigger but easier to interface chip is a better start. Then have a look at the PIC16F88: it has everything you need and more I/O pins, for more LEDs, if needed. The fun of the 16F88 is that it's easier to program it. For the 12F1822, they put everything in a small box and you have to initialize everything (a lot!) correctly, which can be hard, especially for a beginner. The 16F88 is easier to start with.

Something I noticed is that you have the following line to toggle the state:

ioport_toggle_pin_level(IOPORT_CREATE_PIN(PIOA,14));

While technically there's nothing wrong with that most Atmel examples define the port in conf_board.h so if you haven't changed that you've probably also missed configuring the port as an output. Try adding the following to configure the port as an output and it's probably a better practice to define the port name in a define:

#define LED IOPORT_CREATE_PIN(PIOA,14)
ioport_set_pin_dir(LED, IOPORT_DIR_OUTPUT);

Then in your main code:

ioport_toggle_pin_level(LED);

Regardless of whether that works on not it's worth taking a look through some of the ASF generated code in the subdirectories of the project to become familiar with where Atmel normally place the port configuration and initialisation code. There may be other pins being defined as outputs that your board doesn't like. I couldn't find a schematic for the Arduino Due but it might also be worth finding out what crystal frequency it uses, it may be different enough that the clock initialisation code selects a frequency that is too high to work.