Watchdog enabled on power on

[CtrlC-Root]

According to the datasheet the watchdog timer is enabled by default after a power-on reset. It's set to ~ 16 seconds after which it will reset the board (section 15.4 on page 261). If you're just blinking an LED like in this example especially with a long period then you are unlikely to notice it fire and reset the board. I spent an hour debugging my own bare metal program trying to figure out why it was resetting at such a consistent uptime before I figured this out. You can disable it on boot with:

static uint32_t* const WDT_MR = (uint32_t*) 0x400E1A54;

void main() {
  // watchdog timer is actived on boot with a default timeout so disable it
  // note: you can only write to WDT_MR once after power on reset
  // Atmel SAM3X8E Datasheet, section 15.4, page 261
  *WDT_MR |= (1 << 15); // WDDIS (watchdog disable) bit, page 265

  // ... omitted ...
}

Hopefully this helps the next person who comes along and tries to use this project as a starting point from having to debug the same issue.