How can I take look at the inside of the atmega1280?

Question

I want take a look at the memory and at the elements inside the atmega1280. I compiled Ardupilot sketch and I uploaded it with an arduino.

I started avarice with the following command:

$ avarice --mkII --capture --jtag usb :4242

and I started avr-gdb

$ avr-gdb /tmp/build5831285936308447966.tmp/ArduPilotMega.cpp.elf 

I typed:

(gdb)target remote localhost:4242

and this is the answer:

(gdb) target remote localhost:4242
Remote debugging using localhost:4242
0xfffffffe in ?? ()

when I do list it show me

#include <WProgram.h>

int main(void)
{
    init();

    setup();

    for (;;)
        loop();

    return 0;
}

That is not my ardupilot!

I don't understand why I get the ?? symbol after the target command and why I get a different source after the list command.

Could someone explain where is my error, how they work and the reason of those symbols? More important, how can I take a look inside of the atmega1280?

P.S.: I compiled with Arduino, so I compiled with the -g flag.

Edit: I used an unofficial jtagice mkii:

and I follow this guide for the setting http://www.diydronesafety.com/topic/72-articleundocumented-apm2x-jtag-technique-and-jtag-for-apm1x-using-only-the-redboard/

So mine is presented like this:

Answer 1

You should think about investing in JTAGICE MKII, it supports many Atmel device. When you use it with Atmel AVR Studio, debugging is a breeze and it allows you to look inside all the devices.