There is a kind of smart and open emluator -- CooCox Colink,which supports all Arm Cortex-M3 devices(include at91sam3u).
You can just do the hardware yourself,you can find the components you needed and the Circuit Schematic Diagram on http://www.coocox.org/How-to-do-Colink-plugin.htm
If you have finished the hardware,then you can download the plugin for Realview MDK and EWARM IAR from http://www.coocox.org/Colink.htm.
And then,you will have a emluator whose function is similar to ULINK2 and JLINK.You can use it under MDK or IAR.
Have a try,it is interesting and helpful.
Microchip in-system programming solution: SAM-BA
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