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SAM3S peripheral debugging

Hello,

has anybody experienced how to debug peripherals with Keil uVision? The best version so far I have found was MDK 4.11. After this I began to get confused because when I found things from the peripheral debug menue disappeared at least for STM32 devices in versions after 4.11, I had to learn that now the system viewer replaces that.
Now trying to get into the SAM3S4B controller, trying some demo code from atmel and trying to port it to the Olimex eval board I wanted to see what's happening with the peripharls.
Using my favourite version 4.11 I watched GPIO port PIOA. However nothing changed in those flags. So I was wondering if the periperal was in reset or not clocked etc. - just getting familiar with the controller...
However now I have the impression the debug peripherals window doesn't work properly. Because I managed to configure a port for input and it works in the program but no flags set in the window.
So I thought lets give the current 4.23 Version a try but the peripherals windows except Cortex core peripherals have gone also the system viewer shows nothing.
So I wonder how other people have found a solution to this - debgging the peripherals?
I found it so useful beeing able to see how the registers are set and if in doubt manipulate them to try if things would work before changeing my code and recompile all the time.

Help would be very much appreciated.

Thank you.