I am trying to read and write registers on my ARM9 (SAM9X25) following those steps : http://infocenter.arm.com/help/index.jsp?topic=/com.arm.doc.faqs/ka3750.html
I ended
You can't access registers directly, because Linux use MMU and this create for your application virtual address space which is different than physical MCU address space and access outside this virtual address space cause segmentation fault.
Only Way to access these registers in Linux (if you don't want to write kernel drivers) is to open file /dev/mem as file and map it with mmap
For example I have small python library for access GPIO registers on Atmel SAM MCU gpiosam. You can inspire and port it to C.