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My recommendation is to use the JTAG port, as that allows for single stepping and run control. There's a white paper showing how to debug the Linux Kernel, including source level access at the following link.
Source Level Debug using OpenOCD/GDB/Eclipse on... | Intel Communities . Of course the first step in debugging source is to get assembly level, or bare metal access, and you can see that in the screenshots on page 13 of the PDF.
I tried to go through the tutorial and was able to get access to intel quark using olimex debugger. I completed the step 3.1, 3.2, 3.3 and 4.1. but 4.2 mentions the symbol table file. I could not find this file in any package that was mentioned in per-requisites. Also, can anyone help in getting the eclipse environment setup?
I have downloaded the eclipse from intel download section.