I have two development systems set up with uVision for developing on an Atmel Sam9 processor. The output .axf files are not the same, however, and it's a bit puzzling since I have the same version of uVision, development tools and RSX installed. Can anyone know of some sort of checklist of things to make sure two development systems are identical?
The output .axf files are not the same, however, and it's a bit puzzling
It shouldn't be. You should expect the AXF to be different on every build, even on the same machine, building two times in a row. Go ahead and run the experiment: make a copy of your project's entire object folder (.axf, .hex and everything else), and perform a full rebuild. Then see which files are different, and which are the same.
If you want to compare files, do it with HEX files (or BIN files if you absolutely have to). That's what really counts, because that's the code that actually ends up on the microcontroller. The .axf holds all kinds of extra information (time stamps, path names, debug information, even names of temporary files) that can change without affecting the outcome.
Only if the hex file is different is it time to check other files: MAP, LST, source code, and preprocessed source, in that order, to figure out where the difference may have come from.