AS7 does not load breakpoints when debugging with JLink

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I have a Jlink mini edu, I am having an issue where I cannot debug my cortex m3 on it - when I launch debug mode nothing happens. I can see ASM if I attempt to single step but it says "no source file".

 

I had this problem before and somehow fixed it, but it's back and I haven't changed any settings. It's becoming incredibly frustrating since I spend more time debugging debug tools then writing programs. 

 

I should also write, everything works correctly in seggers Embedded studio, and I have gotten it work in Atmel studio before - but for some reason it's now broken. I tried "repairing" my install but nothing happened. 

Last Edited: Thu. Oct 7, 2021 - 07:02 PM
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I think I figured out the problem, basically I did not have "boot from exception table" selected. Normally this would not be a problem but the DUE has a SAM-BA bootloader built into which the chip appears to be booting from. It's very strange since I have "boot-from bank0" checked which should set the appropriate boot bit to prevent the SAM-BA loader from loading.