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When a software breakpoint is set, a Break instruction will be set in flash memory. This will make a checksum calculation over that memory range fail.
Hardware breakpoints or no breakpoints at all should be used if debugging checksum algorithms.
To get control of the usage of the hardware breakpoints check Technical Note 31070.
The J-Link driver can set 'flash breakpoints', and those must be disabled.
When the J-Link Control Panel is open (for example when debugging) the flash breakpoints can be disabled at : Settings > Flash breakpoints.
IAR Embedded Workbench for MSP430 version 5.51 (and newer) has flash breakpoints enabled by default. (So if all hardware breakpoints are in use, then this type of problem can occur).
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