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1, Setup the PLL by executing code (ex: UBoot, etc.) instead of using the GEL file. (preferred)
2, Turn on adaptive clocking XDS100#Q:_How_can_I_turn_on_adaptive_clocking.3F and setup the timeouts to very slow. In this mode, it is still better to "run" the code and not "step" it.
3, Make sure you have the latest CPLD version. To update the XDS100v2 CPLD, please see XDS100#Q:_How_can_I_update_the_CPLD_on_my_XDS100v2.3F