Multiple cores are hardware-wise not synchronized by default after reset.
Synchronization can be enabled by the winIDEA option Synchronize all cores (stop/run) in Hardware / CPU Options / Debugging. This option is enabled by default.
If synchronization of cores is either not needed or unwanted, you can disable it by unchecking the checkbox Synchronize all cores (stop/run) in Hardware / CPU Options / Debugging.
Suspending of peripherals (e.g., timers) is by default disabled. It can be configured with an initialization script <MCU>_CommonInit.ini, which is distributed with winIDEA in the Examples directory.
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