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F29H85X-SOM-EVM: EPWM synchronisation

Part Number: F29H85X-SOM-EVM

I am using an eCAP unit to measure rising and falling edges from an external signal that is triggered  via a 300KHz EPWM on CPU3. The capture unit is ECAP1 and PWM EPWM1. EPWM1 generates a sync out pulse which is used as an input to ECAP1 for sync-in pulse source. This seems to work fine.

However at 100KHz I would like to generate a software interrupt to collect capture data and re-arm the capture unit. To do this EPWM9 has been setup at 100KHZ to generate an interrupt and sync out pulse when the counter hits 0. EPWM1 has a sync in pulse source of EPWM9. However the two EPWM's are not synchronised and I do not understand why. Any suggestions?

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