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The kernel timebase on the Cortex-A9 is always derived from the core's private timer.
FIQ and IRQ signals from the PL
It is not recommended to use the legacy IRQ and FIQ signals from the PL. Instead the 16 general purpose interrupt lines should be used.
It's impossible to use the IRQ line as enabling it will disable all other interrupt source handle by the ucos BSP. However the FIQ line can be used and will generate an FIQ exception which can be handle by defining the UCOS_Int_FIQ_Handler() function in the user application.