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In the ZYNQ section of the BSP settings various initialization steps can be disabled if desired. 

Configuration
Description
ZYNQ_CONFIG_MMUConfigure the MMU with a default page table but leave it disabled
ZYNQ_ENABLE_MMUEnable the MMU after configuration. This also enable the SCU and instruct the current core to join SMP
ZYNQ_CONFIG_CACHESConfigure the caches but leave them disabled
ZYNQ_ENABLE_CACHESEnable the L1 and L2 caches
ZYNQ_ENABLE_PERF_OPTIMSEnable various hardware performance optimizations unique to the Cortex-A9 core
Table - Cortex-A9 Init Configuration

Kernel tick source

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.