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Boot Flash on Zynq is connected to PS only and is not directly accessible from PL or over JTAG. Whenever SPI Flash is programmed on Zynq following actions take place:

1. OCM RAM is re-mapped as single linear memory at high address range, giving 256KByte continuous memory
2. mini-version of u-boot.elf is loaded to this OCM RAM and executed
3. data for programming is copied to Zynq OCM RAM
4. flash tool communicates with u-boot over JTAG using ARM DCC channel

The same process takes place no matter what method is used to flash the SPI on Zynq.

Flash Programming, Zynq UltraScale+

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