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Xilinx Zynq-7000 PS has two USB IP Cores that can be used over dedicated MIO pins only (EMIO multiplexing is not supported). If both USB IP Cores is used then SD Card boot is no longer supported.

 

Linux Devicetree

Petalinux automatically generated devicetree is not sufficient, devicetree top file has to be edited manually for proper USB operation, the changes required depend on the Petalinux version used.