In FMC-to-PCIe Adapter, for the endpoint configuration, the reference clock must be sourced from the host system and the FMC-to-PCIe Adapter does not provide a 100 MHz PCIe reference clock.
Please refer section “Clock Oscillator” from the PCIe FMC Module datasheet for better understanding.
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Zynq™ UltraScale+™ ZU7/ZU5/ZU4 MPSoC System on Module