by ‘separate clock configuration for PCIe’, you meant endpoint sourcing its REFCLK from an external other than RP, then, NO, XavierNX doesn’t support that configuration.
xavier nx maybe is support separate clock for pcie , I follow the connection below and it is successful。
Well, disabling the spread on the REFCLK (of RP) and then using a different REFCLK for EP would work but this is not an officially supported configuration.
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