Hello,
Basically, there are several options for generating clock for i.MX6 PCIe module,
please look at PCIE_AXI_CLK_ROOT Figure 18-2 "Clock Tree" i.MX6DQ
Reference Manual. Note, i.MX6 PCIe module requires 125MHz clock for normal
operation - all other clocks it produces internally - please refer to section 18.5.1.3.6
"Ethernet PLL", it describes Ref_PCIe =125 MHz. Again, 100 MHz PCIe reference
clock is generated from this clock internally.
The PCIe clock signal pair is not part of the PCIe PHY IP (assuming the CLK1N/P are used).
They are configured via PMU_MISC1n register.
Also, please refer to the i.MX6 Datasheet regarding CLK1 hardware specs.
Have a great day,
Yuri
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