The 10G example design use only 1 lane. You might need to double-check which lane that you are actually connected from the board schematic. Perhaps, you may try to connect with a QSFP loopback module to ensure the design is working first before connecting with others.
Besides, you may start with the 10GBASE-R Ethernet design example, and use 322Mhz as a reference clock. See the link below:
Do you refer lane as channel? I modify the example design to support 4 channels, each channel 10G. I also tested the design with QSFP28 Port 0 and Port 1, but neither worked properly.
I already tested the network with an Arria 10 board beforehand. So I am pretty sure it was not the network issue.
My approach (B) is based on the document you have sent. The Intel S10MX board only provide QSFP reference clock of 644.5312 MHz. That's why I modified the ref_clk settings in the PHY, ATX, and fPLL module to 644 MHz.
PHY setting: modifychange CDR reference clock
ATX PLL setting: modify PLL auto mode reference clock
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