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Hi Dave, could you please help me this question "if the board has multiple clkin pins for FPGA chip, if I use two pins for FPGA to drive different modules, the phase of clocks come from these two pins should be exactly same, right?"
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It depends on the board layout. Here's some clocking examples;
1) Single clock routed to a global CLKIN pin on the FPGA.
This clock can route on a global clock network and reach all logic cells in the FPGA.
2) CLKIN pin to PLL
FPGA handbooks list which CLKIN pins can route to specific PLLs. For example, a PLL on the left-side of a large device might only be able to use a clock pin on the left-side of a large device.
3) A common clock to two CLKIN pins to two PLLs
When designing a board, you should first check that your CLKIN and PLLs can meet your design requirements. For example, if I want to use transceivers on both the left and right side of a device, and those transceivers will only accept clocks on the left and right sides of the device, then at the board level I would take a common clock, split it two-ways, and then route those two signals to two clock pins on the FPGA. The transceivers on the left would use the clock on the left, while those on the right would use the clock on the right. Since the external clock sources are in common, I can cross clock domains internal to the FPGA, without worrying that FIFOs will over-flow or under-flow, since the clocks are phase-locked to a common source. The clock phase might not be aligned perfectly, but that is ok, since you can use a FIFO to cross clock domains.
4) Two CLKIN pins with independent clock sources
The link you provided has no details on your board (the link to the user manual is not yet available).
What is it that you are trying to do?
Cheers,
Dave