SDC - What clock should the input pin be relative to?

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Well,

This is exactly what I thought...and did.

I.E: set_input_delay relative to the clock pin (not the Pll output).

But then I started getting setup timing violations on the nets latched by pll_clock_x.

The input delay I set wasn't strict, the design isn't congested and the frequency of clock_x is 40Mhz.

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I take it that io setup/hold are ok but internally setup fails and does so on 40MHz. This is unusual in most devices. You may have some other issues.

you need to describe more details about your design clocking and failed paths.