External clock range

If my target clock is 900MHz, then it is too high to be used as external clock source?
(For Husky)

That’s much too high. Husky supports clocks up to 200 MHz.

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Another question, my target have pin that output each module’s clock for debug purposes, can is be used as input clock for chipwhisperer? or it has to be the target’s input clock signal in order to synchronize with the target?

That is your choice: power traces will be synchronized with the clock that you choose to use.

Another unrelated question. “Synchronous Sampling and Clock Recovery of Internal
Oscillators for Side Channel Analysis and Fault Injection”, the paper introduce the idea of clock recovery, but I don’t see realization in hardware, is it because it requires expensive hardware overhead or it is impossible to achieve in real-time scenarios?

It is possible to do it; the paper shows how. But it’s not currently implemented in ChipWhisperer capture hardware.