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I’ve run a Pi 3 as a PPS clocksource. I used a netbooted aarch64 buildroot on ramdisk, experimenting with rt-linux as well.

I saw similar performance, including those occasional spikes. I found that the flood of interrupts caused by the usb chip - they are handled in the driver rather than on chip - were detrimental to accuracy. Temperature variations were another source of inaccuracy. I didn’t figure out how to connect an rtc together with the gps hat.

I might try again on a Pi 4, I think it’s possible to power off the usb chip without losing ethernet as it does on a Pi 3.

My Raspberry Pi 4 arrived today, so I'll be setting up some similar experiments to see how it performs.

Would love to hear more about the issues you found with the USB chipset though!