Quoting folkert <[email protected]>:
...
Linux has this PPS interface for a while so now that it is easy
configurable in config.txt on the rpi, I thought I give that a try. The
strange thing now is that using that I get very bad jitter. So bad that
ntp discards it as a false ticker!

     remote           refid      st t when poll reach   delay   offset jitter
==============================================================================
x127.127.22.1    .PPS.            0 l    2   16  377    0.000    0.161 0.001

x127.127.22.1    .PPS.            0 l    7   16  377    0.000    0.148 0.006

x127.127.22.1    .PPS.            0 l   13   16  377    0.000    0.147 0.007

x127.127.22.1    .PPS.            0 l    2   16  377    0.000    0.146 0.006

Your kernel pps RPI has a ~147us offset compared to your other time sources. I assume you have the two configured as peers over a local lan. I think ntpd is rejecting the local source because your other source is low enough latency (probably in the 100-200us range).

You could try adjusting the fixed offset of the userland pps to account for the latency between the pps happening and the user process being run.

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