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It might help us to see the "-d -d" output.

If you add the -s option, chronyd should set the system time on start
to the last modification time of the driftfile, and this might avoid
the gpsd/GPS bug. But I'd be curious to know what exactly is
happening.

> root@beaglebone:~# chronyd -d
> 2000-01-01T00:01:29Z chronyd version 2.4 starting (+CMDMON +NTP +REFCLOCK +RTC -PRIVDROP -SCFILTER -SECHASH +ASYNCDNS +IPV6 +DEBUG)
> 2000-01-01T00:01:29Z Setting filter length for PPS to 1
> 2000-01-01T00:01:29Z Setting filter length for NMEA to 2
> 2000-01-01T00:01:29Z Frequency -40.366 +/- 234.206 ppm read from /var/lib/chrony/chrony.drift
> 2000-01-01T00:01:29Z Using right/UTC timezone to obtain leap second data
> 2000-01-01T00:01:36Z Selected source NMEA
> 2000-01-01T00:01:36Z System clock wrong by -11404807.817246 seconds, adjustment started
> 1999-08-22T00:01:28Z System clock was stepped by -11404807.817246 seconds
> 1999-08-22T00:01:55Z Can't synchronise: no selectable sources
> 1999-08-22T00:02:00Z Selected source NMEA
> 1999-08-22T00:02:02Z System clock wrong by -0.029797 seconds, adjustment started
> 1999-08-22T00:02:04Z System clock wrong by 0.020517 seconds, adjustment started
> 1999-08-22T00:02:15Z RTC wrong by 11404807.787 seconds (step)
> 1999-08-22T00:02:15Z Could not set RTC time
> 1999-08-22T00:02:18Z Can't synchronise: no selectable sources
> 1999-08-22T00:02:36Z Selected source NMEA
> 1999-08-22T00:02:36Z System clock wrong by 361331.850290 seconds, adjustment started
> 1999-08-26T04:24:48Z System clock was stepped by 361331.850290 seconds
> 1999-08-26T04:24:50Z Can't synchronise: no selectable sources
> 1999-08-26T04:25:10Z RTC wrong by 11043475.933 seconds (step)
> 1999-08-26T04:25:10Z Could not set RTC time

-- 
Miroslav Lichvar

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