Strange you should mention this - I had the same problem… Some suggestions that I found.
Chrony Version : chronyc (chrony) version 4.6.1 (+READLINE +SECHASH +IPV6 -DEBUG) I also had an issue with Debian (so assume rasping) so check the following.. I had some weird symlinks that were not created - I think the Etc/UCT - but it looks like it might be broken in Debian based distros… cat /usr/share/zoneinfo/right/UTC.src # UTC with leap-second support Zone UTC 0 - UTC root@31perkins:/usr/share/zoneinfo# ls -la total 272 drwxr-xr-x 14 root root 4096 Nov 24 20:52 . drwxr-xr-x 146 root root 4096 Jan 8 22:30 .. drwxr-xr-x 2 root root 4096 Oct 31 21:03 Africa drwxr-xr-x 6 root root 20480 Oct 31 21:03 America drwxr-xr-x 2 root root 4096 Oct 31 21:03 Antarctica drwxr-xr-x 2 root root 4096 Oct 31 21:03 Arctic drwxr-xr-x 2 root root 12288 Oct 31 21:03 Asia drwxr-xr-x 2 root root 4096 Oct 31 21:03 Atlantic drwxr-xr-x 2 root root 4096 Oct 31 21:03 Australia drwxr-xr-x 2 root root 4096 Oct 31 21:03 Etc drwxr-xr-x 2 root root 12288 Oct 31 21:03 Europe -rw-r--r-- 1 root root 116 Aug 25 08:12 Factory lrwxrwxrwx 1 root root 7 Aug 25 08:12 GMT -> Etc/GMT drwxr-xr-x 2 root root 4096 Oct 31 21:03 Indian -rw-r--r-- 1 root root 4791 Sep 7 2023 iso3166.tab -rw-r--r-- 1 root root 3253 Aug 25 08:12 leapseconds -rw-r--r-- 1 root root 5065 Aug 25 08:12 leap-seconds.list lrwxrwxrwx 1 root root 14 Aug 25 08:12 localtime -> /etc/localtime drwxr-xr-x 2 root root 4096 Oct 31 21:03 Pacific lrwxrwxrwx 1 root root 16 Aug 25 08:12 posixrules -> America/New_York drwxr-xr-x 2 root root 4096 Nov 24 20:54 right -rw-r--r-- 1 root root 114396 Aug 25 08:12 tzdata.zi lrwxrwxrwx 1 root root 7 Aug 25 08:12 UTC -> Etc/UTC -rw-r--r-- 1 root root 17597 Mar 21 2025 zone1970.tab -rw-r--r-- 1 root root 8084 Mar 23 2025 zonenow.tab -rw-r--r-- 1 root root 18822 Mar 21 2025 zone.tab root@31perkins:/usr/share/zoneinfo# cat Etc/ GMT GMT0 GMT+10 GMT-11 GMT-13 GMT-2 GMT+4 GMT-5 GMT+7 GMT-8 Greenwich UTC GMT+0 GMT+1 GMT-10 GMT+12 GMT-14 GMT+3 GMT-4 GMT+6 GMT-7 GMT+9 UCT Zulu GMT-0 GMT-1 GMT+11 GMT-12 GMT+2 GMT-3 GMT+5 GMT-6 GMT+8 GMT-9 Universal root@31perkins:/usr/share/zoneinfo# cat Etc/UTC TZif2UTCTZif2UTC UTC0 root@31perkins:/usr/share/zoneinfo# —— cat /etc/chrony/chrony.conf # Welcome to the chrony configuration file. See chrony.conf(5) for more # information about usable directives. # Include configuration files found in /etc/chrony/conf.d. confdir /etc/chrony/conf.d # Primary high-precision reference: PHC (Stratum 1) #refclock PHC /dev/ptp0 poll 0 dpoll 0 offset 0 tai prefer refclock PHC /dev/ptp0 poll 0 dpoll 0 offset 0 tai prefer precision 1e-9 filter 16 minsamples 32 # Optional fallback: public Stratum 1 NTP server (do NOT prefer) server time-a.nist.gov iburst minpoll 6 maxpoll 10 server pool.msltime.measurement.govt.nz iburst minpoll 6 maxpoll 10 # Use time sources from DHCP. sourcedir /run/chrony-dhcp # Allow local LAN access allow # Use NTP sources found in /etc/chrony/sources.d. sourcedir /etc/chrony/sources.d # Authentication key file (if needed) keyfile /etc/chrony/chrony.keys # Store system clock drift driftfile /var/lib/chrony/chrony.drift # Save NTS keys and cookies ntsdumpdir /var/lib/chrony # Logging (optional — uncomment to enable) #log tracking measurements statistics # Log files location logdir /var/log/chrony # Stop bad estimates upsetting machine clock maxupdateskew 5.0 # Kernel RTC synchronization (every 11 minutes) rtcsync # Step the system clock if offset > 1 second, but only in first 3 updates makestep 0.1 -1 # Use TAI / UTC leap seconds from system timezone database leapsectz right/UTC lock_all sched_priority 1 chris@ptp:~$ > On 16 Jan 2026, at 19:28, Simon Plackett <[email protected]> wrote: > > Hi, > > Before I send a lot of detail I wondered if anyone had seen this > phenomenon. I have just upgraded my local chrony server to Trixie on > RPI 5 with chrony 4.6.1. > > I had previously been using the ethernet NIC clock as a time source > with ptp4l and phc2sys, which worked fine. > > During the upgrade I changed to leapseclist from leapsectz as the > latter does not work on Trixie. > > The issue is that on startup the system clock is set by the PHC source > before the TAI-UTC adjustment has been applied which means it jumps > 36+ seconds one way and then back again during the startup. This > obviously trashes the PHC as a source, and it didn't happen > previously. > > Essentially PHC is chosen as the source, updates system clock (wrong > by ~37s) then the TAI-UTC adjustment is found which causes system time > to jump again in the opposite direction by ~37s > > I can see this using systemctl status chrony or using journalctl. > > I have currently turned PHC off again - but happy to turn back on and > send any logs etc that might be useful. > > The other source is PPS from GPS, which is even more accurate on the > new versions :-) > > Thanks > Simon > > -- > To unsubscribe email [email protected] > with "unsubscribe" in the subject. > For help email [email protected] > with "help" in the subject. > Trouble? Email [email protected]. > -- To unsubscribe email [email protected] with "unsubscribe" in the subject. For help email [email protected] with "help" in the subject. Trouble? Email [email protected].
