Why is the computer clock off by few seconds after reboot?

Question

My computer runs 24/7 and does an automatic reboot at night after each kernel/systemd/glibc upgrade. On Fedora this happens every few days.

The system clock is synchronized with NTP protocol using the chrony. The HW clock is synchronized:

# Enable kernel synchronization of the real-time clock (RTC).
rtcsync

and normally I see no difference between system time and HW clock.

But after a reboot:

28.02.2021 00:34:08.657 chronyd: System clock wrong by -4.021024 seconds

or this night:

mar 02 01:48:18 chronyd[990]: chronyd exiting
mar 02 01:48:18 systemd[1]: Stopped NTP client/server.
-- Reboot --
mar 02 01:49:37 systemd[1]: Starting NTP client/server...
mar 02 01:49:37 chronyd[989]: chronyd version 4.0 starting (+CMDMON +NTP +REFCLOCK +RTC +PRIVDROP +SCFILTER +SIGND +ASYNCDNS +NTS +SECHASH +IPV6 +DEBUG)
mar 02 01:49:37 chronyd[989]: Frequency -13.026 +/- 0.008 ppm read from /var/lib/chrony/drift
mar 02 01:49:37 chronyd[989]: Using right/UTC timezone to obtain leap second data
mar 02 01:49:37 systemd[1]: Started NTP client/server.
mar 02 01:49:51 chronyd[989]: Selected source 162.159.200.123 (hu.pool.ntp.org)
mar 02 01:49:51 chronyd[989]: Time smoothing activated (leap seconds only)
mar 02 01:49:51 chronyd[989]: System clock wrong by -9.232765 seconds
mar 02 01:49:42 chronyd[989]: System clock was stepped by -9.232765 seconds

If I manually stop the chrony, wait 2 minutes and restart it, nothing bad happens (as expected).

I searched the net a lot and read many posts, but still cannot understand what I'm doing wrong.

UPDATE, output of timedatectl:

               Local time: St 2021-03-03 14:11:27 CET    
           Universal time: St 2021-03-03 13:11:27 UTC    
                 RTC time: St 2021-03-03 13:11:27        
                Time zone: Europe/Bratislava (CET, +0100)
System clock synchronized: yes                           
              NTP service: active                        
          RTC in local TZ: no  

Output of hwclock --verbose:

hwclock from util-linux 2.36.1
System Time: 1614784382.362288
Trying to open: /dev/rtc0
Using the rtc interface to the clock.
Assuming hardware clock is kept in UTC time.
Waiting for clock tick...
...got clock tick
Time read from Hardware Clock: 2021/03/03 15:13:03
Hw clock time : 2021/03/03 15:13:03 = 1614784383 seconds since 1969
Time since last adjustment is 1614784383 seconds
Calculated Hardware Clock drift is 0.000000 seconds
2021-03-03 16:13:02.344795+01:00

systemd-timesyncd is disabled and inactive.

Answer 1

Try command

timedatectl

to see if RTC clock is ever adjusted, or is off the whole time. You can also use hwclock or similar commands.

For the ntpd service, which is now being deprecated and replaced in many newer distributions, I know that it wrote a drift file on the disk on shutdown, and set the HW clock to the correct time. In the drift file, there were information about system clock accuracy, shutdown time, etc. When you switched on the computer ntpd would check the drift file, and adjusted the system clock according to recorded drift to synchronize quicker.

chrony synchronizes much quicker than ntpd, as that is a need for more and more virtual machines, that do now have a hardware clock. I wonder if chrony adjusts the HW clock on shutdown. Maybe you should check if the discrepancy is only growing. In that case it would be sensible to set HW clock at least on shutdown or see why the system does not adjust HW clock.

Maybe there is some HW problem. I had the strangest case some years ago, when a computer's time was off for about 17 seconds in one minute. The problem was to many HW interrupts, for which I first suspected some special PCI card. It turned out that KVM switch supported some kind of sound via USB, where keyboard and mouse were transferred, too. Without that KVM switch everything worked fine.