ping: Warning: time of day goes back (-203647us), taking countermeasures

Solution 1:

This has happened to me on AMD type processors before, where the clocksource wasn't shared between CPUs (it was set to jiffies for me).

One of the CPU's was a few jiffies ahead of the other causing the time to go backwards when a process moved between CPUs and compared times.

Try setting the clocksource to tsc, hpet or acpi_pm (in that order) as these clocksources tend to be shared between CPUs.

$ cat /sys/devices/system/clocksource/clocksource0/available_clocksource
$ echo 'hpet' > /sys/devices/system/clocksource/clocksource0/current_clocksource

Alternatively you might have an aggressive stepping policy for your timesync (shouldn't occur really after you've booted). Provide the output of /etc/ntp.conf or /etc/chrony.conf for more insight.