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Edit My original answer involves some programming. Maybe you can make the whole setup simpler with some other programming. On my Kubuntu man ntpdate shows that it uses adjtime() system call to gradually adjust the system clock. Consider a program that reads hardware clock and calls adjtime(). Original answer From G-Man's comment: Some (most? all?) ...
This is due to a known bug in LXC regarding the cpuset cgroup. A few workarounds are described here: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824519 .
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