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I managed to run ntpdate at a high priority. My initial thought is to use nice command, like:

nice -n -10 ntpdate -p 8 -u $NTP_TIME_SERVER

However, after checking the nice value of ntpdate command, it stays at -12, regardless of nice -n command.

Did anyone have same experience of modifying priority of ntpdate before? How can I configure ntpdate to make it work at a high priority? Thanks in advance. :-)

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Ntpdate is deprecated (see the disclaimer in the man page) and shouldn't be used. You can use ntpd -q to replicate the functionality of ntpdate. It is however better to setup ntpd to run continuously and adjust the system clock appropriately.

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