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I want to separate the system clock from the hardware clock which I synchronize first. But now I want to change both: hardware clock with the UTC time & system with the GPS time.

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Your question is hard to understand, but whatever you're trying to do will probably involve the hwclock command. This is the command to read or set the harwdare clock. The main ways to use it are:

  • hwclock --systohc: set the hardware clock to the system time
  • hwclock --hctosys: set the system time to the hardware clock
  • hwclock --set --date='…': set the hardware clock to a particular time

Beware of timezones: if you keep your hardware clock in UTC (recommended), pass the --utc option to hwclock.

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