See the explanation of the specific commands Section 22.16, “Configure NTP”.
NTPD must be checking ownership matches the user that NTPD is running as, rather than attempt to write to the drift file.
It doesn't have anything to do with ntpd and shouldn't be used to troubleshoot it. After you use ntpdate to set the clock, use 'hwclock --systohc' to sync "running" time to your hardware clock.
The reason that ntpq was suggested with the -p options to show peering. It is supposed to sync on a reboot but if your machine crashes (or otherwise had a problem doing a proper shutdown) it could not sync it.
If the time difference is greater than X (Sorry I dont remember what X is offhand) than a warning will be printed and time will not be syncd. Resolution: The culprit wasn't local firewall on our server, but firewall settings somewhere in the surrounding network. So we'll be looking at network/firewall settings for this particular server (which is in a different network, accessed over VPN).I have a machine that experienced some troubles with some of the real time stuff that I'm running.One lead that I have is that NTP daemon may have moved the time, causing false timeouts.