I've developed a Windows service which tracks business events. It uses the Windows clock to timestamp events. However, the underlying clock can drift quite dramatically (e.g. losing a few seconds per minute), particularly when the CPUs are working hard. Our servers use the Windows Time Service to stay in sync with domain controllers, which uses NTP under the hood, but the sync frequency is controlled by domain policy, and in any case even syncing every minute would still allow significant drift. Are there any techniques we can use to keep the clock more stable, other than using hardware clocks?
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Clock ticks should be predictable, but on most PC hardware - because they're not designed for real-time systems - other I/O device interrupts have priority over the clock tick interrupt, and some drivers do extensive processing in the interrupt service routine rather than defer it to a deferred procedure call (DPC), which means the system may not be able to serve the clock tick interrupt until (sometimes) long after it was signalled.
Other factors include bus-mastering I/O controllers which steal many memory bus cycles from the CPU, causing it to be starved of memory bus bandwidth for significant periods.
As others have said, the clock-generation hardware may also vary its frequency as component values change with temperature.
Windows does allow the amount of ticks added to the real-time clock on every interrupt to be adjusted: see SetSystemTimeAdjustment. This would only work if you had a predictable clock skew, however. If the clock is only slightly off, the SNTP client ("Windows Time" service) will adjust this skew to make the clock tick slightly faster or slower to trend towards the correct time.
What servers are you running? In desktops the times I've come across this are with Spread Spectrum FSB enabled, causes some issues with the interrupt timing which is what makes that clock tick. May want to see if this is an option in BIOS on one of those servers and turn it off if enabled.
Another option you have is to edit the time polling interval and make it much shorter using the following registry key, most likely you'll have to add it (note this is a DWORD value and the value is in seconds, e.g. 600 for 10min):
Here's a full workup on it: KB816042
Increase the frequency of the re-sync. If the syncs are with your own main server on your own network there's no reason not to sync every minute.
Clock drift may be a consequence of the temperature; maybe you could try to get temperature more constant - using better cooling perhaps? You're never going to loose drift totally, though.
Using an external clock (GPS receiver etc...), and a statistical method to relate CPU time to Absolute Time is what we use here to synch events in distributed systems.
http://www.codinghorror.com/blog/2007/01/keeping-time-on-the-pc.html
You could run "w32tm /resync" in a scheduled task .bat file. This works on Windows Server 2003.