Sounds like the same issue I had with one of my servers, everything  
ran fine, I moved it to a datacenter, and ntp couldn't keep the time  
in sync at all, moved it back, and it was fine again. It was a dual  
cpu computer, and the default timing method used in the kernel on  
freebsd that I was using, kept changing depending on what cpu that  
thread ran on at any given time, giving me the same log messages your  
getting:

> Jan 22 07:15:48 dobby ntpd[51979]: kernel time sync status change 6001
> Jan 22 07:50:10 dobby ntpd[51979]: kernel time sync status change 2001
> Jan 22 11:00:35 dobby ntpd[51979]: kernel time sync status change 6001
> Jan 22 11:49:04 dobby ntpd[51979]: kernel time sync status change 2001

I found that for freebsd atleast, there where 3 different clock source  
options you can configure, and when I changed it, everything behaved  
correctly.

I added this into /etc/sysctl.conf

kern.timecounter.hardware=TSC



Quoting Jeffrey Goldberg <[email protected]>:

> I got an auto notice of problems with my server, and the graphs
> certainly do look dismal.
>
> On Jan 22, 2009, at 10:15 PM, Ask Bjoern Hansen wrote:
>
>> ----------------------------------------------------------------------
>> 72.64.118.118 (current score: -16.0)  http://www.pool.ntp.org/s/1784
>> ----------------------------------------------------------------------
>
>> If you have any questions, just reply to this email.  Otherwise no
>> response is necessary.
>
> I have not been able to diagnose the problem.  From what I see, my
> server is acting properly, but I don't really know what sort of
> diagnostic tools are available to me.
>
> Here is the result of ntpq -c 'rv 0'
>
> $ ntpq -c 'rv 0'
> assID=0 status=06f4 leap_none, sync_ntp, 15 events, event_peer/
> strat_chg,
> version="ntpd 4.2.4p5-a Tue Jan 13 22:16:19 CST 2009 (1)",
> processor="i386", system="FreeBSD/7.1-STABLE", leap=00, stratum=3,
> precision=-19, rootdelay=566.555, rootdispersion=578.905, peer=12437,
> refid=17.151.16.22,
> reftime=cd24718e.09c98675  Fri, Jan 23 2009 10:40:46.038, poll=5,
> clock=cd24721c.da46d092  Fri, Jan 23 2009 10:43:08.852, state=4,
> offset=0.192, frequency=-41.686, jitter=145.186, noise=52.291,
> stability=5.242, tai=0
>
> Every time I've checked in the last few hours, my offset has been less
> than 15ms.  I don't know what are healthy ranges for jitter and
> stability, so I don't know if those give me any clue.
>
> I am getting time resets in my logs.  I assume that these indicate
> that something is wrong.  But again, I don't know where to look.  (Log
> times are -06:00).
>
> Jan 22 07:15:48 dobby ntpd[51979]: kernel time sync status change 6001
> Jan 22 07:50:10 dobby ntpd[51979]: kernel time sync status change 2001
> Jan 22 11:00:35 dobby ntpd[51979]: kernel time sync status change 6001
> Jan 22 11:49:04 dobby ntpd[51979]: kernel time sync status change 2001
> Jan 22 13:48:35 dobby ntpd[51979]: kernel time sync status change 6001
> Jan 22 14:56:56 dobby ntpd[51979]: time reset -0.141398 s
> Jan 22 15:00:44 dobby ntpd[51979]: kernel time sync status change 2001
> Jan 22 18:53:31 dobby ntpd[51979]: time reset -0.154392 s
> Jan 22 22:36:22 dobby ntpd[51979]: time reset -0.147822 s
> Jan 23 04:30:08 dobby ntpd[51979]: time reset -0.129208 s
> Jan 23 10:37:47 dobby ntpd[51979]: time reset +0.159964 s
>
> Any help or advice would be useful.  Nothing really changed on my
> system around the time of the wonkiness, but on another machine on the
> network, I did start using bittorrent (Transmission 1.50b1).  It's
> setting are such that it isn't making more than a dent in my network
> traffic.  But it's only serving about 10 peers, so I don't see how it
> could be confusing my router.
>
> Cheers,
>
> -j
>
>
> --
> Jeffrey Goldberg                        http://www.goldmark.org/jeff/
>
> _______________________________________________
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>



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