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> system clock looping loosely over 4-5 seconds, system clock looping loosely over 4-5 seconds
jptxs
post Nov 4 2006, 09:33 PM
Post #1


Whats this Lie-nix Thing?
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I have a really odd problem. This is also posted at http://www.centos.org/modules/newbb/viewto...21&forum=23.

My clock on a box named bach loops over and over, advancing only 1-2 seconds for every 10-20. My prompt, which displays the time, shows the issue nicely:

08:02:18 jptxs@bach:~$
08:02:18 jptxs@bach:~$
08:02:19 jptxs@bach:~$
08:02:20 jptxs@bach:~$
08:02:20 jptxs@bach:~$
08:02:21 jptxs@bach:~$
08:02:21 jptxs@bach:~$
08:02:21 jptxs@bach:~$
08:02:22 jptxs@bach:~$
08:02:18 jptxs@bach:~$
08:02:18 jptxs@bach:~$
08:02:18 jptxs@bach:~$
08:02:19 jptxs@bach:~$
08:02:19 jptxs@bach:~$
08:02:20 jptxs@bach:~$
08:02:20 jptxs@bach:~$
08:02:20 jptxs@bach:~$
08:02:21 jptxs@bach:~$
08:02:21 jptxs@bach:~$
08:02:22 jptxs@bach:~$
08:02:22 jptxs@bach:~$
08:02:18 jptxs@bach:~$

Now, eventually, it will get to a point where it will move on a second. It would advance to 08:02:23 or maybe 24. But then it will skip back to 19 or 20 and start to loop for a bit again. I wrote a script to track it:

#!/bin/bash

while true
do
echo "bach clock:" >> clockChecks.log
date >> clockChecks.log
echo >> clockChecks.log
echo "wagner clock:" >> clockChecks.log
ssh wagner date >> clockChecks.log
echo >> clockChecks.log
echo ++++++---------------------++++++++ >> clockChecks.log
echo >> clockChecks.log
sleep 10
done

The output compares it to a working box named wagner. I have attached a file [clockChecks.log] that shows the output. Now, what you can see is that they are in sync for quite a while. Then the clock on bach goes out of sync right around when wagner is shutdown for the night (I forgot I was running this test):

bach clock:
Fri Nov 3 23:12:05 EST 2006
wagner clock:
Fri Nov 3 23:12:05 EST 2006
++++++---------------------++++++++

bach clock:
Fri Nov 3 23:12:16 EST 2006
wagner clock:
++++++---------------------++++++++

bach clock:
Fri Nov 3 23:12:27 EST 2006
wagner clock:
++++++---------------------++++++++

bach clock:
Fri Nov 3 23:13:25 EST 2006
wagner clock:
++++++---------------------++++++++

Of course, you could say it may have been due to the wait time for the ssh timeout, but then you see the difference big time once wagner is back up later:

bach clock:
Sat Nov 4 02:27:27 EST 2006
wagner clock:
Sat Nov 4 07:36:26 EST 2006
++++++---------------------++++++++

bach clock:
Sat Nov 4 02:27:42 EST 2006
wagner clock:
Sat Nov 4 07:39:27 EST 2006
+++++---------------------++++++++

bach clock:
Sat Nov 4 02:27:53 EST 2006
wagner clock:
Sat Nov 4 07:42:41 EST 2006

I ran ntpdate and the clock was reset, but immediately slowed down and looped again.

This gets stranger. This all started when I upgraded from a an old Debian install running kernel 2.20 with custom config to Ubuntu 6.06. For various reasons I needed a 2.6 kernel on the box. The box crawled. At that point, I didn't notice the clock issues. I installed over and over. I tried to go back to Debian Sarge. I tried a RedHat AS 3 set of disks I had and that wouldn't boot correctly (seemed like the init scripts were timing out). I finally settled on CentOS 4.4 (Server Disk for the install). That has gotten me to the point where I am now. It seemed to be running fine for 7-8 hours. I reinstalled the services I had had on the box (pdnsd: http://www.phys.uu.nl/~rombouts/pdnsd.html, ejabberd: http://ejabberd.jabber.ru/ and VMWare Server: http://www.vmware.com/products/server/ running an OpenBSD guest OS). Everything seemed fine, but then the clock started going funny again after a few hours more operations. So I searched and searched. I found a ton of stuff about XBox clock skips and loops, but nothing I could find seemed relevant to me. I upgraded my BIOS (http://www-307.ibm.com/pc/support/site.wss/document.do?sitestyle=lenovo&lndocid=MIGR-42952). After that reboot things seemed to be fine again for a bit. That's when I wrote the script to track it. I thought I'd licked it. But then the above unfolded and now I'm here begging for help. I've also no tried replacing the battery on the MB and the same thing happened as with the BIOS, works for a bit and then at 21:06:37 (or there abouts) it goes bad again.

Could this be hardware? Seem too inconsistent for that, in my mind.

How, if at all, could this be somehow be a relationship to the wagner box? It seemed to go out of whack when that went offline. But it was a 100% fresh install in a few cases and still had this issue. I didn't see any errors in /var/log/messages or other logs at that time, either.

Could this be some odd thing I'm just not seeing?

Any suggestions for search terms? I've tried "clock skip" "clock loop" and all sorts of system indicators (kernel: Linux bach 2.6.9-42.EL #1 Sat Aug 12 09:17:58 CDT 2006 i686 i686 i386 GNU/Linux, model: info in dmidecode output attached in zip file).

Anything I'm just plain missing?

Any help appreciated...


jptxs
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DS2K3
post Nov 6 2006, 12:21 PM
Post #2


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To start with the obvious: Have you made sure there is no NTP software running on the computer (perhaps on a CRON schedule) which could be fiddling with the clock.

Do you have an SMP (multi-processor) computer? I have seen this mentioned in conjunction with SMP Ubuntu kernels, it might be related to whatever was causing that issue.

Try booting to single-user mode, that should start with minimal services and software running and might indicate whether or not the problem is related to system load or perhaps a rogue process.

D


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Fixed your problem? Let us know!
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jptxs
post Nov 6 2006, 03:14 PM
Post #3


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[quote name='DS2K3' post='28325' date='Nov 6 2006, 12:21 PM']
To start with the obvious: Have you made sure there is no NTP software running on the computer (perhaps on a CRON schedule) which could be fiddling with the clock.
[/quote]

Yes.

[quote name='DS2K3' post='28325' date='Nov 6 2006, 12:21 PM']
Do you have an SMP (multi-processor) computer? I have seen this mentioned in conjunction with SMP Ubuntu kernels, it might be related to whatever was causing that issue.
[/quote]

No.

[quote name='DS2K3' post='28325' date='Nov 6 2006, 12:21 PM']
Try booting to single-user mode, that should start with minimal services and software running and might indicate whether or not the problem is related to system load or perhaps a rogue process.
[/quote]

Done that as well. No joy. Thought maybe VMWare was to blame, but then I saw the issue without it on. Seems like it may be related to something happening at 21:00 - 21:10 each night, but I can't even find a crontab or any at schedule installed on any user (there are only 2).

Only thing that's com to light is that the RTC clock is way off, but nothing I've read says that should cause any issues at all much less something like this.
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jptxs
post Nov 13 2006, 03:38 PM
Post #4


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RESOLVED(?)

Details at:

http://www.centos.org/modules/newbb/...forumpost18103

In short, a kernel issue. See .config comparison:

old: http://pastebin.com/823567

new: http://pastebin.com/823568
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