I ran into this problem on a system that was unable to obtain NTP sync
because the clock was running very slow (over 10000ppm slow). ntpd had
declared all of its peers 'reject' with 'peer_dist' reason.

On investigation, the tsc_khz variable was significantly incorrect
causing xtime to run slow.  After a reboot tsc_khz was correct so I
did a reboot test to see how often the problem occurred:

Test was done on a 2000 Mhz Xeon system.  Of 689 reboots, 8 of them
had unacceptable tsc_khz values (>500ppm):

 range of tsc_khz  # of boots  % of boots
 ----------------  ----------  ----------
        < 1999750           0      0.000%
1999750 - 1999800          21      3.048%
1999800 - 1999850         166     24.128%
1999850 - 1999900         241     35.029%
1999900 - 1999950         211     30.669%
1999950 - 2000000          42      6.105%
2000000 - 2000000           0      0.000%
2000050 - 2000100           0      0.000%
                   [...]
2000100 - 2015000           1      0.145%  << BAD
2015000 - 2030000           6      0.872%  << BAD
2030000 - 2045000           1      0.145%  << BAD
2045000 <                   0      0.000%

The worst boot was 2032.577 Mhz, over 1.5% off!

It appears that on rare occasions, mach_countup() is taking longer to
complete than necessary.

I suspect that this is caused by the CPU taking a periodic SMI
interrupt right at the end of the 30ms calibration loop.  This would
cause the loop to delay while the SMI BIOS hander runs. The resulting
TSC value is beyond what it actually should be resulting in a higher
tsc_khz.

The below patch makes native_calculate_cpu_khz() take the best
(shortest duration, lowest khz) run of it's 3 calibration loops.  If a
SMI goes off causing a bad result (long duration, higher khz) it will
be discarded.

With the patch applied, 300 boots of the same system produce good
results:

 range of tsc_khz  # of boots  % of boots
 ----------------  ----------  ----------
        < 1999750           0      0.000%
1999750 - 1999800          30     10.000%
1999800 - 1999850         166     55.333%
1999850 - 1999900          89     29.667%
1999900 - 1999950          15      5.000%
1999950 <                   0      0.000%

Problem was found and tested against 2.6.18.  Patch is against 2.6.22.
Signed-off-by: Dave Johnson <djohnson@sw.starentnetworks.com>
Signed-off-by: Ingo Molnar <mingo@elte.hu>
Signed-off-by: Thomas Gleixner <tglx@linutronix.de>