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From: Sergey <a_s_y@sama.ru>
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Date: Fri, 19 Jun 2015 10:52:56 +0400
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On Thursday 18 June 2015, Mikhail Efremov wrote:

> hwclock(8):
>        -r, --show
>        --get
>               Read the Hardware Clock and print the time on standard
>               output.  The time shown is always in local time, even if
>               you keep your Hardware Clock in UTC.  See the --localtime
>               option.
> 
> При отсутствии /etc/adjtime hwclock считает, что время в Hardware Clock
> в UTC и при выводе прибавляет к нему +3.
 
Тогда, вообще, непонятно.

Имеем ядро 3.14.27-std-def-alt1

# hwclock --localtime --systohc
# hwclock -r
Fri Jun 19 09:54:53 2015  -0.860046 seconds
# date
Fri Jun 19 09:54:57 SAMT 2015

Далее делаем так
# service ntpd start
Starting ntpd service:                 [ DONE ]

и ждём:
# sleep 900 ; hwclock -r
Fri Jun 19 06:13:40 2015  -0.813063 seconds

Ядро плевать хотело на /etc/adjtime

-- 
С уважением, Сергей.