500 ms delay in time saved into RTC

[Igor Plyatov <plyatov@gmail.com>]

Hi!

I have board based on AT91SAM9G20 (ARM926EJ-S CPU), Linux-4.9.36 kernel 
and RTC chip DS1340 (rtc-ds1307.c driver).

RTC chip connected by means of I2C-bus, without HW IRQ line connected.

Kernel configured to not use embedded functions for time getting at 
startup and saving at shutdown:
CONFIG_RTC_CLASS=y
# CONFIG_RTC_HCTOSYS is not set
# CONFIG_RTC_SYSTOHC is not set
CONFIG_RTC_INTF_DEV_UIE_EMUL=y
CONFIG_RTC_DRV_DS1307=y
CONFIG_RTC_DRV_DS1307_CENTURY=y

The hwclock utility is from util-linux-2.29.1.

The OS does not have external time synchronization sources like NTP, PTP 
or else.

Generally I need to achieve error within +-20 ms when RTC's time copied 
into OS or back from OS into RTC.

I have made measurements during startup and shutdown of OS and have 
found 500 ms delay introduced into RTC's time, when "hwclock --utc 
--systohc" executed.

Logical analyzer show to me I2C-bus transactions and PPS signal 
generated by Linux. And I see 500 ms delay is between of rising edge of 
PPS signal (start of OS second) and moment when time saved into RTC.

Please explain, why this happens? Is this due to absence of IRQ line for 
RTC or due to a bug in the hwclock, or kernel bug or I have missed 
something else?

Best wishes.
--
Igor Plyatov