RTC drifts when rebooting

Question

I'm working on a project where an RTC (DS3231) is needed since the RPi will not have continuous access to the internet. I've been able to set the clock on time and keep it but I've observed that a delay in time appears when I reboot the system. Around 1 second each 5 reboots.

I've tried to set the clock both with the rc.local method and the overlays method (I'm running Jessie), and none of them solve this delay on reboot issue.

Any idea about why this could happen? It is not a problem with my clock as I've checked two differents DS-3231.

EDIT. What I've tried until now:

1. First Method

   -Including rtc-ds1307 in /etc/modules (It doesn't with "rtc-ds3231", so I use ds1307 driver instead)

   -Including in /etc/rc.local:

   echo ds1307 0x68 > /sys/class/i2c-adapter/i2c-1/new_device
   hwclock -s
   

2. Second Method (recommended for Jessie)

   -Including dtoverlay=i2c-rtc,ds3231 at the end of /boot/config.txt

   -Commenting out the following lines in /lib/udev/hwclock-set:

   #if [ -e /run/systemd/system ] ; then
   #    exit 0
   #fi
   

How I set up and read time

sudo date -s "01 AUG 2017 1:00:00"
sudo hwclock -w
sudo hwclock -r; sudo date

Answer 1

One reason may be that many of the various RTC chips, such as the DS3231, store time only with second prevision, when read from or written to. Thus, I would expect a normal variation of +/- 0.5s depending on when Linux read the hardware clock on each boot. Also, when setting the hardware clock initially, only seconds are stored, so you may end up with +/-1s overall. However, you should see only a random fluctuation in this range, but not accumulated deviation. Except, in case you constantly update the hardware clock from the Linux clock: this would quickly accumulate these errors. As you didn't give details in your question this is only speculation at this time.

Answer 2

Even accurate RTCs have some drift. The DS3231 claims ±2ppm from 0°C to +40°C. A million seconds is about 11½ days, so the clock could be a second off in about a week.

If you need better accuracy than that, you'll need an external precision clock source like a GPS (needs satellite sync, not always possible indoors) or rubidium clock (expensive, power hungry, fiddly).

Do you need to be rebooting so often?