Sync date time and timezone of system and mysql

[Aadil Awan]

We have a web console in PHP where we are giving option to user to change system date time and timezone. He can set the option of manually or automatically from internet. When he check automatic we are starting ntpd service and for manual we are stopping ntpd service. After changing timezone we are restarting mysqld service to sync it with system timezone and time.
The problem is when we change date time manually and then start ntpd service and change timezone then myslqd service does not restart and becomes unresponsive. We have to forcefully kill it and then restart. Error in mysql log is as follow

"[Note] InnoDB: page_cleaner: 1000ms intended loop took 3376912ms. The settings might not be optimal. (flushed=50 and evicted=0, during the time.)"

My question is, does restarting mysqld service is necessary to sync it with system date time and timezone?

If its not necessary then how to sync it with system that does not make it hang.