If you wish to explicitly set the time zone for your MySQL running on an Ubuntu Server, here is how to do it.
First open your global MySQL my.cnf configuration file:
sudo nano /etc/mysql/my.cnf
Scroll down the file to location the [mysqld_safe] section. Add the following line:
timezone = GMT
Obviously you would set it to what you wanted to use, be it UTC, GMT+2 or whatever. Save your changes and restart MySQL:
sudo service mysql restart
Done.
(You can check by creating a table with a timestamp column and then inserting a record with NOW() as the value. This should then show up correctly when queried.)
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