Не в my.cnf нужно писать, а в /etc/mysql/mysql.conf.d
[mysqld]
#
# * Basic Settings
#
default-time-zone = Europe/Moscow
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking