MySQL "wait_timeout" option won't save

MySQL is currently set to a wait_timeout of 28800 on our server which I understand to be the default. I've been attempting to change this to 60 as recommended by a consultant, but the changes don't seem to take for long. Here's what I've tried while logged into Linux as root and MySQL as a database user:

1) Logging into MySQL and:

show variables like '%wait_timeout%';
set wait_timeout=60;

2) Editing the my.cnf file under /etc and adding the following line to both [mysqld] and [mysqld_safe]:

wait_timeout=60

When I try #1 and choose to show the wait_timeout variable right after, it shows correctly as 60. However, if I wait a minute or two, it reverts back to 28800 again. When I try #2, the option doesn't seem to take at all, even after restarting Apache and MySQL.

The my.cnf seems to be the only such version of the file that I can find.

I've tried the following, but no arguments show:

mysql --print-defaults

When restarting Apache, I've been using:

/usr/sbin/apachectl graceful

When restarting MySQL, I've been using:

/etc/init.d/mysqld restart

Any ideas? :-(

I'm afraid you might have run into one of the several gotchas of MySQL. See this bug report.

If I have understood everything right, the MySQL command line client causes mysqld to use interactive_timeout instead of wait_timeout.

What does the following query return to you?

SELECT @@global.wait_timeout, @@session.wait_timeout;

1. Edit my.cnf (the MySQL configuration file).

Ubuntu 16.04

 sudo vi /etc/mysql/mysql.conf.d/mysqld.cnf

Debian

 sudo vi /etc/mysql/my.cnf

Centos

 sudo vi /etc/my.cnf

2. Locate the timeout configuration and adjust it to fit your server.

[mysqld]
wait_timeout = 31536000
interactive_timeout = 31536000

3. Save the changes and exit the editor.

4. Restart MySQL to apply the changes as follows:

sudo /etc/init.d/mysql restart