MySQL – Difference Between wait_timeout and connect_timeout

my.cnfMySQL

I have a my.cnf file. In it I see wait_timeout as well as connect_timeout. What's the difference between these 2?

Right from the MySQL Documentation

wait_timeout : The number of seconds the server waits for activity on a noninteractive connection before closing it.
connect_timeout : The number of seconds that the mysqld server waits for a connect packet before responding with Bad handshake

EXAMPLES

If wait_timeout is 1800 (30 Minutes), the DB Connection will close in 30 minutes if the connection is idle (indicated by Sleep in the command column of the processlist).
If connect_timeout is 10, then mysqld will reject you if you cannot login (authenticate) in 10 seconds.

My immediate suspicion is that there is another my.cnf present on the system. You should run

locate my.cnf

and see if the reports multiple my.cnf files

If there is only one my.cnf, then my.cnf is most likely in the wrong folder.

It should be in one of the following places

Please check for these. Remove extras.

Make the sure the datadir in new cnf file is the same as the old one then restart the service and try again.