Adding also that the mysql timeout might not work always, as presented in manual:

• https://dev.mysql.com/doc/refman/5.5/en/mysql-options.html

Citing:

MYSQL_OPT_READ_TIMEOUT (argument type: unsigned int *)

The timeout in seconds for each attempt to read from the server. There are retries if necessary, so the total effective timeout value is three times the option value. You can set the value so that a lost connection can be detected earlier than the TCP/IP Close_Wait_Timeout value of 10 minutes.

Implementation of this timeout uses mechanisms that may not be available on all platforms. On such a platform, a client that issues a read call might under certain circumstances wait without timing out. For example, a client might not time out if the server is not responding because it is waiting for a “disk full” condition to clear.

Therefore you should also check if there are problems with mysql server.

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