1. Is that the server timed out and closed the connection. By default, the server closes the connection after 8 hours or 28800 seconds if nothing has happened. You can change the time limit by setting the wait_timeout
variable when you start mysqld via your server's /etc/my.cnf
2. Another common reason to receive the MySQL server has gone away error is because you have issued a ``close'' on your MySQL connection and then tried to run a query on the closed connection. You can check that the MySQL hasn't died by executing mysqladmin version and examining the uptime.
i.e. to check mysql uptime, in shell as root user type: