MySQL server has gone away - in exactly 60 seconds
Solution 1:
The php option mysql.connect_timeout
is the reason for this. It's not only used for connect timeout, but as well as waiting for the first answer from the server. You can increase it like this:
ini_set('mysql.connect_timeout', 300);
ini_set('default_socket_timeout', 300);
Solution 2:
When I ran into this problem, it wasn't caused by wait_timeout (which was set to the default 8 hours) but by max_allowed_packet with a large INSERT statement. Changing max_allowed_packet from PHP had no effect, but when I changed it in the mysqld section of /etc/my.cnf and restarted the MySQL server, the problem disappeared.
Solution 3:
There's a whole bunch of things that can cause this. I'd read through these and try each of them
http://dev.mysql.com/doc/refman/5.1/en/gone-away.html
I've worked for several web hosting companies over the years and generally when I see this, it is the wait_timeout on the server end though this doesn't appear to be the case here.
If you find the solution, I hope you post it. I'd like to know.
Solution 4:
This is something I do, (but usually with the MySQLi class).
$link = mysql_connect("$MYSQL_Host","$MYSQL_User","$MYSQL_Pass");
mysql_select_db($MYSQL_db, $link);
// RUN REALLY LONG QUERY HERE
// Reconnect if needed
if( !mysql_ping($link) ) $link = mysql_connect("$MYSQL_Host","$MYSQL_User","$MYSQL_Pass", true);
// RUN ANOTHER QUERY