Then look for
…i-am-a-dummy FALSE
connect_timeout 0
max_allowed_packet 16777216
…

Then, at mysql prompt

mysql> set GLOBAL connect_timeout=259200;
Query OK, 0 rows affected (0.03 sec)

In my web application met this problem while my setup wait_timeout as 30. When it sets to default variable 8 hours which is 28800 seconds its working fine.

i m using c3p0 connection pooling with hibernet in JAVA. Here what happends means the connections goign to kill every 30 seconds which is sleeping state but it live.

So its major problem keep aware with this time out variable on mysql server.

Hope this information usefull for all.

Nah but seriously tho, some mysql_close() calls would be in order, if you are having problems i doubt its one script thats making tons of connections its probably just other connections are being made in other highly used scripts and are not getting closed after. If youre using PHP for example and objects, you can create a destructor like __destruct(){$this->link->close();} to close it at the end of execution because when the object is destroyed it closes the connection then.

In your case, the query selecting rows is probably taking more than 30 seconds, your timeout setting kills the process, so the delete query is not executed anymore.