I have a spider crawling the web written in PHP running constantly to insert and update data in a Mysql database.  Today, it kept stopping on a records with the error message, "Mysql server has gone away".  It certainly did not time out as just starting the process again would result in this message immediately.  The script did not close out the connection to the DB as it had worked just fine for over a year.

Finally, I found that the problem was max_allowed_packet setting in my.cnf was too small.  It was set to 2MB and when Mysql receives a query larger than that, it assumes that something must have gone wrong and closes the connection.  I increased that parameter to 4MB and everything is working fine now.