I have a script that does a lot of legwork nightly.
It uses a PDO prepared statement that executes in a loop.
The first few are running fine, but then I get to a point where they all fail with the error: "MySQL server has gone away".
We run MySQL 5.0.77.
PHP Version 5.2.12
The rest of the site runs fine.
The B.5.2.9. MySQL server has gone away section of the MySQL manual has a list of possible causes for this error.
Maybe you are in one of those situations ? -- Especially considering you are running a long operation, the point about
wait_timeoutmight be interesting...