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_timeout might be interesting...
Most likely you sent a packet to the server that is longer than the maximum allowed packet.
When you try to insert a BLOB that exceeds your server's maximum packet size, even on a local server you will see the following error message on clientside:
MySQL server has gone away
And the following error message in the server log: (if error logging is enabled)
Error 1153 Got a packet bigger than 'max_allowed_packet' bytes
To fix this, you need to decide what is the size of the largest BLOB that you will ever insert, and set max_allowed_packet in my.ini accordingly, for example:
[mysqld]
...
max_allowed_packet = 200M
...