https://bugzilla.wikimedia.org/show_bug.cgi?id=29409

--- Comment #3 from Brion Vibber <[email protected]> 2011-06-15 17:35:46 UTC 
---
'server has gone away' usually means one of:

* some bit of data transferred was too large for mysql's max packet size
setting, thus the connection was cut off

* the connection was idle for too long while waiting for a query to complete,
thus the connection was cut off

The stuff for cl_collation seems to be mostly ALTER TABLE-y so shouldn't
transfer data, so timeout is the most likely. I remember us having that sort of
problem with long-running dump scripts and such in the past... there's a
database::setTimeout() method, which backup.inc's BackupDumper class triggers
on its dedicated DB connection:

    function backupDb() {
        $this->lb = wfGetLBFactory()->newMainLB();
        $db = $this->lb->getConnection( DB_SLAVE, 'backup' );

        // Discourage the server from disconnecting us if it takes a long time
        // to read out the big ol' batch query.
        $db->setTimeout( 3600 * 24 );

        return $db;
    }

Might make sense to bump the timeouts during updates too?

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