In my previous post I mentioned you might need to increase net_write_timeout to avoid connection being aborted and now I think I should have better explained that. MySQL uses a lot of different timeout variables at different stages. For example when connection is just being established connect_timeout is used. When server waits for another query [...]
We often recommend to our clients to convert their current database from MyISAM tables to InnoDB. The transfer by itself in most cases is almost plain, however the application can be broken by new unexpected errors 1205 (ER_LOCK_WAIT_TIMEOUT) Lock wait timeout expired. Transaction was rolled back. 1213 (ER_LOCK_DEADLOCK) Transaction deadlock. You should rerun the transaction.