Magento 1.9.1 with MySQL 5.5 – Compatibility Guide

We have faced similar issues and the most common reasons are one of the following:

1. Reindexall is called from cron.php as per scheduling this on times will eat resources and get stuck or hold some queries( IMPORTANT ).

2. Core Url rewrite indexing is intensive so is product flat table populate process if you have Multistore created or lot many products.

3. Some third party extensions used to populate data externally.

Soltuions: 1. configure Mysql as per available resources and requirement. -- more memory, use of Mysql cache, number of connections allowed etc.

1. Make sure that Flat catalog product and category is on( IMPORTANT ).

2. Indexing not to be run frequently.

3. Improve your caching to reduce data base load.

4. Check for additional modules that might be using lots of resources.

5. Go into server mysql and check for processlist this will give some query list thats not getting executed completely.

Yes, you can. Assuming you open the connection with something like this:

$db = Mage::getSingleton('core/resource')->getConnection('core_read');

You can close the connection with this:

$db->closeConnection();

And then re-open it with this:

$db->getConnection();

When I need to make an api call that could take a long time, I close the connection first, then use getConnection to open it again afterwards, which has solved the "mysql server has gone away" problem for me.