From my experiences, you (the developer) will need to do the last tweaking of the InnoDB config parameters. I’m including the parameters that I constantly apply to my clients and make big difference when it comes to DB performance for Magento.
Magento Performance Archives - ACTIVO
PHP has two directives that typically are turned off by default and can significantly improve your Magento performance by turning them on. Both directives are targeting a feature called ‘realpath cache’ which essentially allows the PHP processes to cache paths to files, hence avoiding expensive disk lookups on every page load.