We have three databases using one mysql server. Two implement connection pool through J2EE architecture and one just uses mysql connection. We need to improve the performance through tuning mysql server parameters such as resetting wait_timeout, max-connections, threads_cache and .... All the information online has directed us to configure my.cnf option file. However, We want the settting only affect the database using normal connections, not the other two with connection pools. Can my.cnf do that and where to put this file? Do settings in my.cnf affect the settings for connection pool in other configuration files? I have been looking up onlines for days and nothing has been found helpful. Please help if anyone knows how to solve the problem.