Performance Tuning

Hi, We started up a new DB that has 50plus tables. Each table may have 10-100's of Gigabytes of data. So the tables are huge. When I join two tables, the query never returns the data - even hours of waiting. I do have indexes on the tables for the fields in my where clause.

In the configuration file, we have set innodb_buffer_pool_size to 128G, innodb_flush_mtheod=O_DIRECT and the tmp-table-size =16G. Are there other parameters in the config file that should be looked at?

How does one determine if the issue is due to hardware, configuration (page swapping, buffer size and etc) or anything else for that matter? What is the best way to try to troubleshoot the performance issue?

Any advice on how to go about tuning our database is greatly appreciated.

Thanks in advance.

Sherry