IBM says here:

Database server performance, typically measured in terms of the transaction throughput and application response time, depends heavily on the I/O subsystem performance. To attain the best possible I/O throughput, database table data layout demands special attention from database and system administrators.

I suggest you examine the file systems in use, the layout and the performance of your disks, and the individual settings related to file system performance. Generally, the ext3 file system is conceived as less performant than, say, XFS. The choice and setup of your file system heavily impacts database performance.