Bonnie is a great tool to use to benchmark your file system. Just a quick tip on using bonnie.
You need to give bonnie how much ram you have have in your system, and when you run bonnie you should run with a size 2x as big as your ram. So using this command will help you speed up that calculation.
bonnie++ -r $(free -m | awk '/^Mem/{print $2}') -s $(echo $(free -m | awk '/^Mem/{print $2}')*2| bc)
We use subcommands to expand and automattically use the right parameters for bonnie. Would be easy enough to stick that into a shell script to make a small wrapper and pass along any other arguments to bonnie like user and directory.