I have been trying to benchmark the sql calls to mysql from an application without success. Even when I set the SELECT statement to SQL_NO_CACHE, the results seemed to be still cached. Apparently, Linux does its own caching of disk reads also. That was giving me incorrect benchmark results if I hit the same data twice.

For those using Linux kernel 2.6.16 or higher, you can clear Linux cache with the following command.
echo 3 > /proc/sys/vm/drop_caches

Unfortunately for me, I am stuck on 2.5.xx and will have to figure out another method.