Mysql DB server hits 400% CPU
InnoDB for MySQL 5.1 exhibits single-threaded behavior because the number of read and write I/O threads are fixed at 4 each. I was just reminded that versions of MySQL before 5.1.38 has only one thread for read and one for write. Therefore, scaling up hardware will not improve performance at all.

You need to upgrade to MySQL 5.5/5.6 because there are settings that will enable InnoDB to engage multiple CPUs and multiple cores (such as innodb_read_io_threads and innodb_write_io_threads).


Sep 20, 2012 : Multi cores and MySQL Performance
Apr 26, 2012 : Is the CPU performance relevant for a database server?
May 26, 2011 : About single threaded versus multithreaded databases performance


CAVEAT : You must tune MySQL 5.5/5.6 properly because left unconfigured MySQL 5.1 is faster than 5.5/5.6 : Why mysql 5.5 slower than 5.1 (linux,using mysqlslap)

Give it a Try !!!