The MySQL optimizer makes the decision of what execution plan to use based on the information provided by the storage engines. That information is not accurate in some engines like InnoDB and they are based in statistics calculations therefore sometimes some tune is needed. In InnoDB these statistics are calculated automatically, check the following blog [...]
Sphinx search performance optimization: multi-threaded search
Queries in MySQL, Sphinx and many other database or search engines are typically single-threaded. That is when you issue a single query on your brand new r910 with 32 CPU cores and 16 disks, the maximum that is going to be used to process this query at any given point is 1 CPU core and [...]

