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I just signed up for BlueHost and one of their PHP config options is PHP5 (FastCGI).

I'm going to start using Codeignitor for as must as I can and was wondering if I should enable FastCGI or now.

Sorry if this is in the wrong place (vs serverfault.com)

A: 

Why dont you setup/migrate/implement the application, and then do a few ab benchmarks with and without FastCGI so you can see for your self?

more info on ab http://www.cyberciti.biz/tips/howto-performance-benchmarks-a-web-server.html

Iraklis