Running PHP as a CGI binary is slower and more resource intensive than running it as a module.
This is because every time you run a script, it has to run through the PHP interpreter before it goes to the webserver. In contrast, when PHP is compiled as a module of Apache (or whatever), it in essence becomes an integral part of the webserver.
Not the best explanation in the world, but the best I can do...
The code is pretty much the same, but some things - like embedded HTTP authentication - are impossible in the CGI binary version, because PHP isn't "hooked" into Apache.
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