This installation method is not yet verified for Shibboleth SP 3.x!
The Shibboleth SP software is an Apache module. Using Shibboleth for a Java Application (or any other application that can be run in container that supports AJP) involves setting up both a Java application server (eg Tomcat) that supports AJP and an Apache frontend server with mod_proxy_ajp. The AJP protocol is used to transport attributes as environment variables to the Java application server. This deployment model is well tested and is know to scale.