Is it possible to have a BOINC server and cluster operating with no connection to the internet? If so, then how would the clients find the application on my server?
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You are proposing to use BOINC to serve compute tasks only to computers on a local network and you do not want external contributors. Yes, this is possible and a very likely scenario when the task itself already gives proprietory information away, e.g. the modeling of a drug target. Besides completely cutting off the server's connection to the outside world, you may also consider to set up a restrictive firewall.
The BOINC client of a participating machine can be configured in two ways. You can use the "BOINC Manager" GUI and as usual and in the "Add Project" dialog box instead of selecting from pre-selected public projects you add the IP number of your server directly into the text field behind "Project URL" followed by a forward slash ("/") and the project name.
The alternative way, which may be appropriate for a headless setup of a cluster, is to use the boinccmd command line interface. The man page of boinccmd (1) gives an overview on the command line options.
The URL to be given is the same that the setup scripts of the BOINC project tell you and that present the web interface to the project. The details on how to create a BOINC project are laid out on the BOINC Wiki pages http://boinc.berkeley.edu/trac/wiki/ProjectMain and of value may also be the shorter descriptions given by the maintainers of the Debian BOINC packages on https://wiki.debian.org/BOINC/Server .