Installing FVCOM
From FVCOM Wiki
This section describes the installation of FVCOM on your system. The preferred environment is Linux with OS X an option as well. Windows installation is possible but senseless.
Windows Users
It is recommended that you download and install the latest version of cygwin (http://www.cygwin.com). Cygwin is a bash shell/Unix emulation program and contains many of the tools such as tar, gzip/gunzip, and cpp which will be useful for installation and compilation of FVCOM. Also, cygwin gives Windows a decent interface with which to setup and run the model. Note that it requires basic familiarity with Unix commands.