The Generic Mapping Tools and netCDF libraries are required to be installed before installing MB-System™. You'll find the GMT package at
Perhaps the easiest way to install GMT and netCDF is using GMT's automated install script. The script needs lots of details about your system and your preferences regarding the installation, so to make answering these questions more straight-forward, the folks at GMT have created a web form. One answers the questions in the web page, and then clicks "GET PARAMETERS". The web page creates a properly formatted parameter file that can be saved and referenced from the GMT install script to semi-automate the rest of the install. The web form can be found at http://gmt.soest.hawaii.edu/gmt/gmt_install_form.html.
One note regarding the GMT web form: Clicking "GET PARAMETERS" results in creation of a text parameter file that is immediately displayed in the browser window. The name of this file is "install_gmt_form.pl", however the file itself is not a script and it is not Perl. It is, in fact, simply a set of parameter-value pairs that must conform to the Bourne shell syntax. It it less confusing if one immediately saves this file with non-perl-script like syntax, perhaps "gmt_install_parameters.d", or whatever you find useful.
With the parameters correctly specified, one can download and install GMT with execution of the GMTinstall script (also available for download from the web form page above):
./install_gmt install_gmt_par.d > install.log 2>&1
This gives you a nice log of everything that's going on during the install which you can monitor with
tail -f install.log