A portable gas fractionalization system with built-in administrative and self-diagnostic functions is provided. The system includes a multiple mode programmable controller which has a operations mode and a diagnostic mode that can be activated by a triggering event. The triggering event can be when a user enters a command input, when one or more process parameters deviate from a nominal value, or when the system is scheduled to perform self-diagnostics. The system also includes a multi-level user interface which is integrally formed with the system. The user interface includes a multi-level display screen and a plurality of user command functions. The diagnostic information displayed on the display screen can be in an abbreviated code form so that only technicians would be able to interpret meaning of the code.