To safely shut down the apogee system, start the agdr software, and
    put the system into warmup mode using the camera...specifications
    ...cooler mode pulldown menu.  Wait until the temperature gets to
    around 0 (the warmest it seems to read).  Then run the program 
    "usershutdown" to halt the operating system on the computer.  There
    is a link to that program in /usr/local/bin so you should find it by
    just typing the program name. Finally, hold the power switch down
    for a few seconds to shut the computer off.