Atlas should take many hours to compile on modern hardware, but not days. You can check the logfile, whose location is printed by the command:
port logfile atlas
but it's possible the end of the log is truncated. You could run the install with the verbose flag to see exactly what it's doing at the time of the hang:
sudo port -v install atlas
Note that single-letter flags like -v must appear between port and the command (install in this case), and have no effect if used elsewhere on the command line.
