Here is an excerpt from a recent post on the PiDP-8 Forum:
The most important thing to know about that is that it is a separate program from the modified SimH+PiDP-8 simulator.
Both need exclusive access to the front panel and switches, so you need to shut one down in order to use the other.
To switch from PDP-8 mode to Deeper Thought 2 mode:
$ sudo systemctl stop pidp8
$ sudo systemctl start deeper
Then vice versa to switch back:
$ sudo systemctl stop deeper
$ sudo systemctl start pidp8
I hope this helps...