11. How Do I Run a Job that Continues after I Log Out?

Generally speaking, you can use the screen command, described in more detail below, to continue having your scripts run on the interactive Yens after logging out.

screen

screen is a window manager that allows you to set up multiple virtual sessions within your terminal session. This can be useful for running multiple processes at the same time, but it can also be used to leave processes running after you log out of any interactive Yen server.

To set up a screen, use:

screen -S <sessionname>

For example, let’s name our session ocr:

screen -S iris 

This will take you to a new terminal with a blank view and a command prompt at the top of the page. Here, you can start issuing commands as usual and in particular, you can start a script that you expect to run for a long time.

Let’s run our serial R script again. This time, we will let it run in a screen (if you had modules loaded, starting a screen preserves these in the new terminal started by screen). So, we can start our R process:

Rscript iris-parallel-bootstrap.R

Once your script is going, you can exit out of this screen session with the keyboard shortcut ctrl + a + d, which will return you to your original terminal.

You should see that the screen was detached:

[detached from 59617.iris]

You can list any screen sessions that you are running on the particular Yen server you are logged onto by typing:

screen -ls

You should see something like:

There is a screen on:
	59617.iris	(04/28/21 13:48:14)	(Detached)
1 Socket in /run/screen/S-nrapstin.

If you exit out of the server here, you can be assured that the scripts in your screen sessions will continue to run, granted they are accessing IFS space.

To return to any existing screen session, you simply need to type:

screen -r <sessionname>

For example, to go back to the screen we detached from earlier:

screen -r iris

If you are actively printing to the console in your script, you may notice that you cannot scroll up through the log of print statements when you are in a screen. In order to activate the “scroll mode”, you can use the keyboard shortcut ctrl + a and then hit esc. In this mode, you can peruse through your print statements with the up and down arrow keys. Once you are finished scrolling, you can exit out of the mode by hitting the q or esc keys.

You may run into a situation where you are disconnected or timed out from the Yens while you are attached to a screen session. When you log back onto the Yens and try to reconnect to that session again, you may find that you cannot re-attach to the screen, since it’s already “attached”. In order to return to that session, you can just use this command:

screen -d -r <sessionname>

This detaches the previous connection to that screen session and then returns you to the screen.

Finally, once you are finished with a screen session, all you have to do is type:

exit