How can I keep a program on a VPS running after SSH session times out?
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screen or tmux
you can use screen or tmux to allow processes to run in the background, detach them from your session and later re-attach them.
I personally like them better than nohup because of the control you have through being able to re-attach those screen-/tmux-sessions later.
A nice wrapper around screen or tmux is byobu (which defaults to using tmux). You can install it by typing apt-get install byobu at a command line.
3
nohup
you can use nohup YOURCOMMAND to prevent the termination of your ssh connection to kill your command. (@byte-commander mentioned it in a comment earlier)