This is not exactly a common issue, but it is an issue that was once mentioned on the GitHub, including myself. Obviously the point of this post is to address any remaining issues. When you launch Karabiner for the first time and the app crash with an error report suggesting failure in creating PID directory, this is the fix you are looking for.
Run the following commands on Terminal: chflags -R nouchg ~/.local/share/karabiner/pid sudo chmod -R 777 ~/.local/share/karabiner/pid
Just to provide context, the bundle of symptoms this issue comes with is following: Karabiner not modifying keys, cannot open the app without sudo command, sudo Karabiner still doesn’t modify keys.
update Nov 10, 2017: complete overhaul of the post for readability.