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I'm struggling to understand boot process on Yocto linux (Dizzy) which I got as pre-built image. It boots in xfce; pidof /sbin/init shows "1" which should mean that it's SysVinit. However, there is no /etc/inittab file and systemd process is started.

I just want to change default runlevel to 3.

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Yocto can create images utilizing either systemd or SysV init. In either case the program used as init will have pid 1. As you are seeing a systemd process on your system you will have a configuration utilizing systemd. Systemd has no run levels perse.

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