Linux – “bus error” when trying to reboot Linux

You should perform a ps aux to see if any of the shutdown scripts are hung waiting for a process to finish. It should look something like this:

/etc/rc6.d/K##procname

You can try manually issuing a kill command for that hung script. Strange though, since there's a timeout set on the scripts where it will force a -KILL signal to any leftover process.

Also, what's the uptime of the server/box? I've experienced an issue in the past where a box that has an uptime of over a year refuses to shut down. In that case, I've killed each process manually, run sync several times to flush all data to disk and forced a reboot (power cycle).

There is already a start-up script for running local commands in /etc/rc.d/local. You can add a line there which executes your program.

If your script requires startup/shutdown/restart capabilities, you can add your own script to /etc/init.d. Start by looking at the existing scripts to figure out how to specify dependencies. Once you've created your script, you can add it to a given run level with update-rc.