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I can do sudo $ service apache2 graceful and it'll do a graceful restart, but looking at /etc/init.d/apache2, the only way I can do a graceful shutdown is is running $ /usr/sbin/apache2ctl -k graceful-stop

But that results in a PID error: httpd (pid xxxxx?) not running

Obviously Ubuntu/Debian does not mean for me to run this command directly.

Basically wat I'd like to do is do a graceful shutdown (as in wait for requests to complete), perform my upgrades, and start the server again.

A: 

The command you are using should be fine. I would guess the error you see might be a watch dog function throwing an error.

apachectl -k graceful-stop

http://httpd.apache.org/docs/2.1/stopping.html

CrazyDart
and I assume you ran this as sudo right?
CrazyDart
Doh! Seems like I didn't. At least when I leave sudo I can reproduce the message, with sudo it's not showing.
Joe