I have recently installed 5.5.28-29.2 Percona Server (GPL), Release 29.2 in a Ubuntu 12.04 OS Desktop. I have tried to stop the server using different methods:
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For those looking at this years after the fact, I had a similar issue and just solved it.
Seems there was a second init script called orig_mysql.conf that existed in the /etc/init directory along with the mysql.conf file. This caused upstart to start two instances and apparently it got confused when one was ended. As such a continuous respawning took place.
My solution:
service mysql stop
telinit u
Once you confirm you have no mysqld processes running and that they are not respawning any longer, restart mysql with service mysql start
.
Hope this helps someone. It took me two years to solve this.