This case was particularly frustrating because the my.cnf file I was using was generated by the Percona Configuration Wizard (https://tools.percona.com/wizard). The Configuration Wizard is a really great tool that takes some input from you about your server and intended use and outputs a config file for Percona. I assumed the configs generated from here would just work, but they don't.
What I figured out in the end is the /etc/init.d/mysql script uses the /etc/mysql/debian.cnf file settings to check if the mysqld server is up or not by pinging on the socket located at /var/run/mysqld/mysqld.sock the config file puts the socket by default into your data directory (on my zfs pool).
Two possible solutions, one verified, one should work in theory:
- Change the config generated from the wizzard to put the socket at the location that debian.cnf expects it. (/var/run/mysqld/mysqld.sock). This is what I ended up doing and it worked very well.
- create a symbolic link between where you socket is, and where the startup script thinks it should be. e.g. sudo ln -s /path/to/your/actual/file/mysqld.sock /var/run/mysqld . This should work in theory and the reason I didn't do it this way is I'm not sure if there is special syntax for creating a symlink to a socket, or if there were any special considerations for reboot scenarios.
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