This question is a bit outdated but I thought I’d post how I resolved this issue when it happened to me on my Mac (OS X El Capitan 10.11.4).

Check the status just to be sure

mysql.server status

ERROR! MySQL is running but PID file could not be found

Find all running mysql processes

ps aux | grep mysql

It will list out all the processes using mysql (including the command you just executed)

Kill off all the mysql pids

sudo kill <pid1> <pid2> <pid3> ...

This should kill off all the mysql processes

Now try to fire mysql up

mysql.server start

Starting MySQL

Hope this helps someone!

EDIT: Alternative solution from @DanielTate

This worked for me JasperSoft Wiki – uninstall-mysql-mac-os-x. I had to brew uninstall mysql then delete ALL of the files then reinstall and follow the home brew install instructions

EDIT 2: Alternative solution from @JanacMeena

There is a nice write-up of their solution in this post on Medium.

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