mysql start error on Yosemite, but sqlpro is reading a db

I have several websites, which use PHP and MySQL, these run with no problems as does SQL Pro.

However I have just written a PHP script which runs from the command line and connects to a MySQL database, but I get the following error when trying to run it:

PHP Warning:  mysqli_connect(): (HY000/2002): No such file or directory

I tried restarting MySQL (on the command line and through System Prefs), on the command line I get his error:

ERROR! The server quit without updating PID file

I think the problem is I have 2 MySQL servers installed: /usr/local/mysql/ /usr/local/mysql-5.6.24-osx10.8-x86_64/

My question is, am I correct in thinking that Apache is using one version of MySQL, but PHP on the command line is using another?

How do I find which versions are being used by Apache, MySQL Pro, PHP?

via Chebli Mohamed