Steb-by-Step to Install Percona Server (Alternative to MySQL) on Mac OS X 10.11.6 (El Capitan)

IntallPerconaOSX.md

Install percona-server.

Install from homebrew

brew install percona-server

chown /usr/local

sudo chown -R <username> /usr/local

Initialize the DB

unset TMPDIR
mysqld --initialize --datadir=/usr/local/var/mysql --user=<username>

Start the server

mysql.server start

Change root password (Optional)

mysql will create temporary password for you and show it in the output of mysql.server start. To change it

mysqladmin -u root -p'<temp_password>' password '<new_password>'

To check whether it is working

mysql -u root -p
<Type in password>

https://dba.stackexchange.com/a/130146
I found a workaround!

Stop your db. Then start it with:
mysqld --skip-grant-tables &
And then, I could finally do my upgrade:
mysql_upgrade