ERROR 2006 (HY000) at line 1: MySQL server has gone away

This usually means that you have "incompatibilities with the current version of MySQL Server", see mysql_upgrade. I ran into this same issue and simply had to run:

mysql_upgrade --password

The documentation states that, "mysql_upgrade should be executed each time you upgrade MySQL".

Change 3 settings in my.cnf file

Under [mysqld]

max_allowed_packet = 64M
wait_timeout = 6000

Under [mysqldump]

max_allowed_packet = 64M

That should fix it