Comment 3 for bug 1658067

Hi,
from the log
mysql_upgrade: Got error: 2002: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) while connecting to the MySQL server
Upgrade process encountered error and will not continue.
mysql_upgrade failed with exit status 11

That means the server did not start, and due to that later processes of the upgrade would fail - therefore it breaks here.

The error log itself doesn't hold too much on that - it seems to start shutting down right after being up:
2017-01-20T11:50:55.797820Z 0 [Note] mysqld: ready for connections.
Version: '5.7.17-0ubuntu0.16.04.1' socket: '/tmp/tmp.4JyEzHaYGM/mysqld.sock' port: 3306 (Ubuntu)
2017-01-20T11:50:55.798261Z 0 [Note] Giving 0 client threads a chance to die gracefully
2017-01-20T11:50:55.798287Z 0 [Note] Shutting down slave threads

Your config at https://launchpadlibrarian.net/303220958/MySQLConf.etc.mysql.mysql.conf.d.mysqld.cnf.txt uses the default socket path, so other than the unexpected immediate shutdown I don't see an issue.
I'd expect more a "error: Reason" anywhere, but this way I'm kind of lost.

The reason the messge shows up over and over again is that it retries every time.

I wonder if anything comes to your mind that this could be any sort of a special case to your custom setup of mysql?