This has moved on.

Increasing innodb_force_recovery to be 3 allowed us to continue.

We were then only able to connect to the DB if we switched from socket to TCP.

mysql_upgrade completed, restarted, still can't use socket, and following error is now preventing replication from starting.

2017-09-25 13:16:03 30267 [Note] Plugin 'FEDERATED' is disabled.
2017-09-25 13:16:03 30267 [Note] InnoDB: Using atomics to ref count buffer pool pages
2017-09-25 13:16:03 30267 [Note] InnoDB: The InnoDB memory heap is disabled
2017-09-25 13:16:03 30267 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-09-25 13:16:03 30267 [Note] InnoDB: Memory barrier is not used
2017-09-25 13:16:03 30267 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-09-25 13:16:03 30267 [Note] InnoDB: Using Linux native AIO
2017-09-25 13:16:03 30267 [Note] InnoDB: Using CPU crc32 instructions
2017-09-25 13:16:03 30267 [Note] InnoDB: Initializing buffer pool, size = 24.0G
2017-09-25 13:16:03 30267 [Note] InnoDB: Completed initialization of buffer pool
2017-09-25 13:16:03 30267 [Note] InnoDB: Highest supported file format is Barracuda.
2017-09-25 13:16:04 30267 [Note] InnoDB: 128 rollback segment(s) are active.
2017-09-25 13:16:04 30267 [Note] InnoDB: Waiting for purge to start
2017-09-25 13:16:04 30267 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.37-82.2 started; log sequence number 6416161641968
2017-09-25 13:16:04 30267 [Note] Recovering after a crash using mysql-bin
2017-09-25 13:16:04 30267 [Note] Starting crash recovery...
2017-09-25 13:16:04 30267 [Note] Crash recovery finished.
2017-09-25 13:16:04 30267 [Note] RSA private key file not found: /home/mysql//private_key.pem. Some authentication plugins will not work.
2017-09-25 13:16:04 30267 [Note] RSA public key file not found: /home/mysql//public_key.pem. Some authentication plugins will not work.
2017-09-25 13:16:04 30267 [Note] Server hostname (bind-address): '*'; port: 3306
2017-09-25 13:16:04 30267 [Note] IPv6 is available.
2017-09-25 13:16:04 30267 [Note]   - '::' resolves to '::';
2017-09-25 13:16:04 30267 [Note] Server socket created on IP: '::'.
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Found an entry in the 'db' table with empty database name; Skipped
2017-09-25 13:16:04 30267 [Warning] Neither --relay-log nor --relay-log-index were used; so replication may break when this MySQL server acts as a slave and has his hostname changed!! Please use '--relay-log=h77-245-67-66-relay-bin' to avoid this problem.
2017-09-25 13:16:04 30267 [ERROR] Failed to open the relay log './mysqld-relay-bin.098231' (relay_log_pos 92593655).
2017-09-25 13:16:04 30267 [ERROR] Could not find target log file mentioned in relay log info in the index file './h77-245-67-66-relay-bin.index' during relay log initialization.
2017-09-25 13:16:04 30267 [ERROR] Failed to initialize the master info structure
2017-09-25 13:16:04 30267 [Note] Check error log for additional messages. You will not be able to start replication until the issue is resolved and the server restarted.
2017-09-25 13:16:04 30267 [Note] Event Scheduler: Loaded 0 events
2017-09-25 13:16:04 30267 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.37-82.2-log'  socket: '/home/mysql/mysql.sock'  port: 3306  Percona Server (GPL), Release 82.2, Revision d1eb51005df
[root@h77-245-67-66 log]# service mysql stop
Shutting down MySQL (Percona Server)...                    [  OK  ]

That is despite the file being present in /home/mysql, as defined in the my.cnf

[root@h77-245-67-66 mysql]# more relay-log.info
./mysqld-relay-bin.098231
92593655
mysql-bin.033015
92593509
9
[root@h77-245-67-66 mysql]# head -n 5 /etc/my.cnf
[mysqld]
datadir=/home/mysql
socket=/home/mysql/mysql.sock
user=mysql
local-infile=0
[root@h77-245-67-66 mysql]# pwd
/home/mysql


My assumption is that somehow the location is not being correctly picked up, but how can we fix this ?

Mike