Remote MySQL server shuts down after upcp command

WHM Server 56 on CentOS 6.7.
Remote MySQL-Server 5.5.49 on CentOS 6.7.

This is ongoing issue since WHM 56, running
/usr/local/cpanel/scripts/upcp, the remote MySQL server is receiving shutdown command and is entering normal shutdown. Once the cPanel update (upcp) is finished, the remote MySQL remains in shutdown state.

mysqld.log

Code:

160507  1:23:08 [Note] /usr/sbin/mysqld: Normal shutdown


160507  1:23:08 [Note] Event Scheduler: Purging the queue. 0 events

160507  1:23:10 [Warning] /usr/sbin/mysqld: Forcing close of thread 164473  user: 'eximstats'


160507  1:23:10 [Warning] /usr/sbin/mysqld: Forcing close of thread 164440  user: 'modsec'


160507  1:23:10 [Warning] /usr/sbin/mysqld: Forcing close of thread 162135  user: 'leechprotect'


160507  1:23:10  InnoDB: Starting shutdown...

160507  1:23:10  InnoDB: Waiting for 56 pages to be flushed

160507  1:23:11  InnoDB: Shutdown completed; log sequence number 115570048662

160507  1:23:11 [Note] /usr/sbin/mysqld: Shutdown complete



160507 01:23:11 mysqld_safe mysqld from pid file /var/lib/mysql/xxx.xxx.com.pid ended

The log timestamp matches those of cPanel upcp update.

 

MySQL profiles are being used, Auto-Migrated active profile.

/root/.my.cnf:

Code:

[client]
host="db1.xxx.xxx"
user="root"
password="xxx"