We have attempted the repair_databases.sh script many times recently to try and resolve this. I ran it again and captured the mysqld.log again during the run as well as ran a reconfigure_nagios.sh.
160301 13:52:10 [Note] /usr/libexec/mysqld: Normal shutdown
160301 13:52:10 [Note] Event Scheduler: Purging the queue. 0 events
160301 13:52:12 InnoDB: Starting shutdown...
160301 13:52:15 InnoDB: Shutdown completed; log sequence number 0 44233
160301 13:52:15 [Note] /usr/libexec/mysqld: Shutdown complete
160301 13:52:15 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
160301 13:54:04 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
160301 13:54:04 InnoDB: Initializing buffer pool, size = 8.0M
160301 13:54:04 InnoDB: Completed initialization of buffer pool
160301 13:54:04 InnoDB: Started; log sequence number 0 44233
160301 13:54:04 [Note] Event Scheduler: Loaded 0 events
160301 13:54:04 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution
160301 13:54:05 [Note] /usr/libexec/mysqld: Normal shutdown
160301 13:54:05 [Note] Event Scheduler: Purging the queue. 0 events
160301 13:54:07 InnoDB: Starting shutdown...
160301 13:54:09 InnoDB: Shutdown completed; log sequence number 0 44233
160301 13:54:09 [Note] /usr/libexec/mysqld: Shutdown complete
160301 13:54:09 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
160301 13:54:11 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
160301 13:54:11 InnoDB: Initializing buffer pool, size = 8.0M
160301 13:54:11 InnoDB: Completed initialization of buffer pool
160301 13:54:11 InnoDB: Started; log sequence number 0 44233
160301 13:54:11 [Note] Event Scheduler: Loaded 0 events
160301 13:54:11 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution
160301 13:54:12 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:12 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:14 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:15 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:15 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
160301 13:54:15 [ERROR] /usr/libexec/mysqld: Table './nagiosxi/xi_events' is marked as crashed and should be repaired
_____________________________________________________________________________________________________________________________________________
WRITE CONFIGS SUCCESSFUL!
OUTPUT:
Nagios Core 4.1.1
Copyright (c) 2009-present Nagios Core Development Team and Community Contributors
Copyright (c) 1999-2009 Ethan Galstad
Last Modified: 08-19-2015
License: GPL
Website:
https://www.nagios.org
Reading configuration data...
Read main config file okay...
Read object config files okay...
Running pre-flight check on configuration data...
Checking objects...
Checked 2062 services.
Checked 267 hosts.
Checked 9 host groups.
Checked 3 service groups.
Checked 10 contacts.
Checked 3 contact groups.
Checked 135 commands.
Checked 17 time periods.
Checked 0 host escalations.
Checked 0 service escalations.
Checking for circular paths...
Checked 267 hosts
Checked 0 service dependencies
Checked 0 host dependencies
Checked 17 timeperiods
Checking global event handlers...
Checking obsessive compulsive processor commands...
Checking misc settings...
Total Warnings: 0
Total Errors: 0
Things look okay - No serious problems were detected during the pre-flight check
RET: 0
Running configuration check...
Stopping nagios:. done.
Starting nagios: done.