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There are two scenarios of how SQL Compliance Manager can work with AlwaysOn availability group databases:

• Listener. Use this scenario when you want to audit a listener (virtual SQL server instance) that works only with a node in the PRIMARY role.
• Nodes. Use this scenario when you want to audit every node that can be in PRIMARY or SECONDARY roles. Note that the secondary role is read-only.

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Review the following links to configure AlwaysOn Availability Groups:

Configuring Listener scenarioListener scenario:

1. Install cluster agent services on all Listener nodes using the SQL Compliance Manager Cluster Configuration Console
2. Install cluster agent services on all Listener nodes using the Failover Cluster Manager
3. Add the Listener to SQL Compliance Manager 

Configuring Nodes scenario: 

• Manually deploy the SQL Compliance Manager Agent

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