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I also faced the same error, i have changed the connection variable as mentioed below:

originally it was under [database] name space with connection as config variable name:

[database]

connection = mysql://heat:<password>@<controller>/heat

I changed it to [DEFAULT] space and variable to sql_connection.

[DEFAULT]

sql_connection=mysql://heat:<password>@<controller>/heat.

not sure it is the root cause but it solved my problem.

my env was centos6.4 and openstack Havana release.

let me know if it helps you as well