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ERROR 1226 (42000): User '' has exceeded the 'max_user_connections' resource (current value: 12)

How do I close all the connections ? Please advise and what is the root cause for this ?

It looks like the root cause is how you manage your db connections. Probably you open them and never close in your code.

This issue happens when I connect to my database using mysql workbench. Please let me know a permament solution to this.

This cannot keep happening when I access the remote database using local machine (mysql)

The quickest way to close all connections would be to reload your website and also to kill all processes from the tables at the bottom of the "Consoles" and "Tasks" pages inside PythonAnywhere.

Ok, but why does this issue occur when I connect to remote SSH. How can I avoid this error ?

What's happening is that something is connecting to the MySQL server and then not closing the connection. You can only make up to twelve concurrent connections to the server.

If you are using MySQL Workbench, perhaps it is the program that is doing that, so you should try closing some of the connections that you have open in it.