Where should I place the one-time operation operation in the Django framework?
__init__.py will be called every time the app is imported. So if you're using mod_wsgi with Apache for instance with the prefork method, then every new process created is effectively 'starting' the project thus importing __init__.py. It sounds like your best method would be to create a new management command, and then cron that up to run every so often if that's an option. Either that, or run that management command before starting the server. You could write up a quick script that runs that management command and then starts the server for instance.
I want to perform some one-time operations such as to start a background thread and populate a cache every 30 minutes as initialize action when the Django server is started, so it will not block user from visiting the website. Where should I place all this code in Django?

Put them into the setting.py file does not work. It seems it will cause a circular dependency.
Put them into the __init__.py file does not work. Django server call it many times (What is the reason?)