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I wrote code like below. It works when I publish it as cloudapp.net, but throw SEHException when I publish it as azurewebsites.net.

String val = RoleEnvironment.GetConfigurationSettingValue("myconfig");

So what's the difference between these 2 domains/publish approaches?

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You need to deploy your application as a Web Site rather than a cloud service. So the RoleEnvironment.IsAvailable = False as expected, which means the application is actually not running with Azure runtime.