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I have published few map services in which I directly publish on server and for remaining services I have created service definition file.

All services are working fine but what exactly difference between "Publish a service" and "Save the service definition file" ? . In case "Publish a service " it also analyze the data and gives the warning message..

In case "Save the service definition file" we know the location of .sd file but in other case we do not.. so which one is best and why OR recommended ?

Software : ArcGIS Server 10.1 and Desktop 10.1

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Generally, you "Save a service definition file' when you can't publish directly to Arcgis Server, or when you want to publish the service at a later time.

The .sd file is a standalone file that stores the information about the service that you enter in the dialog when you publish a service.

When publishing, .sd files are staged in "C:\Users\\AppData\Local\ESRI\Desktop10.1\Staging" by default. They are deleted after the service is published. This is the default location .sd and .sdraft files are saved as well.

In your case it sounds like you generally publish right to the server, you probably don't need to use .sd files.

About Service Definition Files - from ESRI resource centre.

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