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I have a remote server that I can control over a remote desktop connection program. When I open a program on the server remotely (by remote desktop) and then closing the remote desktop, the opened program stopped working and it continues only when I reopen the session to the server.

What do I need to open a program on the remote server and keep it running continuous, even if I close the remote session?

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You need to make that application run as a service.

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This might help

http://support.microsoft.com/kb/251192

basically go into command line on that server

lets say I was going to make notepad.exe run as a background service

so I would do something like

SC Create npadsvc binpath="C:\windows\system32\notepad.exe" start=auto

then this would just run in the background under a system account

an alternative that I've seen done a lot in the past is just to create a generic login for the server / servers, then rather than logging off, just hit the "x" and disconnect the session, processes will continue to run under that user, I do this often when loading various snapshot images that take a long time to mount to a LUN, logon, click click, disconnect, check back later.

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