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An application server is a software framework that provides both facilities to create applications and a server environment to run them. Most application server frameworks contain a comprehensive service layer model, acting as a set of components accessible to the software developer through an API defined by the platform itself. For Web applications, these components are usually performed in the same running environment as their web server(s), and their main job is to support the construction of dynamic pages. However, many application servers target much more than just Web page generation: they implement services like clustering, fail-over, and load-balancing.
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If this doesn't work you'll need to boot off the disk and choose the upgrade option. If you've got a RAID controller you may need to download the drivers to a USB stick and then hit the F6 key to load them.
Obviously you will need to make sure you have a good backup prior to proceeding. Is this machine a VM or on physical hardware? If the latter then I would suggest you disable/uninstall any vendor specific software, e.g. NIC teaming software, HP or Dell system management software, monitoring agents, etc. Also a good idea to disable the A/V on the machine prior upgrading.
If you have SP2 installed on your current 2003 server then you'll also need to make sure the 2003 Enterprise install disk you're using has SP2 slipstreamed into it.