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We are on Win server 2003 and we transfer the files across the same intranet either using CuteFTP or through mapped drives. The problem here is the file transfers start fast and get slower as time progresses and has a great impact on CPU usage which in turn make the website (we do have web site running on same server) less responsive.

We are about to upgrade from Win server 2003 to 2008 and in 2008 we would like to configure the server such that I/O transfer will not have any impact on web site running. Is there any way to do that?

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Using Windows Server 2008, you can likely setup DFSR and simply replicate the data in real time. Generally speaking this will allow the data to move in the background with little or no impact assuming the connection between the two servers is fast enough to handle the traffic. If it isn't, you can schedule the replication to happen between certain hours if needed. If you are planning on running windows server 2008 r2, it will do a block level transfer so if only parts of the files are updated, it does not require the entire file to be resent. I keep over 300,000 user files synced up with almost no traffic, save when a user makes a change to something in their profile/home folders.

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