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What is the best practice when defragmenting an MS application server?

What is the best practice when defragmenting an Exchange, SQL or other Microsoft application server?
Usually, a server application will lock the files it uses. For example, Exchange locks its database files and SQL Server locks its databases. The system has no exclusive access rights to these files and therefore cannot perform an online defragmentation.

To defrag these types of files, you must perform an offline defragmentation. Several defraggers offers options like "Boot-time defragmentation" to defrag certain files during the system startup. During this phase of the boot process no other application can access the files and, therefore, it is then safe to defrag them.

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