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Understanding Windows Vista Disk Defragmenting Utility.
The Windows Vista Disk Defragmenting Utility is considered an improvement on its predecessor XP. The defrag engine and the manageability of fragmentation has been improved. The Disk Defragmenter runs as a low priority task in the background without affecting the performance of the computer. It runs only when the machine is idle ! It uses the Task Scheduler to automatically keep the hard disk defragmented. This automated defragmentation does not affect the performance of the Windows. What is sadly missed by most is the colorful display showing you the progress.
 
Now, by default, the defrag tool only defragments files smaller than 64 MB, for according to Microsoft’s benchmarks, fragments of this size, which already consist of at least 16000 contiguous clusters, have a negligible impact on performance. This means that games and large media files are effectively left as they are ! So if you still want to defrag files larger than 64 MB too, you need to use the -w parameter mentioned below to defragment files of all size.
The Disk Defragmenter process starts according to a schedule that you can adjust. You can view the current settings of the by clicking on All Programs > Accessories > System Tools > Disk Defragmenter Shortcut or by rt-clicking on a Drive's icon.
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Here, you can set or modify the schedule or choose to defragment "now' ! There is NO option to choose a Drive here, however.
Some Points To Remember:
Disk Defragmenter does not defragment files in the Recycle Bin. Best to run Disk Cleaner first and then empty the Recycle Bin, before defragmenting
Disk Defragmenter will also not defragment files which are in use. Best to try and shut down as many processes as possible and then defragment.
Disk Defragmenter does not defragment the following files:
Bootsect dos, Safeboot fs, Safeboot csv, Safeboot rsv, Hiberfil sys, Memory dmp and the Windows page file.
However using the -b parameter, as mentioned below, will optimize the boot files.
There are various options for you to exercise control over the defragmentation process.
To defrag a specific drive, say Drive C, type
defrag c:
at a command prompt.
You can use the following parameters or switches with the Defrag command to further fine-tune your control:

-r
This is the default setting and defragments file fragments that less than 64 MB.

-a
Analyze the selected drive / volume & display a summary report, consisting of analysis and defragmentation reports.

-c
Defragments all volumes on the computer. Don't specify a drive letter while using this.

-w
Perform FULL defragmentation of files of ALL sizes.

-f
Forced defragmentation even when there is less amount of free space on the drive being defragmented. A volume must have at least 15 % free space before Disk Defragmenter can completely defragment it.

-i
This makes Defrag run in the background & operate only if the computer is idle, like when run as a scheduled task.

-v
Displays complete reports.

-b
It optimizes boot files and applications only.

The only indication you will get is a blinking cursor. This means that the process is going. To interrupt the defragmentation process, press Ctrl + C in the command window.
If you find that you are unable to defragment or cannot run the defragment utility in Vista or that a drive or volume has been marked by Vista as having errors, run chdsk by entering
chkdsk c: /f
at any command prompt; where c is the drive letter. You will be able to then run Defrag after Chkdsk has repaired the file system.

SP1 in Vista now gives you the option to select which Drives you want to defrag

These Links may Interest You:
List of Common Errors encountered during Vista Activation.
What to do : If ChkDsk Runs On Every StartUp..
 
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