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You need a good defragger to keep your disk running smoothly. The ones that ship with Windows aren't generally that good. The one that ships with Windows 9x is - well, supply your own word. Its basic weakness is that when it starts crunching it can add to your swap file, but as soon as something gets added to your swap file, it wants to start all over again. Vicious circle. And the one that ships with Windows 2000 - a watered-down version of Diskeeper - isn't all that hot either, what we've seen. It lacks a number of important functions you need. A good guess is that the makers of Diskeeper, Executive Software, still want you to buy the full product.
When we first started using Windows NT, there was only one defragger on the market that could handle NTFS: Diskeeper from Executive Software. So there wasn't much deliberation about which product to choose. We used ExecSoft's Diskeeper Lite for quite some time.
Today we use Diskeeper 4.0 Workstation, because it can consolidate directories, something Diskeeper Lite will not do. Although we've tried Diskeeper 4.0 Server, we weren't happy with it: it kept crashing on us all the time. And we have tried O&O Defrag, RAXCO's defragger, and Norton's defragger too, and we don't like any of them. It's hard to trust a defragger, it's harder still to switch defraggers when the one you've got hasn't let you down, and these other defraggers seemed to mess up our disks more than clean them up. Some of them took eons to get nowhere at all, and for all the foibles in the Diskeeper user interface, it's still miles ahead of the pack.
We've tried Diskeeper 5.0 too, but this is a monstrous package; it insists on installing the Microsoft Management Console, and our own take is that Diskeeper 4.0 is a lot more versatile and does a lot of things well that the successor product doesn't do at all, or at the very best rather poorly.
Consolidating directories on an NTFS volume can be dicey. NTFS has security on directories, and files and sub-directories assume by default the security scheme of their parent directory. Mucking about with directories while logged on can be tricky.
Diskeeper 4.0 does its directory consolidation before you log on - right after the initial boot sequence. It pays to break up your disk into as many partitions as you can, because the time needed to consolidate is geometric in proportion to the volume's size and the number of files on it. With as many as 50,000 files on a 4GB partition, Diskeeper might need upwards of an hour to complete this phase.
It pays to consolidate often too. And although Diskeeper issues monstrous message boxes about consolidating more than one volume on any boot, we generally do it anyway, and just take an extended coffee break. The reason it's good to keep the directories consolidated is that defragging the files themselves becomes easier, and directories strewn around a volume can break up contiguous free disk space just like files do.
Things We've Noticed
Diskeeper doesn't attempt to 'optimize' a disk, only 'improve' it, meaning it is going to be a lot faster than any other defragger out there. Diskeeper has a number of algorithms which all in their own way attempt to 'improve' things. Because of this, it can sometimes be worthwhile to run a defrag successive times. You'll learn with time when this is a profitable idea or not. But because it (at least with NTFS) never attempts to pack everything at the logical start of a volume, it's going to be a lot faster than the competition.
The first time you defrag a really large disk, Diskeeper can seem to hang forever in 'Phase 2', and you might begin to wonder if everything is all right; but it is: Diskeeper simply has to go through this phase completely at least once to optimize your disk its own way. Once that's done, and provided you defrag often and regularly, it should never take so long ever again.
On install Diskeeper will put a service in your system and set it for automatic startup. Go into your services applet and change this to manual startup. The Diskeeper application will start this service itself if it has not already been started anyway, and upon completion of your defragging session you can go into your services applet and turn it off again.
Be very careful of Diskeeper when it is initializing. Don't do anything at all, don't even try to close it, until it has completely initialized and entered its idle state. Failure to do so may result in a 'thread fight' within the application, racing your CPU and locking you completely out. In general, thread management in Diskeeper is 'not that good', so avoid doing anything concurrent with it. This includes starting more than one analysis or defrag run at the same time.