Defragment a RAID 5, 4Kb cluster size NTFS partition on Windows 2000 server

Posted on 2006-04-05
Last Modified: 2013-11-15
I am trying to find a tool to defragment RAID 5, 4Kb cluster NTFS size partitions. Windows defragger included in Windows 2000 server works on a FAT 32 partition, but if I run it on one of the NTFS partitions the following happens:
It stays fragmented:Volume (C:):
      Volume size      =      4,996 MB
      Cluster size      =      4 KB
      Used space      =      3,170 MB
      Free space      =      1,826 MB
      Percent free space      =      36 %
Volume fragmentation
      Total fragmentation      =      14 %
      File fragmentation      =      28 %
      Free space fragmentation      =      0 %
File fragmentation
      Total files      =      20,364
      Average file size      =      894 KB
      Total fragmented files      =      11
      Total excess fragments      =      144
      Average fragments per file      =      1.00
Pagefile fragmentation
      Pagefile size      =      0 bytes
      Total fragments      =      0
Directory fragmentation
      Total directories      =      1,459
      Fragmented directories      =      1
      Excess directory fragments      =      1
Master File Table (MFT) fragmentation
      Total MFT size      =      26,930 KB
      MFT record count      =      21,867
      Percent MFT in use      =      81 %
      Total MFT fragments      =      2

This is also the O/S partition. Following this incomplete job, windows defrag program requests further defragmentation, but rerun lasts 3 seconds after which partition remains in the same state, fragmented.

I know one way of defragmenting can be achieved by backup/delete/restore of data partitions but this requires to much management, especially for O/S partition.

I researched the web a bit this morning and found resizing cluster size to 64K could do the trick, albight I would loose compression functionnality. I 'm worried about implementation of solution (would I need to format partition beforehand, what effect it would have on system files, and on partition size since an 80Gig 4k cluster size partition is not equal to the same data in 64k cluster size ...). I'm also not sure if I can do it in Windows (Disk management) or would I need a 3rd party software.

The best answer would give the solution as to what program/utility could I use to defrag RAID 5, 4Kb cluster size NTFS partitions on my Windows 2000 servers, without having to change cluster size at all (Remember I tried with Windows defragger and it does not work with these parameters).

I want a for sure answer, no guesses as these are production servers.

Please help :)

Question by:pascal_p
    LVL 1

    Expert Comment

    The parameters you listed, indicate a non-fragmented volume.
    see these ones:

     --- File fragmentation
     --- --- Average fragments per file     =     1.00

     --- Volume fragmentation
     --- --- Free space fragmentation     =     0 %

    11 fragmented files you mention are most likely the OS files, which are locked/unmovable.
    You may want to try full Diskeeper at
    it may be able to consolidate those files (and directories) upon reboot.

    Alternative is O&O Defrag at

    Author Comment

    What about :

    Total fragmentation     =     14 %
    File fragmentation     =     28 %
    Directory fragmentation
    Total directories     =     1,459
    Fragmented directories     =     1
    Excess directory fragments     =     1

    And why does it keep recommending to defrag the drive given these parameters. Even if I do re-defrag, it does so for a couple of seconds, tells me its finished with the same parameters. It then still recommends to defrag once more.

    You are right about the system files as rest of report output suggests:
    Fragments       File Size       Most fragmented files
    2               56 KB           \WINNT\system32\dhcp\backup\DhcpCfg
    2               1,814 KB        \WINNT\WindowsUpdate.log
    2               425 KB          \WINNT\Debug\NtFrs_0005.log
    23              16 KB           \WINNT\system32\config\software.LOG
    3               1 KB            \WINNT\system32\config\default.LOG
    3               1 KB            \WINNT\system32\config\SECURITY.LOG
    2               117 KB          \WINNT\SoftwareDistribution\ReportingEvents.log
    2               726 KB          \WINNT\ShellIconCache
    2               249 MB          \Documents and Settings\rwebster\Local Settings\Temp\~WRF0000.tmp
    2               148 MB          \Documents and Settings\rwebster\My Documents\Localisation géni civil.doc
    2               300 KB          \Documents and Settings\pascal\NTUSER.DAT
    2               1,032 KB        \WINNT\system32\dhcp\backup\Jet\new\dhcp.mdb
    3               32 KB           \Documents and Settings\pascal\Local Settings\Temp\MMC30E.tmp

    Still doesn't explain why it keeps recommending defrags.

    LVL 1

    Expert Comment

    These files are in use and can be defragmented when the system is running. The Diskeeper will defragment these on reboot, and also seems to have somewhat better algorithms in handling free space.

    1. I would be quite happy with the current condition
    2. Overall volume fragmentation (reported at 14%) may have something to do with an uneven/unoptimal distribution of a free space, but built in defragmenter does not handle that real well.
    3. Why it reports 28% of file fragmentation, I have no idea.
    4. It probably keeps suggesting re-defrag because of that 28% readout (which seems to be in error).
    5. btw, has you tried chkdsk on that drive?

    And your options are
    1. Leave it as is
    2. Get a trial of Diskeeper (or O&O) and see if it can improve the situation.
    3. Run CHKDSK against this volume just for the case.

    I personally would do (3) and then (1).


    Author Comment

    I would have liked to put a screen print that shows the defrag box:
    Asside from the system files which are displayed in green, half of the files are in red, which means they are fragmented.
    LVL 1

    Accepted Solution

    These in green not a "system files" in a typical sense. These are MFT, pagefile (swap), hiberfil.sys (if any), possibly directories, filesystem log file, filesystem security indexes, and quota indexes. Maybe I forgot something but you get the drift - most of this stuff is not even visible via normal means.

    I checked my own machine. I have an average 1.5 fragments per file (i.e. moderate to heavy fragmentation) and the screen is, really, half red. It seems that something is wrong in the report.

    1. Run CHKDSK to check that volume.
    2. Evaluate the possibilty that filesystem permissions does not allow something to be defragmented.
    2.1. Are you the only user on the machine?
    2.2. Are you running under an administrative account?
    2.3. Is it reasonably possible that on some part of a folder tree the permissions are configured in such a way that you cannot access this?
    2.4. Check how much space is allocated for System Restore (Control Panel -- System -- System Restore -- Disk space usage). What is the upper limit, in megabytes?
    LVL 1

    Expert Comment

    Also, how came you have a system installed on a RAID5? As far as I recall, it would not allow to place a system on a RAID5 array.
    LVL 76

    Expert Comment

    It is not a question of allowed or not allowed, during the installation of the OS it sees a single "drive".  Placing the OS on a Raid 5 is often discouraged, but some do it anyway.

    You could try to boot the system into "safe mode" and perform your defrag.  There should be fewer files in use.  Or like advised by others try the other defragmenters.
    LVL 17

    Expert Comment

    LVL 8

    Expert Comment

    delete all temporary files and empty ie temp files and remove any files you don't need, empty the recycle bin.  Your actually somewhat low on disk space.  Disk defragmenters like at least 25% free space to perfrom there duties.

    defrag the drive - reboot and defrag again.

    You might want to invest in purchasing Diskeeper - it has a lot more features and boot-time services that help manage fragmentation.

    Author Comment

    Thanks to you all for your help especially to AlexGGGG who worked hard on it. I'll give you the points. You're right about the system partition on RAID 5. These servers were installed at least 3 yrs ago. Don't know what the impact will be if we get a defunct drive. We're going to replace them in the next couple of years and system files will be on mirror partition.

    As far as the defrag goes, I will get Diskkeeper because wether defragging the system partition or other data partitions on the servers, it never seems to complete the job properly. On one partition, not all data is defragged but it does not require further defrags. On another data partition, same result but it does recommend further defrags and I end up in the same situation as the system partition.

    I won't try to reboot into safe mode and defrag with Diskeeper as I'm a little worried it might damage normally active files. I have plenty of room to defrag on both servers. By the way, system restore does not apply as far as I know since we're talking about Win 2K servers.

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