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Files that cannot be defragmented - 80% space free hard drive

Last response: in Windows XP
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May 16, 2011 8:42:38 PM

I ran the XP's defrag GUI tool on a fairly new Dell's e6410 laptop and bellow is the result.


- Is the fragmentation acceptable or too high? I feel that the laptop is sluggish lately.
- I also ran it in a safe mode with network and the results where the same.
- If the HD's fragmentation is too high, how do I defragment it, especially the CiFile with 2,424 fragments?

Thank you!

  1. Volume Default (C:)
  2. Volume size = 149 GB
  3. Cluster size = 4 KB
  4. Used space = 27.72 GB
  5. Free space = 121 GB
  6. Percent free space = 81 %
  7.  
  8. Volume fragmentation
  9. Total fragmentation = 21 %
  10. File fragmentation = 42 %
  11. Free space fragmentation = 0 %
  12.  
  13. File fragmentation
  14. Total files = 95,440
  15. Average file size = 430 KB
  16. Total fragmented files = 6,554
  17. Total excess fragments = 29,689
  18. Average fragments per file = 1.31
  19.  
  20. Pagefile fragmentation
  21. Pagefile size = 3.42 GB
  22. Total fragments = 1
  23.  
  24. Folder fragmentation
  25. Total folders = 14,359
  26. Fragmented folders = 788
  27. Excess folder fragments = 3,738
  28.  
  29. Master File Table (MFT) fragmentation
  30. Total MFT size = 209 MB
  31. MFT record count = 110,112
  32. Percent MFT in use = 51 %
  33. Total MFT fragments = 2


  1. Fragments File Size Files that cannot be defragmented
  2. 334 48 MB \Documents and Settings\All Users\Application Data\Microsoft\Search\Data\Applications\Windows\GatherLogs\SystemIndex\SystemIndex.4.gthr
  3. 2,424 206 MB \Documents and Settings\All Users\Application Data\Microsoft\Search\Data\Applications\Windows\Projects\SystemIndex\Indexer\CiFiles\0001000A.ci
  4. 402 54 MB \Documents and Settings\All Users\Application Data\Symantec\Symantec Endpoint Protection\000009A3
  5. 706 4 MB \Documents and Settings\userxxxx\Application Data\Mozilla\Firefox\Profiles\ezac9xk8.default\places.sqlite
  6. 626 39 MB \Documents and Settings\userxxxx\Local Settings\Application Data\Microsoft\Communicator\sip_xxxx.xxxxxx@xxxxxxxxx.com\GalContacts.db
  7. 172 19 MB \Documents and Settings\userxxxx\Local Settings\Application Data\Microsoft\Communicator\sip_xxxx.xxxxxx@xxxxxxxxx.com\GalContacts.db.idx
  8. 133 233 MB \Documents and Settings\userxxxx\Local Settings\Application Data\Microsoft\Outlook\outlook.ost
  9. 117 2 MB \Documents and Settings\userxxxx\Local Settings\Temporary Internet Files\Content.IE5\index.dat
  10. 114 15 MB \Documents and Settings\userxxxx\My Documents\xxx\schemas\xxx\xx\xxx_xx_xx_xxxxx_xxx.xx.x.xx_xxxxxxxxxxxx.zip
  11. 224 112 MB \Documents and Settings\userxxxx\My Documents\xxx\schemas\xxx\xx\xxx_xxxxxxxxxxxxxxxxxxxxxxxxxxx.zip
  12. 159 71 MB \Documents and Settings\userxxxx\My Documents\xxx\schemas\xxx\xx\xxx_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.zip
  13. 113 11 MB \Documents and Settings\userxxxx\My Documents\xxx\schemas\xxx\xxx\xxx_xxx_x.x.x.x_xxxxx_xxxxxxxxxxxxxxxxxx.zip
  14. 119 7 MB \Program Files\DGAgent\dg.log
  15. 537 43 MB \Program Files\Java\jre6\lib\rt.jar
  16. 119 7 MB \Program Files\Microsoft Office Communicator\OcApi.dll
  17. 127 8 MB \Program Files\Microsoft Office\Office12\1033\WINWORD.HXS
  18. 156 10 MB \Program Files\Microsoft Office\Office12\MSACCESS.EXE
  19. 158 10 MB \WINDOWS\Installer\{26A24AE4-039D-4CA4-87B4-2F83216025FF}\sp1033.MST
  20. 365 2 MB \WINDOWS\Microsoft.NET\Framework\v4.0.30319\ngen_service.log
  21. 151 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_1034.xml
  22. 125 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_1244.xml
  23. 152 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_1844.xml
  24. 151 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_1964.xml
  25. 143 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_2143.xml
  26. 109 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_704.xml
  27. 112 9 MB \WINDOWS\PCHealth\HelpCtr\DataColl\CollectedData_854.xml
  28. 117 467 KB \WINDOWS\ntbtlog.txt
  29. 156 1 KB \WINDOWS\system32\config\software.LOG
  30. 229 1 KB \WINDOWS\system32\config\system.LOG
  31. 127 57 MB \WINDOWS\system32\wbem\Repository\FS\OBJECTS.DATA
  32.  
  33. (some file names were X-ed for privacy reasons)

Best solution

May 17, 2011 7:44:07 PM
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1. There are other reasons an old laptop will become sluggish, and not just fragmentation. NTFS is not affected by fragmentation as badly as FAT, but it is a little high and I would defrag.
2. The Windows defrag utility skips files that are in use. Some files can be defragged during boot-up by a free utility called PageDefrag.
May 18, 2011 2:56:59 AM

For a thorough defrag (even alonside other programs running) download the free trial of a good automatic commercial defragger and let it run in the background. Mine defragged completely the very first time leaving no fragmentation.
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May 18, 2011 3:15:49 AM

For a thorough defrag (even alonside other programs running) download the free trial of a good automatic commercial defragger and let it run in the background. Mine defragged completely the very first time leaving no fragmentation.
May 18, 2011 6:17:24 PM

oztom said:
I ran the XP's defrag GUI tool on a fairly new Dell's e6410 laptop and bellow is the result.


- Is the fragmentation acceptable or too high? I feel that the laptop is sluggish lately.
- I also ran it in a safe mode with network and the results where the same.
- If the HD's fragmentation is too high, how do I defragment it, especially the CiFile with 2,424 fragments?

Thank you!

  1. Volume Default (C:)
  2. Volume size = 149 GB
  3. Cluster size = 4 KB
  4. Used space = 27.72 GB
  5. Free space = 121 GB
  6. Percent free space = 81 %
  7.  
  8. Volume fragmentation
  9. Total fragmentation = 21 %
  10. File fragmentation = 42 %
  11. Free space fragmentation = 0 %



21% total fragmentation with 42% file fragmentation is high

The CiFile appears to be a system file so you will need to get a third party defragmenter that can perform a "Boot Time Defrag" as system files are not safely accessible while windows is running.

There are many third party programs available, but I would recommend using a good program from a reputable company as I have seen posts of people using a freebie that turned out to be a virus in disguise.

I agree with PhilFrisbie that there are several reasons for a PC to slow down. Here is a routine I compiled over the years addressing common issues behind computer slow-downs (including defrag solutions):

0. Ensure the Hard Disc Drive is not damaged or faulty.
Solution - Run CheckDisk:
a. Start> Computer >select C Drive>Right Click C Drive>select "Properties">"Tools" > click "Check Now"> Select both boxes and click "Start".
b. This can take a long time, so let it complete (may take all night or longer. Be patient.)

1. Ensure your PC has as much memory (RAM) as possible.
Solution -- Find out how much RAM your PC has:
a. Go to Start > Right Click "Computer" > Properties
b. This will list the processor type and speed as well as how much RAM is installed and what version of windows is running along with the Service Pack #. Write all this down as it may be needed later.
c. Go to your search engine and input your PC's name and model # followed by "memory" and see what's listed. This tells you what kind of memory you need and how many "Sticks" your PC will accept.
d. Get the maximum amount of memory your computer can hold and install it (you can search "How to install memory on a (your model name and #" to find some videos on how to do this).

2. Ensure the PC is protected.
Solution - Update existing Anti-Malware software or install if there are none.
a. Open the Anti-Virus program and ensure it is up to date.
b. Open the Anti-Spyware program and ensure it is up to date.
c. If no Anti-Virus or Anti-Spyware, get good programs.
d. If getting another AV program, remove the old one before installing the replacement one.

Note: some Antivirus programs include Anti-Spyware, so you may not need both.

3. Remove Malware from your PC
Solution - Run the Antivrus and then the Antispyware scans (can take a while if never done. Be patient):
a. Scan the whole system with the Anti-Virus;
b.Scan the whole system with the Anti-Spyware;

4. Next, ensure the Registry is clean.
Solution: Get and run a good registry cleaner.
a. Check to see if there is a registry cleaner already on the system;
b. if none, get CCleaner here: http://download.cnet.com/ccleaner/
c. Run the Registry cleaner till it finds and corrects all errors.

5. Now you can defragment the drive.
Solution - Get a good third party program that will defrag your drive and keep it defragmented.

Fragmentation is basically broken-up pieces of files and free space randomly scattered all over your disk. The disk has to work a lot harder to save files in pieces and then to find them again and this really slows your computer down. It also wears out your disk, as the more the disk is used, the faster it wears out.

Basic defragmenting finds all the pieces of a file and puts them together, saving time.

Windows has a built-in defrag tool in the accessories area under "All Programs", but it is very slow and you cannot use the PC while it is running (some users complain that it did not completely defrag their disks despite running all night).

a. Here is a Top 10 Reviews side-by-side comparison of the best defrag programs around:

http://disk-defragmenter-software-review.toptenreviews....

b. Select a program and install it. Most of the better ones offer a free trial so you can see what it will do for you before buying. Good defragmenters are automatic and the better ones defrag while you use the PC. The better programs are very fast. You will be able to see the progress and you can use the PC while these are working with no problems. The best defrag program prevents fragmentation (see the review for details).

c. Defragment your disk drives using the program of your choice.

Once this all is done, your PC will be in the best shape possible.

Good luck and let us know if you have any questions (post your questions and I'll answer then as best as I can).

Bill R TechSpec




May 18, 2011 6:55:24 PM

I did use PageDefrag but it left the HD badly fragmented.

I have had many PCs and never seen such high defragmentation after defrag has been ran.

I have 4GB on the laptop running the latests XP SP and all the patches. The slowness is not due to a lack of memory or high CPU utilization.

The laptop is protected by a corporate license of Symantec Endpoint Protection suite. Does it catch all the threats? I do not know.

The HD is highly fragmented by looking at the visual map of the HD from the defrag GUI. It got to be one of the reasons why the laptop is sluggish IMO.

I can't install any SW that is not approved/purchased by the company I work for. So I can't install the recommended SW.

Any idea how to remove the highly fragmented file?

2,424 206 MB \Documents and Settings\All Users\Application Data\Microsoft\Search\Data\Applications\Windows\Projects\SystemIndex\Indexer\CiFiles\0001000A.ci

If I call our help desk with the issue, I am sure their reaction would be: "Huh?"
May 18, 2011 7:41:00 PM

oztom said:
Any idea how to remove the highly fragmented file?

2,424 206 MB \Documents and Settings\All Users\Application Data\Microsoft\Search\Data\Applications\Windows\Projects\SystemIndex\Indexer\CiFiles\0001000A.ci

I cannot tell you how to defragment it, but I can maybe tell you how to stop accessing it and speed up your system a little. I think that file is related to the Indexing Service which monitors all file writes to maintain an index of all file contents. It makes searching files faster while slightly slowing down hard drive access always. You can effectively deactivate it by right clicking on your C: drive, unchecking the box "Allow Indexing Service....", hit apply, then on the next window make sure to apply to all subfolders and click OK. It will take several minutes to apply the change.
May 18, 2011 9:59:03 PM

oztom said:
I did use PageDefrag but it left the HD badly fragmented.

I have had many PCs and never seen such high defragmentation after defrag has been ran.

I have 4GB on the laptop running the latests XP SP and all the patches. The slowness is not due to a lack of memory or high CPU utilization.

The laptop is protected by a corporate license of Symantec Endpoint Protection suite. Does it catch all the threats? I do not know.

The HD is highly fragmented by looking at the visual map of the HD from the defrag GUI. It got to be one of the reasons why the laptop is sluggish IMO.

I can't install any SW that is not approved/purchased by the company I work for. So I can't install the recommended SW.

Any idea how to remove the highly fragmented file?

2,424 206 MB \Documents and Settings\All Users\Application Data\Microsoft\Search\Data\Applications\Windows\Projects\SystemIndex\Indexer\CiFiles\0001000A.ci

If I call our help desk with the issue, I am sure their reaction would be: "Huh?"



You really should not remove system files as it could render the machine inoperable.

If it's not your PC, I would show this thread to the powers that be and ask for an OK to download a free trial of the top placer in the above review.

In my experience, if you pester them with complaints that the machine is slow, they will usually cave-in (especisally for a free trial).

Once it has been defragmented, then you can let the trial run out or convince the company they should spring for the $40 or so to keep it.

But definitely don't remove systme files unless you thoroughly research what it does and know it will not mess up the machine.

Besides, if you can't install software, you probably don't have enough eights to remove a system file anyway.....

PS: Did you do all the other steps mentioned?
May 19, 2011 3:11:58 PM

Indexing service of the hard drive is already turned off. I have also uninstalled Windows Search. Both of these have no effect on the fragmentation.
May 19, 2011 10:23:51 PM

oztom said:
Indexing service of the hard drive is already turned off. I have also uninstalled Windows Search. Both of these have no effect on the fragmentation.

OK, that means you are no longer accessing that file, so it does not matter how fragmented it is.
May 19, 2011 10:50:02 PM

I think if the file is scatter across the HD, it causes that the HD has limited continual space to work with. There are bits and pieces of free HD space here and there with others files filling up the spaces. When the HD reads it needs to skip a lot.

The defrag GUI screen shows mostly red color. That got to kill the PC's performance.
May 24, 2011 4:50:38 PM

The issue was caused by a software that encrypts the content of the hard drive for security reasons.

Once this SW was removed, the defrag started to move all the fragmented files. Once it is over, the encryptor would have to be turn back on.

Thank you all for your help!
May 26, 2011 1:07:52 PM

Yes you fragmentation percentage is high.My PC after using Windows built in defrag utility leaves me at aprx 10%-11% fragmentation. Thats on a 250G.B. Hard Drive. I always recieve a prompt that some files could not be defragmented "see report".Then when I view the report it does no list any files that where not defragmented ,go figure? Some will disagree with me however I feel now that degrfragmenting to often can do more harm then good. I believee by using a freeware application I downladed to defrag my PC caused my boot.ini file to become corrupt and unable to boot into Windows,causing me to perform a fresh re-install of the O/S. I now have a 320G.B. externial H.D. and a complete backup of my system. I have read that fragmentation is non issuse in WindowsXP and NTFS filing system,however many will argue this point with you !
Good Luck ,NicRic
June 24, 2011 4:05:48 AM

NicRic said:
Yes you fragmentation percentage is high.My PC after using Windows built in defrag utility leaves me at aprx 10%-11% fragmentation. Thats on a 250G.B. Hard Drive. I always receive a prompt that some files could not be defragmented "see report".Then when I view the report it does no list any files that where not defragmented, go figure? Some will disagree with me however I feel now that defragmenting to often can do more harm then good. I believe by using a freeware application I downladed to defrag my PC caused my boot.ini file to become corrupt and unable to boot into Windows,causing me to perform a fresh re-install of the O/S. I now have a 320G.B. externial H.D. and a complete backup of my system. I have read that fragmentation is non issuse in WindowsXP and NTFS filing system,however many will argue this point with you !
Good Luck ,NicRic


A suggestion. Burn yourself a CD Recovery Disk or USB (many are free and typically Linux based - I use an Ubuntu "Live CD"). You will be able to copy and save the boot.ini and any other "root" files to a USB, other HD, CD, etc. You can then use the recovery disk to restore your "root" files.

As far as fragmentation, I am still searching for a utility or copy function that will copy a large file (virtual disk) that takes up over half the available free space. I have used Ultradefrag ( http://ultradefrag.sourceforge.net/ ) to consolidate all "smaller files" to the "start" of the HD, leaving a free space area larger than the "large file" to be copied. The large file always ends up being fragmented and with gaps between the fragments. This causes performance problems when the virtual disk is "used". I have also used "Defraggler" (www.piriform.com or free from http://www.filehippo.com/download_defraggler ), which will defrag individual files (assuming you have sufficient free space for the file). I have also used "MyDefrag"( http://www.mydefrag.com/ (does have hokey graphics) or http://download.cnet.com/MyDefrag/3000-18512_4-10701976... ), which can consolidate free space, although it will fragment files in doing so, requiring defragging them (Defraggler helps).

BTW, the site http://www.ntfs.com/ has good information on the MS filesystem ( http://www.ntfs.com/ntfs_optimization.htm ).
July 4, 2011 1:38:00 AM

Best answer selected by oztom.
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