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Defrag With Many Holes - Normal?

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I typically use defraggler to defrag my virtual machine guest hard drives. This usually lets me have an very large expanding hdd, but, after defrag I can "Compact" the hdd to only take up the space it actually uses before archiving it. Typically I just restart+defrag and all the blue dots gets put at the beginning, and "Compact" works great (often turning 80GB vmdk files to 20GB).

However I just recently did this HDD and there are so many holes everywhere, including files put at the very end of the HDD (which doesn't do well with "Compact"):image.png.8c5d0e9ccad71ddda6ecec5663d78575.png


Note: I did a normal "Defrag" (typically all I do), and after seeing all the holes I did a "Defrag Freespace" and then a "Defrag Freespace (allow fragmentation)". The end result is above. Note at one point i had 700kB fragmented files (12 total fragments) and it still looked very similar to the above (little less red).

Is there anything I can do to make the fragmentation more optimized for virtual machine compacting (no freespace holes, everything at the beginning)? Settings or such? Everything right now is default (or is defraggler just not going to do what I want it to do in some cases?). Thanks.

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- I agree. Defraggler doesn't always behave as it should, I know what you're talking about. The most likely reason is that the program gets "entangled" in "complicated situations" with other parts of Windows and other pieces of software.

- Are there (large) differences between the two computer systems ? Like: Programs running in the background, additional Services running (did you tell DF to disable the Shadow Volume Service/VSS ?), Antivirus program running, etc.  There're differences between a normal system and a virtual machine (don't ask me what those differences are. Can anyone provide more details ??)

- Do a socalled "Clean Boot" and run the program. Are there major differences in behaviour ? (Does Defraggler run after a "Clean Boot" ?)

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I think that we are talking about the difference between defragmenting a disk and compacting (not compressing) a disk.

I came across this explanation of the 2 different processes:


Defragmenting a disk will move all the blocks that make up each file to a consecutive sequence of blocks on the disk, but will not necessarily attempt to eliminate free areas between files.
Compacting a disk will consolidate all of the free areas by moving data from later parts of the disk to unused locations in earlier parts, but may cause fragmentation of existing files.

In other words:

Defragmenting puts (or tries to) each file in one 'place' instead of it being spread about the disk, but each individual file may be anywhere on the disk with free space between them.
Compacting puts (or tries to) all files at the start of the disc, but may need to fragment some files to achieve this.

Which to use depends on what you are trying to achieve.


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  • 1 month later...

Sorry, I kinda forgot about this topic. There could of been differences with that VM... most my VM's are the "Standard"/"Basic"/"Pro" versions, this one was "Windows Ultimate", so, very likely had a bunch of services on that the other editions/vm do not have... that said all my VM's are basically the same when archiving (Fresh install of windows, windows update, defrag, compact; aka no 3rd party installs or services).

Next time I run into a problem like that I'll definitely try a clean boot+defraggler, the services could definitely of had something to do with it. Thanks.

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  • 2 months later...

Is this discussion closed?  I have the exact same issue and have tried everything to resolve it.  I think that something is wrong with the program (defraggler).  Sometimes (and quite often) it will report 0% fragmentation while at the same time display HUGE amounts of red squares, 10's of files fragmented. and megabytes affected.  I too would like to see my drive like I was use to seeing it after an old Windows defrag, (mostly all blue and very few spaces).  Why is this too unrealistic?  Defraggler don't touch some of my system files and will never touch my page file - I don't understand?

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That's a different issue to what was discussed here but fair enough.

Defraggler cannot touch any Windows system files that are in use, including the page file.
Because it can't defrag them it usually ignores them in the percentage figure.

Sometimes it will report files as fragmented but can't defrag them because Windows has started using them again or has protected them from change.

Try using the 'Boot time Defrag' option.

From the menu at the top right select Settings>Boot time Defrag>Run once.

It will ask to restart your computer and will run a defrag of the Windows/system files before Windows is loaded into memory, (which should also take care of  pagefile).

Obviously there are no fancy graphics to see, just a black screen with text, because Windows isn't loaded.

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