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I know that one of the main drawing points for ex3 and other journaling filesystems is that they do not fragment like NTFS and such.

I once heard someone say that ext3 actually would fragment when operated at near-full capacity for a length of time. Is there any truth to this? I've been running my main home ext3 partition at 95%+ capacity for at least a year and would like to know if this is actually causing any fragmentation, and if so does it clean up after itself automatically?

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I don't know the specifics, but yes, it can fragment if there is not much free space available, and no, it doesn't clean up after itself. Here is an article about how to defrag a Linux system if you are really interested, but chances are it is not affecting your system to a noticeable degree, so you don't need to worry about it.

This article was extremely helpful to me in understanding how the file system works (although it's a lot to take in at once).

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For some reason the host gives an error accessing the link above. Just shorten the URL and it works, e.g.: geekblog.oneandoneis2.org/index.php/2006/08/17 – casualcoder Nov 24 at 2:34
Thanks for noticing, I fixed it. – musicfreak Nov 24 at 4:59
According to man page, -a does nothing re: fragmentation, afaik only reports frag levels – ptor Nov 24 at 15:21
Ah, okay. Found a more legit article that shows how to defrag a Linux system using Shake. Just note that I wouldn't recommend doing this in most cases, as it's probably unnecessary. – musicfreak Nov 24 at 23:28

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