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When I first installed Linux, I let it dual boot with Windows 98. I have sense removed Win98, but all of my important data (docs, mp3s, pixtures, etc) is on my VFAT drive. In windows, I would defrag it every so often, but sense removing windows from my system, this hasn't been an option.
The partition has really been slowing down and I'm sure I need to defrag it. Is there anyway to do this under Linux, without putting (POS) Win98 back on my system?
This doesn't sound like a fragmentation problem. Fragmentation occurs because files are relocated after alteration which would generally not be the case in this situation (music, pics etc). They would be only in a read mode and not read/write. Documents that you need to change frequently should be moved to /home/user and then just use the partition as an archive. I think there may be something else wrong such as the drive starting to die. Perhaps you need to get a diagnostics disk from the manufacturer and run some tests on it. If it is dying and you want/need the info then you need to get it off.
One way to "defrag" your windows drive would be to copy all the files to your linux partition, (Check that they have all been copied correctly!!), then delete all the files on your windows partition, then copy them back. But why not just copy them to a linux filesystem, and be done with it?
tredegar is right, if you don't have win, so what for a fat partition?? copy the data of this partotion elsewhere, then format it to be ext2 (or ext3 if you have a "recent" kernel) and copy your data back to that partition, you won't have to botter about defragmentation never more!!
All of the above, and -- if you still have it -- you could boot Win98 from a floppy or CD and check the fragmentation level there.
Also, does you vfat drive support SMART? If so, make sure you've turned on your BIOS SMART support, or, alternatively, run the smartd service. (I do both.) That can catch (some) hard disk problems, and at least warn you of potential (or actual) problems.