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When I got my pc up and running, out of curiosity I ran a frag
analysis (Auslogics) on my E: drive. The results showed a block of
about 250Gb containing 3 files which were completely fragmented.
These were old system backups, but I didnt think they took up that
I then ran the defrag on the disk and nothing happened, the block was
not defragged although the rest of the disk was.
I deleted the folder containing these 3 files and since then, apart
from the disk not showing up in File Manager which sorted itself out
on the next reboot, I have had no problems at all.
I realise that it is only a week since I did this, so it is still
early days, but possibly these files were the root of the problem ?
I carried out Seagate and HDSentinel tests on the drive and there
were no problems found.
Defragmentation can only use the non-reserved parts of a partition.
With NTFS, there are journaling files that cannot be moved. You think
there is a big chunk of continuous free space where a file could get
moved into to defrag it. However, the file is too large and has to jump
over the journal file(s).
In the past, and to get around the unmovable journal files, I saved a
backup image, formatted the partition, and restored the image and did
the defrag. Another solution I remember reading was to open a command
shell with admin privileges and run "fsutil usn deletejournal /d c:".
That deletes the journaling, do the defrag, and reboot.
Journaling maintains a persistent log of changes on the drive. You can
delete the journal files but they get regenerated. More info at:
You would first defrag then delete the journal files and then do another
defrag. The journal files will get recreated but at different spots, so
there might be enough space between the new journal files within which
your large files will fit. However, because the files are so huge, a
couple breaks in them (i.e., more than 1 fragment) won't much affect the
time to access them. For example, you might have a huge video file but
having multiple fragments won't affect playback since all players have a
buffer to read ahead in the video file to ensure smooth playback.
The defrag didn't do anything because those files were defragmented as
best they could be using whatever layout that defrag tool prefers to
use. You didn't say which defrag tool you used, and different ones use
different layouts which compete with each other resulting in one defrag
changing the layout for a different defrag tool.
"Completely fragmented" doesn't say how many fragments were encompassed
by each of the 3 huge files. The OS doesn't have any 250GB sized file.
Even with 3 files occupying 250GB, the OS doesn't have any files sized
at 66GB. Those 3 files are data files, like backups, zip archives,
videos, ISO images, VHD files for virtual machines, and the like. Those
data files aren't involved in booting Windows. While getting rid of
them solved the problem, the problem is still lurking. You worked on
something unrelated, the computer now boots okay, but nothing you did
addressed the problem. In fact, on the next reboot after the file
deletions you said the problem remained: the drive was unseen on the
You did not mention if you have yet bothered to run chkdsk.exe with its
/r option to test the sectors on the disk. Defrag doesn't move any
files that don't have over 1 fragment or those already that fit within
the layout the defrag tool likes to use. Since the system files rarely
ever get moved to a different sector, they never get rewritten to
refresh those sectors. All magnetic media loses retentivity (i.e.,
signal strength wanes) due to dipole stress. Data isn't written
permanently into the disk but as magnetic moments on the disk. Take a
couple of magnetic sticks and put them on your desk. If the norths and
souths align then the sticks push away. If they are not aligned, the
sticks pull toward each other. Magnetic dipoles do the same on disks.
There is magnetic stress that will unalign them over time, so those bits
do not produce as high a signal strength on reading them until
eventually they are too unaligned to read reliably. Magnetic data needs
to get refreshed: data read, media erased, data rewritten. That
realigns the dipoles.
There are many tools to refresh a magnetic drive (e.g., Spinrite @ $89,
HDD Regenerator @ $100). However, as a cheap but not thorough check,
you can first use "chkdsk c: /r" as I previously mentioned to check if
each sector is reliably readable. If flaky, the data gets moved to a
pretested sector and the old sector is marked bad. That will check the
readability of the disk. It does not refresh the dipoles if the result
is okay because that means the data never got rewritten.
Most system files are never rewritten, so the magnetic media for them
never gets refreshed. The good tools that do refresh (rewrite to
realign the dipoles) cost money, enough that you need to consider
whether to buy the tool and see if it helps with reliability of the
drive or to buy a new drive. For techs, this type of software should be
in their software toolbox because it would get applied across multiple
drives hence making the software affordable per device. It's like the
plumber that buys all his tools to use for multiple jobs, not buying all
the tools needed for just one job and then doing the same for every job.
I've heard of but not used MHDD (free) but it's old (2005) and
discontinued but that doesn't mean it stopped working. I'm using 40tude
Dialog to post to Usenet and its author abandoned it back in 2005. I
have HD Sentinel but only the Standard version for monitoring the health
of the HDDs and SSDs. The Pro version ($30) can do a surface scan which
includes their "reinitialization" method (another wording for refresh).
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