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Messed external APFS

Any ideas why the disk looks like this?

Estimations should it be just wiped of fixed?

If both works which is faster, wiping includes cloning 460GB of homers to another drive and then back?

Posted on Sep 2, 2019 3:08 AM

Reply
Question marked as Top-ranking reply

Posted on Sep 2, 2019 6:56 PM

Boot into Internet Recovery Mode using Command + Option + R and run Disk Utility First Aid again to see if it will repair the volume.


One part of the message looks like one of the APFS snapshots may have issues. It might be possible to delete the APFS snapshots using the Terminal command line utility "tmutil". I have no idea how this could affect your Time Machine backups or other backup software.


Since Apple has not released the necessary APFS documentation third party utilities cannot repair an APFS volume. So if Disk Utility cannot repair the volume, then you will need to erase it and reinstall macOS or restore it from backup.


Before attempting any repairs you should make sure everything is backed up.

7 replies
Question marked as Top-ranking reply

Sep 2, 2019 6:56 PM in response to Toke Lahti

Boot into Internet Recovery Mode using Command + Option + R and run Disk Utility First Aid again to see if it will repair the volume.


One part of the message looks like one of the APFS snapshots may have issues. It might be possible to delete the APFS snapshots using the Terminal command line utility "tmutil". I have no idea how this could affect your Time Machine backups or other backup software.


Since Apple has not released the necessary APFS documentation third party utilities cannot repair an APFS volume. So if Disk Utility cannot repair the volume, then you will need to erase it and reinstall macOS or restore it from backup.


Before attempting any repairs you should make sure everything is backed up.

Sep 2, 2019 10:03 AM in response to Toke Lahti

Interesting lines are at the end:

Performing deferred repairs

warning: found physical extent corruption but repairs are disabled

The volume /dev/rdisk5s1 appears to be OK

File system check exit code is 0

Restoring the original state found as mounted

Finished file system repair on disk5s1 SSDhomeDir


Now,

Does this mean that distil is unable to repair those few thousand errors in the disk?

Sep 3, 2019 7:58 AM in response to HWTech

I've tried Disk Utility with recovery mode and booting from another disk.

Recovery mode is worse since you can't monitor if OS is doing anything since you don't have Activity Monitor.

It gets stuck every time after few minutes and does not complete even after 30 hours.

Maybe it's buffer for diskutil's output gets full?


So diskutil works better than Disk Utility.

Just if somebody would have the insight to those lines, I'd like to know what they mean.

Of course Apple has no public documentation of those...


Tmutil does not show any local backups on that ssd.

Sep 3, 2019 7:19 PM in response to Toke Lahti

The Disk Utility log in your first post shows there are two snapshots. The first snapshot appears to have some issues:

Checking snapshot 1 of 2
[LINES 17-249:]
error: Cross Check : ExtentRef physical extent (0xXXXXXXX + XXX) has kind APFS_KIND_UPDATE but was not referenced previously
[LINES 250-2015:]
error: Cross Check : FSroot tree references extent (0xXXXXXXX + XXX) which is not present in the ExtentRef tree
[LINES 2016-7316:]
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0xXXXXXXX + XXX)



Use the following article as a guide to check for APFS snapshots and how to delete them using "tmutil". Make sure you are checking the correct drive volume when issuing the "tmutil" command.

https://derflounder.wordpress.com/2019/05/08/creating-managing-and-using-apple-file-system-snapshots-for-startup-drive-backups/


Verifying allocated space
warning: Overallocation Detected on Main device: (27277961+8) bitmap address (7cb0)
...

If Disk Utility still shows these errors even after repairs, then you will need to erase the physical drive.


I've seen several other threads on these forums mentioning how Disk Utility reports APFS issues and tells people to boot into Recovery Mode to repair them. In Recovery Mode Disk Utility First Aid doesn't find any APFS errors. It seems Apple is still working out the kinks with APFS and Disk Utility. We as regular users have no idea if these errors are real or not. The APFS errors mentioned in the other threads are not the same as what you've listed here. I believe your errors are real and should be addressed.


It gets stuck every time after few minutes and does not complete even after 30 hours.
Maybe it's buffer for diskutil's output gets full?

Your Disk Utility log in the original post actually mentions "too many warnings generated; suppressing subsequent ones" so it is entirely possible. If running Disk Utility First Aid multiple times doesn't shorten the list of errors, then I think you have no choice but to backup the files and erase the drive.

Sep 4, 2019 2:30 AM in response to HWTech

Thanks for the input,

maybe you didn't notice, that the output I posted, came from diskutil, not from Disk Utility (which gets stuck, every time).

And there's no local snapshots in the drive.


You are right, that I accidentally snipped away the notice for 2nd snapshot (the whole output is too long for this forum, 7400 lines):

...

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0xa3f98f1 + 12)

Checking snapshot 2 of 2

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x1b81a30 + 1)

...


What bugs me, is that I get same result with multiple runs.

So it seems, that nothing gets fixed, and what I'm really trying to ask, is why?

Those last lines might tell something to somebody, but not me...

Messed external APFS

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