APFS, fsck_apfs and 'physical extent corruption' - what's up with my MacBook Pro?

Hi All

I believe the problem is due to corrupt local timemachine snapshots (when timemachine can't backup to the storage device - example when its not present, it creates a snapshot). I had the same problem and manual remove all snapshots using the following command.

Launch the Terminal (from Applications > Utilities), and then copy and paste this command and press Return:

tmutil listlocalsnapshots /

The Terminal will show a list of local snapshots with names like com.apple.TimeMachine.2018-03-01-002010. To remove a snapshot:

1. Copy and paste this command: sudo tmutil deletelocalsnapshots
2. Type a space and then paste in the date portion of the snapshot.
3. Press Return, and finally press Return.

Altogether, using the example snapshot above, that looks like:

sudo tmutil deletelocalsnapshots 2018-03-01-002010

If it deletes properly, you’ll see Delete local snapshot '2018-03-01-002010' in the Terminal as the response.

Run FirstAid again, this should produce a better report with no snapshot errors.

Catchyou

I had a similar problem a few days ago. Three month old Mac Mini 2014 (1TB hard drive) with 10.14.4 upgrade a week earlier. All was well. But I powered it on in the morning and it would panic and restart. I was able to boot in Safe Mode but even then it would panic after a while. More disk error output than yours but same stuff, particularly the contradictory "...repairs disabled..." output at the end. I could not repair the disk errors in Recovery mode.

I spoke with Apple support several times and we first tried an OS reinstall, which did not help. Ultimately, at their suggestion, I had to erase the main drive and reinstall the OS. (In this case a recent backup is your savior.) I summarized the events with Apple support but they had no worthwhile insight.

Computer has been running fine for the last few days. I run First Aid twice a day with no errors reported. But I sit here, presumably like you, wondering what happened. Was it a disk error that will reoccur? Was it caused by some app failure, Apple or third-party? Needless to say, I do my Time Machine and CCC backups more frequently now and hope that the problem is behind me.

Well I spoke too soon I guess. I just ran First Aid and got this output:

Running First Aid on “Macintosh HD” (disk1s1)

NOTE: First Aid will temporarily lock the startup volume.

Verifying file system.

Volume could not be unmounted.

Using live mode.

Performing fsck_apfs -n -l -x /dev/rdisk1s1

Checking the container superblock.

Checking the EFI jumpstart record.

Checking the space manager.

Checking the space manager free queue trees.

Checking the object map.

Checking volume.

Checking the APFS volume superblock.

The volume Macintosh HD was formatted by diskmanagementd (945.250.134) and last modified by apfs_kext (945.250.134).

Checking the object map.

Checking the snapshot metadata tree.

Checking the snapshot metadata.

Checking snapshot 1 of 1.

error: Cross Check : ExtentRef physical extent (0x2cba70 + 2) has kind APFS_KIND_UPDATE but was not referenced previously

error: Cross Check : ExtentRef physical extent (0x2cba73 + 3) has kind APFS_KIND_UPDATE but was not referenced previously

error: Cross Check : FSroot tree references extent (0x2cba70 + 1) which is not present in the ExtentRef tree

error: Cross Check : FSroot tree references extent (0x2cba71 + 1) which is not present in the ExtentRef tree

error: Cross Check : FSroot tree references extent (0x2cba73 + 3) which is not present in the ExtentRef tree

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba70 + 1)

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba71 + 1)

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba73 + 3)

Checking the extent ref tree.

Checking the fsroot tree.

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba70 + 1)

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba71 + 1)

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x2cba73 + 3)

Verifying allocated space.

Performing deferred repairs.

warning: found physical extent corruption but repairs are disabled

The volume /dev/rdisk1s1 appears to be OK.

File system check exit code is 0.

Restoring the original state found as mounted.

Operation successful.

I restarted the computer in normal mode, ran First Aid again and got no errors:

Running First Aid on “Macintosh HD” (disk1s1)

NOTE: First Aid will temporarily lock the startup volume.

Verifying file system.

Volume could not be unmounted.

Using live mode.

Performing fsck_apfs -n -l -x /dev/rdisk1s1

Checking the container superblock.

Checking the EFI jumpstart record.

Checking the space manager.

Checking the space manager free queue trees.

Checking the object map.

Checking volume.

Checking the APFS volume superblock.

File system check exit code is 0.

Restoring the original state found as mounted.

Operation successful.

So I am also hoping someone can help diagnose this problem.

G.C.Thompson wrote:

To try and fix the issue I ran Internet Recovery and ran First Aid from there, and while the issues were found, fsck_apfs is reporting "warning: found physical extent corruption but repairs are disabled". It then reports "The volume /dev/rdisk2s1 appears to be OK," which sounds like a contradiction.

Performing deferred repairs.

warning: found physical extent corruption but repairs are disabled

The volume /dev/rdisk2s1 appears to be OK.

File system check exit code is 0.

Restoring the original state found as mounted.

Operation successful.

Have you run Disk Utility from your Macintosh HD— and let it run

Is there still an issue?

The disk errors I reported are permanent now - they do not go away after a restart. I clearly don't understand why they briefly went away after the first restart. I am not having restart panics - yet. I fear I will soon however.

Well now, isn't that a helpful response. The format of the disk drive in this case is clearly relevant and a potential alternate format would be a possible workaround. Regardless, may I suggest a more appropriate response if you disagree:

"No, the only main drive format used in Mojave is APFS. If you want to discuss the various disk formats used in Mojave I recommend you start a new thread."

You certainly know the answer to the question. Ridiculous.

Hi Nick,

When I ran the command tmutil listlocalsnapshots / I received NO list of local snapshots. I then entered Time Machine and there were ZERO backups to restore from. Not sure how, I've NOT manually disabled the snapshot time machine on this system. Do I need to run the listed command in Safe or Recovery mode?

Thanks,

John

Hi John

I believe local timemachine snapshots only happen on apfs file system and only if disk space permits. please check what file system you formatted you hard disk with and space free. I also have a system format with apple_hfs extended journal and the command tmutil listlocalsnapshots / list nothing.

Thats why this threads is about "Q:APFS, fsck_apfs and 'physical extent corruption'" when you run disk firstaid. do you have a corrupt harddisk, reporting this error?.

Catchyou

Nick

Hi! I have same problem with MacBook Pro 13, 2017. (Mojave) Whenever I run FirstAid I get a lot of errors like:

error: Cross Check : Mismatch between extentref entry reference count (1) and calculated fsroot entry reference count (0) for extent (0x2e620f + 2)

and

warning: found physical extent corruption but repairs are disabled

I deleted all local snapshots but still get same errors. This part "0x2e620f + 2 " of error message is always different. Like in next error message number will be 0x2e621f + 2 and etc.

Please help

GeezerFella wrote:

Operation successful.

So I am also hoping someone can help diagnose this problem.

Hard to diagnosis a successful operation.

Does anyone know if I can format my main hard drive in Mac OS Extended (Journaled) instead of APFS?

Mac Mini SATA 1TB

macOS Mojave 10.14.4

Thanks.

GeezerFella wrote:

Does anyone know if I can format my main hard drive in Mac OS Extended (Journaled) instead of APFS?

You need to start your own thread instead of hijacking this one.