How to fix my corrupted APFS container?

Question

I'm using MBP late 11 running 10.13.2 on Samsung Evo 850 250GB internally.

Everything was fine for months but few days ago something horrible occurred. I'm so shocked and urgently need your help.

Finder wasn't responding and I had to restart it by force. But it didn't boot again and just showed a black screen. Tried several times without success which finally I had to install another High Sierra on my 2nd drive (a healthy HDD)

• Here's few shots which convince me that the APFS container is damaged (SSD=disk0):

Disk0s2 - part1

Disk0s2 - part2

Container

Weird thing called Synthesized

Diskutil list

Diskutil apfs list

Diskutil repairDisk/repairVloume

• Here's few notes which probably help you know where the error lies:

▸ Note1: Used a third party app and it found 4 partitions including VM , Recovery , macSSD , Preboot. Tried to recover data from macSSD partition and fortunately almost all important data was intact and almost all files were healthy and readable/playable. That's why I think it may just be a corruption of the APFS container.

4 lost partitions found by a recovery app

▸ Note2: diskutil verifyVolume disk2

MacBook-Pro:~ rainyhighsierra$ diskutil verifyVolume disk2
Started file system verification on disk2
Verifying storage system
Performing fsck_apfs -n -x /dev/disk0s2
Checking volume
Checking the container superblock
error: object (oid 0x1): o_cksum (0x7f23daf6f220955d) is invalid for object
warning: checkpoint 247 fsck_obj_phys failed
error: object (oid 0x107): o_cksum (0xe096dd51deca9041) is invalid for object
warning: checkpoint 262 fsck_obj_phys failed
error: object (oid 0x10b): o_cksum (0x661d289dd9202cbd) is invalid for object
warning: checkpoint 266 fsck_obj_phys failed
Checking the EFI jumpstart record
error: (oid 0x2aac6) nrl: invalid o_cksum (0x8eaa1aec711175bb)
error: verification/reading of the nx_reaper object failed
The volume /dev/disk0s2 could not be verified completely
Storage system check exit code is 0
Finished file system verification on disk2

▸ Note3: Trying to add an empty volume SAM to synthesized container (disk2) to see what may happen

MacBook-Pro:~ rainyhighsierra$ diskutil ap addVolume disk2 apfs SAM
Exporting new APFS Volume "SAM" from APFS Container Reference disk2
Started APFS operation on disk2
Preparing to add APFS Volume to APFS Container disk2
Error: -69620: Unable to get capacity info for an APFS Container or APFS Volume
MacBook-Pro:~ rainyhighsierra$

▸ Note4: GPT strucure of disk0

MacBook-Pro:~ rainyhighsierra$ sudo gpt show /dev/disk0
Password:
      start       size  index  contents
          0          1         PMBR
          1          1         Pri GPT header
          2         32         Pri GPT table
         34          6      
         40     409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
     409640  487987488      2  GPT part - 7C3457EF-0000-11AA-AA11-00306543ECAC
  488397128          7      
  488397135         32         Sec GPT table
  488397167          1         Sec GPT header
MacBook-Pro:~ rainyhighsierra$

▸ Note5: I had ~3-5 GB free space on the SSD at the time of crashing

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Please help me repair the disk and take back the OS. The drive looks like healthy and repairable.

Answer 1

Your GPT Structure looks ok but just to be sure, there are a few things you can do. However, before proceeding, back up all of your data (time machine works well). Then proceed to

1. Download Gdisk for mac
2. Install the package
3. Open up your terminal application
4. enter the command sudo gdisk /dev/disk0
5. Enter your administrator password

6. A message will appear. If something is broken it should auto-repair itself and look something like this

   GPT fdisk (gdisk) version 1.0.3

   Warning: Devices opened with shared
   lock will not have their partition table automatically reloaded! The
   protective MBR's 0xEE partition is oversized! Auto-repairing.
   

7. Press x, hit enter

8. Press p, hit enter

9. Press o, hit enter

10. Press q

11. Copy and paste the results in your answer.

12. Close terminal

13. Go to the App store

14. Download Mac OS High Sierra

15. Get a USB stick

16. Go to https://support.apple.com/en-us/HT201372 and follow the instructions on the site.

17. Restart your mac with your newly created bootable USB of High Sierra (or corresponding OS)plugged in, while holding down the 'Alt' key.

18. A boot screen will appear.

19. Select the option "Install Mac OS High Sierra"

20. Once in your installation screen, go to the "Utilities" menu and select "Disk Utility"

21. Click on your hard drive and hit the "First Aid" button. Then use the first aid button/tool on each of it's partitions/containters.

22. Exit Disk Utility. Reboot. Check if things are fixed. If not, continue with instructions....

23. Reboot with USB inserted again, and go back to "Install Mac OS High Sierra".

24. Once in the install screen, click the "Install Mac OS"

25. !IMPORTANT! - DO NOT FORMAT THE HARD DRIVE OR ITS PARTITIONS.

26. At the "Select the disk in which to install" screen, select your disk, but DO NOT FORMAT. Then hit the "Install" button.

27. Wait for the installer to finish.

28. Reboot.

29. Check and see if things are working. They should be. Done.

Answer 2

Here is how I fixed some corrupted internal APFS SSD system drives for a Mac mini and macBook Pro running Ventura 13.2.

Caution: This information may or may not apply to (or resolve) your situation. Use as your own risk.

First, make sure that a reliable and complete backup has been made of the computer. I used Carbon Copy Cloner 6. However, Time Machine (and perhaps SuperDuper!) should work as alternatives.

Disk Utility "First Aid"

1. Run Disk Utility "First Aid" in a normal running configuration.

Note: This did not fix either of my cases. However, it did find and list the issues present.

Disk Utility "First Aid" in Recovery Mode

1. Boot the machine in Recovery Mode.
   • cmd-R while booting a Mac mini
   • continue holding the power button while booting a MacBook.
2. Run Disk Utility "First Aid".

Note: In my case, this resolved the issue for one machine, but not the other.

Create Bootable Full-Image Recovery Drive

Note: I found this process to work with a quality external USB-C SSD drive formatted to the APFS file system.

1. Make an image backup of the system to an external APFS USB-C SSD drive. (Carbon Copy Cloner)
2. Make the back drive bootable by running the official Apple Venture installer on the image backup just created. (Look for "Ventura macOS" in the App Store.)
   • Choose the type of system install which leaved the users, data, and applications in place.
   • Run Disk Utilities "First Aid" on the external drive to verify that the drive has no issues.
3. Boot the machine in Recovery Mode. Enable the computer to boot from an external drive by changing the Security Settings which are available while in the recovery mode.
4. Boot the machine with the external bootable recovery drive (just created in steps 1 and 2) as the startup disk.

Note: If the hardware is found to required repairs or replacement, then this bootable, full-image, up-to-date, external SSD drive could be used as a system boot drive until the hardware issues are resolved. … in which case, make sure to have another separate backup of the system.

Restore from Bootable Recovery Drive

Note: I had a full image backup separate from this recovery drive to allow for alternate approaches in the event the following steps did not work as expected.

1. Boot the machine with the bootable, verified, external recovery drive.
2. fully erase the internal machine SSD with APFS format.
3. verify the internal SSD has no issues with the Disk Utilities "First Aid"
   • If the freshly, fully formatting the internal SSD drive still has issues, then new hardware be needed.
4. restore the internal drive from the recovery drive
5. install macOS Ventura with the official Apple macOS installer
6. again verify the internal SSD has no issues with the Disk Utilities "First Aid"
7. change the startup disk to the internal drive and reboot.
8. After booting with the internal drive, unmount the recovery drive and run Disk Utilities "First Aid" for a final check.

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Notes:

• While backup software like CCC may make a copy of the system files, the Apple macOS system official installer is required to perform a number of security and proprietary operations to make the disk bootable.
• The above process should also work with some external boot drive and a separate Time Machine drive. This approach would use a system clean install and the Migration Assistant to restore users and data. (… per instructions but not what I actually did.)
• Another option should be to (1) erase the internal drive while Recovery Mode, (2) install macOS over the internet which still in Recovery Mode, and (3) restore from a Time Machine-compatible backup. (… also per instructions but not what I actually did.)

Resources:

Apple Support

• Disk Volumes
  • Add, delete or erase APFS volumes in Disk Utility on Mac ⇗
  • Partition a physical disk in Disk Utility on Mac ⇗
• How to repair a Mac disk with Disk Utility ⇗
• How to reinstall macOS ⇗ … via recovery mode and an internet connection.
• Use macOS Recovery on a Mac with Apple silicon ⇗

Carbon Copy Cloner

• Creating legacy bootable copies of macOS (Big Sur and later)
• How to restore from your backup
• Identifying and Troubleshooting Hardware-Related Problems