MacOS – How to fix the corrupted APFS container

apfsdisk-utilityhigh sierramacosssd

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

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

Best Answer

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

Download Gdisk for mac
Install the package
Open up your terminal application
enter the command sudo gdisk /dev/disk0
Enter your administrator password

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.

Press x, hit enter
Press p, hit enter
Press o, hit enter
Press q
Copy and paste the results in your answer.
Close terminal
Go to the App store
Download Mac OS High Sierra
Get a USB stick
Go to https://support.apple.com/en-us/HT201372 and follow the instructions on the site.
Restart your mac with your newly created bootable USB of High Sierra (or corresponding OS)plugged in, while holding down the 'Alt' key.
A boot screen will appear.
Select the option "Install Mac OS High Sierra"
Once in your installation screen, go to the "Utilities" menu and select "Disk Utility"
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.
Exit Disk Utility. Reboot. Check if things are fixed. If not, continue with instructions....
Reboot with USB inserted again, and go back to "Install Mac OS High Sierra".
Once in the install screen, click the "Install Mac OS"
!IMPORTANT! - DO NOT FORMAT THE HARD DRIVE OR ITS PARTITIONS.
At the "Select the disk in which to install" screen, select your disk, but DO NOT FORMAT. Then hit the "Install" button.
Wait for the installer to finish.
Reboot.
Check and see if things are working. They should be. Done.

Related Solutions

I think I messed up the Fusion Drive on the 1TB iMac (with BootCamp)

Theoretically everything is fine with your Fusion Drive. Fusion Drives look like this. Disk0 is your SSD with 121 GB and disk1 is your HDD with ~1 TB (~1.121 TB summed up).

The larger parts of your SSD (disk0s2) and your HDD (disk1s2) are pooled to a CoreStorage LVG (Fusion Drive: disk3) with a size of 967.8 GB. The rest is reserved for EFIs, a Recovery HD (alltogether ~1.3 GB) and your old Windows partition - now probably free space (~152 GB).

The logical volume 'Macintosh HD' (967.8 GB) spans disk0s2 and disk1s2. This is the first 'Macintosh HD' in picture 1. The volume 'Macintosh HD' - it's the one visible on the desktop - should ideally also have about 967.8 GB. This is the second 'Macintosh HD' in picture 1.
In fact it has only 852.67 GB (see picture 3).

In the second picture the logical volume 'Macintosh HD' is the first listed in black, the volume 'Macintosh HD' is the second listed in black, the other two 'Macintosh HD's listed in grey are the parts of your SSD and HDD dedicated to the logical volume 'Macintosh HD'.

In my opinion something went wrong after deleting various partitions with the Bootcamp Assistant/Disk Utility or in Windows.

Preparation:

Detach any external drive (especially your external Time Machine backup drive)
Restart to Internet Recovery Mode by pressing alt cmd R at startup.
The prerequisites are the latest firmware update installed, either ethernet or WLAN (WPA/WPA2) and a router with DHCP activated.
On a 50 Mbps-line it takes about 4 min (presenting a small animated globe) to boot into a recovery netboot image which usually is loaded from an apple/akamai server.

I recommend ethernet because it's more reliable. If you are restricted to WIFI and the boot process fails, just restart your Mac until you succeed booting.

Alternatively you may start from a bootable installer thumb drive (preferably Mavericks or Yosemite) or a thumb drive containing a full system (preferably Mavericks or Yosemite).

Now you may either repair CoreStorage or rebuild your Fusion Drive:

'Repair CoreStorage' (not recommended):

First i would try to check the volume 'Macintosh HD' with Disk Utility. If the volume is corrupted consider a reinstall of Mac OS X.
If the volume is ok quit Disk Utility
Open Terminal and enter diskutil unmountDisk /dev/LVIdentifier and both diskutil unmountDisk /dev/DiskContainingApple_CoreStorageIdentifier
In your case: first diskutil unmountDisk /dev/disk3 then diskutil unmountDisk /dev/disk0 and diskutil unmountDisk /dev/disk1
remove the EFI NO NAME partition with gpt remove -i IndexNumberOfEFINoName DiskIdentifier:
gpt remove -i 4 disk1
Remount the CoreStorage disks and then the Logical Volume:
In your case: first diskutil mountDisk /dev/disk0 and diskutil mountDisk /dev/disk1 and then diskutil mount /dev/disk3.

enter gpt -r -vvv show /dev/diskIdentfierOfApple_CoreStorage to get infos of your HDD CoreStorage disk.
In your case: gpt -r -vvv show /dev/disk1
It should look like this:

-bash-3.2# gpt -r -vvv show /dev/disk1
gpt show: /dev/disk1: mediasize=1000204886016; sectorsize=512;         blocks=1953525168
gpt show: /dev/disk1: PMBR at sector 0
gpt show: /dev/disk1: Pri GPT at sector 1
gpt show: /dev/disk1: GPT partition: type=C12A7328-F81F-11D2-BA4B-00A0C93EC93B, start=40, size=409600
gpt show: /dev/disk1: GPT partition: type=53746F72-6167-11AA-AA11-00306543ECAC, start=409640, size=1671210848
gpt show: /dev/disk1: GPT partition: type=426F6F74-0000-11AA-AA11-00306543ECAC, start=1671620488, size=1269760
gpt show: /dev/disk1: Sec GPT at sector 1953525167                               
     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    1671210848      2 GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
1671620488       1269760      3 GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
1672890248     280634887
1953525135            32        Sec GPT table
1953525167             1        Sec GPT header

The free space on your HDD has 280634887 blocks. Please calculate the biggest block number dividable through 8. That's 280634880 blocks (á 512 bytes) which equals 143685058560 B or ~143.7 GB. Add the size of your HDD CoreStorage Physical Volume (852666400768 B) The result is 143685058560 B + 852666400768 B = 996351459328 B
Resize your HDD CoreStorage physical volume with diskutil cs resizeDisk HDDPVUUID newsize
In your case: diskutil cs resizeDisk 93892BE8-2B7F-4ABD-A4C3-984495DCD98D 996351459328b
Calculate the maximal size of your CoreStorage Logical Volume in diskutil cs list: (size disk0s2) + (size disk1s2) In your case that's 120988852224 B + 996351459328 B = 1117340311552 B. That should be the size of your refreshed Logical Volume Group.
Resize your Logical Volume with diskutil cs resizeVolume LVUUID LVGSize-128 MB In your case that's diskutil cs resizeVolume D237FFDC-7DA4-41D7-AC13-4CC7E5E8C0A0 1117212311552b. If you get an error (There is not enough free space...) choose a smaller size like 1117148311552b.
Quit Terminal and open Disk Utility.
Check your expanded CoreStorage Volume for errors.
Quit Disk Utility, choose your CS volume as startup disk and restart your Mac

'Rebuild Fusion Drive' (recommended if you have a Time Machine backup)

Booted to Internet Recovery Mode open Utilities → Terminal in the menubar and enter:
diskutil cs list to get the CoreStorage listing.
Copy the Logical Volume UUID, it's the fifth listed.
Now delete the Logical Volume with diskutil cs deleteVolume LVUUID.
In your case: diskutil cs deleteVolume D237FFDC-7DA4-41D7-AC13-4CC7E5E8C0A0.
Copy the Logical Volume Group UUID, it's the first listed in the listing of diskutil cs list.
Then delete the Logical Volume Group with diskutil cs delete LVGUUID.
In your case: diskutil cs delete 1EFE58BC-3613-44C4-86EE-D816F3B66E3E
Enter exit and quit 'Terminal'
Open 'Disk Utility'. Enter 'Ignore' if you are asked to fix the drives.
Choose your SSD and partition it: 1 Partition Mac OS X Extended (Journaled), hit the Options button and choose GUID Partiton table and hit OK and Apply.
Please check that the size is ~121 GB

Example:
Choose your HDD and partition it: 1 Partition Mac OS X Extended (Journaled), hit the Options button and choose GUID Partiton table and hit OK and Apply.
Please check that the size is ~1 TB

Example:
Quit Disk Utility and open Terminal
Enter diskutil list

Example (your disk identifiers and sizes are different of course: Your volume SSD probably has the Identifier disk0s2 and the size 121 GB and your volume HDD probably has the Identifier disk1s2 and the size 1.0 TB):
Enter diskutil cs create "Name" IdentifierSSD IdentifierHDD
In your case probably diskutil cs create "Macintosh HD" disk0s2 disk1s2.

Copy the resulting LVGUUID

Example:
Enter diskutil cs CreateVolume LVGUUID jhfs+ "Macintosh HD" 100%.

Example:
Enter diskutil cs list
Check the size of your Logical Volume. It should have the size ~1.121 TB

Example:
Quit Terminal
Open 'Disk Utility' and check your newly created volume for errors
Quit 'Disk Utility'
Attach your external Time Machine backup drive or check this answer if you use NAS or another network share.
Open 'Restore from Time Machine Backup'
Choose the appropriate Time Machine backup and restore your system
Reboot to your restored system.
Unmount and detach your Time Machine backup drive
Open 'Terminal' and enter 'diskutil list'
Check if your 'Recovery HD' is listed.
If your 'Recovery HD' is missing, usually reinstalling your current system with the latest available system installer (e.g. 'Install OS X Mavericks (10.9.5)' if Mavericks is currently installed) will recreate it without loosing any data. AFAIK Recovery Partition Creator 3.8 will NOT create a Recovery HD on CoreStorage volumes.
After reinstalling the system with the latest available system installer open App Store and install the latest security fixes.

MacOS – APFS partition inaccessible, container missing

Note: Posting images of the output from the Terminal application can often lead to users not posting an answer to a question. You should copy and paste the text to your question. Once pasted, highlight the text, then click on the code sample button {} to format the text.

Your current APFS partition (disk0s2) does not appear to be valid for several reasons. Below are three reasons.

The magic number stored in the header is incorrect. Also, the header defines the block size to be 2,385,839,421 bytes and the APFS container to be 2,777,634,813,198,357 TB in size. The magic number should be BSXN. The block size should be 4096 bytes and the container should be less than or equal to 883,222,061,056 bytes in size.
The APFS partition size of 1,725,043,095 logical sectors is not divisible by 8.
The APFS partition should appear either immediately and soon after the EFI partition (disk0s1). Here, the partition starts 116,773,068,800 bytes after the end of the EFI partition.

It appears that an APFS partition of 960,018,657,280 bytes in size did occur immediately after the EFI partition (disk0s1). The problem is the data stored in the APFS partition was partially overwritten by the data now stored in disk0s3. The type and location of disk0s3 would indicate that macOS Sierra may have been installed close or immediately before disk0s3. If this is true, then additional data stored in the APFS partition may have been overwritten.

Note: The partition entries stored in the GPT are not in ascending order. While this does not create problems for Ubuntu, this condition oftend leads to an incorrectly functioning macOS.

To correct the GPT, you need to remove the second and third entries. The commands are given below.

Note: You must unmount all volumes from disk0 before entering the commands given below.

sudo gpt remove -i 2 /dev/disk0
sudo gpt remove -i 3 /dev/disk0

The command below will add the APFS container to the GPT.

sudo gpt add -i 2 -b 409640 -s 1875036440 -t apfs /dev/disk0

There is no guarantee fixing the GPT will automatically lead to a correctly functioning APFS partition.

When finished, the output from sudo gpt -r show /dev/disk0 should appear as shown below.

     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  1875036440      2  GPT part - 7C3457EF-0000-11AA-AA11-00306543ECAC
1875446080    78079055         
1953525135          32         Sec GPT table
1953525167           1         Sec GPT header

Best Answer

Related Solutions

I think I messed up the Fusion Drive on the 1TB iMac (with BootCamp)

MacOS – APFS partition inaccessible, container missing

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