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User profile for user: pomme-homme
pomme-homme Author
User level: Level 2
443 points

Trying to figure out how to proceed and diagnose APFS problem

Today my MacPro started to reset the audio volume to minimum repeatedly,

so I tried to reset the NVRAM. After that, the computer would start up

but nothing would appear on the monitor, and in about 3-5 minutes it

would shut itself down. So I booted into Recovery and ran Disk Utility

to repair the startup disk. I received the dreaded "fs root tree is invalid" message. Because I have good CCC and Backblaze backups, I chose to re-install Mojave. I restarted and things seemed to be working OK, but I was getting a lot of spinning beachballs where they didn't used to appear. I ran Disk Utility and received this message:


Repairing file system

Volume was successfully unmounted

Can't repair volume because other APFS Volumes in its Container are mounted. Unmount them, or perform a repair while running from another macOS system (such as the Recovery System.)

Restoring the original state found as mounted.

Unable to unmount volume for repair.

Operation failed...


This is a little concerning. I am trying to decide whether this is a hardware and/or software issue and how to treat after diagnosis. I thought that re-installing Mojave would have fixed this, but it does not appear to have done so.


Thanks!




Mac Pro, macOS 10.14

Posted on Aug 12, 2020 4:30 PM

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User profile for user: DiZoE
DiZoE
User level: Level 4
2,991 points

Posted on Aug 12, 2020 10:45 PM

Hey there! Agree with HWTech, typically if the file system can’t repair itself for one reason or another, the volume or drive needs to be erased to fix. It could be hardware, a clean install, while set up as new might be a clue but you can also run Apple Diagnostics beforehand to check the hardware:


https://support.apple.com/en-us/HT202731


Are there any external hard drives connected? If so, I might disconnect them and test it out.


Also, does the same happen in safe boot?:


https://support.apple.com/en-gb/HT201262


To me it sounds like maybe the recovery partition version may be different than the corresponding OS version, as if you’re booting to recovery mode from an external disk with a different OS installed, that could cause a conflict.


Anyhow, you have everything backed up as you said, I’d probably do as said previously and erase the main drive, to remove any extra partitions, (You May have to select View > Show all devices to see it. (Just make sure the format, if High Sierra or later is going to be installed is APFS, otherwise Mac OS Extended Journaled). After that, you should be good to Reinstalll Mac OS.


If you get an error, in particular a server/network error:


Check the System date and time, so after quitting Disk Utility, hit Utilities > Terminal and type “date” and hit Return, it’s usually showing UTC time, but whatever it shows, if incorrect you can correct it using Terminal if you need to and know the procedure. Another possible way to try and correct this, (If using Internet Recovery), is you can select “Get Help Online”, make sure you’re connected to your network, and go to to AppleID.apple.com or iCloud.com and sign in while connected, that can possibly correct the date/time problem.


You should be good to reinstall afterwards!


The hardware test maybe a good first test, if that comes back positive, might save you some time! Otherwise hope all works out!

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User profile for user: DiZoE
DiZoE
User level: Level 4
2,991 points

Aug 12, 2020 10:45 PM in response to pomme-homme

Hey there! Agree with HWTech, typically if the file system can’t repair itself for one reason or another, the volume or drive needs to be erased to fix. It could be hardware, a clean install, while set up as new might be a clue but you can also run Apple Diagnostics beforehand to check the hardware:


https://support.apple.com/en-us/HT202731


Are there any external hard drives connected? If so, I might disconnect them and test it out.


Also, does the same happen in safe boot?:


https://support.apple.com/en-gb/HT201262


To me it sounds like maybe the recovery partition version may be different than the corresponding OS version, as if you’re booting to recovery mode from an external disk with a different OS installed, that could cause a conflict.


Anyhow, you have everything backed up as you said, I’d probably do as said previously and erase the main drive, to remove any extra partitions, (You May have to select View > Show all devices to see it. (Just make sure the format, if High Sierra or later is going to be installed is APFS, otherwise Mac OS Extended Journaled). After that, you should be good to Reinstalll Mac OS.


If you get an error, in particular a server/network error:


Check the System date and time, so after quitting Disk Utility, hit Utilities > Terminal and type “date” and hit Return, it’s usually showing UTC time, but whatever it shows, if incorrect you can correct it using Terminal if you need to and know the procedure. Another possible way to try and correct this, (If using Internet Recovery), is you can select “Get Help Online”, make sure you’re connected to your network, and go to to AppleID.apple.com or iCloud.com and sign in while connected, that can possibly correct the date/time problem.


You should be good to reinstall afterwards!


The hardware test maybe a good first test, if that comes back positive, might save you some time! Otherwise hope all works out!

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User profile for user: HWTech
HWTech
User level: Level 9
60,080 points

Aug 12, 2020 9:26 PM in response to pomme-homme

Did you perform a clean install by first erasing the drive? If not, then the file system was not modified by reinstalling macOS over top of itself. Personally I would recommend erasing the whole physical drive as opposed to just erasing the volume. If you have a backup, then you should be able to restore from a backup after erasing the drive.

https://support.apple.com/en-us/HT208496


Try running the Apple Diagnostics.


If the Mac is booting you can run DriveDx and EtreCheck. Post the reports here using the "Additional Text" icon which looks like a piece of paper.




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User profile for user: pomme-homme
pomme-homme Author
User level: Level 2
443 points

Aug 13, 2020 9:56 AM in response to DiZoE

Thanks! The MacPro is a mid-2010 2 x 2.4 GHz Quad-Core Intel Xeon, so I think that Apple Diagnostics won't work on a device that old. My CCC backups are, indeed, on a different hard disk that is formatted with High Sierra, so I am not sure if that will be a problem with trying to restore after reinstalling Mojave (I have a ticket out to CCC right now with that very question.) I will try disconnecting external drives and try safe booting before doing anything drastic, as things seem to be limping along for now. It is a little disconcerting that these spontaneous problems can arise without warning and cannot be addressed without a clean reinstall and recovery of backed-up data; that is going to take quite a while.

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Trying to figure out how to proceed and diagnose APFS problem

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