APFS Snapshot metadata tree "Unable to mark physical extent range allocated for space verification"

Question

APFS Snapshot metadata tree "Unable to mark physical extent range allocated for space verification"

Hi all,

I seem to be experiencing issues similar, but not identical, to those discussed here:

https://discussions.apple.com/thread/8564919

https://discussions.apple.com/thread/8092082

My MBP Retina (2014, 15", hybrid graphics) is running insanely hot. The fans are permanently on. Checking Activity Monitor shows that kernel_task is consuming 100% CPU perpetually. Opening Console, I see an eternally scrolling list of error messages from the kernel about allocating space.

I ran Disk Utility First Aid on the disk, but it failed abysmally:

First Aid output

Searching for the error message led me to the two threads listed above, however I folllowed the instructions but didn't find any Time Machine local snapshots, dataless or otherwise, on my disk - the tmutil command gave no output. As such, the fix that worked for others isn't relevant to me.

The machine has the original Apple SSD installed. I last ran a Time Machine backup about 2 weeks ago, but my NAS isn't working very well. The machine's full spec, if relevant, is: i7 2.5GHz, 16GB RAM, 256GB PCIe SSD, hybrid Geforce GTX 750, running 10.13.6. It was originally installed with Sierra, then upgraded to High Sierra. I cannot upgrade to Mojave due to the current fuss with nVidia drivers.

I have a second Mac available, as well as a Thunderbolt cable to use Target Disk Mode. I am also extremely at home behind a bash prompt (Linux sysadmin by trade) so not afraid to get my hands dirty.

Can this machine be rescued, or is my only option to wipe it and reinstall? If the latter, is there any way to stop this happening again?

MacBook Pro Retina

Posted on Jan 5, 2019 7:16 AM

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Answer 1

BDAqua

Level 10

250,259 points

Jan 5, 2019 11:26 AM in response to mypublicselfdestruction

How much free space is on the SSD?

https://discussions.apple.com/thread/8094732?answerId=32667743022#32667743022

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Answer 2

BDAqua

Level 10

250,259 points

Jan 5, 2019 12:56 PM in response to mypublicselfdestruction

Yeah, I suspect you need far more space for DU to complete, it doesn't look like DU is really finding errors, but erring in having space to do it's checks, what does Memory in Activity Monitor show when running DU?

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Answer 3

Jan 6, 2019 2:07 PM in response to mypublicselfdestruction

On the suggestion of a friend, I fired up an Ubuntu live USB stick and ran some SMART tests on the SSD. All of them reported no problems. So I'm hoping this is not the disk itself failing, but is purely the filesystem on it.

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Answer 4

Jan 5, 2019 11:39 AM in response to BDAqua

There was about 10GB free on the disk when the issues started. The disk space has been going up and down by itself like a yoyo ever since - as of the last time I had the machine powered on earlier, it was about 4.6GB free. I think I'm seeing the symptom of deleted space not being freed as mentioned in the other threads.

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Answer 5

Jan 6, 2019 1:31 PM in response to BDAqua

Okay, so, I did all this from the second Mac with the broken one in Target Disk Mode.

I nuked my Steam library, which totals about 90GB, since I can at least re-download it if everything goes right. However `df -h` only showed around 30GB free afterwards. Something is really broken on this disk.

I then re-ran `fsck_apfs -y /dev/rdisk3s1` from the command line, since it kept crashing Disk Utility. This is the result:

fsck

I'm guessing the disk is unrecoverable at this point?

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Answer 6

Jan 6, 2019 2:32 PM in response to BDAqua

I've noticed. Although this is Apple in a nutshell, I can't help but wonder why they built an entirely new filesystem, one of the core things that has to be tested to destruction and back in every possible way, and release it together with the OS, versus adaopting, say, an open-source filesystem with the necessary features. The latter will have considerably more support tools and testing.

Rolling APFS straight out as the default filesystem, considering the beta version in Sierra is not compatible with the 'production' version in High Sierra, doesn't sit comfortably with me.

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