Fusion disk full, freed space not becoming available.

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Fusion disk full, freed space not becoming available.

I’ve run into an issue with my 2014 iMac 5k, 1TB fusion disk (running Catalina). About three weeks ago, a modal popped up saying I’d run out of application memory and the system became unresponsive. This appeared to mean the disk was full. After cycling on an off (system appeared to hang completely while attempting a restart), I cleaned ~100GB off the disk, and thought nothing more of it.

Then on Wed last, the same message showed up again. It’s highly unlikely anything like 100GB of extra space has been used in the last three weeks. But hey ho, I more thoroughly cleaned up the disk and moved files off to an external disk, paying attention to how many files were moved / deleted. I moved in excess of 100GB of files on the external disk and deleted two old VMs ~50GB and sundry other files, for freeing up 150GB-200GB of space. I also went into disk utility and deleted a 120GB boot camp partition(*) and removed local snapshots. The system started working again, although reporting a negligible change in the amount of available space on the disk (~40GB).

Two days later, the same modal appeared again. Mail also reporting inability to read mail as there was no disk space available. I freed another ~100GB, mostly moving files to an external disk and deleting them from the main disk. No significant change in the reported available space, still at about 40GB on startup.

The next day, mail again reported inability to save new messages due to no available space.

Thinking this has gotten crazy, and there is no point trying to free more space, I made used carbon copy Cloner to clone the disk. The clone size is 659GB. That seems reasonable.

What is going on and how can I make the ‘missing’ space available?

(*) I now know I shouldn't have used disk utility to delete the bootcamp partition (It would be nice if diskutil gave you an alert, "this appears to be a bootcamp disk and may not be able to deleted correctly with disk utility. It can be removed correctly using the bootcamp assistant. Do you want to continue." Now that has happened, what can I do to reclaim that space?

Thanks in advance for any help or advice.

iMac Line (2012 and Later)

Posted on Oct 25, 2020 5:18 AM

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Answer 1

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Chris..S Author

Level 1

8 points

Oct 27, 2020 5:05 AM in response to Chris..S

The key seems to have been the invalid local snapshots which couldn't be deleted. All the space I was freeing up, would have been still in use in those snapshots, so I wasn't freeing up anything.

The advice to delete local snapshots is good, but couldn't remove the invalid snapshots.

This post describes a similar problem and provides more detail (https://apple.stackexchange.com/questions/384070/apfs-snapshot-is-invalid)

The possible solution #2, didn't fly. In recovery mode, I couldn't find any snapshots.

My solution,

clone disk
in recovery mode, diskutil resetFusion (effectively erase and recreate the fusion disk)
at this point you can choose between
1. re-install os only
2. re-install os, restore from timemachine
3. restart on clone disk, use CCC to restore fusion drive from clone disk

I chose to restore from clone. My fusion drive is now back in good shape, with the correct amount of free space.

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Answer 2

Oct 25, 2020 8:15 AM in response to Chris..S

Chris..S wrote:

I’ve run into an issue with my 2014 iMac 5k, 1TB fusion disk (running Catalina).

(*) I now know I shouldn't have used disk utility to delete the bootcamp partition

There is an issue manually deleting the Bootcamp partition— have you resolved this issue?

It may be the way forward is erasing/reformatting/initializing the parent drive(s) and restoring your user data.

Disk Utility>View>Show All Devices

https://support.apple.com/guide/disk-utility/erase-and-reformat-a-storage-device-dskutl14079/19.0/mac/10.15

Remove Windows from your Mac using Boot Camp - Apple ...

https://support.apple.com/guide/bootcamp-assistant/remove-windows-from-your-mac-using-boot-camp-bcmp59c41c31/mac

How to fix a split Fusion Drive - Apple Support

https://support.apple.com/en-us/HT207584

How to use Time Machine to... restore your Mac - Apple Support

https://support.apple.com/en-us/HT201250

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Answer 3

Chris..S Author

Level 1

8 points

Oct 25, 2020 7:51 AM in response to TonyCollinet

Recycle bin is empty. I've been emptying it frequently (and after every clean up). CCC doesn't include it in clones.

There are some local snapshots for today. 3GB worth. I've deleted all of them as part of the second and third clean ups. List attached is from CCC, as tmutil doesn't include space (it shows the same snapshot times).

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Answer 4

Oct 25, 2020 6:26 AM in response to Chris..S

You have removed stuff from the recycle bin haven't you? (I've no idea if CCC is intelligent enough not to clone this).

Do you use time machine local snapshots - or do you use time machine, but your time machine disk is not available. Try entering this from a terminal:

tmutil listlocalsnapshots /

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Answer 5

Chris..S Author

Level 1

8 points

Oct 25, 2020 8:20 AM in response to Chris..S

In addition. I deleted those snapshots and ran first aid on the fusion volume. It still finds two snapshots, the first of which has errors, lots of them. It concludes the snapshot is invalid and it looks like it decides it can't complete its checks.

Checking the Fusion data structures.
error: fusion mt: total RC blocks count (2876100) is smaller than number of blocks found in MT (2876101)
Checking volume.
Checking the APFS volume superblock.
The volume Macintosh HD - Data was formatted by hfs_convert (1412.61.1) and last modified by apfs_kext (1412.141.1).
Checking the object map.
Checking the snapshot metadata tree.
Checking the snapshot metadata.
Checking snapshot 1 of 2 (com.apple.apfs.purgatory.4d8b9f)
error: Cross Check : ExtentRef physical extent (0x4000007f68938 + 4) has kind APFS_KIND_UPDATE but was not referenced previously 
error: Cross Check : ExtentRef physical extent (0x4000007f68944 + 4) has kind APFS_KIND_UPDATE but was not referenced previously 
error: Cross Check : ExtentRef physical extent (0x4000007f68956 + 17) has kind APFS_KIND_UPDATE but was not referenced previously 

... lots of these with different ExtentRef physical extent numbers... 

error: Cross Check : ExtentRef physical extent (0x4000006369691 + 1) has kind APFS_KIND_UPDATE but was not referenced previously 
error: Cross Check : ExtentRef physical extent (0x4000006369694 + 1) has kind APFS_KIND_UPDATE but was not referenced previously 
error: (oid 0x224653) apfs_extentref: btn: invalid o_oid (0x13bf841)
error: (oid 0x224653) apfs_extentref: btn: invalid o_subtype (0xe, expected 0xf)
error: (oid 0x224653) apfs_extentref: btn: invalid o_type (0x3, expected 0x40000003)
Snapshot is invalid.
The volume /dev/disk1s2 could not be verified completely.

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Answer 6

Chris..S Author

Level 1

8 points

Oct 25, 2020 8:15 AM in response to leroydouglas

leroydouglas wrote:

It may be the way forward is erasing/reformatting/initilizing the parent drive(s) and restoring your user data.

Yes, I am coming to that conclusion.

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Fusion disk full, freed space not becoming available.

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