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After upgrading to Sonoma I've been running out of disk space (and application memory) even tho Finder shows 300+GB free. I read about it being a common problem with too much Time Machine snapshots in the disk, but I deleted it all and still didn't free almost any space. In fact, even after recreating the snapshot the size DiskUtility shows is still not very big to explain the 300gb vanishing gigs (see img below).

Finder

enter image description here

DiskUtility

enter image description here

Some other facts (with unclear to me at present math):

  • DiskUtility shows only 25GB free, while Finder shows 300GB
  • Finder shows my Home folder with 960GB
  • OTOH du -h . at home dir gives 621GB
  • I have a 1TB SSD on a M1 Mac Mini
  • I'm sure DiskUtility is the right one because i'm having low space warnings often
  • it seems that deleting the snapshot doesn't fully show in neither totals
  • Grand Perspective shows 902GB used
  • In DiskUtility I can see a "purgeable space" that kind of matches the "black matter" I'm looking for (see above)
  • diskutil apfs list output (warning: I removed 100GB+ icloud files after posting some screen shots so I could work, free increased but "purgeable" is still the same, still ~300GB difference between DiskUtility and Finder free space):
APFS Containers (4 found)
|
+-- Container disk3 DFC7C2F9-82AF-4D43-BE11-1B7B963CAC69
|   ====================================================
|   APFS Container Reference:     disk3
|   Size (Capacity Ceiling):      994662584320 B (994.7 GB)
|   Capacity In Use By Volumes:   856211038208 B (856.2 GB) (86.1% used)
|   Capacity Not Allocated:       138451546112 B (138.5 GB) (13.9% free)
|   |
|   +-< Physical Store disk0s2 C4152987-7B2B-489C-9C0E-15D8E77A2FF5
|   |   -----------------------------------------------------------
|   |   APFS Physical Store Disk:   disk0s2
|   |   Size:                       994662584320 B (994.7 GB)
|   |
|   +-> Volume disk3s1 E09E7634-90F6-424A-AEE0-2B47E205DB98
|   |   ---------------------------------------------------
|   |   APFS Volume Disk (Role):   disk3s1 (System)
|   |   Name:                      Macintosh HD (Case-insensitive)
|   |   Mount Point:               Not Mounted
|   |   Capacity Consumed:         10122260480 B (10.1 GB)
|   |   Sealed:                    Yes
|   |   FileVault:                 Yes (Unlocked)
|   |   Encrypted:                 No
|   |   |
|   |   Snapshot:                  AADC1822-4545-48C8-82FA-0C198CB4881B
|   |   Snapshot Disk:             disk3s1s1
|   |   Snapshot Mount Point:      /
|   |   Snapshot Sealed:           Yes
|   |
|   +-> Volume disk3s2 AAC21E83-E0F5-462F-8C8B-931D11104B23
|   |   ---------------------------------------------------
|   |   APFS Volume Disk (Role):   disk3s2 (Preboot)
|   |   Name:                      Preboot (Case-insensitive)
|   |   Mount Point:               /System/Volumes/Preboot
|   |   Capacity Consumed:         6054576128 B (6.1 GB)
|   |   Sealed:                    No
|   |   FileVault:                 No
|   |
|   +-> Volume disk3s3 6225A76B-5840-489C-AB82-A9200364D387
|   |   ---------------------------------------------------
|   |   APFS Volume Disk (Role):   disk3s3 (Recovery)
|   |   Name:                      Recovery (Case-insensitive)
|   |   Mount Point:               Not Mounted
|   |   Capacity Consumed:         907165696 B (907.2 MB)
|   |   Sealed:                    No
|   |   FileVault:                 No
|   |
|   +-> Volume disk3s5 F8E3078B-F197-43C2-92E1-7E2D571BEEC3
|   |   ---------------------------------------------------
|   |   APFS Volume Disk (Role):   disk3s5 (Data)
|   |   Name:                      Data (Case-insensitive)
|   |   Mount Point:               /System/Volumes/Data
|   |   Capacity Consumed:         836679122944 B (836.7 GB)
|   |   Sealed:                    No
|   |   FileVault:                 Yes (Unlocked)
|   |
|   +-> Volume disk3s6 C08EE347-7A71-49BB-B4EB-95817CECE5BB
|       ---------------------------------------------------
|       APFS Volume Disk (Role):   disk3s6 (VM)
|       Name:                      VM (Case-insensitive)
|       Mount Point:               /System/Volumes/VM
|       Capacity Consumed:         2148384768 B (2.1 GB)
|       Sealed:                    No
|       FileVault:                 No

Another weirdness: iCloud Drive in Finder changes to "Mobile Documents" with the warning "iCloud is not syncing. There are pending items to sync." This behavior was observed after Sonoma (3 or 4 days ago).

So, what am I missing here?

PS: the suggested DaisyDisk work really well, it showed the following to me:

enter image description here

There were some purgeable stuff which were not snapshots and I could use DaisyDisk to remove it. Weird is how MacOS's didn't purge it automatically when getting the "high tide" alarm.

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1 Answer 1

Reset to default
2

In Disk Utility - you have Command 2 to show all devices. Then top to bottom, some of the "disks" are full even though I have plenty of space on the Mac. Also, with Copy on write and linked files, many tools over estimate the storage, so you can not trust Grand Perspective, du, and to some extent Finder as they will count a 1 GB file that's linked to three others with small changes as 4 GB when in reality it might only occupy 1.0000001 GB of free space on the disk.

me@m2 ~ % diskutil apfs list
APFS Containers (3 found)
|
+-- Container disk3 8B17D8A0-997A-4FFA-BCDB-86E654ADF12A
    ====================================================
    APFS Container Reference:     disk3
    Size (Capacity Ceiling):      494384795648 B (494.4 GB)
    Capacity In Use By Volumes:   343976984576 B (344.0 GB) (69.6% used)
    Capacity Not Allocated:       150407811072 B (150.4 GB) (30.4% free)
    |
    +-< Physical Store disk0s2 50C7540C-0198-4A18-A58C-85CDF759292D
    |   -----------------------------------------------------------
    |   APFS Physical Store Disk:   disk0s2
    |   Size:                       494384795648 B (494.4 GB)
    |
    +-> Volume disk3s1 8A305B86-DC98-42BE-A1BB-3A3DAA0436B5
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s1 (System)
    |   Name:                      Macintosh HD (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         10125135872 B (10.1 GB)
    |   Sealed:                    Yes
    |   FileVault:                 Yes (Unlocked)
    |   Encrypted:                 No
    |   |
    |   Snapshot:                  061D1544-37AC-4EF3-87AB-6EFDB81A5401
    |   Snapshot Disk:             disk3s1s1
    |   Snapshot Mount Point:      /
    |   Snapshot Sealed:           Yes
    |
    +-> Volume disk3s2 C37789A8-9DE5-4176-8677-609917109E6B
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s2 (Preboot)
    |   Name:                      Preboot (Case-insensitive)
    |   Mount Point:               /System/Volumes/Preboot
    |   Capacity Consumed:         6050476032 B (6.1 GB)
    |   Sealed:                    No
    |   FileVault:                 No
    |
    +-> Volume disk3s3 F5FB25A5-1DBC-41A3-B1E6-46EA0C6EFB73
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s3 (Recovery)
    |   Name:                      Recovery (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         923299840 B (923.3 MB)
    |   Sealed:                    No
    |   FileVault:                 No
    |
    +-> Volume disk3s5 86AFA8F6-A217-4F4C-B370-210E0E5EC958
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s5 (Data)
    |   Name:                      Data (Case-insensitive)
    |   Mount Point:               /System/Volumes/Data
    |   Capacity Consumed:         323434283008 B (323.4 GB)
    |   Sealed:                    No
    |   FileVault:                 Yes (Unlocked)
    |
    +-> Volume disk3s6 F495DA9D-0504-4F57-960A-967333E4D0E3
        ---------------------------------------------------
        APFS Volume Disk (Role):   disk3s6 (VM)
        Name:                      VM (Case-insensitive)
        Mount Point:               /System/Volumes/VM
        Capacity Consumed:         3221303296 B (3.2 GB)
        Sealed:                    No
        FileVault:                 No

In your case, you really have 138.7 GB totally free and some of the occupied space is purgeable (cloud backed, temporary files, etc...) when disk space grows even lower free. I believe Finder reports the free and easily purgeable in your case so 300 GB or thereabouts.

Setting aside container disk5 (your 2 TB backup) everything else looks just normal. System is not bloated, you're not so low on free space that bad things happen like bad spotlight and other "lack of space" concerns.

Here are the two items I would focus on for your situation and not the image you posted from Disk Utility:

Macintosh HD synthesized disk utility storage information

and below

Container disk3 disk utility storage information

If you need a third party tool, the only one I know that works well with the new APFS is Daisy Disk - there may be a free trial on the website and then if you purchase the version on the Mac App Store, you get a license for the direct download version automagically.

Daisy Disk - showing free + purgeable to match Finder available

I think what you seek is what I see in the image above: ~ free + purgable (333.1 GB) aligning well with what Finder shows for available in your user folder (333.07 GB)

Daisy Disk free + purgable Finder available

I think you can trust the above equivalents on your Mac as well as the system information - storage section:

macOS Storage from System Settings app

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  • 1
    so, should I disregard finder's status bar readings? well, that would solve the case, but is weird anyway right?
    – Henry Mazza
    Commented Dec 14, 2023 at 17:52
  • 1
    Not so fast, if your external backup is good - eject and physically disconnect it (if possible) and then carefully I would delete ALL the snapshots on each of container disk3 using Disk Utility and then shut down completely. Next boot to recovery and run disk utility on the disk3 items / start with the top disk (remember command + 2 - show all disks) and end up repairing the data volume last. @HenryMazza You're getting very close to the issue now.
    – bmike ♦
    Commented Dec 14, 2023 at 17:55
  • well, I must do a follow up question called "Now IT IS snapshots" because diskutility gimme 50MB free, and Finder ~200GB. Every 2 days I have to fire up Daisy Disk to erase some snapshots (using DiskUtility doesn't work afaict; says busy resource). Any idea? i can create the new question if it is going to help.
    – Henry Mazza
    Commented Jun 2 at 15:46
  • New would be my advice. Lay out the situation as an update, incorporating all the relevant items. We can always decide later to merge or close one
    – bmike ♦
    Commented Jun 2 at 18:03

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