Battle of the Disk Utilities (Multi-Boot APFS Internal SSD)

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Level 1

41 points

Battle of the Disk Utilities (Multi-Boot APFS Internal SSD)

Hello all,

I recently upgraded an internal Fusion drive to a 2TB SSD in a 2017 iMac. The fusion drive contained three volumes/partitions: HFS+ (High Sierra/32-bit app support), Catalina (APFS) and Ventura (APFS sub-container).

I used Carbon Copy Cloner for High Sierra and Catalina but decided to skip the Ventura APFS container because I intend to upgrade Catalina and no longer want a third macOS.

First thing I notice after booting my upgraded iMac up, is that a 28GB partition showed up on the SSD. It appeared as a third choice when holding down "option" at startup, but upon selecting it the boot did not complete. Then, upon running Disk Utility, it didn't even *see* this partition. After a lot of hunting around to figure out how to "reveal" the partition using Terminal, I can now erase or re-partition the 28GB in Disk Utility — but am unable to delete it. I tried a force-removal in Terminal, multiple boots into Safe Mode, running Disk Utility in Recovery, reinstalling macOS on the bootable partitions — and still I can't get rid of this 28GB partition and return the free space to the remaining volumes.

As part of the troubleshooting, I noted that despite booting successfully with no apparent issue into High Sierra and Catalina, Disk Utility throws all kinds of errors. It ranges from the apparently common issue of drives refusing to dismount so that First Aid can execute repairs to reporting that one of the volumes (Disk3s1) is corrupt.

In booting from an external USB key containing various macOS installers, and launching Disk Utility from there, I was able to delete faulty Time Machine snapshots, and that got rid of the scariest message about my High Sierra volume being corrupt. (I was on the verge of wiping the drive because that sort of message from Disk Utility tends to mean there is no fix. Fortunately, there was.)

Unfortunately, there's more: When I "view all" in Disk Utility (Ventura edition) to test the parent SSD while booted from a thumb drive, it reports errors on the parent volume but when I run other versions of Disk Utility, it does not. Conversely, when I run Ventura's version of Disk Utility on the individual APFS containers, there are no warnings/errors but when I use earlier versions of Disk Utility there are so many warnings on Disk3 (High Sierra container) that Disk Utility reports that it has suppressed the duplicating error entries.

Depending on the version of Disk Utility, I get results that are all over the map, ranging from nothing found to orphaned files, warnings about invalid files (inode_val: object…), dstream, unable to verify the drive completely, references to suppressed warnings, etc. — only for Disk Utility to report that my volumes are "OK".

I then decided to boot into Single User Mode, only to find that fsck_apfs -y can't be run in Single User Mode (unable to dismount the volume). However, I did find in Single User Mode a repeating entry called "sanity check" that reports an "fs_alloc_count mismatch" at the root nodes. (Caveat being, I can't be sure if that's a valid error, either, because it's not running off a fully dismounted SSD.)

My last ditch effort was to search for an alternative to Disk Utility. I ended up buying an app called DriveDX. It reports that the drive health is good, with no errors of any kind. (Back in the day, I would have turned to the likes of TechTool Pro or DiskWarrior but apparently Apple never released the full APFS documentation so competitors to Disk Utility are unable to rebuild APFS volumes. Consequently, I am unaware of any third-party software that overcomes these limitations.)

The original Fusion drive was itself new and had no Disk Utility errors before cloning. (I say "new" because this 2017 iMac was purchased off of an auction site still new in a sealed Apple box less than two months ago, probably one of the last 2017s on the planet with no mileage on it. My only reason for upgrading was to get a larger internal drive. Ugh.)

In the end, I suspect this ties into the fact that I failed to exactly duplicate the original fusion drive. Although I can't be sure why I ended up with a persistent 28GB partition that I can't delete, I suspect the presence of allocation mismatches reported in Single User mode may explain some (if not all) of this.

Q: Since the latest version of Disk Utility available to me (Ventura) doesn't find a problem with the bootable containers, should I worry about the fact that other versions of Disk Utility report numerous "warnings"?

iMac 27″ 5K

Posted on Oct 11, 2023 8:31 PM

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Answer 1

Top-ranking reply

HWTech

Level 9

60,380 points

Oct 12, 2023 8:19 AM in response to NewsView

The 28GB SSD partition is actually the SSD part of the original Fusion Drive as mentioned by @MartinR and you cannot delete it since it is a physical drive unless you physically remove that SSD from the Mac which would be a major undertaking since it requires removing every internal component in order to pull the Logic Board out (SSD is mounted on the back of the Logic Board) so this is not recommended.

Otherwise you can prevent the 28GB SSD from mounting automatically during boot which requires using the command line to add an entry to "fstab". You would still see the physical SSD within Disk Utility. I wrote instructions in this other post on how to create such an entry (ignore the first line in that post since it does not apply to you):

Can't rename internal hd - Apple Community

FYI, DriveDx is completely different than Disk Utility or Disk Warrior. Disk Utility & Disk Warrior are utilities which can scan & repair the file system while DriveDx accesses & tries to analyze the drive's physical health. Neither Disk Utility or Disk Warrior analyzes the drive's physical health (at least not in any meaningful way). Unfortunately drive health monitoring apps like DriveDx don't accurately summarize the health of an SSD (hard drives yes), but are only useful to be alerted to a change in the SSD's health which requires human examination & interpretation to determine if the change is something to worry about. Most SSD failures will never show up in the health report because it is the SSD's controller which typically fails which has no health monitoring available.

Alsoft is currently working on adding APFS support for Disk Warrior, but I would expect it will be a while before it will be available.

Also, you should only use the same or newer version of Disk Utility when repairing the file system since newer versions of macOS may have made changes to the file system which older versions of Disk Utility won't be aware of and could possibly damage the file system if repairs are performed. Also, just run First Aid on the hidden Container since First Aid will scan each of the APFS volumes within it plus it will scan the container itself which may not occur when running First Aid on individual volumes. It also means you only have to run First Aid one time on one single item instead of manually selecting & scanning individual volumes.

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Answer 2

Oct 11, 2023 8:52 PM in response to NewsView

Personally, I believe you've created this problem by using multiple volume formats on a single SSD. While it's obvious that yes, technically you can do this, I believe it just invites trouble of the sort that you're experiencing now and possibly worse. I suggest you reconsider this configuration.

It would be best to use a separate bootable external drive for the legacy 32-bit macOS High Sierra with its HFS+ format. I assume this would not be your daily driver, so to speak, so you would only plug it it for use when you felt the need to use that vintage OS.

Finally, erase and reformat the internal SSD using APFS. This will reintegrate all of the available drive space, eliminate any format conflict and allow you to move forward with installation and use of macOS Ventura without the need to worry about what multiple disk utilities have to report.

I'm a firm believer in the KISS principle... keep it simple.

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Answer 3

NewsView Author

Level 1

41 points

Oct 11, 2023 9:38 PM in response to D.I. Johnson

I posted here not because I think there is a solution for everything I have documented — maybe if I'm lucky a suggestion for how to get rid of the 28GB partition? — but because users deserve to know that Disk Utility behavior may differ depending on which version is running, and that in some cases (i.e. bad Time Machine snapshots), Disk Utility will suggest the drive is corrupt, causing the appearance of a hardware problem (and all the related time/expense) when, in fact, it's a fixable problem.

Coming from an even older 2009 iMac, I made the mistake with the 2017 (didn't want the T2 security chip or the 32-bit macOS limitations) of failing to appreciate that the fusion drive was smaller than my old SATA drive. I got everything set up with fresh installs (partitioned and working for over a month even though HFS/APFS were sharing space on the same internal drive) only to realize I needed to upgrade the fusion drive in order to bring over the rest of my files from the older iMac via Time Machine.

In this case, even the 28GB partition and the High Sierra install are APFS (no longer HFS+ after doing a High Sierra reinstall as part of this troubleshooting process). I have a large format photo printer, flatbed scanner and the aforementioned Adobe software tied up in my "vintage" system, with Correl Draw 2021 on the second partition. In fact, I only need a current macOS for security purposes (i.e. web browsing).

The problem seems to be A) It's a clone consisting of only two out of three of the original bootable volumes, B) it's APFS and by all accounts APFS is difficult for Disk Utility to repair even when it is a stand-alone (single volume) install.

I have been using Macs, exclusively, since the early 1990s. In my opinion, if I was able to run a multi-boot setup and successfully execute First Aid in HFS for years on end — one learns the value of a partitioned drive upon realizing that Apple's annual macOS updates can unexpectedly break stuff! — the same multi-boot setup should be possible in APFS — but APFS isn't there yet.

Disk Utility is clearly struggling to deal with APFS, which tells me that APFS is flawed — so much so that Apple still hasn't released the full developer documentation years after the fact. This has left consumers without alternatives such as TechTool Pro and DiskWarrior, the latter of which was the king of third-party disk utilities for over two decades.

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Answer 4

NewsView Author

Level 1

41 points

Oct 12, 2023 12:53 AM in response to NewsView

Anybody care to take a crack at the actual question?

Q: Since the latest version of Disk Utility available to me (Ventura) doesn't find a problem with the bootable containers, should I worry about the fact that other versions of Disk Utility report numerous "warnings"?

BTW, I shouldn't have to state this but… Please refrain from slamming the OP for setting up a partitioned system in the first place. If Apple didn't intend for anyone to have multi-boot setups, they could easily remove the ability for Disk Utility to partition an internal disk or for the macOS installer to install to a partitioned drive. (In fact, APFS theoretically should have made such a setup that much more flexible because one can add or delete a scale-able container within an existing volume vs. a fixed drive partition. However, getting rid of those containers at a later date, having the system reclaim the free space and accurately rewrite the allocation map is another thing entirely, so despite being a "late adopter" of this format, this OP feels like a beta tester.)

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Answer 5

MartinR

Level 7

21,655 points

Oct 12, 2023 7:37 AM in response to BDAqua

+1 I also suspect that this is the core of the OP's problem.

Fusion drives consist of a baked-in SSD (24GB, 32GB or 128GB depending on the iMac model) and an HDD that are "fused" by software into a single logical device. Only the actual drive hardware could be replaced. Portions of macOS are cached on the SSD portion of the Fusion drive. Fusion drives had a lot of problems with APFS and many users ended up with a split Fusion drive with the SSD showing up as a separate drive. I suspect that's what the OP has ended up with.

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Answer 6

NewsView Author

Level 1

41 points

Oct 13, 2023 1:13 AM in response to HWTech

Thank you, HWTech, for the helpful tips on Disk Utility and to all those who pointed out that the unremovable "partition" was a fusion drive leftover. (It was slow to dawn on me because I didn't install the SSD upgrade myself — didn't want to mess with the adhesive that holds the display together on this model — so wasn't aware that the fusion drive consists of two distinct parts.)

I read somewhere that Apple recommends running Disk Utility/First Aid on the container, then the volume, then the disk. Is that correct?

I also forgot to mention in the OP a huge chunk of the warnings were traceable to Microsoft OneDrive, which was apparently an common issue under Mojave. (Interesting because I have never run Mojave.) At any rate, I got rid of a lot of warnings by getting rid of all traces of OneDrive. (Another chunk of them disappeared after I manually deleted Time Machine snapshots. I didn't delete every last one, however, which might account for why I am still getting other errors.)

Rather than migrate all my data from the older iMac straightaway, I was initially content to test the waters on a preliminary install of Ventura using the stock fusion drive (reason why there was a third container prior to the clone; normally I run a dual-boot, not a triple one!). For now, however, I am putting the upgraded SSD through the paces before I migrate the rest of my files.

The entry in Single User mode that refers to "fs_alloc_count mismtach fs rootnodes" is the one that jumped out at me the most because it seems to suggest a problem with the file map. (Although from what I hear, Apple no longer recommends using Single User Mode anymore, either, so not sure how much stock I should put in it.)

Knock on wood, the dual-boot macOS seems to be working well so far. (Plus, I always have a TM backup drive connected and the iCloud storage.) So as long as the same or newer version of Disk Utility is exiting with "Ok" and "0", should I be good — or is it advisable to do a complete re-do of the drive?

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Answer 7

HWTech

Level 9

60,380 points

Oct 17, 2023 5:32 PM in response to NewsView

NewsView wrote:

I read somewhere that Apple recommends running Disk Utility/First Aid on the container, then the volume, then the disk. Is that correct?

For most issues you only need to run First Aid on the hidden Container. If you look as the First Aid report details, then you will see that First Aid runs first on the container, then every APFS volume located within the container including APFS snapshots. It is one and done.

You can run First Aid on the whole physical drive if you want, but that is rarely needed. It makes sense to first scan the whole drive since it will make sure the partitions & container structures are fine before proceeding inside each partition/container. However, I have seen several contributors mention doing it the other way.

The entry in Single User mode that refers to "fs_alloc_count mismtach fs rootnodes" is the one that jumped out at me the most because it seems to suggest a problem with the file map. (Although from what I hear, Apple no longer recommends using Single User Mode anymore, either, so not sure how much stock I should put in it.)

Apple has supposedly gotten rid of Single User Mode with the later Intel Macs. If your Mac and macOS support Single User Mode, then it is fine to use it as it can make some things simpler than performing them in Recovery Mode.

So as long as the same or newer version of Disk Utility is exiting with "Ok" and "0", should I be good — or is it advisable to do a complete re-do of the drive?

Don't trust the First Aid summary since I have seen it lie. Even if First Aid says everything is "Ok", click "Show Details" and scroll back through the report to see if there are any unfixed errors listed. If there are any unfixed errors listed, then you will need to try running First Aid from Recovery Mode, otherwise it would require erasing the drive. Theoretically you can ignore "Warnings" as long as the "Warnings" are not causing a problem.

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