Disk Utility: 'error: Cross Check' failures during check

[djivatma]

Hi guys,

I need your help with solving this issue. Any suggestions on how to fix the system volume?

After multiple power outages in one day, system freezes appeared. I checked system volume with Disk Utility and the following errors have been found:

Running First Aid on “NVMe MacOS” (disk4s1) NOTE: First Aid will temporarily lock the startup volume. Verifying file system. Volume could not be unmounted. Using live mode. Performing fsck_apfs -n -l -x /dev/rdisk4s1 Checking the container superblock. Checking the EFI jumpstart record. Checking the space manager. Checking the space manager free queue trees. Checking the object map. Checking volume. Checking the APFS volume superblock. The volume NVMe MacOS was formatted by hfs_convert (945.275.7) and last modified by apfs_kext (945.275.9). Checking the object map. Checking the snapshot metadata tree. Checking the snapshot metadata. Checking snapshot 1 of 1. Checking the extent ref tree. error: Cross Check : ExtentRef physical extent (0x313f0e + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x313f12 + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x313f16 + 4) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x313f1c + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x313fb4 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x313fc7 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314709 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314714 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314752 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314758 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x3147cf + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x3147d6 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x3147db + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x3147de + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x3147e1 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314818 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314820 + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314826 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314834 + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31483a + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314845 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314849 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31484e + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314851 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314854 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314858 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31485a + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31485c + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31485e + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314861 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314863 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314866 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31486b + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31486d + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314871 + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314878 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31487c + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314914 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314920 + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31494e + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x314973 + 2) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0x31497d + 1) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0xba142d5 + 140) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0xba14363 + 72) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0xba143ac + 259) has kind APFS_KIND_UPDATE but was not referenced previously error: Cross Check : ExtentRef physical extent (0xba1656a + 9) has kind APFS_KIND_UPDATE but was not referenced previously Checking the fsroot tree. error: Cross Check : FSroot tree references extent (0xba142d5 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142d6 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142d7 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142d8 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1656a + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142d9 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142da + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142db + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142dc + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142dd + 8) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142e5 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1656b + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142e6 + 2) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142e8 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142e9 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142ea + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142eb + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142ec + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142ed + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142ee + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142ef + 2) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f1 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f2 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f3 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f4 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f5 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba142f6 + 19) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14309 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430a + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430b + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430c + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430d + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430e + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1430f + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14310 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14311 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14312 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14313 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14314 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14315 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14316 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14317 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14318 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14319 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431a + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431b + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431c + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431d + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431e + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1431f + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14320 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14321 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14322 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14323 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14324 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14325 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14326 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14327 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14328 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14329 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432a + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432b + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432c + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432d + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432e + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1432f + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14330 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14331 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1656c + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba1656d + 3) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14332 + 1) which is not present in the ExtentRef tree error: Cross Check : FSroot tree references extent (0xba14333 + 1) which is not present in the ExtentRef tree ~~...~~ error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f0e + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f12 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f13 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f16 + 4) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f1c + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313fb4 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313fc7 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314709 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314714 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314752 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314758 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147cf + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147d6 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147db + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147de + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147e1 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314818 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314820 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314821 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314826 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314834 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314835 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31483a + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314845 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314849 + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31484e + 1) error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31484f + 1) ~~...~~ Verifying allocated space. Performing deferred repairs. warning: found physical extent corruption but repairs are disabled The volume /dev/rdisk4s1 appears to be OK. File system check exit code is 0. Restoring the original state found as mounted. Operation successful.

 

[Fishrrman]

What I'd do:

Get an external drive to serve as a backup.

Use either CarbonCopyCloner or SuperDuper to create a BOOTABLE cloned backup of your current install on a backup drive.
IMPORTANT: DO NOT USE time machine. You need to create a BOOTABLE backup!

CCC and SD are FREE to use for 30 days.
Doing what I suggest will cost you nothing.

Now... BOOT FROM the cloned backup drive.

Open Disk Utility. Go to the view menu and choose "show all devices" (VERY important step).

Select "the top line" that represents the physical drive inside your Mac.

ERASE it.
- For High Sierra and earlier, choose Mac OS extended with journaling enabled, GUID partition format.
- For Mojave and later, choose APFS with GUID partition format.
(Looks like you need APFS)

Now try disk utility's "first aid" function again.
Do you still get the same errors, or have they been "cleaned up".

If they're gone, and the disk now looks good, quit Disk Utility and re-open CCC (or SD).

Next, RE-clone the contents of the cloned backup BACK TO the internal drive.

That should do it.

I realize this is "some work" and will take some time, but sometimes the only way to clear up problems with disk corruption is to just erase it and start over.

 

[Taz Mangus]

Boot into Recovery Mode and run Disk Utility First Aid again.

If you can't start up from macOS Recovery - Apple Support

Learn what to do if you can't get your Mac to start up from macOS Recovery.

support.apple.com

 

[djivatma]

Thanks A LOT for your quick reply!

Do you think I may expect problems if continue using the system as it is right now?

Also, will the Time Machine backup be damaged bu these errors or I can continue doing backup with no issues if I need to restore it in the future?

What I'd do:

Get an external drive to serve as a backup.

Use either CarbonCopyCloner or SuperDuper to create a BOOTABLE cloned backup of your current install on a backup drive.
IMPORTANT: DO NOT USE time machine. You need to create a BOOTABLE backup!

CCC and SD are FREE to use for 30 days.
Doing what I suggest will cost you nothing.

Now... BOOT FROM the cloned backup drive.

Open Disk Utility. Go to the view menu and choose "show all devices" (VERY important step).

Select "the top line" that represents the physical drive inside your Mac.

ERASE it.
- For High Sierra and earlier, choose Mac OS extended with journaling enabled, GUID partition format.
- For Mojave and later, choose APFS with GUID partition format.
(Looks like you need APFS)

Now try disk utility's "first aid" function again.
Do you still get the same errors, or have they been "cleaned up".

If they're gone, and the disk now looks good, quit Disk Utility and re-open CCC (or SD).

Next, RE-clone the contents of the cloned backup BACK TO the internal drive.

That should do it.

I realize this is "some work" and will take some time, but sometimes the only way to clear up problems with disk corruption is to just erase it and start over.

 

[djivatma]

Thanks! I've made it three times already without any changes. I suppose this won't help

Boot into Recovery Mode and run Disk Utility First Aid again.

If you can't start up from macOS Recovery - Apple Support

Learn what to do if you can't get your Mac to start up from macOS Recovery.

support.apple.com

 

[DeltaMac]

Yes, running Disk Utility while you are booted to the recovery system, is what you should try now.

 

[Taz Mangus]

I would also suggest to do a SMC reset and then boot into Recovery Mode and perform Disk Utility First Aid.

Reset the SMC of your Mac - Apple Support

The SMC is responsible for managing power on your Mac. Resetting it can resolve certain uncommon issues related to power or thermal management.

support.apple.com

 

[djivatma]

So... guys... I followed all the steps provided by Fishrrman and it helped me! Many thanks! ❤️

 

[Thehum]

Had this problem on my MBP 2015 w/ Big Sur. My resolution involved similar steps to Fisherman’s but instead of using disk utility first aid, I went to terminal and zero-fill erased the entire disk.

- clone HD t external using Carbon Copy Cloner
- reboot and boot into external clone w/ option key
- open terminal and check disk# using the command: diskutil list
-verified disk0 was my internal disk
-ran the zerofill erase using command for disk0: zerodisk disk0
-Open disk utility and “erase” the now blank HD And as a Blank APFS volume
-Open CCC and clOne the external volume back to internal disk.
-unplug external and boot into internal Hd
-run boot camp assistant
Voila!

 

[DeltaMac]

Just to remind other readers here: There's a reason that you can't "zero" an SSD through the Disk Utility. It's not a recommended procedure, as it will shorten the potential life of that SSD.
A simple erase would likely have fixed you up just as well

 

[tintinUK]

Hi,

I had errors similar to the OP. Because I'm running Big Sur I used the latest version of CCC to clone my MacBook Pro 2018's SSD to an external drive. I then booted from the clone, reformatted the SSD, and restored it.

(Note that I didn't wipe the entire drive as I didn't want to lose the Bootcamp partition so I just reformatted the Mac container and let CCC do it's thing.)

Booting from the restored internal SSD everything seemds to be working fine but I've noticed that Disk Utility now shows my SSD in a different way: Before it would just show 'Macintosh HD' and 'Macintosh HD - Data' but now Macintosh HD appears to be unmounted and says: System Snapshot Mounted. The mounted aspect below goes by the name of: com.apple.os.update..... blah blah (See screenshot.)

Is this setup normal or have I screwed up along the way?

 

[dlfuller]

My occasional crash and repetitive Disk Utility errors were similar to djivatma's. Different restore and command line fsck techniques didn't help.

So I followed Fishrrman's recommendation. The cloning took a little time, but the result was the best. Back to normal on 10.14.6 with a cleaner, reorganized boot SSD.

Thank you Fishrrman!

 

[zlloyd1]

I have heard that sometimes, not always, if you keep trying First Aid over and over, it may eventually clean up this problem....
This seems a LOT more desirable than completely wiping out your hard drive to me, but it IS a Macintrash, some a complete wipe may be your only real option, Sorry.
For the outrageous amount of money Apple charges for their devices, you would think that a complete reformat would not be needed for almost every bug, but hey, we were the ones who were stupid enough to buy these things!!

 

[vett93]

I am having the same problem and have tried First Aid 7 times in the Recovery Mode. But the problem does not go away. Guess I'll erase the system/Mac SSD next.

 

[DeltaMac]

I think the First Aid tool in Big Sur is a little glitchy.
Here's what I do:
While booted to the Recovery system, run Disk Utility/First Aid on the container once. If there are errors reported, shut down (not just a restart), then boot back into the Recovery system, and run First Aid again. I will sometimes do this 3 times. The error may disappear. If you continue to get similar errors, even after 3 times through (with power cycles each time), you likely need to replace the SSD.

 

[vett93]

The errors are about snapshots. The Disk Utility First Aid exits with code 0 and it states the SSD is fine. Do I still need to replace the SSD? Or an erase and reformat would do?

What is the benefit of using CCC to clone the SSD? Why can't I just reboot from Discovery Mode over the Internet, erase the SSD, reinstall MacOS, and then recover the rest from the Time Machine?

 

[DeltaMac]

I would not attempt to boot to Discovery Mode, (not sure why you would do that) but I'm guessing you mean Internet Recovery, which would likely work better!

The "benefit" of using CCC is usually speed. It's normally faster to do the whole process, compared to recovering through Time Machine.

Just curious -- which Mac is giving you the First Aid errors?
Are you running Big Sur? or Monterey (beta)?

 

[vett93]

Yes, I mean Internet Recovery Mode.

It is my 2013 Mac Pro that is having problems. It has First Aid errors in the System SSD snapshots and both backup HDs. These two backup HDs are LaCie drives I bought from Apple Store less than a year ago.

If one uses CCC to clone the System SSD to an external drive, would the bad snapshots from System SSD get cloned over there too?

I have owned the 2013 Mac Pro since it first came out in early 2014. I am hoping to prolong its life until M1x or M2 Mac comes out. The 2020 M1 MBP is a laptop from work. I like my 2013 MP better and use it as my main computer still.

 

[DeltaMac]

Question:
When you boot to the Internet Recovery system, what macOS version is running? You can tell easily by launching Reinstall macOS. You get the first installer screen telling you if it is Big Sur, or Monterey, or maybe something older in Internet Recovery. If it is OLDER than the system that you are normalling booted to, that may mean that you can still choose to ignore those errors. For example, Catalina Disk Utility might not know how to repair problems on a Big Sur drive.

If you choose to ignore those reported errors in First Aid - what kind of problems are you actually experiencing?
How are you backing up to the two backup HHDs?

 

[vett93]

Internet Recovery Mode would take me to install Big Sur. I did reinstall Big Sur. But it has not solved the problem.

I run into all USB devices ejected problems from time to time. These are random ejections. All USB devices, including HDs, microphone, webcam, and speaker, would get disconnected from the MP.

I have been using two HDs to backup my MP for years. All you have to do is adding a HD to the Time Machine. TM would back up to them alternatively. It would use one HD and then use the other HD next, and then back to the first one.

 

[vett93]

Update: I ended up erasing the System SSD and reinstalling the MacOS. It has resolved the cross-check errors. However, the backup HDs still have errors from Disk Utility's first aid. I erased these two LaCie HDs using secure erase 2. It randomly wrote data to the HDs twice. After that, they passed Disk Utility. However, after backing up the data, the same problem has returned.

It seems very unlikely that both HDs (less than 1 year old) would fail like this at the same time. I am wondering if this is a bug in MacOS 11.5.2

 

[zlloyd1]

I am once again seeing this happening every time i try to run First Aid....
It stopped for a while after i made a backup using Time Machine on an external drive I got, but now it is back with a vengeance.
It is infuriating because I truthfully do not even really use Time Machine that often, mainly because I do not trust anything that Apple coded to work without messing up the already overpriced mess of a computer I bought from them.
Regardless, hopefully my previous post was correct, and it will just go away eventually if you keep trying First Aid, but as noted, Macintosh systems are ridiculously complex, and nearly impossible to figure out if you are not a software engineer, which is ludicrous for a home computer sold to laymen.
Good Luck yo, hope you don't end up having to completely wipe your device, and start over, but that seems to be the main fix for any problems with a Mac, as even they do not seem to understand how they work!!

 

[zlloyd1]

Honestly, I am getting similar errors to yours from the snapshots portion of running the First Aid utility, and so it is basically these errors thaat pop up at random snapshot numbers:

error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f0e + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f12 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f13 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f16 + 4)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313f1c + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313fb4 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x313fc7 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314709 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314714 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314752 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314758 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147cf + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147d6 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147db + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147de + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x3147e1 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314818 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314820 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314821 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314826 + 1)
?error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314834 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314835 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31483a + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314845 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x314849 + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31484e + 1)
error: Cross Check : Mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (1) for extent (0x31484f + 1)

Which is very odd to me because before upgrading from High Sierra to Mojave, I never even saw anything about snapshots when running First Aid.
So, it must be some new stupidity the devs down at Apple Macintosh came up with causing this foolishness, but not having any clue what it means!!

I swear, I wish to Lord Above that I could just go back to High Sierra, back when I was happy to have a Mac, because every since then the systems have gotten more and more screwy, and less and less user friendly....??

 

[zlloyd1]

Alright, I realize that i am just ranting, and not adding anything to this discussion, so let me throw this out there,,,,

How to manually delete Time Machine local snapshots

Open Terminal.
Enter the command tmutil listlocalsnapshots /
Press enter. This will bring up a list of all snapshots on the disk, date and time-stamped.
For each snapshot, enter the command sudo tmutil deletelocalsnapshots followed by the date and timestamp. For example, sudo tmutil deletelocalsnapshots 2021-06-26-123740
if asked, enter your password for the user account, and press enter.
Once you see the statement "Delete local snapshot" followed by the date and time stamp, the local snapshot has been deleted.

How to delete Time Machine local snapshots in macOS | AppleInsider

Apple's Time Machine is an essential file backup tool for macOS, but it too has a backup that works off your Mac's primary drive. Here's how Time Machine's local snapshots work, and how to get rid of them if you want them gone.

appleinsider.com

This seems to work, at least for running First Aid, just be sure to delete every single one of them listed as they do not truly do anything useful except take up space, and create confusing errors!!

 

[zlloyd1]

As you can see here, it completely skips Checking Snapshots, because they are all gone....

You just need to make sure, when using the above method, that you remove every single one of them in the Terminal.
Plus, that may clear up other stupid problems associated with that mountain garbage that is Time Machine snapshots on your device!!