Disk utility and FSCK failed, shall I format boot HDD?

I have encountered problems with my late 2012 iMac 3TB Fusion drive running Mojave. Disk utility in macOS as well as in Recovery mode as well as FSCK in Single User ends with approx. 100 errors and these lines in the end:

Verifying allocated space.
Performing deferred repairs.
warning: found physical extent corruption but repairs are disabled
The volume /dev/rdisk2s1 appears to be OK.
File system check exit code is 0.
Restoring the original state found as mounted.


Can't use Disk Warrior or similar software since it is AFPS.

So my question is: Is there a chance that these issues would be solved by formatting the HDD?


Any piece of advice would be highly appreciated!

Posted on Apr 18, 2019 2:42 PM

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10 replies

Apr 18, 2019 4:41 PM in response to jamike2

I agree with rkaufmann87 on his assessment. If you want better confirmation, run DriveDX to check the hard drive's health. If it shows as healthy, then please post a screenshot or report of all the "Health Indicators" for both of your drives. You can also use DriveDX to run the drive's long or extended selftest for the hard drive (and for the SSD if the selftest option is available).


Sometimes the Apple Diagnostic will catch some types of failures, but many are not caught.

Apr 19, 2019 11:38 AM in response to jamike2

It is a little hard to read the results as some of the values are broken due to posting it inline, but both drives appear to be healthy as far as I can tell. At least they don't have any reallocated sectors. It is difficult to tell, but your SSD's Wear Level may be declining a bit much. Unfortunately Apple's SSDs don't really provide enough SMART data. I would suggest running the "Long" or "Extended" selftest on each drive if it is available in DriveDX. The Apple SSD may not support the internal selftest.


Of course some types of drive failures may not show up clearly in these attributes, but nothing major stands out with your drives.


You can try repairing the drive with Disk Utility by booting into Recovery Mode or Internet Recovery Mode. If Disk Utility is unable to repair the damage, then your only option is to backup your data and Erase the drive and re-install clean or from a backup since I'm not aware of any APFS filesystem utilities which can repair APFS yet.

Apr 18, 2019 11:41 PM in response to HWTech

Large classic HDD:

   1   Raw Read Error Rate                           Pre-fail    online            0x6CC4C00             116           6     99                       -   96.5%  OK          
   3   Spin Up Time                                  Pre-fail    online                0                  95           0     94                       -   95.0%  OK          
   4   Start Stop Count                              Life-span   online              9 117                92          20     92                       -   90.0%  OK          
   5   Reallocated Sector Count                      Pre-fail    online                0                 100          36    100                       -    100%  OK          
   7   Seek Error Rate                               Pre-fail    online           0x10517B1CD             79          30     60                       -    100%  OK          
          


I need to find out whether these disk utility errors are software-related (e.g. could be solved by formatting), or hardware-related.

Apr 18, 2019 11:42 PM in response to HWTech

Large classic HDD (part 2/3):

   9   Power On Hours                                Life-span   online              17 681               80           0     80                       -   80.0%  OK          
  10   Spin Retry Count                              Pre-fail    online                0                 100          97    100                       -    100%  OK          
  12   Power Cycle Count                             Life-span   online              10 686               90          20     90                       -   87.5%  OK          
 184   End-to-End Error                              Life-span   online                0                 100          99    100                       -    100%  OK          
 187   Reported Uncorrectable Errors                 Life-span   online                0                 100           0    100                       -    100%  OK          
 188   Command Timeout                               Life-span   online                0                 100           0    100                       -    100%  OK          
 189   High Fly Writes                               Life-span   online                3                  97           0     97                       -    100%  OK          
 190   Airflow Temperature Celsius                   Life-span   online                48                 52          45     46                       -   12.7%  OK          
 191   G-Sense Error Rate                            Life-span   online                0                 100           0    100                       -    100%  OK          
 192   Power-Off Retract Count                       Life-span   online               123                100           0    100                       -    100%  OK          
 193   Load Cycle Count                              Life-span   online              10 695               95           0     95                       -   95.0%  OK          
 194   Temperature (Celsius)                         Life-span   online                48                 52          35     46                       -   26.2%  OK          
 197   Current Pending Sector Count                  Life-span   online                0                 100           0    100                       -    100%  OK          
 198   Offline Uncorrectable Sector Count            Life-span   offline               0                 100           0    100                       -    100%  OK          


Apr 22, 2019 1:19 PM in response to HWTech

Well, all indicators for both disks are OK (no warning, failing or failed) according to DriveDX. A have also ran short self-test (do not have licence for full test) and it was also completed without error.


As I have written in the beginning, Disk Utility and FSCK -FY in both Recovery Mode and Single User Mode ended with same results as Disk Utility in normal macOS. I would like to know what exactly alle these errors mean.

Waiting for utility that would be able to repair AFPS seems to have no sense.

Apr 23, 2019 1:19 AM in response to HWTech

Thank you for the detailed instructions. Here are results of smartctl -l selftest command (I've amended short test results for comparison):

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Completed without error       00%     16221         -
# 2  Short offline       Completed without error       00%     16210         -


Both disks (HDD + SSD = Fusion Drive) are shown in Disk Utility and System Info with one indentifier only: disk2s1


So I think I will try the formatting after many days of lenghty backing up. Unfortunately, I haven't found any procedure how to revert AFPS back to HFS in case of Fusion Drives. Therefore I will keep the AFPS.

Apr 18, 2019 11:40 PM in response to HWTech

Thank you for the tip!

DriveDX shows both drives as OK.

Here are health indicators reports:


SSD:

   1   Raw Read Error Rate                           Life-span   online               0x0                200           0    200                       -    100%  OK          
   5   Retired Block Count                           Pre-fail    online                0                 100           0    100                       -    100%  OK          
   9   Power On Hours                                Life-span   online              16 127               96           0     96                       -   96.0%  OK          
  12   Power Cycle Count                             Life-span   online              6 825                93           0     93                       -   93.0%  OK          
 169   Total Bad Block Count                         Pre-fail    online           0x9E0CC00C80           253          10    253                       -    100%  OK          
 173   Wear Leveling Count                           Life-span   online          0x3A705310433           156         100    156                       -   56.0%  OK          
 192   Unsafe Shutdown Count                         Life-span   online              5 572                98           0     98                       -   98.0%  OK          
 194   Temperature (Celsius)                         Life-span   online                55                 45          30     39                       -   21.4%  OK          
 197   Current Pending Block Count                   Life-span   online                0                 100           0    100                       -    100%  OK          
 199   UDMA CRC Error Count                          Life-span   online                0                 200           0    200                       -    100%  OK 

Apr 18, 2019 11:45 PM in response to HWTech

Large classic HDD (part 3/3):

 199   UDMA CRC Error Count                          Life-span   online                0                 200           0    200                       -    100%  OK          
 240   Head Flying Hours                             Life-span   offline             19 409              100           0    253                       -    100%  OK          
 241   Total LBAs Written                            Life-span   offline    35 998 325 141 (16.8 TB)     100           0    253                       -    100%  OK          
 242   Total LBAs Read                               Life-span   offline    18 576 220 092 024 (8650.2 TB)     100           0    253                       -    100%  OK


Apr 22, 2019 2:15 PM in response to jamike2

Well, all indicators for both disks are OK (no warning, failing or failed) according to DriveDX. A have also ran short self-test (do not have licence for full test) and it was also completed without error. 

Using Disk Utility or Apple System Profiler, get the drive designator for the drive you want to test which will be in the form of "disk0". You will need this in a minute.


In the Finder, Right-click (or Control-click) on the DriveDX app and select "Show package contents". Then navigate to "Contents/Resources". Open the Terminal app and type "sudo " without the quotes, then drag & drop "smartctl" onto the Terminal to auto populate the path to the actual tool. Then type the following without the quotes " -t long /dev/diskN" where you replace "diskN" with the drive designator for the drive you want to test. Here is an example using "disk0" where "0" is a zero:

sudo  <path-to-DriveDX.app>/Contents/Resources/smartctl  -t  long  /dev/disk0


To view the results of the selftest, you would use replace the "-t long" with "-l selftest", where "l" is a lowercase "L". Example using "disk0":

sudo  <path-to-DriveDX.app>/Contents/Resources/smartctl  -l selftest  /dev/disk0


It may be a good idea to check the selftest log first so you know what is already listed there since it may not show the current test until it is completed. It will likely take 4+ hours to test your 3TB drive, even longer if the system is actively using the drive.


If the SSD supports the selftest you can also use this method to run the extended or long test on the SSD.


Note: These commands will prompt you for your user password as the commands need administrator privileges to run.


Like I said the information provided by DriveDX does alert users to many types of drive failures, but not to all of them so one of the drives could still have an issue not easily detected even if the selftests pass which is mostly a surface level scan of the blocks/sectors.


Unfortunately APFS is still a very new filesystem so it really isn't surprising to see these types of issues. Plus the necessary documentation needed to create utilities to repair APFS has not been released by Apple yet so third parties are unable to update their tools to work with APFS.

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Disk utility and FSCK failed, shall I format boot HDD?

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