Ubuntu – My files permissions change spontaneously to read-only, sometimes

fsckhard drivemountread-only

This is very common, i have been doing my things when my files permissions changed to read-only. I reboot my pc immediately and this won't start, so i forced power off, then I typed fsck /dev/sda2. Where is the problem? Why this always happens? The pc is eight months old.

I am worried because my last time when I typed sudo fsck -f /dev/sda2 in Live Ubuntu, the output showed me this:

Pass 1: Checking inodes, blocks, and sizes 
Inode 19411393 seems to contain garbage.  Clear? yes 
...
Inode 19412112 seems to contain garbage.  Clear? yes 

...

Pass 2: Checking directory structure 
Entry 'Captura de pantalla de 2020-04-14 17-02-34.png' in /home/pasta/ImM-CM-!genes (19398749) has deleted/unused inode 19411936.  Clear? yes 

...

Entry 'bdcc59467787cae82ff54abaec1dd5497e4d0d' in /home/pasta/.cache/mesa_shader_cache/35 (19398823) has deleted/unused inode 19411992.  Clear? yes 
...

Pass 5: Checking group summary information 
Block bitmap differences:  -(625760--625791) ... -(500 OF THESE, MORE OR LESS) ... -(159426726--159426729) 
Fix? yes

The output of dmesg, what caught my attention:

[   39.721010] pcieport 0000:00:1c.5: AER: PCIe Bus Error: severity=Corrected, type=Physical Layer, (Receiver ID)
[   39.721019] pcieport 0000:00:1c.5: AER:   device [8086:9d15] error status/mask=00000001/00002000
[   39.721024] pcieport 0000:00:1c.5: AER:    [ 0] RxErr            
...
[  170.652599] blk_update_request: I/O error, dev sdb, sector 4096 op 0x0:(READ) flags 0x80700 phys_seg 1 prio class 0
[  170.652736] blk_update_request: I/O error, dev sdb, sector 4096 op 0x0:(READ) flags 0x0 phys_seg 1 prio class 0
[  170.652744] Buffer I/O error on dev sdb1, logical block 256, async page read

Output of sudo smartctl -a /dev/sda2 after sudo smartctl -t long /dev/sda2 :

smartctl 6.6 2016-05-31 r4324 [x86_64-linux-5.3.0-46-generic] (local build) 
Copyright (C) 2002-16, Bruce Allen, Christian Franke, www.smartmontools.org 

=== START OF INFORMATION SECTION === 
Device Model:     TOSHIBA MQ04ABF100 
Serial Number:    X8JBP3K2T 
LU WWN Device Id: 5 000039 8d268714d 
Firmware Version: JU001J 
User Capacity:    1.000.204.886.016 bytes [1,00 TB] 
Sector Sizes:     512 bytes logical, 4096 bytes physical 
Rotation Rate:    5400 rpm 
Form Factor:      2.5 inches 
Device is:        Not in smartctl database [for details use: -P showall] 
ATA Version is:   ACS-3 T13/2161-D revision 5 
SATA Version is:  SATA >3.2 (0x1ff), 6.0 Gb/s (current: 6.0 Gb/s) 
Local Time is:    Tue Apr 14 22:33:42 2020 -04 
SMART support is: Available - device has SMART capability. 
SMART support is: Enabled 

=== START OF READ SMART DATA SECTION === 
SMART overall-health self-assessment test result: PASSED 

General SMART Values: 
Offline data collection status:  (0x00) Offline data collection activity 
                    was never started. 
                    Auto Offline Data Collection: Disabled. 
Self-test execution status:      (   0) The previous self-test routine completed 
                    without error or no self-test has ever  
                    been run. 
Total time to complete Offline  
data collection:        (  120) seconds. 
Offline data collection 
capabilities:            (0x5b) SMART execute Offline immediate. 
                    Auto Offline data collection on/off support. 
                    Suspend Offline collection upon new 
                    command. 
                    Offline surface scan supported. 
                    Self-test supported. 
                    No Conveyance Self-test supported. 
                    Selective Self-test supported. 
SMART capabilities:            (0x0003) Saves SMART data before entering 
                    power-saving mode. 
                    Supports SMART auto save timer. 
Error logging capability:        (0x01) Error logging supported. 
                    General Purpose Logging supported. 
Short self-test routine  
recommended polling time:    (   2) minutes. 
Extended self-test routine 
recommended polling time:    ( 172) minutes. 
SCT capabilities:          (0x003d) SCT Status supported. 
                    SCT Error Recovery Control supported. 
                    SCT Feature Control supported. 
                    SCT Data Table supported. 

SMART Attributes Data Structure revision number: 16 
Vendor Specific SMART Attributes with Thresholds: 
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE 
  1 Raw_Read_Error_Rate     0x000b   100   100   050    Pre-fail  Always       -       0 
  2 Throughput_Performance  0x0005   100   100   050    Pre-fail  Offline      -       0 
  3 Spin_Up_Time            0x0027   100   100   001    Pre-fail  Always       -       1294 
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       636 
  5 Reallocated_Sector_Ct   0x0033   100   100   050    Pre-fail  Always       -       0 
  7 Seek_Error_Rate         0x000b   100   095   050    Pre-fail  Always       -       0 
  8 Seek_Time_Performance   0x0005   100   100   050    Pre-fail  Offline      -       0 
  9 Power_On_Hours          0x0032   096   096   000    Old_age   Always       -       1743 
 10 Spin_Retry_Count        0x0033   112   100   030    Pre-fail  Always       -       0 
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       451 
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       1359 
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       23 
193 Load_Cycle_Count        0x0032   095   095   000    Old_age   Always       -       50104 
194 Temperature_Celsius     0x0022   100   100   000    Old_age   Always       -       35 (Min/Max 13/45) 
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0 
197 Current_Pending_Sector  0x0032   100   100   000    Old_age   Always       -       0 
198 Offline_Uncorrectable   0x0030   100   100   000    Old_age   Offline      -       0 
199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always       -       0 
220 Disk_Shift              0x0002   100   100   000    Old_age   Always       -       0 
222 Loaded_Hours            0x0032   097   097   000    Old_age   Always       -       1533 
223 Load_Retry_Count        0x0032   100   100   000    Old_age   Always       -       0 
224 Load_Friction           0x0022   100   100   000    Old_age   Always       -       0 
226 Load-in_Time            0x0026   100   100   000    Old_age   Always       -       264 
240 Head_Flying_Hours       0x0001   100   100   001    Pre-fail  Offline      -       0 

SMART Error Log Version: 1 
ATA Error Count: 1 
    CR = Command Register [HEX] 
    FR = Features Register [HEX] 
    SC = Sector Count Register [HEX] 
    SN = Sector Number Register [HEX] 
    CL = Cylinder Low Register [HEX] 
    CH = Cylinder High Register [HEX] 
    DH = Device/Head Register [HEX] 
    DC = Device Command Register [HEX] 
    ER = Error register [HEX] 
    ST = Status register [HEX] 
Powered_Up_Time is measured from power on, and printed as 
DDd+hh:mm:SS.sss where DD=days, hh=hours, mm=minutes, 
SS=sec, and sss=millisec. It "wraps" after 49.710 days. 

Error 1 occurred at disk power-on lifetime: 1096 hours (45 days + 16 hours) 
  When the command that caused the error occurred, the device was active or idle. 

  After command completion occurred, registers were: 
  ER ST SC SN CL CH DH 
  -- -- -- -- -- -- -- 
  04 31 00 02 59 d7 a9 

  Commands leading to the command that caused the error were: 
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name 
  -- -- -- -- -- -- -- --  ----------------  -------------------- 
  ea 00 00 00 00 00 a0 00      05:01:42.830  FLUSH CACHE EXT 
  61 58 30 38 f9 20 40 00      05:01:42.830  WRITE FPDMA QUEUED 
  61 08 80 08 f9 1b 40 00      05:01:42.829  WRITE FPDMA QUEUED 
  61 08 78 a0 b8 52 40 00      05:01:42.788  WRITE FPDMA QUEUED 
  61 30 70 58 0c 50 40 00      05:01:42.788  WRITE FPDMA QUEUED 

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%      1743         - 
# 2  Extended offline    Completed without error       00%      1728         - 

SMART Selective self-test log data structure revision number 1 
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS 
    1        0        0  Not_testing 
    2        0        0  Not_testing 
    3        0        0  Not_testing 
    4        0        0  Not_testing 
    5        0        0  Not_testing 
Selective self-test flags (0x0): 
  After scanning selected spans, do NOT read-scan remainder of disk. 
If Selective self-test is pending on power-up, resume after 0 minute delay.

Best Answer

The OS remounts your root partition as read-only when it detected a file system problem during boot time or during runtime if the access to disk was lost for more than a certain time. The output of smartctl you've shown does not indicate problems on the disk counters (yet) but the SMART logs show a disk access problem in the no so far past.

Try running a full SMART check on your drive: smartctl -t long /dev/sda. If that doesn't find anything, you should boot a Live Linux (e.g. Knoppix, Linux Mint, etc) and run a fsck -f on your non-mounted drive.

Losing access to the drive is in most cases caused by a defective drive, much less caused by a defective SATA cable or controller.

Disable `uas` without rebooting

First, unplug all USB devices that might be using it. Then, remove the uas and usb-storage modules:

sudo modprobe -r uas
sudo modprobe -r usb-storage

Then, load usb-storage module with a parameter that tells it to not use uas for a given device:

sudo modprobe usb-storage quirks=VendorId:ProductId:u

VendorId and ProductId must be replaced by your device vendor and product id, which can be obtained with lsusb command (they are the characters after ID).

For example, I have the following device:

Bus 002 Device 011: ID 0bc2:3320 Seagate RSS LLC SRD00F2 [Expansion Desktop Drive]

So my vendor id is 0bc2, and my product id is 3320. My command is:

sudo modprobe usb-storage quirks=0bc2:3320:u

The last u tells usb-storage to ignore uas for the device (see source).

At this point, you can insert the USB device, and it will know not to use uas, making S.M.A.R.T work properly. You will see lines like these in dmesg when inserting the USB device:

usb 2-2: UAS is blacklisted for this device, using usb-storage instead
usb-storage 2-2:1.0: USB Mass Storage device detected
usb-storage 2-2:1.0: Quirks match for vid 0bc2 pid 3320: 800000
scsi host12: usb-storage 2-2:1.0

Make the change permanent

The previous quirk will only last until you reboot the system. To make it persistent, you need to follow the steps described here, which I copy below:

First, create a file named ignore_uas.conf in the /etc/modprobe.d/ directory with the following content:

options usb-storage quirks=VendorId:ProductId:u

As before, substitute VendorId and ProductId by your device vendor and product id obtained from lsusb.

Next, regenerate your inital ramdisk:

mkinitcpio -p linux

or, on newer Ubuntu versions:

sudo update-initramfs -u

Finally, reboot your computer.

Edit: More background on the issue, and another way to get around it without disabling uas (which has better throughput than usb-storage) can be found here: https://www.smartmontools.org/ticket/971#comment:12

It seems that kernel is blacklisting SAT ATA PASS-THROUGH on some devices when running in uas mode, as they have broken firmware.

So, the blacklisting can be disabled (at your own risk) by using the previous method I mention in the answer, but removing the final u from the quirk, ie:

quirks=VendorId:ProductId:

Please note, however, that I have not tested this approach.

Best Answer

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Disable uas without rebooting

Make the change permanent

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Disable `uas` without rebooting