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I'm facing an issue with my server running CentOS. The system partition "md3" (raid1) is full due to a backup script error that failed to delete old data. As a result, my CentOS system has become inaccessible.

When I try to reboot the server, the system fails to mount /sysroot, which is associated with the "md3" partition. The process eventually times out, preventing the system from booting up.

I've also tried accessing "md3" in rescue mode to perform some cleanup, but the mount command fails to mount the partition. The process hangs indefinitely without displaying any errors. (i try mount in read mode only and verbose, nothing show).

For additional context, I've checked the RAID1 and hard disk statuses, anything is ok (verified with support of hosting).

root@rescue-customer-eu (/////) ~ # free --mega
              total        used        free      shared  buff/cache   available
Mem:          33266        2256       30356          15         653       30101
Swap:             0           0           0
root@rescue-customer-eu (/////) ~ # dmidecode -q -t memory | grep Size
        Size: No Module Installed
        Size: 16384 MB
        Size: No Module Installed
        Size: 16384 MB
root@rescue-customer-eu (/////) ~ # fdisk -l
Disk /dev/ram0: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram1: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram2: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram3: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram4: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram5: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram6: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram7: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram8: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram9: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram10: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram11: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram12: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram13: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram14: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram15: 50 MiB, 52428800 bytes, 102400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/sda: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Disk model: HGST HUS724020AL
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 5F909BBA-6950-429A-BB7E-BBBCC2C704EA

Device          Start        End    Sectors  Size Type
/dev/sda1        2048    1048575    1046528  511M EFI System
/dev/sda2     1048576    2095103    1046528  511M Linux RAID
/dev/sda3     2095104 3907026943 3904931840  1.8T Linux RAID
/dev/sda5  3907026944 3907028991       2048    1M Linux filesystem


Disk /dev/sdb: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Disk model: HGST HUS724020AL
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 71084CB3-27E5-4CBF-A406-98371DDCFB44

Device       Start        End    Sectors  Size Type
/dev/sdb1     2048    1048575    1046528  511M EFI System
/dev/sdb2  1048576    2095103    1046528  511M Linux RAID
/dev/sdb3  2095104 3907029134 3904934031  1.8T Linux RAID


Disk /dev/md3: 1.8 TiB, 1999325036544 bytes, 3904931712 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/md2: 511 MiB, 535756800 bytes, 1046400 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

root@rescue-customer-eu (/////) ~ # smartctl -a /dev/sda
smartctl 7.2 2020-12-30 r5155 [x86_64-linux-6.1.38-mod-std] (local build)
Copyright (C) 2002-20, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Hitachi/HGST Ultrastar 7K4000
Device Model:     HGST HUS724020ALA640
Serial Number:    PN1134P6H1DGLN
LU WWN Device Id: 5 000cca 22dcebab0
Firmware Version: MF6OABY0
User Capacity:    2,000,398,934,016 bytes [2.00 TB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    7200 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA8-ACS T13/1699-D revision 4
SATA Version is:  SATA 3.0, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Mon Sep 11 07:08:28 2023 UTC
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:  (0x82) Offline data collection activity
                                        was completed without error.
                                        Auto Offline Data Collection: Enabled.
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:                (   24) 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:        (   1) minutes.
Extended self-test routine
recommended polling time:        ( 319) 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   016    Pre-fail  Always       -       0
  2 Throughput_Performance  0x0005   136   136   054    Pre-fail  Offline      -       82
  3 Spin_Up_Time            0x0007   214   214   024    Pre-fail  Always       -       274 (Average 308)
  4 Start_Stop_Count        0x0012   100   100   000    Old_age   Always       -       264
  5 Reallocated_Sector_Ct   0x0033   100   100   005    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000b   100   100   067    Pre-fail  Always       -       0
  8 Seek_Time_Performance   0x0005   142   142   020    Pre-fail  Offline      -       25
  9 Power_On_Hours          0x0012   092   092   000    Old_age   Always       -       58834
 10 Spin_Retry_Count        0x0013   100   100   060    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       264
192 Power-Off_Retract_Count 0x0032   099   099   000    Old_age   Always       -       1257
193 Load_Cycle_Count        0x0012   099   099   000    Old_age   Always       -       1257
194 Temperature_Celsius     0x0002   171   171   000    Old_age   Always       -       35 (Min/Max 15/75)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0022   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0008   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x000a   200   200   000    Old_age   Always       -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Completed without error       00%     33143         -
# 2  Short offline       Completed without error       00%     33142         -
# 3  Short offline       Completed without error       00%     33141         -
# 4  Short offline       Completed without error       00%     33141         -
# 5  Short offline       Completed without error       00%     33133         -
# 6  Short offline       Completed without error       00%     33133         -
# 7  Short offline       Completed without error       00%     33115         -
# 8  Short offline       Completed without error       00%     33099         -
# 9  Short offline       Completed without error       00%     33091         -
#10  Short offline       Completed without error       00%     30865         -
#11  Short offline       Completed without error       00%     30847         -
#12  Short offline       Completed without error       00%     30811         -
#13  Short offline       Completed without error       00%     30803         -
#14  Short offline       Completed without error       00%     30803         -
#15  Short offline       Completed without error       00%     30794         -
#16  Short offline       Completed without error       00%     30794         -
#17  Short offline       Completed without error       00%     26924         -
#18  Short offline       Completed without error       00%     26921         -
#19  Short offline       Completed without error       00%     26921         -
#20  Short offline       Completed without error       00%     26888         -
#21  Short offline       Completed without error       00%     26880         -

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.

root@rescue-customer-eu (/////) ~ # smartctl -a /dev/sdb
smartctl 7.2 2020-12-30 r5155 [x86_64-linux-6.1.38-mod-std] (local build)
Copyright (C) 2002-20, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Hitachi/HGST Ultrastar 7K4000
Device Model:     HGST HUS724020ALA640
Serial Number:    PN2134P6HEY5NP
LU WWN Device Id: 5 000cca 22dd46de0
Firmware Version: MF6OABY0
User Capacity:    2,000,398,934,016 bytes [2.00 TB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    7200 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA8-ACS T13/1699-D revision 4
SATA Version is:  SATA 3.0, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Mon Sep 11 07:09:41 2023 UTC
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:  (0x82) Offline data collection activity
                                        was completed without error.
                                        Auto Offline Data Collection: Enabled.
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:                (   28) 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:        (   1) minutes.
Extended self-test routine
recommended polling time:        ( 326) 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   016    Pre-fail  Always       -       0
  2 Throughput_Performance  0x0005   137   137   054    Pre-fail  Offline      -       79
  3 Spin_Up_Time            0x0007   215   215   024    Pre-fail  Always       -       274 (Average 306)
  4 Start_Stop_Count        0x0012   100   100   000    Old_age   Always       -       120
  5 Reallocated_Sector_Ct   0x0033   100   100   005    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000b   100   100   067    Pre-fail  Always       -       0
  8 Seek_Time_Performance   0x0005   140   140   020    Pre-fail  Offline      -       26
  9 Power_On_Hours          0x0012   090   090   000    Old_age   Always       -       70019
 10 Spin_Retry_Count        0x0013   100   100   060    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       120
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       1114
193 Load_Cycle_Count        0x0012   100   100   000    Old_age   Always       -       1114
194 Temperature_Celsius     0x0002   166   166   000    Old_age   Always       -       36 (Min/Max 14/52)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0022   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0008   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x000a   200   200   000    Old_age   Always       -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Completed without error       00%     44327         -
# 2  Short offline       Completed without error       00%     44325         -
# 3  Short offline       Completed without error       00%     44325         -
# 4  Short offline       Completed without error       00%     44324         -
# 5  Short offline       Completed without error       00%     44316         -
# 6  Short offline       Completed without error       00%     44316         -
# 7  Short offline       Completed without error       00%     44298         -
# 8  Short offline       Completed without error       00%     44282         -
# 9  Short offline       Completed without error       00%     44274         -

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.

root@rescue-customer-eu (/////) ~ # cat /proc/mdstat
Personalities : [linear] [raid0] [raid1] [raid10] [raid6] [raid5] [raid4] [multipath] [faulty]
md2 : active raid1 sda2[0] sdb2[1]
      523200 blocks [2/2] [UU]

md3 : active raid1 sda3[0] sdb3[1]
      1952465856 blocks [2/2] [UU]

unused devices: <none>

root@rescue-customer-eu (/////) ~ # mdadm -D /dev/md3
/dev/md3:
           Version : 0.90
     Creation Time : Fri Oct 16 14:46:33 2020
        Raid Level : raid1
        Array Size : 1952465856 (1862.02 GiB 1999.33 GB)
     Used Dev Size : 1952465856 (1862.02 GiB 1999.33 GB)
      Raid Devices : 2
     Total Devices : 2
   Preferred Minor : 3
       Persistence : Superblock is persistent

       Update Time : Sun Sep 10 12:37:01 2023
             State : clean
    Active Devices : 2
   Working Devices : 2
    Failed Devices : 0
     Spare Devices : 0

Consistency Policy : resync

              UUID : e9ffe126:3edcd095:a4d2adc2:26fd5302
            Events : 0.681359

    Number   Major   Minor   RaidDevice State
       0       8        3        0      active sync   /dev/sda3
       1       8       19        1      active sync   /dev/sdb3

Does anyone have any suggestions on how to resolve this issue?

Thank you very much for your advice and assistance.

1 Answer 1

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Quick update, after several tests, I ran:

xfs_repair -L /dev/md3

This aims to remove the damaged XFS journal. Obviously, be cautious: it's always necessary to have a backup, as this could lead to corruption or additional data loss.

Thank you.

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