RAID rebuilding seems to have stopped

mdadmraid

My server was running a RAID 1 array with two disks. One of those disk failed today and was replaced.

I've copied the GPT partition to the new hard disk (sda) with:

sgdisk -R /dev/sda /dev/sdb

and changed the UDID with

sgdisk -G /dev/sda

I've then added both partitions to the RAID array:

mdadm /dev/md4 -a /dev/sda4

and

mdadm /dev/md5 -a /dev/sda5

/dev/md4 was rebuilt correctly, but not /dev/md5.

When I run cat /proc/mdstat shortly after running those commands, it showed this:

Personalities : [raid1]
md5 : active raid1 sda5[2] sdb5[1]
      2820667711 blocks super 1.2 [2/1] [_U]
      [>....................]  recovery =  0.0% (2109952/2820667711) finish=423.0min speed=111050K/sec

md4 : active raid1 sda4[2] sdb4[0]
      15727544 blocks super 1.2 [2/2] [UU]

unused devices: <none>

Which was correct; it was trying to rebuild md5, but a few minutes later, it stopped and now cat /proc/mdstat returns:

Personalities : [raid1]
md5 : active raid1 sda5[2](S) sdb5[1]
      2820667711 blocks super 1.2 [2/1] [_U]

md4 : active raid1 sda4[2] sdb4[0]
      15727544 blocks super 1.2 [2/2] [UU]

unused devices: <none>

Why did it stop rebuilding on that new disk? Here's what I get when running mdadm --detail /dev/md5

    /dev/md5:
        Version : 1.2
  Creation Time : Sun Sep 16 15:26:58 2012
     Raid Level : raid1
     Array Size : 2820667711 (2690.00 GiB 2888.36 GB)
  Used Dev Size : 2820667711 (2690.00 GiB 2888.36 GB)
   Raid Devices : 2
  Total Devices : 2
    Persistence : Superblock is persistent

    Update Time : Sat Dec 27 04:01:26 2014
          State : clean, degraded
 Active Devices : 1
Working Devices : 2
 Failed Devices : 0
  Spare Devices : 1

           Name : rescue:5  (local to host rescue)
           UUID : 29868a4d:f63c6b43:ee926581:fd775604
         Events : 5237753

    Number   Major   Minor   RaidDevice State
       0       0        0        0      removed
       1       8       21        1      active sync   /dev/sdb5

       2       8        5        -      spare   /dev/sda5

Thanks @Michael Hampton for your answer. I'm back at it after a night of sleep đŸ™‚ So I checked dmesg and I get this:

[Sat Dec 27 04:01:04 2014] md: recovery of RAID array md5
[Sat Dec 27 04:01:04 2014] md: minimum _guaranteed_  speed: 1000 KB/sec/disk.
[Sat Dec 27 04:01:04 2014] md: using maximum available idle IO bandwidth (but not more than 200000 KB/sec) for recovery.
[Sat Dec 27 04:01:04 2014] md: using 128k window, over a total of 2820667711k.
[Sat Dec 27 04:01:04 2014] RAID1 conf printout:
[Sat Dec 27 04:01:04 2014]  --- wd:2 rd:2
[Sat Dec 27 04:01:04 2014]  disk 0, wo:0, o:1, dev:sdb4
[Sat Dec 27 04:01:04 2014]  disk 1, wo:0, o:1, dev:sda4
[Sat Dec 27 04:01:21 2014] ata2.00: exception Emask 0x0 SAct 0x1e000 SErr 0x0 action 0x0
[Sat Dec 27 04:01:21 2014] ata2.00: irq_stat 0x40000008
[Sat Dec 27 04:01:21 2014] ata2.00: cmd 60/80:68:00:12:51/03:00:0d:00:00/40 tag 13 ncq 458752 in
[Sat Dec 27 04:01:21 2014]          res 41/40:80:68:14:51/00:03:0d:00:00/00 Emask 0x409 (media error) <F>
[Sat Dec 27 04:01:21 2014] ata2.00: configured for UDMA/133
[Sat Dec 27 04:01:21 2014] sd 1:0:0:0: [sdb] Unhandled sense code
[Sat Dec 27 04:01:21 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:21 2014] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE
[Sat Dec 27 04:01:21 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:21 2014] Sense Key : Medium Error [current] [descriptor]
[Sat Dec 27 04:01:21 2014] Descriptor sense data with sense descriptors (in hex):
[Sat Dec 27 04:01:21 2014]         72 03 11 04 00 00 00 0c 00 0a 80 00 00 00 00 00 
[Sat Dec 27 04:01:21 2014]         0d 51 14 68 
[Sat Dec 27 04:01:21 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:21 2014] Add. Sense: Unrecovered read error - auto reallocate failed
[Sat Dec 27 04:01:21 2014] sd 1:0:0:0: [sdb] CDB: 
[Sat Dec 27 04:01:21 2014] Read(16): 88 00 00 00 00 00 0d 51 12 00 00 00 03 80 00 00
[Sat Dec 27 04:01:21 2014] end_request: I/O error, dev sdb, sector 223417448
[Sat Dec 27 04:01:21 2014] ata2: EH complete
[Sat Dec 27 04:01:24 2014] ata2.00: exception Emask 0x0 SAct 0x8 SErr 0x0 action 0x0
[Sat Dec 27 04:01:24 2014] ata2.00: irq_stat 0x40000008
[Sat Dec 27 04:01:24 2014] ata2.00: cmd 60/08:18:68:14:51/00:00:0d:00:00/40 tag 3 ncq 4096 in
[Sat Dec 27 04:01:24 2014]          res 41/40:08:68:14:51/00:00:0d:00:00/00 Emask 0x409 (media error) <F>
[Sat Dec 27 04:01:24 2014] ata2.00: configured for UDMA/133
[Sat Dec 27 04:01:24 2014] sd 1:0:0:0: [sdb] Unhandled sense code
[Sat Dec 27 04:01:24 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:24 2014] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE
[Sat Dec 27 04:01:24 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:24 2014] Sense Key : Medium Error [current] [descriptor]
[Sat Dec 27 04:01:24 2014] Descriptor sense data with sense descriptors (in hex):
[Sat Dec 27 04:01:24 2014]         72 03 11 04 00 00 00 0c 00 0a 80 00 00 00 00 00 
[Sat Dec 27 04:01:24 2014]         0d 51 14 68 
[Sat Dec 27 04:01:24 2014] sd 1:0:0:0: [sdb]  
[Sat Dec 27 04:01:24 2014] Add. Sense: Unrecovered read error - auto reallocate failed
[Sat Dec 27 04:01:24 2014] sd 1:0:0:0: [sdb] CDB: 
[Sat Dec 27 04:01:24 2014] Read(16): 88 00 00 00 00 00 0d 51 14 68 00 00 00 08 00 00
[Sat Dec 27 04:01:24 2014] end_request: I/O error, dev sdb, sector 223417448
[Sat Dec 27 04:01:24 2014] ata2: EH complete
[Sat Dec 27 04:01:24 2014] md/raid1:md5: sdb: unrecoverable I/O read error for block 4219904
[Sat Dec 27 04:01:24 2014] md: md5: recovery interrupted.
[Sat Dec 27 04:01:24 2014] RAID1 conf printout:
[Sat Dec 27 04:01:24 2014]  --- wd:1 rd:2
[Sat Dec 27 04:01:24 2014]  disk 0, wo:1, o:1, dev:sda5
[Sat Dec 27 04:01:24 2014]  disk 1, wo:0, o:1, dev:sdb5
[Sat Dec 27 04:01:24 2014] RAID1 conf printout:
[Sat Dec 27 04:01:24 2014]  --- wd:1 rd:2
[Sat Dec 27 04:01:24 2014]  disk 1, wo:0, o:1, dev:sdb5

So it does seem to be a read error. But SMART doesn't seem to be too bad (if I understand it correctly):

SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   088   087   006    Pre-fail  Always       -       154455820
  3 Spin_Up_Time            0x0003   096   096   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       5
  5 Reallocated_Sector_Ct   0x0033   084   084   036    Pre-fail  Always       -       21664
  7 Seek_Error_Rate         0x000f   072   060   030    Pre-fail  Always       -       38808769144
  9 Power_On_Hours          0x0032   071   071   000    Old_age   Always       -       26073
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       5
183 Runtime_Bad_Block       0x0032   099   099   000    Old_age   Always       -       1
184 End-to-End_Error        0x0032   100   100   099    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   001   001   000    Old_age   Always       -       721
188 Command_Timeout         0x0032   100   099   000    Old_age   Always       -       4295032833
189 High_Fly_Writes         0x003a   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   063   061   045    Old_age   Always       -       37 (Min/Max 33/37)
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       0
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       3
193 Load_Cycle_Count        0x0032   095   095   000    Old_age   Always       -       10183
194 Temperature_Celsius     0x0022   037   040   000    Old_age   Always       -       37 (0 21 0 0)
197 Current_Pending_Sector  0x0012   088   088   000    Old_age   Always       -       2072
198 Offline_Uncorrectable   0x0010   088   088   000    Old_age   Offline      -       2072
199 UDMA_CRC_Error_Count    0x003e   200   200   000    Old_age   Always       -       0
240 Head_Flying_Hours       0x0000   100   253   000    Old_age   Offline      -       157045479198210
241 Total_LBAs_Written      0x0000   100   253   000    Old_age   Offline      -       4435703883570
242 Total_LBAs_Read         0x0000   100   253   000    Old_age   Offline      -       5487937263078

SMART Error Log Version: 1
ATA Error Count: 6 (device log contains only the most recent five errors)

Anyway thanks for your answer. And yes, if I was setting up the server again I definitely would not use more than one partition for my RAID array (in this case actually md5 is even using LVM.

Thanks,

Best Answer

It looks like you physically removed the faulty disk without Linux being fully aware of it, thus when you added the new disk it was marked as a spare (and the system is still waiting for you to put the old disk back in). It is likely that /dev/md4 failed and Linux detected the failure, but since /dev/md5 is a separate array (that didn't itself fail) Linux still believed it was good.

To recover from this situation, you need to tell the system to start using the spare, and to forget about the removed disk.

First, grow the RAID array to three devices, so that it can make use of the spare.

mdadm --grow /dev/md5 --raid-devices=3

At this point it should begin syncing to the spare, which will be listed as spare rebuilding in mdadm --detail, and you should see the sync operation in /proc/mdstat.

When the sync completes, you'll tell mdadm to forget about the device that is no longer present.

mdadm --remove /dev/md5 detached

Finally, you set the number of devices back to 2.

mdadm --grow /dev/md5 --raid-devices=2

How your system got into this state, I can't be sure. But it could be that your other disk had a read error, causing the resync to stop and this failed state to occur. If this is the case, you'll see log entries to that effect in dmesg when the sync operation dies. If this turns out to be case you'll need some deeper magic (update your question if this happens) and possibly to have your backups handy.

You may also want to read this virtually identical question on Super User as it contains some other possible solutions.

Finally, it is a best practice to use whole disks as RAID array members, or at most a single partition of the disk, you can then divide up the RAID block device with LVM if necessary. This configuration would have prevented this problem.

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