RAID5 member disks shrunk

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Dear list,

I hope you all had a good festive period. Happy New Year!

Sorry to burden you with this, but I'm in real need of some help! I recently suffered from a failed hard disk in my RAID5 array, and have made some rookie errors since.. I'll try and detail what I did as accurately and concisely as possible. Some help in recovering data from my ext4 partition would be greatly appreciated!

Set up:-
1. RAID0 was pre-configured on new machine, with 2x300GB WD Velociraptors. (2010) 2. Got another, identical drive and upgrade to RAID5 using Windows Intel Matrix Manager. (2011)

RAID Partitions (roughly):
  1. 100MB windows boot loader.
  2. 342GB NTFS Windows installation partition
  3. 256GB ext4 partition with Kubuntu 12.10, and dmraid.

Non-RAID Partitions (for completeness):
  Backup Drive: 2TB.
     1. 200GB Ubuntu 12.10 ext4 (recovabuntu) with dmraid.
     2. 1800GB NTFS backup and media partition.
  SAS drive: 600GB
     1. 600GB ext4 partition, for SQL and other databases.


Problem, started about two weeks ago:
  1. Suffer an IO error on member disk, whilst in Kubuntu. Array DEGRADED.
2. Goes unnoticed for at most a day. Shut down immediately, replace HD with new, identical disk. 3. Boot into Windows, use Matrix Storage manager to rebuild array on to new disk. Array now fine. 4. At some point after the array was rebuilt, back in Kubuntu, the new disk also raised an IO error. DEGRADED again.

Stop gap:
5. Panic, and boot into recovabuntu on non-raid disk. The 2TB drive is not a drive I want to (over-)use when not strictly necessary, as this has all my media on it and a couple of (old) backups. 6. WD have been stalling the RMA on the failed drive(s) over Christmas, and I didn't want to stress out my 2TB drive too much.
  7. Decide to get an SSD and use that as primary boot device.
8. Whilst at it, I also bought and installed a 5 bay Icy Box HD backplane, upgrading from a 3 bay version. This was trickier than I thought; I had to completely disassemble the PC and mod the 5.25" bays in the case, with drill, dremel, rivet gun, and some spray paint for good measure :)

Human error:
9. Putting it back together, I accidentally connected one of the good RAID member drives to the SAS controller, and the SAS drive into one of the SATA ports, which has an Intel ICH10R controller. 10. Took a couple boots into BIOS and recovabuntu to realise what I'd done wrong. Array now wants to rebuild on to good disk, using data from the drive that IO Error'd on me. Don't like the sound of that, so I leave it degraded.

(Botched) Recovery:
11. Install Arch Linux and Windows onto separate partitions on the SSD drive. 12. Read that Intel now support mdadm over dmraid, so install that on Arch.
  13. Backup some information:

    $ sudo mdadm -D /dev/md/RAID5

/dev/md/RAID5:
      Container : /dev/md/imsm0, member 0
     Raid Level : raid5
     Array Size : 586066944 (558.92 GiB 600.13 GB)
  Used Dev Size : 293033600 (279.46 GiB 300.07 GB)
   Raid Devices : 3
  Total Devices : 2

          State : active, degraded
 Active Devices : 2
Working Devices : 2
 Failed Devices : 0
  Spare Devices : 0

         Layout : left-asymmetric
     Chunk Size : 64K


           UUID : 789c5fd2:da9dd3d2:b57d7def:89f68d3c
    Number   Major   Minor   RaidDevice State
       1       8        0        0      active sync   /dev/sda
       1       0        0        1      removed
       0       8       16        2      active sync   /dev/sdb


    $ sudo mdadm -D /dev/md/imsm0

/dev/md/imsm0:
        Version : imsm
     Raid Level : container
  Total Devices : 3

Working Devices : 3


           UUID : 4528e473:abbe0e9f:25a8bb6b:bb9e9999
  Member Arrays : /dev/md/RAID5

    Number   Major   Minor   RaidDevice

       0       8        0        -        /dev/sda
       1       8       96        -        /dev/sdg
       2       8       16        -        /dev/sdb


    $ sfdisk -d /dev/sda > sda.out (and same for sdg and sdb)
    $ ls -l /dev/sd[agb].out
-rw-r--r-- 1 albl500 users   259 Dec 18 10:45 sda.out
-rw-r--r-- 1 albl500 users     0 Dec 18 10:47 sdb.out
-rw-r--r-- 1 albl500 users     0 Dec 18 10:47 sdg.out

    $ cat sda.out

# partition table of /dev/sda
unit: sectors

/dev/sda1 : start=     2048, size=   204800, Id= 7, bootable
/dev/sda2 : start=   206848, size=667994112, Id= 7
/dev/sda3 : start=668200960, size=503928832, Id= 7
/dev/sda4 : start=        0, size=        0, Id= 0

14. Figure I should zero the superblocks and re-create the array. Really should have backed up as much as possible before this...
    $ sudo mdadm --misc --zero-superblock /dev/sd[agb]

$ sudo mdadm --create /dev/md/imsm0 --raid-devices=2 --uuid='4528e473:abbe0e9f:25a8bb6b:bb9e9999' --metadata=imsm /dev/sda /dev/sdg /dev/sdb
mdadm: container /dev/md/imsm0 prepared.

$ sudo mdadm --create --verbose /dev/md/RAID5 --raid-devices=3 --level=5 --chunk=64 --layout=la --size=293033600 --uuid='789c5fd2b57d7def:89f68d3c' -e imsm /dev/sda /dev/sdg /dev/sdb
mdadm: /dev/sdb not enough space (586066062 < 586067200)
mdadm: /dev/sdb is smaller than given size. 0K < 293033600K + metadata
mdadm: /dev/sdc not enough space (586066062 < 586067200)
mdadm: /dev/sdc is not suitable for this array.
mdadm: create aborted


15. If I leave off the size option, then the array gets built, and verifies all 3 drives without a single IO error. So the drives seem to be okay now. But when they are assembled, the Array Size and Used Dev Size come out smaller than with the previous array, whose details are above. Now, after re-creating and verifying (with no size option), I get these results:

    $ sudo mdadm -D /dev/md/RAID5

/dev/md/RAID5:
      Container : /dev/md/imsm0, member 0
     Raid Level : raid5
     Array Size : 586065920 (558.92 GiB 600.13 GB)
  Used Dev Size : 293033024 (279.46 GiB 300.07 GB)
   Raid Devices : 3
  Total Devices : 3

          State : clean
 Active Devices : 3
Working Devices : 3
 Failed Devices : 0
  Spare Devices : 0

         Layout : left-asymmetric
     Chunk Size : 64K


           UUID : 2cdc3f5c:7d91eb7d:51b57c72:bdbfc1fb
    Number   Major   Minor   RaidDevice State
       2       8       16        0      active sync   /dev/sda
       1       8      112        1      active sync   /dev/sdg
       0       8       32        2      active sync   /dev/sdb

    $ sudo sfdisk -d /dev/md126  # this is: /dev/md/RAID5

# partition table of /dev/md126
unit: sectors

/dev/md126p1 : start=     2048, size=   204800, Id= 7, bootable
/dev/md126p2 : start=   206848, size=667994112, Id= 7
/dev/md126p3 : start=668200960, size=503928832, Id= 7
/dev/md126p4 : start=        0, size=        0, Id= 0

16. When I saw these partitions in /dev, I was very happy! I thought I had everything back, but I couldn't mount a single one of the file systems. I used testdisk to try and recover the partitions, and this changed the partition table to point to different start and end positions for p1 and p2, deleting p3. I could mount and recover data from my NTFS windows partition, but the ext4 partition could not be recovered at all; I suspect because of the new Minor numbers and the apparent reduced device and array sizes.

17. It seems the Used Dev size has reduced by 576kB ( = 512kB + 64kB), which I thought could be partially explained by an MBR being present on the disks, but I have been unable to think where the extra 64kB could be taken up.

18. So I backup the first 512kB of each member disk, and write zeros to those areas, with dd.

    $ sudo dd if=/dev/sdX of=sdX.out bs=512 count=1
    $ sudo dd if=/dev/zero of=/dev/sdX bs=512 count=1

19. Still unable to create an array with the right size (after zeroing superblocks). Updating the super-minor doesn't seem to apply to imsm containers, and I can't think of any other way to get this to re-assemble correctly.

So, I've got myself into a real mess here. I don't have the space to backup every disk image, which I've seen recommended pretty much everywhere.
Any help getting me out of this mess would be really, really appreciated!

Kind regards,
Alex

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