My system had these partitions:

  • DellUtility
  • Windows 7
  • Ubuntu 14.04 (64bit) - extended
  • /home - extended
  • virtualbox - extended
  • swap - extended

(A Dell box with Ubuntu dual-boot and seperate home / "other data" partitions)

Sequence of Events

  • Distro upgrade to 16.04.1, apparently successful
  • reboot and end up in Emergency Mode as described e.g. here
  • use of systemctl etc. was unsuccessful; a suggestion was using Upstart via GRUB, which booted to desktop
  • the next boot (into Emergency Mode) did not succeed; now the /home partition was unavailable
  • boot via USBDrive; /home still unavailable, listed as "unknown partition" by gparted
  • lengthy investigation via fdisk, testdisk etc. wiki, a howto showed that all superblocks were corrupted, no backups available. I'm not a recovery expert but this seems unusual.
  • Make a testdisk image into "virtualbox" partition
  • Follow process described here without success, including last-ditch use of mke2fs -S.
  • testdisk deeper search finds partition, but not the superblocks; alogn with messages like No ext2, JFS, Reiser, cramfs or XFS marker
  • Tools like photorec can retrieve some files, but they are garbled, miss filename / structure, and many are encrypted due to it being a /home partition
  • Decide that as I have a backup of the partition, and the original data, delete and replace the /home partition, which succeeds. Boot into "home-new" and set it up...
  • and on the next boot, imagine my surprise to find both "home-new" and the "virtualbox" partition are unavailable. Same superblock issue. Well, great.
  • Using USBDrive, re-re-create home partition in a different disk location; this appears stable. Delete "home-new".
  • Realise that the backup of /home, and some critical data, are on that now-unreadable partition; obtain a USB disk and make an image on there

Current Situation

My partitions are:

  • DellUtility (OK)
  • Windows 7 (OK)
  • Ubuntu 16.04 (OK)
  • /home-new (bad, deleted, in same disk location as original /home) - extended
  • /home (seems OK, at different disk location) - extended
  • virtualbox (bad) - extended
  • swap (OK) - extended

The "virtualbox" partition is ~550GB. It is unreadable and has no valid superblocks.

Important data on it: * a testdisk image of my original /home partiton , ~50GB, itself unreadable with no valid superblocks * some original data from /home that wasn't handled by Crashplan. Not enough to be a critical problem, but enough to be annoying.

Note that first boots were fine - it was on the next boot the issues occurred. The "virtualbox" partition has been backed up as a Testdisk image on a USB drive.


sudo fdisk -l /dev/sda
Disk /dev/sda: 931.5 GiB, 1000204886016 bytes, 1953525168 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
Disklabel type: dos
Disk identifier: 0x15642c74

Device     Boot      Start        End    Sectors   Size Id Type
/dev/sda1  *            63      80324      80262  39.2M  6 FAT16
/dev/sda2         18395136  427995135  409600000 195.3G  7 HPFS/NTFS/exFAT
/dev/sda3        427995136 1920120831 1492125696 711.5G  f W95 Ext'd (LBA)
/dev/sda4       1920122880 1953523711   33400832  15.9G 82 Linux swap / Solaris
/dev/sda5        438233088  489433087   51200000  24.4G 83 Linux
/dev/sda6        773240832 1920120831 1146880000 546.9G 83 Linux
/dev/sda7        633921536  736321535  102400000  48.8G 83 Linux

Partition 1 does not start on physical sector boundary.
Partition table entries are not in disk order.


sudo dumpe2fs /dev/sda6
dumpe2fs 1.42.13 (17-May-2015)
dumpe2fs: Bad magic number in super-block while trying to open /dev/sda6
Couldn't find valid filesystem superblock.


sudo parted -l
Model: ATA ST1000DM003-1CH1 (scsi)
Disk /dev/sda: 1000GB
Sector size (logical/physical): 512B/4096B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type      File system     Flags
 1      32.3kB  41.1MB  41.1MB  primary   fat16           boot
 2      9418MB  219GB   210GB   primary   ntfs
 3      219GB   983GB   764GB   extended                  lba
 5      224GB   251GB   26.2GB  logical   ext4
 7      325GB   377GB   52.4GB  logical   ext4
 6      396GB   983GB   587GB   logical
 4      983GB   1000GB  17.1GB  primary   linux-swap(v1)


As you can imagine, this is very frustrating. Note the "Partition 1 does not start on physical sector boundary." warning in fdisk, which did not appear before.

Going by Partition does not start on physical sector boundary? , I suspect there is some alignment issue which confuses low-level disk utilities, introduced by the 16.04 upgrade, but that's just a suspicion.


sudo gdisk -l /dev/sda
GPT fdisk (gdisk) version 1.0.1

Partition table scan:
  MBR: MBR only
  BSD: not present
  APM: not present
  GPT: not present

Found invalid GPT and valid MBR; converting MBR to GPT format
in memory. 

Disk /dev/sda: 1953525168 sectors, 931.5 GiB
Logical sector size: 512 bytes
Disk identifier (GUID): 8C15FD44-F839-4637-853E-C092F0959C48
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 1953525134
Partitions will be aligned on 8-sector boundaries
Total free space is 209964007 sectors (100.1 GiB)

Number  Start (sector)    End (sector)  Size       Code  Name
   1              63           80324   39.2 MiB    0700  Microsoft basic data
   2        18395136       427995135   195.3 GiB   0700  Microsoft basic data
   4      1920122880      1953523711   15.9 GiB    8200  Linux swap
   5       438233088       489433087   24.4 GiB    8300  Linux filesystem
   6       773240832      1920120831   546.9 GiB   8300  Linux filesystem
   7       633921536       736321535   48.8 GiB    8300  Linux filesystem


  1. How can I identify the cause? My system now seems stable, but am wary of further low-level disk writes.
  2. Is it possible to recover the superblock-less "virtualbox" partition - and then hopefully the superblock-less "home" partition image within?

Perhaps the superblocks are intact, but via an offset that the system isn't aware of.

  • e2fs utilities are for linux filesystems, which utilize superblocks, and journaling. basicly, youre using the wrong tool for the job. Try using testdisk. Additionaly, it would appear you are trying to recover to a filesystem currently in use. Dont do that. Boot via a live disk, and do your recovery with the disk not mounted, using testdisk and gparted.
    – j0h
    May 15, 2020 at 15:34

1 Answer 1


Have made some progress (and a partial answer):

Noticed that in some applications (e.g. System Monitor), at some point the swap became reported as 546.9GB. The swap should be 15.9GB, and that's a number suspiciously near the broken "virtualbox" partition.

lsblk showed that /dev/sda6 - the partition - was also mapped via cryptswap1 to swap.

/etc/crypttab had:

cryptswap1 /dev/sda6 /dev/urandom swap,cipher=aes-cbc-essiv:sha256

The smoking gun! So hypothesis now is the 16.04 upgrade failed to re-configure swap correctly, and on later boots the swap startup broke the partition (which would explain why first boots were successful).

  • Disable swap everywhere (used technique in What to do about "the disk drive for /dev/mapper/cryptswap1 is not ready yet or not present"? )
  • Reboot and confirm swap-less state
  • Use testdisk to investigate. It attempts to mark active partitions as deleted and can't find the partition, so quit.
  • Confirm state unchanged with sudo dumpe2fs /dev/sda6
  • dumpe2fs: Bad magic number in super-block while trying to open /dev/sda6 Couldn't find valid filesystem superblock.
  • So use the last ditch method described above:
  • sudo /sbin/mkfs.ext4 -S -v /dev/sda6
  • sudo mount /dev/sda6 /media/USER/virtualbox-image/
  • ... and ls lists some of the files / directories!

Well, hooray!!

I couldn't access the files, so ran fsck. There were so many errors I gave up with preen and interactive modes and just used -y. Here are some fsck messages for reference:

  • Group descriptor 4349 checksum is 0xf6d0, should be 0x2ed1. FIXED.
  • /dev/sda6: Inode 13434881 is in use, but has dtime set. FIXED.
  • /dev/sda6: Inode 13434881 has an extra size (336) which is invalid FIXED.
  • /dev/sda6: Inode 13434881 has INDEX_FL flag set but is not a directory. HTREE INDEX CLEARED.
  • /dev/sda6: Inode 13434881, i_blocks is 137157068659908, should be 0. FIXED.
  • Inodes that were part of a corrupted orphan linked list found. Fix? yes
  • Inode 13434886 was part of the orphaned inode list. FIXED.
  • Inode 13434886 has imagic flag set. Clear? yes
  • Inode 13434886 has an extra size (62340) which is invalid Fix? yes
  • Inode 13434886 has compression flag set on filesystem without compression support. Clear? yes
  • Inode 13434886 has INDEX_FL flag set but is not a directory. Clear HTree index? yes
  • Inode 13434886, i_size is 18440780219561279704, should be 0. Fix? yes
  • Inode 13434886, i_blocks is 219803506189340, should be 0. Fix? yes
  • Inode 13495674 has a bad extended attribute block 21496064. Clear? yes
  • Inode 13495674 has illegal block(s). Clear? yes
  • Illegal block #0 (1376321536) in inode 13495674. CLEARED.
  • File /image_new_superblock.dd (inode #45605, mod time Wed Oct 28 12:58:24 2015) has 1 multiply-claimed block(s), shared with 1 file(s): ... (inode #13455772, mod time Thu Jul 4 03:48:32 1996) Clone multiply-claimed blocks? yes

Many screens of the above, timestamps all over the place. fsck actually aborted several times due to memory allocation, LOL. Eventually it ran clean, with messages:

  • Running additional passes to resolve blocks claimed by more than one inode...
  • Pass 1B: Rescanning for multiply-claimed blocks
  • Pass 1C: Scanning directories for inodes with multiply-claimed blocks
  • Pass 1D: Reconciling multiply-claimed blocks

Can now mount the partition and copy data. A lot of files still seem intact.

But there's more to do; this partition has been affected for 3 weeks. Presumably if I repeat this on the image made initially, I can recover more or nearly all the data. And still need to investigate "Partition 1 does not start on physical sector boundary." But, looking good!

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