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I'm running Debian Wheezy (Linux wheezy3.2.0-4-amd64 #1 SMP Debian 3.2.63-2+deb7u1 x86_64 GNU/Linux) as an encrypted LVM with hardware raid 1 (Adaptec 6405E) on a supermicro server.

I was encounting the following errors during the the kernel update:

Running depmod.
Examining /etc/kernel/postinst.d.
run-parts: executing /etc/kernel/postinst.d/initramfs-tools 3.2.0-4-amd64 /boot/vmlinuz-3.2.0-4-amd64
update-initramfs: Generating /boot/initrd.img-3.2.0-4-amd64
run-parts: executing /etc/kernel/postinst.d/zz-update-grub 3.2.0-4-amd64 /boot/vmlinuz-3.2.0-4-amd64
error: unknown LVM metadata header.
error: unknown LVM metadata header.
Generating grub.cfg ...
Found linux image: /boot/vmlinuz-3.2.0-4-amd64
Found initrd image: /boot/initrd.img-3.2.0-4-amd64
error: unknown LVM metadata header.
error: unknown LVM metadata header.
error: unknown LVM metadata header.
error: unknown LVM metadata header.
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
done

Here is the output for pvdisplay, vgdisplay, lvdisplay, df, pvs, lvs, vgs:

root@wheezy:~# pvdisplay -v
    Scanning for physical volume names
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
  --- Physical volume ---
  PV Name               /dev/dm-0
  VG Name               wheezy
  PV Size               111.37 GiB / not usable 2.00 MiB
  Allocatable           yes (but full)
  PE Size               4.00 MiB
  Total PE              28510
  Free PE               0
  Allocated PE          28510
  PV UUID               8DEe3m-NaQC-mRia-cMfv-OO2O-Foog-XXTLeU

  "/dev/sda1" is a new physical volume of "243.00 MiB"
  --- NEW Physical volume ---
  PV Name               /dev/sda1
  VG Name
  PV Size               243.00 MiB
  Allocatable           NO
  PE Size               0
  Total PE              0
  Free PE               0
  Allocated PE          0
  PV UUID               fnKsgr-KC2h-inYi-jhli-YFil-edTh-RsRTzK

root@wheezy:~# vgdisplay -v
    Finding all volume groups
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
    Finding volume group "wheezy"
  --- Volume group ---
  VG Name               wheezy
  System ID
  Format                lvm2
  Metadata Areas        1
  Metadata Sequence No  10
  VG Access             read/write
  VG Status             resizable
  MAX LV                0
  Cur LV                3
  Open LV               3
  Max PV                0
  Cur PV                1
  Act PV                1
  VG Size               111.37 GiB
  PE Size               4.00 MiB
  Total PE              28510
  Alloc PE / Size       28510 / 111.37 GiB
  Free  PE / Size       0 / 0
  VG UUID               nq8fye-SpVe-cHrd-AM99-YWdA-7SPp-L3S2Hm

  --- Logical volume ---
  LV Path                /dev/wheezy/SWAP
  LV Name                SWAP
  VG Name                wheezy
  LV UUID                VbC1TX-2Ppz-1003-VFqU-0o0X-otwu-qy5Xam
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:36:55 +0000
  LV Status              available
  # open                 2
  LV Size                7.45 GiB
  Current LE             1907
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:1

  --- Logical volume ---
  LV Path                /dev/wheezy/TMP
  LV Name                TMP
  VG Name                wheezy
  LV UUID                btQknc-WeBv-q2xA-dhz0-GsqR-G2hn-gKwCh0
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:37:05 +0000
  LV Status              available
  # open                 1
  LV Size                10.79 GiB
  Current LE             2761
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:2

  --- Logical volume ---
  LV Path                /dev/wheezy/base
  LV Name                base
  VG Name                wheezy
  LV UUID                dWD7ro-ACQ6-04O2-rKd2-iMCe-HddW-kX1mt6
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:37:13 +0000
  LV Status              available
  # open                 1
  LV Size                93.13 GiB
  Current LE             23842
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:3

  --- Physical volumes ---
  PV Name               /dev/dm-0
  PV UUID               8DEe3m-NaQC-mRia-cMfv-OO2O-Foog-XXTLeU
  PV Status             allocatable
  Total PE / Free PE    28510 / 0

root@wheezy:~# lvdisplay -v
    Finding all logical volumes
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
  --- Logical volume ---
  LV Path                /dev/wheezy/SWAP
  LV Name                SWAP
  VG Name                wheezy
  LV UUID                VbC1TX-2Ppz-1003-VFqU-0o0X-otwu-qy5Xam
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:36:55 +0000
  LV Status              available
  # open                 2
  LV Size                7.45 GiB
  Current LE             1907
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:1

  --- Logical volume ---
  LV Path                /dev/wheezy/TMP
  LV Name                TMP
  VG Name                wheezy
  LV UUID                btQknc-WeBv-q2xA-dhz0-GsqR-G2hn-gKwCh0
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:37:05 +0000
  LV Status              available
  # open                 1
  LV Size                10.79 GiB
  Current LE             2761
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:2

  --- Logical volume ---
  LV Path                /dev/wheezy/base
  LV Name                base
  VG Name                wheezy
  LV UUID                dWD7ro-ACQ6-04O2-rKd2-iMCe-HddW-kX1mt6
  LV Write Access        read/write
  LV Creation host, time wheezy, 2014-11-24 16:37:13 +0000
  LV Status              available
  # open                 1
  LV Size                93.13 GiB
  Current LE             23842
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:3


root@wheezy:~# df -h
Filesystem                   Size  Used Avail Use% Mounted on
rootfs                        92G   25G   63G  28% /
udev                          10M     0   10M   0% /dev
tmpfs                        3.2G  1.3M  3.2G   1% /run
/dev/mapper/wheezy-base   92G   25G   63G  28% /
tmpfs                        5.0M  4.0K  5.0M   1% /run/lock
tmpfs                        6.3G     0  6.3G   0% /run/shm
/dev/sda1                    228M   30M  187M  14% /boot
/dev/mapper/wheezy-TMP    11G  172M   10G   2% /tmp

root@wheezy:~# pvs
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
  PV         VG         Fmt  Attr PSize   PFree
  /dev/dm-0  wheezy lvm2 a--  111.37g      0
  /dev/sda1             lvm2 a--  243.00m 243.00m

root@wheezy:~# vgs
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
  VG         #PV #LV #SN Attr   VSize   VFree
  wheezy   1   3   0 wz--n- 111.37g    0

root@wheezy:~# lvs
  Incorrect metadata area header checksum on /dev/sda1 at offset 4096
  LV   VG         Attr     LSize  Pool Origin Data%  Move Log Copy%  Convert
  SWAP wheezy -wi-ao--  7.45g
  TMP  wheezy -wi-ao-- 10.79g
  base wheezy -wi-ao-- 93.13g

What would be the best workaround to fix the corrupted metadata header? I have an identical machine (same hardware, same partitions, same wheezy installation, same apt sources) running without any problems.

The second machine doesn't have this output in the pvdislay-command:

  "/dev/sda1" is a new physical volume of "243.00 MiB"
  --- NEW Physical volume ---
  PV Name               /dev/sda1
  VG Name
  PV Size               243.00 MiB
  Allocatable           NO
  PE Size               0
  Total PE              0
  Free PE               0
  Allocated PE          0
  PV UUID               fnKsgr-KC2h-inYi-jhli-YFil-edTh-RsRTzK
  • I have the exact same problem as your first machine. As I understand this metadata is some leftovers from the installation part, when you are configuring partitions and LVMs. I still do not have a solution. Regarding your second machine, you do not have this problem cause you did not configure any LVMs. As you can see the pvdislay returns a physical drive only – Athafoud Apr 8 '15 at 15:04
0

You may have leftover metadata from earlier partitioning. Like a boot partition that is used without LVM but which has LVM metadata because an installer prepared it to be used via LVM.

https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/452350

(German) https://debianforum.de/forum/viewtopic.php?f=33&t=154131

Yes this is not a full-blown solution, but progress.

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