f16 gpt corrupt header, repair it and later the other one gets corrupted

[rtguille]

I recently installed F16, later i noticed that one of the gpt header get corrupted
and i am tring to find why.

# gdisk -l /dev/sda
GPT fdisk (gdisk) version 0.8.1

Caution: invalid backup GPT header, but valid main header; regenerating
backup header from main header.

Partition table scan:
MBR: protective
BSD: not present
APM: not present
GPT: damaged

************************************************** **************************
Caution: Found protective or hybrid MBR and corrupt GPT. Using GPT, but disk
verification and recovery are STRONGLY recommended.
************************************************** **************************
Disk /dev/sda: 625142448 sectors, 298.1 GiB
Logical sector size: 512 bytes
Disk identifier (GUID): 4F85375A-FCC5-4582-B687-916C9DE4D12B
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 625142414
Partitions will be aligned on 2048-sector boundaries
Total free space is 2669 sectors (1.3 MiB)

Number Start (sector) End (sector) Size Code Name
1 2048 4095 1024.0 KiB EF02
2 4096 2101247 1024.0 MiB EF00 ext4
3 2101248 75501567 35.0 GiB 0700
4 75501568 390381567 150.1 GiB 0700
5 390381568 474267647 40.0 GiB 0700
6 474267648 482656255 4.0 GiB 8200
7 482656256 625141759 67.9 GiB 0700


# parted -l
Error: The backup GPT table is corrupt, but the primary appears OK, so that will
be used.
OK/Cancel? ok
Model: ATA SAMSUNG HM320HJ (scsi)
Disk /dev/sda: 320GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt

Number Start End Size File system Name Flags
1 1049kB 2097kB 1049kB bios_grub
2 2097kB 1076MB 1074MB ext4 ext4 boot
3 1076MB 38.7GB 37.6GB ext4
4 38.7GB 200GB 161GB ext4
5 200GB 243GB 42.9GB
6 243GB 247GB 4295MB linux-swap(v1)
7 247GB 320GB 73.0GB ext4


Model: Linux device-mapper (crypt) (dm)
Disk /dev/mapper/luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f: 42.9GB
Sector size (logical/physical): 512B/512B

Partition Table: loop

Number Start End Size File system Flags
1 0.00B 42.9GB 42.9GB ext4


Something happens at boot, that either the main or backup gpt header "corrupts". One time the main, the other
the backup. I created the gpt partitions with anaconda at install time, with custom partitioning.

To repair it, i do:

# gdisk /dev/sda
GPT fdisk (gdisk) version 0.8.1

Caution: invalid backup GPT header, but valid main header; regenerating
backup header from main header.

Partition table scan:
MBR: protective
BSD: not present
APM: not present
GPT: damaged

************************************************** **************************
Caution: Found protective or hybrid MBR and corrupt GPT. Using GPT, but disk
verification and recovery are STRONGLY recommended.
************************************************** **************************

Command (? for help): r

Recovery/transformation command (? for help): ?
b use backup GPT header (rebuilding main)
c load backup partition table from disk (rebuilding main)
d use main GPT header (rebuilding backup)
e load main partition table from disk (rebuilding backup)
f load MBR and build fresh GPT from it
g convert GPT into MBR and exit
h make hybrid MBR
i show detailed information on a partition
l load partition data from a backup file
m return to main menu
o print protective MBR data
p print the partition table
q quit without saving changes
t transform BSD disklabel partition
v verify disk
w write table to disk and exit
x extra functionality (experts only)
? print this menu

Recovery/transformation command (? for help): d

Recovery/transformation command (? for help): p
Disk /dev/sda: 625142448 sectors, 298.1 GiB
Logical sector size: 512 bytes
Disk identifier (GUID): 4F85375A-FCC5-4582-B687-916C9DE4D12B
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 625142414
Partitions will be aligned on 2048-sector boundaries
Total free space is 2669 sectors (1.3 MiB)

Number Start (sector) End (sector) Size Code Name
1 2048 4095 1024.0 KiB EF02
2 4096 2101247 1024.0 MiB EF00 ext4
3 2101248 75501567 35.0 GiB 0700
4 75501568 390381567 150.1 GiB 0700
5 390381568 474267647 40.0 GiB 0700
6 474267648 482656255 4.0 GiB 8200
7 482656256 625141759 67.9 GiB 0700

Recovery/transformation command (? for help): w

Final checks complete. About to write GPT data. THIS WILL OVERWRITE EXISTING
PARTITIONS!!

Do you want to proceed? (Y/N): y
OK; writing new GUID partition table (GPT).
Warning: The kernel is still using the old partition table.
The new table will be used at the next reboot.
The operation has completed successfully.

# partprobe

# gdisk -l /dev/sda
GPT fdisk (gdisk) version 0.8.1

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

Found valid GPT with protective MBR; using GPT.
Disk /dev/sda: 625142448 sectors, 298.1 GiB
Logical sector size: 512 bytes
Disk identifier (GUID): 4F85375A-FCC5-4582-B687-916C9DE4D12B
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 625142414
Partitions will be aligned on 2048-sector boundaries
Total free space is 2669 sectors (1.3 MiB)

Number Start (sector) End (sector) Size Code Name
1 2048 4095 1024.0 KiB EF02
2 4096 2101247 1024.0 MiB EF00 ext4
3 2101248 75501567 35.0 GiB 0700
4 75501568 390381567 150.1 GiB 0700
5 390381568 474267647 40.0 GiB 0700
6 474267648 482656255 4.0 GiB 8200
7 482656256 625141759 67.9 GiB 0700

# parted -l
Model: ATA SAMSUNG HM320HJ (scsi)
Disk /dev/sda: 320GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt

Number Start End Size File system Name Flags
1 1049kB 2097kB 1049kB bios_grub
2 2097kB 1076MB 1074MB ext4 ext4 boot
3 1076MB 38.7GB 37.6GB ext4
4 38.7GB 200GB 161GB ext4
5 200GB 243GB 42.9GB
6 243GB 247GB 4295MB linux-swap(v1)
7 247GB 320GB 73.0GB ext4


Model: Linux device-mapper (crypt) (dm)
Disk /dev/mapper/luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f: 42.9GB
Sector size (logical/physical): 512B/512B
Partition Table: loop

Number Start End Size File system Flags
1 0.00B 42.9GB 42.9GB ext4


I belive that sometimes it gets corrupted. Sometimes, but not allways,
when i power-on the laptop, systemd ask for root password or to press ctrl+d
for root login, with no visible cause of the question (no error), i just
press ctrl+d and it boots ok. Also grub2 adds like 10-15 seconds to the 'start'
boot process (which is more than the 5 seconds, since it is the first
time i do use it, i will not change it for now.)

[srs5694]

What, if anything, is installed on the computer other than Fedora 16? Are you using any unusual boot loaders or other pre-boot software? Some such programs, especially if they're GPT-unaware, will overwrite some of the sectors used by the primary GPT data, which could be at least part of the problem.

You might try running Boot Info Script and posting the RESULTS.TXT file that it generates. That provides information on your boot loaders and other low-level boot information. (Please post using code tags, though -- [ code ] before the text and [ /code ] after, but closing up the spaces within the brackets. That preserves columnar formatting, which the forum software otherwise removes.)

Another possibility is that you're running into hardware problems -- a bad hard disk, disk interface, RAM, or even CPU. You could try checking your SMART data (accessible from Palimpsest Disk Utility or other tools), or check dmesg output for hints of hardware problems.

[rtguille]

F16 uses the whole drive. The partitions where created by anaconda (using custom partitioning).
Boot time is unusually high compared to F15 (which was previously installed), specially the time it takes
to grub2 menu to appear is just gigantic (it seems like 10s) and then it waits other 5s.
I do not execute anything in particular regarding to bootloaders, i suspect that something at boot time corrupts it, probably grub2.

# cat /etc/grub2.cfg
#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub2-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#

### BEGIN /etc/grub.d/00_header ###
if [ -s $prefix/grubenv ]; then
load_env
fi
set default="0"
if [ "${prev_saved_entry}" ]; then
set saved_entry="${prev_saved_entry}"
save_env saved_entry
set prev_saved_entry=
save_env prev_saved_entry
set boot_once=true
fi

function savedefault {
if [ -z "${boot_once}" ]; then
saved_entry="${chosen}"
save_env saved_entry
fi
}

function load_video {
insmod vbe
insmod vga
insmod video_bochs
insmod video_cirrus
}

set timeout=5
### END /etc/grub.d/00_header ###

### BEGIN /etc/grub.d/10_linux ###
menuentry 'Fedora (3.1.1-2.fc16.x86_64)' --class fedora --class gnu-linux --class gnu --class os {
load_video
set gfxpayload=keep
insmod gzio
insmod part_gpt
insmod ext2
set root='(hd0,gpt2)'
search --no-floppy --fs-uuid --set=root f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc
echo 'Loading Fedora (3.1.1-1.fc16.x86_64)'
linux /vmlinuz-3.1.1-2.fc16.x86_64 root=UUID=7a5bcedb-cbc1-4c07-962a-b44c86be8c0d ro rd.md=0 rd.lvm=0 rd.dm=0 quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 KEYTABLE=es LANG=en_US.UTF-8
echo 'Loading initial ramdisk ...'
initrd /initramfs-3.1.1-2.fc16.x86_64.img
}
menuentry 'Fedora (3.1.1-1.fc16.x86_64)' --class fedora --class gnu-linux --class gnu --class os {
load_video
set gfxpayload=keep
insmod gzio
insmod part_gpt
insmod ext2
set root='(hd0,gpt2)'
search --no-floppy --fs-uuid --set=root f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc
echo 'Loading Fedora (3.1.1-1.fc16.x86_64)'
linux /vmlinuz-3.1.1-1.fc16.x86_64 root=UUID=7a5bcedb-cbc1-4c07-962a-b44c86be8c0d ro rd.md=0 rd.lvm=0 rd.dm=0 quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 KEYTABLE=es LANG=en_US.UTF-8
echo 'Loading initial ramdisk ...'
initrd /initramfs-3.1.1-1.fc16.x86_64.img
}
menuentry 'Fedora Linux, with Linux 3.1.0-7.fc16.x86_64' --class fedora --class gnu-linux --class gnu --class os {
load_video
set gfxpayload=keep
insmod gzio
insmod part_gpt
insmod ext2
set root='(hd0,gpt2)'
search --no-floppy --fs-uuid --set=root f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc
echo 'Loading Linux 3.1.0-7.fc16.x86_64 ...'
linux /vmlinuz-3.1.0-7.fc16.x86_64 root=UUID=7a5bcedb-cbc1-4c07-962a-b44c86be8c0d ro rd.md=0 rd.lvm=0 rd.dm=0 quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 KEYTABLE=es LANG=en_US.UTF-8
echo 'Loading initial ramdisk ...'
initrd /initramfs-3.1.0-7.fc16.x86_64.img
}
menuentry 'Fedora Linux, with Linux 3.1.0-7.fc16.x86_64 (recovery mode)' --class fedora --class gnu-linux --class gnu --class os {
load_video
set gfxpayload=keep
insmod gzio
insmod part_gpt
insmod ext2
set root='(hd0,gpt2)'
search --no-floppy --fs-uuid --set=root f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc
echo 'Loading Linux 3.1.0-7.fc16.x86_64 ...'
linux /vmlinuz-3.1.0-7.fc16.x86_64 root=UUID=7a5bcedb-cbc1-4c07-962a-b44c86be8c0d ro single rd.md=0 rd.lvm=0 rd.dm=0 quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 KEYTABLE=es LANG=en_US.UTF-8
echo 'Loading initial ramdisk ...'
initrd /initramfs-3.1.0-7.fc16.x86_64.img
}
### END /etc/grub.d/10_linux ###

### BEGIN /etc/grub.d/20_linux_xen ###
### END /etc/grub.d/20_linux_xen ###

### BEGIN /etc/grub.d/30_os-prober ###
### END /etc/grub.d/30_os-prober ###

### BEGIN /etc/grub.d/40_custom ###
# This file provides an easy way to add custom menu entries. Simply type the
# menu entries you want to add after this comment. Be careful not to change
# the 'exec tail' line above.
### END /etc/grub.d/40_custom ###

### BEGIN /etc/grub.d/41_custom ###
if [ -f $prefix/custom.cfg ]; then
source $prefix/custom.cfg;
fi
### END /etc/grub.d/41_custom ###

### BEGIN /etc/grub.d/90_persistent ###
### END /etc/grub.d/90_persistent ###


# cat /etc/default/grub
GRUB_TIMEOUT=5
GRUB_DISTRIBUTOR="Fedora"
GRUB_DEFAULT=saved
GRUB_CMDLINE_LINUX="rd.md=0 rd.lvm=0 rd.dm=0 quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 KEYTABLE=es LANG=en_US.UTF-8"

dmesg:
[ 1.959237] scsi 1:0:0:0: CD-ROM MAT****A DVD+-RW UJ8A2 1.02 PQ: 0 ANSI: 5
[ 1.986195] Alternate GPT is invalid, using primary GPT.
[ 1.986250] sda: sda1 sda2 sda3 sda4 sda5 sda6 sda7

[srs5694]

Please post the Boot Info Script results. Also, please use code tags!

[rtguille]

                  Boot Info Script 0.60    from 17 May 2011


============================= Boot Info Summary: ===============================

 => Grub2 (v1.99) is installed in the MBR of /dev/sda and looks at sector 2048 
    of the same hard drive for core.img. core.img is at this location and 
    looks for ?? on this drive.

sda1: __________________________________________________________________________

    File system:       BIOS Boot partition
    Boot sector type:  Grub2's core.img
    Boot sector info:  

sda2: __________________________________________________________________________

    File system:       ext4
    Boot sector type:  -
    Boot sector info:  
    Operating System:  
    Boot files:        /grub2/core.img

sda3: __________________________________________________________________________

    File system:       ext4
    Boot sector type:  -
    Boot sector info:  
    Operating System:  Fedora release 16 (Verne) 
                       Kernel on an ()
    Boot files:        /etc/fstab /boot/grub2/core.img

sda4: __________________________________________________________________________

    File system:       ext4
    Boot sector type:  -
    Boot sector info:  
    Operating System:  
    Boot files:        

sda5: __________________________________________________________________________

    File system:       crypto_LUKS
    Boot sector type:  Unknown
    Boot sector info:  

sda6: __________________________________________________________________________

    File system:       swap
    Boot sector type:  -
    Boot sector info:  

sda7: __________________________________________________________________________

    File system:       ext4
    Boot sector type:  -
    Boot sector info:  
    Operating System:  
    Boot files:        

============================ Drive/Partition Info: =============================

Drive: sda _____________________________________________________________________

Disk /dev/sda: 320.1 GB, 320072933376 bytes
255 heads, 63 sectors/track, 38913 cylinders, total 625142448 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes

Partition  Boot  Start Sector    End Sector  # of Sectors  Id System

/dev/sda1                   1   625,142,447   625,142,447  ee GPT


GUID Partition Table detected.

Partition    Start Sector    End Sector  # of Sectors System
/dev/sda1           2,048         4,095         2,048 BIOS Boot partition
/dev/sda2           4,096     2,101,247     2,097,152 EFI System partition
/dev/sda3       2,101,248    75,501,567    73,400,320 Data partition (Windows/Linux)
/dev/sda4      75,501,568   390,381,567   314,880,000 Data partition (Windows/Linux)
/dev/sda5     390,381,568   474,267,647    83,886,080 Data partition (Windows/Linux)
/dev/sda6     474,267,648   482,656,255     8,388,608 Swap partition (Linux)
/dev/sda7     482,656,256   625,141,759   142,485,504 Data partition (Windows/Linux)

"blkid" output: ________________________________________________________________

Device           UUID                                   TYPE       LABEL

/dev/mapper/luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f d258aa4c-e613-4491-a226-45bd1863e294   ext4       
/dev/sda2        f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc   ext4       
/dev/sda3        7a5bcedb-cbc1-4c07-962a-b44c86be8c0d   ext4       _Fedora-16-x86_6
/dev/sda4        e21fac71-cc35-4c18-a736-1284b04ebccd   ext4       
/dev/sda5        0de9acb9-cb50-4a89-b93e-f9bc74b5724f   crypto_LUKS 
/dev/sda6        a0e6bd27-80e6-43b7-928b-4a39e1963654   swap       
/dev/sda7        db0a257a-83a4-48e6-a640-c4278b26eb89   ext4       

========================= "ls -R /dev/mapper/" output: =========================

/dev/mapper:
control
luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f

================================ Mount points: =================================

Device           Mount_Point              Type       Options

/dev/mapper/luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f /home                    ext4       (rw,relatime,seclabel,user_xattr,acl,barrier=1,data=ordered)
/dev/sda2        /boot                    ext4       (rw,relatime,seclabel,user_xattr,acl,barrier=1,data=ordered)
/dev/sda3        /                        ext4       (rw,relatime,seclabel,user_xattr,barrier=1,data=ordered)
/dev/sda4        /virtual                 ext4       (rw,relatime,seclabel,user_xattr,acl,barrier=1,data=ordered)
/dev/sda7        /data1                   ext4       (rw,relatime,seclabel,user_xattr,acl,barrier=1,data=ordered)


=================== sda2: Location of files loaded by Grub: ====================

           GiB - GB             File                                 Fragment(s)

   0.158065796 = 0.169721856    initramfs-3.1.0-7.fc16.x86_64.img              1
   0.181510925 = 0.194895872    initramfs-3.1.1-1.fc16.x86_64.img              1
   0.205032349 = 0.220151808    initramfs-3.1.1-2.fc16.x86_64.img              1
   0.135044098 = 0.145002496    vmlinuz-3.1.0-7.fc16.x86_64                    1
   0.164344788 = 0.176463872    vmlinuz-3.1.1-1.fc16.x86_64                    1
   0.187652588 = 0.201490432    vmlinuz-3.1.1-2.fc16.x86_64                    1

================= sda2: Location of files loaded by Syslinux: ==================

           GiB - GB             File                                 Fragment(s)

   0.129699707 = 0.139264000    extlinux/cat.c32                               1
   0.130611420 = 0.140242944    extlinux/chain.c32                             1
   0.129665375 = 0.139227136    extlinux/cmd.c32                               1
   0.129814148 = 0.139386880    extlinux/config.c32                            1
   0.129707336 = 0.139272192    extlinux/cpuid.c32                             1
   0.130130768 = 0.139726848    extlinux/cpuidtest.c32                         1
   0.130554199 = 0.140181504    extlinux/disk.c32                              1
   0.129787445 = 0.139358208    extlinux/dmitest.c32                           1
   0.130462646 = 0.140083200    extlinux/elf.c32                               1
   0.129852295 = 0.139427840    extlinux/ethersel.c32                          1
   0.130592346 = 0.140222464    extlinux/gfxboot.c32                           1
   0.130210876 = 0.139812864    extlinux/gpxecmd.c32                           1
   0.130882263 = 0.140533760    extlinux/hdt.c32                               1
   0.130226135 = 0.139829248    extlinux/host.c32                              1
   0.129806519 = 0.139378688    extlinux/ifcpu64.c32                           1
   0.129871368 = 0.139448320    extlinux/ifcpu.c32                             1
   0.129890442 = 0.139468800    extlinux/ifplop.c32                            1
   0.130622864 = 0.140255232    extlinux/kbdmap.c32                            1
   0.130432129 = 0.140050432    extlinux/linux.c32                             1
   0.130168915 = 0.139767808    extlinux/ls.c32                                1
   0.130119324 = 0.139714560    extlinux/lua.c32                               1
   0.130207062 = 0.139808768    extlinux/mboot.c32                             1
   0.129821777 = 0.139395072    extlinux/meminfo.c32                           1
   0.130542755 = 0.140169216    extlinux/menu.c32                              1
   0.130413055 = 0.140029952    extlinux/pcitest.c32                           1
   0.130569458 = 0.140197888    extlinux/pmload.c32                            1
   0.130546570 = 0.140173312    extlinux/pwd.c32                               1
   0.130172729 = 0.139771904    extlinux/reboot.c32                            1
   0.130485535 = 0.140107776    extlinux/rosh.c32                              1
   0.129791260 = 0.139362304    extlinux/sanboot.c32                           1
   0.130157471 = 0.139755520    extlinux/sdi.c32                               1
   0.129749298 = 0.139317248    extlinux/sysdump.c32                           1
   0.129882812 = 0.139460608    extlinux/vesainfo.c32                          1
   0.130378723 = 0.139993088    extlinux/vesamenu.c32                          1
   0.129798889 = 0.139370496    extlinux/vpdtest.c32                           1
   0.129753113 = 0.139321344    extlinux/whichsys.c32                          1


============== sda2: Version of COM32(R) files used by Syslinux: ===============

 extlinux/cat.c32                   :  COM32R module (v4.xx)
 extlinux/chain.c32                 :  COM32R module (v4.xx)
 extlinux/cmd.c32                   :  COM32R module (v4.xx)
 extlinux/config.c32                :  COM32R module (v4.xx)
 extlinux/cpuid.c32                 :  COM32R module (v4.xx)
 extlinux/cpuidtest.c32             :  COM32R module (v4.xx)
 extlinux/disk.c32                  :  COM32R module (v4.xx)
 extlinux/dmitest.c32               :  COM32R module (v4.xx)
 extlinux/elf.c32                   :  COM32R module (v4.xx)
 extlinux/ethersel.c32              :  COM32R module (v4.xx)
 extlinux/gfxboot.c32               :  COM32R module (v4.xx)
 extlinux/gpxecmd.c32               :  COM32R module (v4.xx)
 extlinux/hdt.c32                   :  COM32R module (v4.xx)
 extlinux/host.c32                  :  COM32R module (v4.xx)
 extlinux/ifcpu64.c32               :  COM32R module (v4.xx)
 extlinux/ifcpu.c32                 :  COM32R module (v4.xx)
 extlinux/ifplop.c32                :  COM32R module (v4.xx)
 extlinux/kbdmap.c32                :  COM32R module (v4.xx)
 extlinux/linux.c32                 :  COM32R module (v4.xx)
 extlinux/ls.c32                    :  COM32R module (v4.xx)
 extlinux/lua.c32                   :  COM32R module (v4.xx)
 extlinux/mboot.c32                 :  COM32R module (v4.xx)
 extlinux/meminfo.c32               :  COM32R module (v4.xx)
 extlinux/menu.c32                  :  COM32R module (v4.xx)
 extlinux/pcitest.c32               :  COM32R module (v4.xx)
 extlinux/pmload.c32                :  COM32R module (v4.xx)
 extlinux/pwd.c32                   :  COM32R module (v4.xx)
 extlinux/reboot.c32                :  COM32R module (v4.xx)
 extlinux/rosh.c32                  :  COM32R module (v4.xx)
 extlinux/sanboot.c32               :  COM32R module (v4.xx)
 extlinux/sdi.c32                   :  COM32R module (v4.xx)
 extlinux/sysdump.c32               :  COM32R module (v4.xx)
 extlinux/vesainfo.c32              :  COM32R module (v4.xx)
 extlinux/vesamenu.c32              :  COM32R module (v4.xx)
 extlinux/vpdtest.c32               :  COM32R module (v4.xx)
 extlinux/whichsys.c32              :  COM32R module (v4.xx)

=============================== sda3/etc/fstab: ================================

--------------------------------------------------------------------------------

#
# /etc/fstab
# Created by anaconda on Fri Nov 18 22:22:17 2011
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
UUID=7a5bcedb-cbc1-4c07-962a-b44c86be8c0d /                       ext4    defaults        1 1
UUID=f09f1c85-31ca-48d6-a2d3-825b2b8bd4cc /boot                   ext4    defaults        1 2
UUID=db0a257a-83a4-48e6-a640-c4278b26eb89 /data1                  ext4    defaults        1 2
/dev/mapper/luks-0de9acb9-cb50-4a89-b93e-f9bc74b5724f /home                   ext4    defaults        1 2
UUID=e21fac71-cc35-4c18-a736-1284b04ebccd /virtual                ext4    defaults        1 2
UUID=a0e6bd27-80e6-43b7-928b-4a39e1963654 swap                    swap    defaults        0 0
--------------------------------------------------------------------------------

=================== sda3: Location of files loaded by Grub: ====================

           GiB - GB             File                                 Fragment(s)

   1.158065796 = 1.243463680    boot/initramfs-3.1.0-7.fc16.x86_64.img         1
   1.181510925 = 1.268637696    boot/initramfs-3.1.1-1.fc16.x86_64.img         1
   1.205032349 = 1.293893632    boot/initramfs-3.1.1-2.fc16.x86_64.img         1
   1.135044098 = 1.218744320    boot/vmlinuz-3.1.0-7.fc16.x86_64               1
   1.164344788 = 1.250205696    boot/vmlinuz-3.1.1-1.fc16.x86_64               1
   1.187652588 = 1.275232256    boot/vmlinuz-3.1.1-2.fc16.x86_64               1

================= sda3: Location of files loaded by Syslinux: ==================

           GiB - GB             File                                 Fragment(s)

   1.129699707 = 1.213005824    boot/extlinux/cat.c32                          1
   1.130611420 = 1.213984768    boot/extlinux/chain.c32                        1
   1.129665375 = 1.212968960    boot/extlinux/cmd.c32                          1
   1.129814148 = 1.213128704    boot/extlinux/config.c32                       1
   1.129707336 = 1.213014016    boot/extlinux/cpuid.c32                        1
   1.130130768 = 1.213468672    boot/extlinux/cpuidtest.c32                    1
   1.130554199 = 1.213923328    boot/extlinux/disk.c32                         1
   1.129787445 = 1.213100032    boot/extlinux/dmitest.c32                      1
   1.130462646 = 1.213825024    boot/extlinux/elf.c32                          1
   1.129852295 = 1.213169664    boot/extlinux/ethersel.c32                     1
   1.130592346 = 1.213964288    boot/extlinux/gfxboot.c32                      1
   1.130210876 = 1.213554688    boot/extlinux/gpxecmd.c32                      1
   1.130882263 = 1.214275584    boot/extlinux/hdt.c32                          1
   1.130226135 = 1.213571072    boot/extlinux/host.c32                         1
   1.129806519 = 1.213120512    boot/extlinux/ifcpu64.c32                      1
   1.129871368 = 1.213190144    boot/extlinux/ifcpu.c32                        1
   1.129890442 = 1.213210624    boot/extlinux/ifplop.c32                       1
   1.130622864 = 1.213997056    boot/extlinux/kbdmap.c32                       1
   1.130432129 = 1.213792256    boot/extlinux/linux.c32                        1
   1.130168915 = 1.213509632    boot/extlinux/ls.c32                           1
   1.130119324 = 1.213456384    boot/extlinux/lua.c32                          1
   1.130207062 = 1.213550592    boot/extlinux/mboot.c32                        1
   1.129821777 = 1.213136896    boot/extlinux/meminfo.c32                      1
   1.130542755 = 1.213911040    boot/extlinux/menu.c32                         1
   1.130413055 = 1.213771776    boot/extlinux/pcitest.c32                      1
   1.130569458 = 1.213939712    boot/extlinux/pmload.c32                       1
   1.130546570 = 1.213915136    boot/extlinux/pwd.c32                          1
   1.130172729 = 1.213513728    boot/extlinux/reboot.c32                       1
   1.130485535 = 1.213849600    boot/extlinux/rosh.c32                         1
   1.129791260 = 1.213104128    boot/extlinux/sanboot.c32                      1
   1.130157471 = 1.213497344    boot/extlinux/sdi.c32                          1
   1.129749298 = 1.213059072    boot/extlinux/sysdump.c32                      1
   1.129882812 = 1.213202432    boot/extlinux/vesainfo.c32                     1
   1.130378723 = 1.213734912    boot/extlinux/vesamenu.c32                     1
   1.129798889 = 1.213112320    boot/extlinux/vpdtest.c32                      1
   1.129753113 = 1.213063168    boot/extlinux/whichsys.c32                     1

============== sda3: Version of COM32(R) files used by Syslinux: ===============

 boot/extlinux/cat.c32              :  COM32R module (v4.xx)
 boot/extlinux/chain.c32            :  COM32R module (v4.xx)
 boot/extlinux/cmd.c32              :  COM32R module (v4.xx)
 boot/extlinux/config.c32           :  COM32R module (v4.xx)
 boot/extlinux/cpuid.c32            :  COM32R module (v4.xx)
 boot/extlinux/cpuidtest.c32        :  COM32R module (v4.xx)
 boot/extlinux/disk.c32             :  COM32R module (v4.xx)
 boot/extlinux/dmitest.c32          :  COM32R module (v4.xx)
 boot/extlinux/elf.c32              :  COM32R module (v4.xx)
 boot/extlinux/ethersel.c32         :  COM32R module (v4.xx)
 boot/extlinux/gfxboot.c32          :  COM32R module (v4.xx)
 boot/extlinux/gpxecmd.c32          :  COM32R module (v4.xx)
 boot/extlinux/hdt.c32              :  COM32R module (v4.xx)
 boot/extlinux/host.c32             :  COM32R module (v4.xx)
 boot/extlinux/ifcpu64.c32          :  COM32R module (v4.xx)
 boot/extlinux/ifcpu.c32            :  COM32R module (v4.xx)
 boot/extlinux/ifplop.c32           :  COM32R module (v4.xx)
 boot/extlinux/kbdmap.c32           :  COM32R module (v4.xx)
 boot/extlinux/linux.c32            :  COM32R module (v4.xx)
 boot/extlinux/ls.c32               :  COM32R module (v4.xx)
 boot/extlinux/lua.c32              :  COM32R module (v4.xx)
 boot/extlinux/mboot.c32            :  COM32R module (v4.xx)
 boot/extlinux/meminfo.c32          :  COM32R module (v4.xx)
 boot/extlinux/menu.c32             :  COM32R module (v4.xx)
 boot/extlinux/pcitest.c32          :  COM32R module (v4.xx)
 boot/extlinux/pmload.c32           :  COM32R module (v4.xx)
 boot/extlinux/pwd.c32              :  COM32R module (v4.xx)
 boot/extlinux/reboot.c32           :  COM32R module (v4.xx)
 boot/extlinux/rosh.c32             :  COM32R module (v4.xx)
 boot/extlinux/sanboot.c32          :  COM32R module (v4.xx)
 boot/extlinux/sdi.c32              :  COM32R module (v4.xx)
 boot/extlinux/sysdump.c32          :  COM32R module (v4.xx)
 boot/extlinux/vesainfo.c32         :  COM32R module (v4.xx)
 boot/extlinux/vesamenu.c32         :  COM32R module (v4.xx)
 boot/extlinux/vpdtest.c32          :  COM32R module (v4.xx)
 boot/extlinux/whichsys.c32         :  COM32R module (v4.xx)


======================== Unknown MBRs/Boot Sectors/etc: ========================

Unknown BootLoader on sda5

00000000  4c 55 4b 53 ba be 00 01  61 65 73 00 00 00 00 00  |LUKS....aes.....|
00000010  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000020  00 00 00 00 00 00 00 00  78 74 73 2d 70 6c 61 69  |........xts-plai|
00000030  6e 36 34 00 00 00 00 00  00 00 00 00 00 00 00 00  |n64.............|
00000040  00 00 00 00 00 00 00 00  73 68 61 31 00 00 00 00  |........sha1....|
00000050  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000060  00 00 00 00 00 00 00 00  00 00 10 00 00 00 00 40  |...............@|
00000070  a0 46 63 f9 ed a9 13 1b  28 06 e5 14 cf 71 ca 71  |.Fc.....(....q.q|
00000080  0b 41 39 78 3a e4 12 37  99 84 aa 91 40 03 7c 94  |.A9x:..7....@.|.|
00000090  e8 a4 c7 a4 ea 03 8e 6f  2a 74 52 5a b1 58 9a ad  |.......o*tRZ.X..|
000000a0  a2 d2 ef 70 00 00 a6 81  30 64 65 39 61 63 62 39  |...p....0de9acb9|
000000b0  2d 63 62 35 30 2d 34 61  38 39 2d 62 39 33 65 2d  |-cb50-4a89-b93e-|
000000c0  66 39 62 63 37 34 62 35  37 32 34 66 00 00 00 00  |f9bc74b5724f....|
000000d0  00 ac 71 f3 00 02 9b 7b  ae ce e2 07 96 56 04 c9  |..q....{.....V..|
000000e0  69 8c a9 04 ef 21 06 82  c2 75 25 11 38 07 7d be  |i....!...u%.8.}.|
000000f0  66 e6 c7 7c f0 e8 94 2d  00 00 00 08 00 00 0f a0  |f..|...-........|
00000100  00 ac 71 f3 00 02 ac e3  b6 7d d7 30 b6 c6 05 fa  |..q......}.0....|
00000110  ba e5 6f da 45 11 4a ad  e8 da cc e1 68 7b 45 b2  |..o.E.J.....h{E.|
00000120  f4 47 42 a9 19 bf 04 bf  00 00 02 00 00 00 0f a0  |.GB.............|
00000130  00 00 de ad 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000140  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000150  00 00 00 00 00 00 00 00  00 00 03 f8 00 00 0f a0  |................|
00000160  00 00 de ad 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000170  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000180  00 00 00 00 00 00 00 00  00 00 05 f0 00 00 0f a0  |................|
00000190  00 00 de ad 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001a0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001b0  00 00 00 00 00 00 00 00  00 00 07 e8 00 00 0f a0  |................|
000001c0  00 00 de ad 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001d0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001e0  00 00 00 00 00 00 00 00  00 00 09 e0 00 00 0f a0  |................|
000001f0  00 00 de ad 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000200


=============================== StdErr Messages: ===============================

File descriptor 7 (pipe:[81051]) leaked on lvscan invocation. Parent PID 7712: /bin/bash
  No volume groups found
mdadm: No arrays found in config file or automatically

ok, it is all of it.

[srs5694]

I don't see anything in your Boot Info Script output that clearly identifies the source of the problem. I only have one idea at this point, and it's a long shot: I see you're using LUKS for disk encryption. I know very little about LUKS, but if it were misconfigured to access the whole disk rather than just /dev/sda5, it's conceivable that it would damage the partition table data. You might therefore look into your LUKS configuration, but as I know next to nothing about it, I can't help you with more precise suggestions.

[chrismurphy]

This is a physical machine, not a VM? I know nothing about LUKS either but if it were misconfigured for whole disk instead of just sda5, I think it would in short order hose the entire disk and make it unbootable.

It's interesting that something is causing just a problem with the backup GPT. I'd look at smartctl:

smartctl -s on /dev/sda enable SMART
smartctl -x /dev/sda show all info on device

I'd check the SMART Attributes section and see if you're getting any errors: raw read error, seek error, reallocation events, pending sectors, CRC or zone errors. And in any event I'd do a long test, and walk away from the computer - you can boot in recovery mode and do this, which will avoid services interrupting the testing since it's an offline test (i.e. the test occurs when the disk is idle).

smartctl -t long /dev/sda

It will give you a time estimate for completion as a result. After that time you can:
smartctl -x /dev/sda

And see if any new errors have appeared. If so, just get rid of the disk. If there are no errors, realize SMART is only catching something like 40% of drive failures in advance of failure.

I wonder if it would be useful to see the full main and backup GPT entries if you're able to reproduce this problem, to see exactly how the backup GPT is being hosed.

[srs5694]

Chris has some good suggestions. If you care to show us the raw GPT data, you'll need to use dd to create two files:

dd if=/dev/sda of=primary.gpt bs=512 count=34
dd if=/dev/sda of=backup.gpt bs=512 count=33 skip=625142415

I'm not sure how the forum software copes with attaching raw binary files of a type that it doubtless would consider unknown, but you can e-mail them to me, if you like. (rodsmith@rodsbooks.com)

[rtguille]

for some strange reason, my post did not show up. (it was rejected due to being to big, i just
assumed it worked...)

It seems that -x is very much better than just -a (as i normally check the drives).

I extrated the gpt headers, then repaired backup, then extracted them again for comparison.
after poweroff and booted sysrescdd, backup was also corrupted.

It is a laptop, a dell e4310.

[rtguille]

Here are:

* main ok, backup bad
* main ok, backup ok
after fixing it, i power-off the laptop and booted into sysrescd, it reported that
backup was bad again
* backup bad again

[chrismurphy]

Someone correct me if I'm reading the attached smartctl report incorrectly!!

I am seeing four problems: a few read errors; but 3200+ spin up time errors. If either of these get a a certain threshold, they will cause the drive to give you a prefailure. So in a sense maybe you're in pre-pre-failure?

But then there's the g-sense error rate and free fall rate. Looks like maybe the drive has been dropped or banged around a bit?

I would for sure do a long test:

smartctl -t long /dev/sda

And come back and do another -a or -x to see if any of the attributes have changed. I'm wondering if you just so happen to have a bad sector right where this backup GPT is located. It's strange for the same thing to keep happening. Could still also be a bug somewhere. But I'd try to track it down. Bad sectors tend to grow.

[chrismurphy]

Only difference between good and bad backup GPTs I'm seeing is in the screen shot attached.

[rtguille]

Thanks, i did use hexedit and noticed it after posting.

Currently i managed to boot without corruption.
I will try to reboot several times and also perform several power-cycles to confirm.

Currently i installed just F16, but previously there was a dualboot work-setup.
I switched from RAID to AHCI since it is no longer necessary.
Was it a RAID mode "metadata" issue from the long gone other-os? (too suspicious to
be a faulty sector, but murphy is between us every time...)

I will start testing reboot & power cycle intermediately.

---------- Post added at 10:59 PM ---------- Previous post was at 10:36 PM ----------

I power cycled it two times and rebooted other three times.
Both main and backup gpt headers are ok for now.

I think it was related to RAID mode in the sata controller.
The firmware was slow to boot f16, i thought it was grub2... but evidently it was de firmware itself.
The controller comes in RAID mode , no option when dual-booting, but as i installed f16 on the whole disk i was
able to try with ahci.

Thanks everybody for the help provided.
I will mark it as resolved if all is ok for the following 10 reboots or power-cycles.

[chrismurphy]

I still suggest a long smartctl test. The spin up numbers alone concern me. But you'd have to dig up a technical document from the manufacturer on this drive delineating the meaning of the SMART raw values, which aren't the same between vendors.

[rtguille]

I confirmed that it was the SATA controller in RAID mode. In AHCI i found no problems,
rebooted several times, power-cycled, all ok, no gpt corruption.
Then i switched back to RAID and the corruption of the secondary header returned in the
first boot and went away after switching to AHCI (and repairing it, of course).


So:

When the SATA controller in a Dell e4310 with FW/BIOS A05 (in my case) is set to RAID,
it corrupts the secondary/backup gpt header at poweron, a big pause -5 or more seconds-
is added to the time it takes to grub2 menu to appear.

There was no problem with MBR boot and RAID with dual-boot, using F15.
F16 was installed with the whole disk, using custom partitioning.


The issue manifested with these partitions:

# gdisk -l /dev/sda
GPT fdisk (gdisk) version 0.8.1

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

Found valid GPT with protective MBR; using GPT.
Disk /dev/sda: 625142448 sectors, 298.1 GiB
Logical sector size: 512 bytes
Disk identifier (GUID): 4F85375A-FCC5-4582-B687-916C9DE4D12B
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 625142414
Partitions will be aligned on 2048-sector boundaries
Total free space is 2669 sectors (1.3 MiB)

Number  Start (sector)    End (sector)  Size       Code  Name
   1            2048            4095   1024.0 KiB  EF02  
   2            4096         2101247   1024.0 MiB  EF00  ext4
   3         2101248        75501567   35.0 GiB    0700  
   4        75501568       390381567   150.1 GiB   0700  
   5       390381568       474267647   40.0 GiB    0700  
   6       474267648       482656255   4.0 GiB     8200  
   7       482656256       625141759   67.9 GiB    0700

# fdisk -l /dev/sda

WARNING: GPT (GUID Partition Table) detected on '/dev/sda'! The util fdisk doesn't support GPT. Use GNU Parted.


Disk /dev/sda: 320.1 GB, 320072933376 bytes
255 heads, 63 sectors/track, 38913 cylinders, total 625142448 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 identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1   625142447   312571223+  ee  GPT

SATA Controller in RAID mode:
  00:1f.2 RAID bus controller [0104]: Intel Corporation Mobile 82801 SATA RAID Controller [8086:282a] (rev 05)

SATA Controller in AHCI mode:
  00:1f.2 SATA controller [0106]: Intel Corporation 5 Series/3400 Series Chipset 6 port SATA AHCI Controller [8086:3b2f] (rev 05)

Regarding the disk:

The only option i have is for it to wait for it to fail, making sure to make backups, because it wont be changed if it is not 'broken' or
if the other os works, etc. And the hdd actual situation does not help at all.

I really appreciate the help provided. I have learned that RAID mode can also corrupt disks.
Thanks for the support provided.