Updates keep destroying initrd and boot config

**drfunky69** · 24-Aug-2009, 04:35

Hi everyone,

I'm running a dual-boot Vista/OpenSuSE machine. It normally works fine, but occasionally after updating the system rebooting fails. Obviously, this is both frustrating and a bit scary.

The first time, both /boot/grub/menu.lst and /boot/initrd were missing or corrupted. The 2nd and 3rd time it seems to be only /boot/initrd with problems. I have managed to fix it each time using the dvd repair utility followed by Super Grub Disk.

Does anyone have an idea how to fix this? The only thing that I can think may be exotic about my configuration is the fact that I use Vista's bootloader to call grub (in my root linux partition). Could Super Grub Disk have done something even stranger?

Here is all the info that I can think would be useful (I would be happy to provide more):

Code:

> sudo /sbin/sfdisk -l /dev/sda
Disque /dev/sda: 30394 cylindres, 255 t�tes, 63 secteurs/piste
AVERTISSEMENT: la partition �tendue ne d�bute pas sur une fronti�re de.
cylindres DOS et Linux interpr�teront les contenus diff�remment.
Unit�s= cylindres de 8225280 octets, blocs de 1024 octets, d�compte � partir de 0

   P�riph Amor D�but     Fin   #cyls    #blocs    Id  Syst�me
/dev/sda1   *      0+   6373    6374-  51198131    7  HPFS/NTFS
/dev/sda2       6374+  25815-  19441- 156159832    7  HPFS/NTFS
                d�but: (c,h,s) expect� (1023,254,63) trouv� (1023,59,22)
/dev/sda3      25815+  30393    4579-  36778949    f  W95 Etendu (LBA)
/dev/sda4          0       -       0          0    0  Vide
/dev/sda5      25815+  26077-    262-   2102646+  82  Linux swap / Solaris
/dev/sda6      26077+  30393    4317-  34676271   83  Linux

/etc/fstab:

Code:

/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part5 swap    swap    default
s 0 0
/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 /       ext3    acl,use
r_xattr 1 1
/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part1 /windows/c      ntfs-3g
 users,gid=users,locale=fr_FR.UTF-8,exec 0 0
/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part2 /windows/d      ntfs-3g
 users,gid=users,locale=fr_FR.UTF-8,exec 0 0
proc    /proc   proc    defaults 0 0
sysfs   /sys    sysfs   noauto 0 0
debugfs /sys/kernel/debug       debugfs noauto 0 0
devpts  /dev/pts        devpts  mode=0620,gid=5 0 0

/boot/grub/menu.lst:

Code:

# Modified by YaST2. Last modification on Mon Aug 24 13:44:50 CEST 2009
default 0
timeout 8
gfxmenu (hd0,5)/boot/message
##YaST - activate

###Don't change this comment - YaST2 identifier: Original name: linux###
title SUSE LINUX
    root (hd0,5)
    kernel /boot/vmlinuz root=/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892
-part6    repair=1 resume=/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-par
t5 splash=silent showopts vga=0x31a
    initrd /boot/initrd

###Don't change this comment - YaST2 identifier: Original name: failsafe###
title Failsafe -- SUSE LINUX
    root (hd0,5)
    kernel /boot/vmlinuz root=/dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892
-part6 showopts ide=nodma apm=off noresume edd=off powersaved=off nohz=off highres=off
processor.max_cstate=1 x11failsafe vga=0x31a
    initrd /boot/initrd

Thanks in advance,
Jesse

PS: I was once able to repair the system using zypper, but I can't remember or find the exact command again. Does anyone know what it is?

**Knurpht** · 24-Aug-2009, 12:58

Don't know the zypper command, but it must have been something like installing a rpm that calls mkinitrd.

Just today this happened to me, updating Milestone 6 with the latest updates. Repaired it through NET-install CD.

**drfunky69** · 25-Aug-2009, 10:19

I don't know if this helps, but I just checked

Code:

/var/log/YaST2/y2logmkinitrd

and see this but at the end:

Code:

Kernel image:   /boot/vmlinuz-2.6.27.29-0.1-trace
Initrd image:   /boot/initrd-2.6.27.29-0.1-trace
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/s
da6) (mounted on / as ext3)
FATAL: Module ata_generic not found.
WARNING: no dependencies for kernel module 'ata_generic' found.
FATAL: Module piix not found.
WARNING: no dependencies for kernel module 'piix' found.
FATAL: Module ide_pci_generic not found.
WARNING: no dependencies for kernel module 'ide_pci_generic' found.
FATAL: Module usbhid not found.
WARNING: no dependencies for kernel module 'usbhid' found.
Kernel Modules: dock scsi_mod libata ahci ata_piix jbd mbcache ext3 crc-t10dif sd_mod u
sbcore ohci-hcd uhci-hcd ehci-hcd
Features:       block usb resume.userspace resume.kernel
Bootsplash:     openSUSE (1280x1024)
25834 blocks

What can make these fail, and what can I do?

**eldar_g** · 25-Aug-2009, 23:32

I experienced the same problem. The update left my system with RAID unbootable for a wheek.

**Knurpht** · 26-Aug-2009, 03:25

Usually when upgrading a kernel, mkinitrd is run a couple of times: for kernel-"flavor", kernel-"flavor"-base, kernel-"flavor"-extra; the first time mkinitrd is called not all new kernel modules are available yet, therefor the errors. AFAIK.

I have decided to call mkinitrd manually after each kernel upgrade, just to make sure.

**drfunky69** · 26-Aug-2009, 03:33

I see. In that case, thought, shouldn't the mkinitrd errors happen only with the first few passes, and not with the last?

I should have included the whole log file before. As you can see, errors have several times, including on the last pass. Here it is:

Code:

jesse-local@alix:~> sudo cat /var/log/YaST2/y2logmkinitrd
root's password:                                         

Kernel image:   /boot/vmlinuz-2.6.27.7-9-default
Initrd image:   /boot/initrd-2.6.27.7-9-default 
Root device:    /dev/sda6 (mounted on / as ext3)
Kernel Modules: hwmon thermal_sys processor thermal fan jbd mbcache ext3 dock scsi_mod libata ahci edd crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid                                                                                       
Features:       block usb resume.userspace resume.kernel                                
Bootsplash:     openSUSE (1280x1024)                                                    
26580 blocks                                                                            

Kernel image:   /boot/vmlinuz-2.6.27.7-9-default
Initrd image:   /boot/initrd-2.6.27.7-9-default 
Root device:    /dev/sda6 (mounted on / as ext3)
Kernel Modules: hwmon thermal_sys processor thermal fan jbd mbcache ext3 dock scsi_mod libata ahci edd crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid                                                                                       
Features:       block usb resume.userspace resume.kernel                                
Bootsplash:     openSUSE (1280x1024)                                                    
26580 blocks                                                                            
2009-01-16 15:08:21 WARNING: GRUB::GrubDev2UnixDev: No partition found for /dev/sda with 3.                                                                                     

Kernel image:   /boot/vmlinuz-2.6.27.7-9-default
Initrd image:   /boot/initrd-2.6.27.7-9-default 
Root device:    /dev/sda6 (mounted on / as ext3)
Kernel Modules: hwmon thermal_sys processor thermal fan jbd mbcache ext3 dock scsi_mod libata ahci edd crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid                                                                                       
Features:       block usb resume.userspace resume.kernel                                
Bootsplash:     openSUSE (1280x1024)                                                    
26580 blocks                                                                            
2009-01-16 15:09:00 WARNING: GRUB::GrubDev2UnixDev: No partition found for /dev/sda with 3.                                                                                     

Kernel image:   /boot/vmlinuz-2.6.27.25-0.1-default
Initrd image:   /boot/initrd-2.6.27.25-0.1-default 
node name not found                                
Root device (/dev/sda6) not found                  

Kernel image:   /boot/vmlinuz-2.6.27.25-0.1-default
Initrd image:   /boot/initrd-2.6.27.25-0.1-default 
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)                                                              
Kernel Modules: dock scsi_mod libata ahci ata_piix ata_generic ide-core piix ide-pci-generic jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid                                                                                
Features:       block usb resume.userspace resume.kernel                                
Bootsplash:     openSUSE (1280x1024)                                                    
26613 blocks                                                                            

Kernel image:   /boot/vmlinuz-2.6.27.25-0.1-trace
Initrd image:   /boot/initrd-2.6.27.25-0.1-trace 
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)                                                              
FATAL: Module ata_generic not found.                                                    
WARNING: no dependencies for kernel module 'ata_generic' found.                         
FATAL: Module piix not found.                                                           
WARNING: no dependencies for kernel module 'piix' found.                                
FATAL: Module ide_pci_generic not found.                                                
WARNING: no dependencies for kernel module 'ide_pci_generic' found.                     
FATAL: Module usbhid not found.                                                         
WARNING: no dependencies for kernel module 'usbhid' found.                              
Kernel Modules: dock scsi_mod libata ahci ata_piix jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd                                                        
Features:       block usb resume.userspace resume.kernel                                
Bootsplash:     openSUSE (1280x1024)                                                    
25832 blocks                                                                            

Kernel image:   /boot/vmlinuz-2.6.27.29-0.1-default
Initrd image:   /boot/initrd-2.6.27.29-0.1-default 
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)                                                              
Kernel Modules: dock scsi_mod libata ahci ata_piix ata_generic ide-core piix ide-pci-generic jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid                                                                                
Features:       block usb resume.userspace resume.kernel
Bootsplash:     openSUSE (1280x1024)
26616 blocks

Kernel image:   /boot/vmlinuz-2.6.27.29-0.1-trace
Initrd image:   /boot/initrd-2.6.27.29-0.1-trace
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)
FATAL: Module ata_generic not found.
WARNING: no dependencies for kernel module 'ata_generic' found.
FATAL: Module piix not found.
WARNING: no dependencies for kernel module 'piix' found.
FATAL: Module ide_pci_generic not found.
WARNING: no dependencies for kernel module 'ide_pci_generic' found.
FATAL: Module usbhid not found.
WARNING: no dependencies for kernel module 'usbhid' found.
Kernel Modules: dock scsi_mod libata ahci ata_piix jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd
Features:       block usb resume.userspace resume.kernel
Bootsplash:     openSUSE (1280x1024)
25834 blocks

Kernel image:   /boot/vmlinuz-2.6.27.29-0.1-default
Initrd image:   /boot/initrd-2.6.27.29-0.1-default
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)
Kernel Modules: dock scsi_mod libata ahci ata_piix ata_generic ide-core piix ide-pci-generic jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd ff-memless hid usbhid
Features:       block usb resume.userspace resume.kernel
Bootsplash:     openSUSE (1280x1024)
26616 blocks

Kernel image:   /boot/vmlinuz-2.6.27.29-0.1-trace
Initrd image:   /boot/initrd-2.6.27.29-0.1-trace
Root device:    /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6 (/dev/sda6) (mounted on / as ext3)
FATAL: Module ata_generic not found.
WARNING: no dependencies for kernel module 'ata_generic' found.
FATAL: Module piix not found.
WARNING: no dependencies for kernel module 'piix' found.
FATAL: Module ide_pci_generic not found.
WARNING: no dependencies for kernel module 'ide_pci_generic' found.
FATAL: Module usbhid not found.
WARNING: no dependencies for kernel module 'usbhid' found.
Kernel Modules: dock scsi_mod libata ahci ata_piix jbd mbcache ext3 crc-t10dif sd_mod usbcore ohci-hcd uhci-hcd ehci-hcd
Features:       block usb resume.userspace resume.kernel
Bootsplash:     openSUSE (1280x1024)
25834 blocks

**hedge_hog** · 29-Sep-2009, 22:29

I've seen the same mkinitrd partition error in openSUSE...
Can you post the results of running (as root):

Code:

# hwinfo --partition|grep --context=15 /dev/sda

**hedge_hog** · 30-Sep-2009, 00:19

You may like to track the mkinitrd warning issue here:

https://bugzilla.novell.com/show_bug.cgi?id=543076

**drfunky69** · 30-Sep-2009, 01:44

Hi hedge_hog, thanks for getting back to me. Here's the result that you asked for.

Also, thanks for posting the bug. I'll follow it for sure.

Jesse

Code:

> sudo hwinfo --partition|grep --context=15 /dev/sda
21: None 00.0: 11300 Partition
  [Created at block.412]
  UDI: /org/freedesktop/Hal/devices/volume_uuid_4452153E52153660
  Unique ID: bdUI.SE1wIdpsiiC
  Parent ID: 3OOL.UK5FR6qJlS2
  SysFS ID: /class/block/sda/sda1
  Hardware Class: partition
  Model: "Partition"
  Device File: /dev/sda1
  Device Files: /dev/sda1, /dev/disk/by-id/scsi-SATA_WDC_WD2500AAJS-_WD-WMAT15666892-part1, /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part1, /dev/disk/by-path/pci-0000:00:1f.2-scsi-0:0:0:0-part1, /dev/disk/by-uuid/4452153E52153660
  Config Status: cfg=no, avail=yes, need=no, active=unknown
  Attached to: #20 (Disk)

22: None 00.0: 11300 Partition
  [Created at block.412]
  UDI: /org/freedesktop/Hal/devices/volume_uuid_EC883AB8883A815E
  Unique ID: 2pkM.SE1wIdpsiiC
  Parent ID: 3OOL.UK5FR6qJlS2
  SysFS ID: /class/block/sda/sda2
  Hardware Class: partition
  Model: "Partition"
  Device File: /dev/sda2
  Device Files: /dev/sda2, /dev/disk/by-id/scsi-SATA_WDC_WD2500AAJS-_WD-WMAT15666892-part2, /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part2, /dev/disk/by-path/pci-0000:00:1f.2-scsi-0:0:0:0-part2, /dev/disk/by-uuid/EC883AB8883A815E, /dev/disk/by-label/DATA
  Config Status: cfg=no, avail=yes, need=no, active=unknown
  Attached to: #20 (Disk)

23: None 00.0: 11300 Partition
  [Created at block.412]
  UDI: /org/freedesktop/Hal/devices/volume_part3_size_1024
  Unique ID: W__Q.SE1wIdpsiiC
  Parent ID: 3OOL.UK5FR6qJlS2
  SysFS ID: /class/block/sda/sda3
  Hardware Class: partition
  Model: "Partition"
  Device File: /dev/sda3
  Device Files: /dev/sda3, /dev/disk/by-id/scsi-SATA_WDC_WD2500AAJS-_WD-WMAT15666892-part3, /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part3, /dev/disk/by-path/pci-0000:00:1f.2-scsi-0:0:0:0-part3
  Config Status: cfg=no, avail=yes, need=no, active=unknown
  Attached to: #20 (Disk)

24: None 00.0: 11300 Partition
  [Created at block.412]
  UDI: /org/freedesktop/Hal/devices/volume_uuid_ec6389b3_078d_40e3_962c_0835e39c7346
  Unique ID: QLVZ.SE1wIdpsiiC
  Parent ID: 3OOL.UK5FR6qJlS2
  SysFS ID: /class/block/sda/sda5
  Hardware Class: partition
  Model: "Partition"
  Device File: /dev/sda5
  Device Files: /dev/sda5, /dev/disk/by-id/scsi-SATA_WDC_WD2500AAJS-_WD-WMAT15666892-part5, /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part5, /dev/disk/by-path/pci-0000:00:1f.2-scsi-0:0:0:0-part5, /dev/disk/by-uuid/ec6389b3-078d-40e3-962c-0835e39c7346
  Config Status: cfg=no, avail=yes, need=no, active=unknown
  Attached to: #20 (Disk)

25: None 00.0: 11300 Partition
  [Created at block.412]
  UDI: /org/freedesktop/Hal/devices/volume_uuid_fbb07455_3e0e_4cdf_8cba_7b7cb51d4e06
  Unique ID: tWld.SE1wIdpsiiC
  Parent ID: 3OOL.UK5FR6qJlS2
  SysFS ID: /class/block/sda/sda6
  Hardware Class: partition
  Model: "Partition"
  Device File: /dev/sda6
  Device Files: /dev/sda6, /dev/root, /dev/disk/by-id/scsi-SATA_WDC_WD2500AAJS-_WD-WMAT15666892-part6, /dev/disk/by-id/ata-WDC_WD2500AAJS-75B4A0_WD-WMAT15666892-part6, /dev/disk/by-path/pci-0000:00:1f.2-scsi-0:0:0:0-part6, /dev/disk/by-uuid/fbb07455-3e0e-4cdf-8cba-7b7cb51d4e06
  Config Status: cfg=no, avail=yes, need=no, active=unknown
  Attached to: #20 (Disk)

**Akoellh** · 30-Sep-2009, 01:51

Originally Posted by drfunky69

Code:

> sudo /sbin/sfdisk -l /dev/sda
Disque /dev/sda: 30394 cylindres, 255 t�tes, 63 secteurs/piste
AVERTISSEMENT: la partition �tendue ne d�bute pas sur une fronti�re de.
cylindres DOS et Linux interpr�teront les contenus diff�remment.
Unit�s= cylindres de 8225280 octets, blocs de 1024 octets, d�compte � partir de 0

   P�riph Amor D�but     Fin   #cyls    #blocs    Id  Syst�me
/dev/sda1   *      0+   6373    6374-  51198131    7  HPFS/NTFS
/dev/sda2       6374+  25815-  19441- 156159832    7  HPFS/NTFS
                d�but: (c,h,s) expect� (1023,254,63) trouv� (1023,59,22)
/dev/sda3      25815+  30393    4579-  36778949    f  W95 Etendu (LBA)
/dev/sda4          0       -       0          0    0  Vide
/dev/sda5      25815+  26077-    262-   2102646+  82  Linux swap / Solaris
/dev/sda6      26077+  30393    4317-  34676271   83  Linux

Well, my french isn't good (and never was) but in short I would translate the warnings with "your partition table is seriously messed up" (and this is a potential cause for such strange behavior).

Run

Code: