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#1 2020-03-18 01:29:49

NSW
Member
Registered: 2020-03-18
Posts: 5

Updating older system results in unbootable "failed: I/O error"...

Hello everyone, i have a system that hasn't been updated in several months that i'm trying to bring current. Trying to go straight to current is resulting in an unbootable system with the error "../vmlinuz-linux... failed: I/O error".

I have the ability to rollback the file system and i've been able to walk the updates to November 1 with the use of the Arch Linux Archive. As soon as i attempt to update beyond this point, i get the aforementioned error. The only thing of note between Nov 1 and Dec 1 on the main blog is "2019-11-10 - New kernel packages and mkinitcpio hooks".

Anyone have a good starting point to troubleshoot this issue? I'm not sure if something in the kernel has changed or if something else is causing the error. The storage drives are fine and i can boot backup versions of the previous working kernel just fine. Not getting any noticeable failure errors during the pacman update and the update completes successfully. Seems like the newer kernel wants to just instantly fail when called.

Any help, guidance or suggestions to resolve the issue are appreciated.

System Info:
BIOS based older system with no UEFI.
/boot on ext4 partition, root file system is on zfs

Gigabyte 990FXA-UD5
AMD FX8350 Eight-Core Processor
32GB RAM

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#2 2020-03-18 11:15:27

sabroad
Member
Registered: 2015-05-24
Posts: 118

Re: Updating older system results in unbootable "failed: I/O error"...

NSW wrote:

resulting in an unbootable system with the error "../vmlinuz-linux... failed: I/O error".

This looks like an error with syslinux loading the kernel before execution (so not a kernel issue).

NSW wrote:

Anyone have a good starting point to troubleshoot this issue? [...]The storage drives are fine

Check the filesystem (/boot unmounted), if you haven't done so:

# fsck -f /dev/sdxX

Reinstall syslinux (/boot mounted) for updates:

# syslinux-install_update -i -a -m

Last edited by sabroad (2020-03-18 11:16:29)


--
saint_abroad

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#3 2020-03-19 04:46:32

NSW
Member
Registered: 2020-03-18
Posts: 5

Re: Updating older system results in unbootable "failed: I/O error"...

sabroad wrote:
NSW wrote:

resulting in an unbootable system with the error "../vmlinuz-linux... failed: I/O error".

This looks like an error with syslinux loading the kernel before execution (so not a kernel issue).

I had considered this but didn't think it was probable because syslinux happily loads the backup kernel and ramdisk from the same drive and location.

sabroad wrote:

Check the filesystem (/boot unmounted), if you haven't done so:

# fsck -f /dev/sdxX

Ran fsck again just to be sure and it returned no errors.

sabroad wrote:

Reinstall syslinux (/boot mounted) for updates:

# syslinux-install_update -i -a -m

This completed without errors. Rebooted without updating to make sure everything was working, it was. After updating it still fails with "../vmlinuz-linux... failed: I/O error".

I really wish syslinux or the kernel would actually output more information then just "I/O error", would make fixing this a million times easier. Haha. I do appreciate the attempt though, thanks!

I'm at a loss as to why this would happen. The only other oddity i've noticed on this upgrade is a reduction in "Net Upgrade Size" with pacman only replacing one package. Dropping 487.95MB seems like a lot without really removing packages, but it could also be perfectly normal.

:: Synchronizing package databases...
 core                                      134.8 KiB  66.8 KiB/s 00:02 [########################################] 100%
 extra                                    1646.6 KiB   109 KiB/s 00:15 [########################################] 100%
 community                                   4.7 MiB   229 KiB/s 00:21 [########################################] 100%
 multilib                                  164.8 KiB   358 KiB/s 00:00 [########################################] 100%
 archzfs is up to date
:: Starting full system upgrade...
warning: discord: local (0.0.10-2) is newer than community (0.0.9-5)
:: Replace pygobject2-devel with extra/python2-gobject2? [Y/n] y
resolving dependencies...
looking for conflicting packages...

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               smbclient-4.10.10-2  smplayer-19.10.2-1  solid-5.64.0-1  sonnet-5.64.0-1  sord-0.16.4-1
               speech-dispatcher-0.9.1-3  sqlite-3.30.1-2  sratom-0.6.4-1  steam-native-runtime-1.0.0.61-2
               subversion-1.13.0-1  suil-0.10.6-2  suitesparse-5.6.0-1  sysfsutils-2.1.0-11
               syslinux-6.04.pre2.r11.gbf6db5b4-3  systemd-243.162-2  systemd-libs-243.162-2
               systemd-sysvcompat-243.162-2  talloc-2.3.0-1  tar-1.32-3  tdb-1.3.18-4  telegram-desktop-1.8.15-2
               tevent-1:0.9.39-4  texinfo-6.7-2  thin-provisioning-tools-0.8.5-3  thunar-1.8.11-1  tiled-1.3.1-1
               traceroute-2.1.0-5  twolame-0.4.0-2  tzdata-2019c-3  unrar-1:5.8.4-1  usbutils-012-2
               util-linux-2.34-8  vamp-plugin-sdk-2.9.0-1  vde2-2.3.2-13  vi-1:070224-4  vim-8.1.2268-2
               vim-runtime-8.1.2268-2  virtualbox-6.0.14-4  virtualbox-host-dkms-6.0.14-4  vlc-3.0.8-6
               volume_key-0.3.12-2  vte-common-0.58.3-1  vte3-0.58.3-1  vulkan-icd-loader-1.1.127-1
               webkit2gtk-2.26.2-2  which-2.21-5  wine-staging-4.20-1  wireless_tools-30.pre9-3
               wpa_supplicant-2:2.9-2  wpebackend-fdo-1.4.0-2  x264-3:0.157.r2980.34c06d1-2  xcb-proto-1.13-4
               xdg-utils-1.1.3+18+g0547886-4  xfburn-0.6.1-1  xfce4-screenshooter-1.9.7-1  xfsprogs-5.2.1-3
               xine-lib-1.2.9-11  xinetd-2.3.15-6  xorg-server-1.20.6-1  xorg-server-common-1.20.6-1
               xorg-xprop-1.2.4-1  xz-5.2.4-2  yelp-xsl-3.34.2-1  zlib-1:1.2.11-4  zstd-1.4.3-2

Total Download Size:   1919.92 MiB
Total Installed Size:  8476.46 MiB
Net Upgrade Size:      -487.95 MiB

:: Proceed with installation? [Y/n] n

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#4 2020-03-19 08:43:14

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 8,993

Re: Updating older system results in unbootable "failed: I/O error"...

A mkinitcpio hook should run after the update that generates the kernel image, what is it's output ?

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#5 2020-03-20 00:20:09

sabroad
Member
Registered: 2015-05-24
Posts: 118

Re: Updating older system results in unbootable "failed: I/O error"...

NSW wrote:

Rebooted without updating to make sure everything was working, it was. After updating it still fails with "../vmlinuz-linux... failed: I/O error".

I see you've got syslinux-6.04.pre2.r11.gbf6db5b4-3 in the list of updates. Did you run

# syslinux-install_update -i -a -m

after the package update?

Can you post your config?

cat /boot/syslinux/syslinux.cfg

--
saint_abroad

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#6 2020-03-20 05:06:58

NSW
Member
Registered: 2020-03-18
Posts: 5

Re: Updating older system results in unbootable "failed: I/O error"...

V1del wrote:

A mkinitcpio hook should run after the update that generates the kernel image, what is it's output ?

Here is the post-transaction hooks section, including mkinitcpio...

:: Running post-transaction hooks...
( 1/29) Creating system user accounts...
( 2/29) Registering binary formats...
( 3/29) Updating journal message catalog...
( 4/29) Reloading system manager configuration...
( 5/29) Updating udev hardware database...
( 6/29) Applying kernel sysctl settings...
( 7/29) Creating temporary files...
( 8/29) Reloading device manager configuration...
( 9/29) Arming ConditionNeedsUpdate...
(10/29) Updating module dependencies...
(11/29) Install DKMS modules
==> dkms install vboxhost/6.0.14_OSE -k 5.3.13-arch1-1
==> dkms install zfs/0.8.3 -k 5.3.13-arch1-1
(12/29) Restarting cronie for libc upgrade...
(13/29) Updating linux initcpios...
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
==> Starting build: 5.3.13-arch1-1
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [autodetect]
  -> Running build hook: [modconf]
  -> Running build hook: [block]
  -> Running build hook: [zfs]
  -> Running build hook: [usr]
  -> Running build hook: [filesystems]
  -> Running build hook: [keyboard]
  -> Running build hook: [shutdown]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
==> Image generation successful
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
==> Starting build: 5.3.13-arch1-1
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [autodetect]
  -> Running build hook: [modconf]
  -> Running build hook: [block]
  -> Running build hook: [zfs]
  -> Running build hook: [usr]
  -> Running build hook: [filesystems]
  -> Running build hook: [keyboard]
  -> Running build hook: [shutdown]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
==> Image generation successful
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
==> Starting build: 5.3.13-arch1-1
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [modconf]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: aic94xx
==> WARNING: Possibly missing firmware for module: wd719x
  -> Running build hook: [zfs]
  -> Running build hook: [usr]
  -> Running build hook: [filesystems]
  -> Running build hook: [keyboard]
  -> Running build hook: [shutdown]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-fallback.img
==> Image generation successful
(14/29) Reloading system bus configuration...
(15/29) Warn about old perl modules
(16/29) Updating fontconfig cache...
(17/29) Updating 32-bit fontconfig cache...
(18/29) Probing GDK-Pixbuf loader modules...
(19/29) Updating GIO module cache...
(20/29) Compiling GSettings XML schema files...
(21/29) Probing GTK3 input method modules...
(21/29) Probing GTK3 input method modules...
(22/29) Updating icon theme caches...
(23/29) Reloading GVFS config...
(24/29) Updating the info directory file...
(25/29) Rebuilding certificate stores...
(26/29) Updating the desktop file MIME type cache...
(27/29) Updating the MIME type database...
(28/29) Updating the vlc plugin cache...
(29/29) Updating X fontdir indices...

It completes without any errors and returns to the command prompt.

Here is the boot partition with files after update. The .bak files are my copies before the update. The sizes look good for the newly generated files.

drwxr-xr-x  5 root root     1024 Mar 19 21:37 .
drwxr-xr-x 19 root root       27 Mar 17 17:54 ..
-rw-r--r--  1 root root 11550720 Dec 16  2012 boot
drwxr-xr-x  5 root root     1024 Mar 15 13:28 grub
-rw-r--r--  1 root root 35356598 Mar 19 21:36 initramfs-linux-fallback.img
-rw-r--r--  1 root root 35555189 Mar 17 20:17 initramfs-linux-fallback.img.bak
-rw-r--r--  1 root root 12836557 Mar 19 21:35 initramfs-linux.img
-rw-r--r--  1 root root 12837841 Mar 17 20:17 initramfs-linux.img.bak
drwx------  2 root root    12288 Dec 14  2012 lost+found
drwxr-xr-x  2 root root     3072 Mar 19 21:38 syslinux
-rw-r--r--  1 root root  6285696 Mar 19 21:35 vmlinuz-linux
-rw-r--r--  1 root root  6289792 Mar 17 20:16 vmlinuz-linux.bak

Also checked both boot partition and zfs root for errors again...

sudo fsck -f /dev/sda1
fsck from util-linux 2.34
e2fsck 1.45.4 (23-Sep-2019)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
/dev/sda1: 407/128016 files (0.5% non-contiguous), 153827/512000 blocks
sudo zpool status
  pool: archpool
 state: ONLINE
status: Some supported features are not enabled on the pool. The pool can
	still be used, but some features are unavailable.
action: Enable all features using 'zpool upgrade'. Once this is done,
	the pool may no longer be accessible by software that does not support
	the features. See zpool-features(5) for details.
  scan: scrub repaired 0B in 0 days 00:07:27 with 0 errors on Thu Mar 19 21:54:04 2020
config:

	NAME        STATE     READ WRITE CKSUM
	archpool    ONLINE       0     0     0
	  mirror-0  ONLINE       0     0     0
	    sda2    ONLINE       0     0     0
	    sdb2    ONLINE       0     0     0

errors: No known data errors

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#7 2020-03-20 05:15:09

NSW
Member
Registered: 2020-03-18
Posts: 5

Re: Updating older system results in unbootable "failed: I/O error"...

sabroad wrote:

I see you've got syslinux-6.04.pre2.r11.gbf6db5b4-3 in the list of updates. Did you run

# syslinux-install_update -i -a -m

after the package update?

I didn't before, but i did on this run. Same result. smile

sabroad wrote:

Can you post your config?

cat /boot/syslinux/syslinux.cfg

Sure! I haven't touched this file in years outside of setting the backup entry last week.

# Config file for Syslinux -
# /boot/syslinux/syslinux.cfg
#
# Comboot modules:
#   * menu.c32 - provides a text menu
#   * vesamenu.c32 - provides a graphical menu
#   * chain.c32 - chainload MBRs, partition boot sectors, Windows bootloaders
#   * hdt.c32 - hardware detection tool
#   * reboot.c32 - reboots the system
#   * poweroff.com - shutdown the system
#
# To Use: Copy the respective files from /usr/lib/syslinux to /boot/syslinux.
# If /usr and /boot are on the same file system, symlink the files instead
# of copying them.
#
# If you do not use a menu, a 'boot:' prompt will be shown and the system
# will boot automatically after 5 seconds.
#
# Please review the wiki: https://wiki.archlinux.org/index.php/Syslinux
# The wiki provides further configuration examples

DEFAULT arch
PROMPT 0        # Set to 1 if you always want to display the boot: prompt
TIMEOUT 50
# You can create syslinux keymaps with the keytab-lilo tool
#KBDMAP de.ktl

# Menu Configuration
# Either menu.c32 or vesamenu32.c32 must be copied to /boot/syslinux
UI menu.c32
#UI vesamenu.c32

# Refer to http://syslinux.zytor.com/wiki/index.php/Doc/menu
MENU TITLE Arch Linux
#MENU BACKGROUND splash.png
MENU COLOR border       30;44   #40ffffff #a0000000 std
MENU COLOR title        1;36;44 #9033ccff #a0000000 std
MENU COLOR sel          7;37;40 #e0ffffff #20ffffff all
MENU COLOR unsel        37;44   #50ffffff #a0000000 std
MENU COLOR help         37;40   #c0ffffff #a0000000 std
MENU COLOR timeout_msg  37;40   #80ffffff #00000000 std
MENU COLOR timeout      1;37;40 #c0ffffff #00000000 std
MENU COLOR msg07        37;40   #90ffffff #a0000000 std
MENU COLOR tabmsg       31;40   #30ffffff #00000000 std

# boot sections follow
#
# TIP: If you want a 1024x768 framebuffer, add "vga=773" to your kernel line.
#
#-*

LABEL arch
        MENU LABEL Arch Linux
        LINUX ../vmlinuz-linux
        INITRD ../initramfs-linux.img
        APPEND zfs=archpool/ROOT/archfs rw zfs_force=1

LABEL archfallback
        MENU LABEL Arch Linux Fallback
        LINUX ../vmlinuz-linux
        INITRD ../initramfs-linux-fallback.img
        APPEND zfs=archpool/ROOT/archfs zfs_force=1

LABEL archbak
        MENU LABEL Arch Linux Backup
        LINUX ../vmlinuz-linux.bak
        INITRD ../initramfs-linux.img.bak
        APPEND zfs=archpool/ROOT/archfs rw zfs_force=1

LABEL hdt
        MENU LABEL HDT (Hardware Detection Tool)
        COM32 hdt.c32

LABEL reboot
        MENU LABEL Reboot
        COM32 reboot.c32

LABEL off
        MENU LABEL Power Off
        COMBOOT poweroff.com

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