How can I repair boot process (so that it uses my SSD)?

Question

I use Lubuntu 20.04, which boots from an SSD.

Today I allowed the system to do upgrades, and subsequently got an error message saying that update-initramfs failed. I googled the error message and found this link which suggested the problem could be resolved by freeing some space on /boot and reinstalling a package. I think I made a mistake trying to do both fixes in one procedure.

I did:

sudo apt remove initramfs-tools
sudo apt-get auto-remove 
sudo apt-get clean 
sudo apt install initramfs-tools
sudo apt-get update

Everything appeared to be fixed until I rebooted the machine. The machine could not reboot automatically, but I entered the boot menu and picked an older kernel. That worked. Inspecting the broken and working boot commands, I believe that I am no longer booting off the SSD (I could also be wrong).

The broken boot option (which used to work) is:

menuentry 'Ubuntu, with Linux 5.4.0-86-generic' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-86-generic-advanced-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        gfxmode $linux_gfx_mode
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-86-generic ...'
        linux   /vmlinuz-5.4.0-86-generic root=/dev/nvme0n1p3 ro  quiet splash $vt_handoff
    }

... and the working option is:

menuentry 'Ubuntu, with Linux 5.4.0-84-generic' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-84-generic-advanced-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        gfxmode $linux_gfx_mode
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-84-generic ...'
        linux   /vmlinuz-5.4.0-84-generic root=UUID=f81f27eb-c1f2-467c-a62b-fdd60b4f0592 ro  quiet splash $vt_handoff
        echo    'Loading initial ramdisk ...'
        initrd  /initrd.img-5.4.0-84-generic
    }

Is there any way I can repair the damage and get Lubuntu back to booting from the SSD ? I now think that the autoremove operation may have destroyed some vital information on the SSD.

The broken boot option produces this output before crashing:

If I use the working boot option, I now get the following response from df (/boot appears to be on the SSD, so looks like my idea that this option was booting via the hard drive is probably wrong).

df -h
Filesystem      Size  Used Avail Use% Mounted on
udev             16G     0   16G   0% /dev
tmpfs           3.2G  2.1M  3.2G   1% /run
/dev/nvme0n1p3  468G  121G  324G  28% /
tmpfs            16G   92M   16G   1% /dev/shm
tmpfs           5.0M  4.0K  5.0M   1% /run/lock
tmpfs            16G     0   16G   0% /sys/fs/cgroup
tmpfs            16G   11M   16G   1% /tmp
/dev/loop1      128K  128K     0 100% /snap/bare/5
/dev/loop3       62M   62M     0 100% /snap/core20/1081
/dev/loop2       56M   56M     0 100% /snap/core18/2128
/dev/loop4      165M  165M     0 100% /snap/gnome-3-28-1804/161
/dev/loop5      243M  243M     0 100% /snap/gnome-3-38-2004/76
/dev/loop0       56M   56M     0 100% /snap/core18/2074
/dev/loop6       66M   66M     0 100% /snap/gtk-common-themes/1515
/dev/loop7       66M   66M     0 100% /snap/gtk-common-themes/1519
/dev/loop8      699M  699M     0 100% /snap/libreoffice/227
/dev/nvme0n1p2  510M  318M  155M  68% /boot
/dev/nvme0n1p1  532M  5.3M  527M   1% /boot/efi
/dev/loop9      163M  163M     0 100% /snap/gnome-3-28-1804/145
/dev/loop10      33M   33M     0 100% /snap/snapd/13170
/dev/loop11      33M   33M     0 100% /snap/snapd/12883
/dev/loop12     701M  701M     0 100% /snap/libreoffice/229
/dev/loop13     242M  242M     0 100% /snap/gnome-3-38-2004/70
tmpfs           3.2G  8.0K  3.2G   1% /run/user/1000
/dev/sdb1       1.9T 1008G  856G  55% /media/paul/Seagate Backup Plus Drive

My complete grub.cfg is:

#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#
BEGIN /etc/grub.d/00_header
if [ -s $prefix/grubenv ]; then
  set have_grubenv=true
  load_env
fi
if [ "${initrdfail}" = 2 ]; then
   set initrdfail=
elif [ "${initrdfail}" = 1 ]; then
   set next_entry="${prev_entry}"
   set prev_entry=
   save_env prev_entry
   if [ "${next_entry}" ]; then
      set initrdfail=2
   fi
fi
if [ "${next_entry}" ] ; then
   set default="${next_entry}"
   set next_entry=
   save_env next_entry
   set boot_once=true
else
   set default="0"
fi
if [ x"${feature_menuentry_id}" = xy ]; then
  menuentry_id_option="--id"
else
  menuentry_id_option=""
fi
export menuentry_id_option
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 initrdfail {
    if [ -n "${have_grubenv}" ]; then if [ -n "${partuuid}" ]; then
      if [ -z "${initrdfail}" ]; then
        set initrdfail=1
        if [ -n "${boot_once}" ]; then
          set prev_entry="${default}"
          save_env prev_entry
        fi
      fi
      save_env initrdfail
    fi; fi
}
function recordfail {
  set recordfail=1
  if [ -n "${have_grubenv}" ]; then if [ -z "${boot_once}" ]; then save_env recordfail; fi; fi
}
function load_video {
  if [ x$feature_all_video_module = xy ]; then
    insmod all_video
  else
    insmod efi_gop
    insmod efi_uga
    insmod ieee1275_fb
    insmod vbe
    insmod vga
    insmod video_bochs
    insmod video_cirrus
  fi
}
if [ x$feature_default_font_path = xy ] ; then
   font=unicode
else
insmod part_gpt
insmod ext2
if [ x$feature_platform_search_hint = xy ]; then
  search --no-floppy --fs-uuid --set=root  f81f27eb-c1f2-467c-a62b-fdd60b4f0592
else
  search --no-floppy --fs-uuid --set=root f81f27eb-c1f2-467c-a62b-fdd60b4f0592
fi
    font="/usr/share/grub/unicode.pf2"
fi
if loadfont $font ; then
  set gfxmode=auto
  load_video
  insmod gfxterm
  set locale_dir=$prefix/locale
  set lang=en_GB
  insmod gettext
fi
terminal_output gfxterm
if [ "${recordfail}" = 1 ] ; then
  set timeout=30
else
  if [ x$feature_timeout_style = xy ] ; then
    set timeout_style=hidden
    set timeout=0
Fallback hidden-timeout code in case the timeout_style feature is
unavailable.
elif sleep --interruptible 0 ; then
    set timeout=0
  fi
fi
END /etc/grub.d/00_header
BEGIN /etc/grub.d/05_debian_theme
set menu_color_normal=white/black
set menu_color_highlight=black/light-gray
END /etc/grub.d/05_debian_theme
BEGIN /etc/grub.d/10_linux
function gfxmode {
    set gfxpayload="${1}"
    if [ "${1}" = "keep" ]; then
        set vt_handoff=vt.handoff=7
    else
        set vt_handoff=
    fi
}
if [ "${recordfail}" != 1 ]; then
  if [ -e ${prefix}/gfxblacklist.txt ]; then
    if hwmatch ${prefix}/gfxblacklist.txt 3; then
      if [ ${match} = 0 ]; then
        set linux_gfx_mode=keep
      else
        set linux_gfx_mode=text
      fi
    else
      set linux_gfx_mode=text
    fi
  else
    set linux_gfx_mode=keep
  fi
else
  set linux_gfx_mode=text
fi
export linux_gfx_mode
menuentry 'Ubuntu' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-simple-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
    recordfail
    load_video
    gfxmode $linux_gfx_mode
    insmod gzio
    if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
    insmod part_gpt
    insmod ext2
    if [ x$feature_platform_search_hint = xy ]; then
      search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
    else
      search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
    fi
    linux   /vmlinuz-5.4.0-86-generic root=/dev/nvme0n1p3 ro  quiet splash $vt_handoff
}
submenu 'Advanced options for Ubuntu' $menuentry_id_option 'gnulinux-advanced-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
    menuentry 'Ubuntu, with Linux 5.4.0-86-generic' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-86-generic-advanced-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        gfxmode $linux_gfx_mode
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-86-generic ...'
        linux   /vmlinuz-5.4.0-86-generic root=/dev/nvme0n1p3 ro  quiet splash $vt_handoff
    }
    menuentry 'Ubuntu, with Linux 5.4.0-86-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-86-generic-recovery-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-86-generic ...'
        linux   /vmlinuz-5.4.0-86-generic root=/dev/nvme0n1p3 ro recovery nomodeset dis_ucode_ldr 
    }
    menuentry 'Ubuntu, with Linux 5.4.0-84-generic' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-84-generic-advanced-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        gfxmode $linux_gfx_mode
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-84-generic ...'
        linux   /vmlinuz-5.4.0-84-generic root=UUID=f81f27eb-c1f2-467c-a62b-fdd60b4f0592 ro  quiet splash $vt_handoff
        echo    'Loading initial ramdisk ...'
        initrd  /initrd.img-5.4.0-84-generic
    }
    menuentry 'Ubuntu, with Linux 5.4.0-84-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-5.4.0-84-generic-recovery-f81f27eb-c1f2-467c-a62b-fdd60b4f0592' {
        recordfail
        load_video
        insmod gzio
        if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi
        insmod part_gpt
        insmod ext2
        if [ x$feature_platform_search_hint = xy ]; then
          search --no-floppy --fs-uuid --set=root  504e9392-5142-456a-852d-7838c4a522bc
        else
          search --no-floppy --fs-uuid --set=root 504e9392-5142-456a-852d-7838c4a522bc
        fi
        echo    'Loading Linux 5.4.0-84-generic ...'
        linux   /vmlinuz-5.4.0-84-generic root=UUID=f81f27eb-c1f2-467c-a62b-fdd60b4f0592 ro recovery nomodeset dis_ucode_ldr 
        echo    'Loading initial ramdisk ...'
        initrd  /initrd.img-5.4.0-84-generic
    }
}
END /etc/grub.d/10_linux
BEGIN /etc/grub.d/10_linux_zfs
END /etc/grub.d/10_linux_zfs
BEGIN /etc/grub.d/20_linux_xen
END /etc/grub.d/20_linux_xen
BEGIN /etc/grub.d/20_memtest86+
END /etc/grub.d/20_memtest86+
BEGIN /etc/grub.d/30_os-prober
END /etc/grub.d/30_os-prober
BEGIN /etc/grub.d/30_uefi-firmware
menuentry 'UEFI Firmware Settings' $menuentry_id_option 'uefi-firmware' {
    fwsetup
}
END /etc/grub.d/30_uefi-firmware
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  ${config_directory}/custom.cfg ]; then
  source ${config_directory}/custom.cfg
elif [ -z "${config_directory}" -a -f  $prefix/custom.cfg ]; then
  source $prefix/custom.cfg;
fi
END /etc/grub.d/41_custom

Why do you think you're no longer booting from the SSD? No, apt autoremove does absolutely nothing to the boot settings nor any of the other commands. — ChanganAuto, Sep 23 '21 at 18:33
You should have provided the actual error message; my guess from your description is you ran out of disk space, where subsequent commands are likely to fail as well, or potentially make the issue worse. Read the actual error message (esp. if it's disk space) and act appropriately (ie. if it's lack of disk space, you need to create more disk space). Ubuntu desktop recommends 25GB as the minimum to avoid issues like this; yet 3rd party blog sites often recommend less which tend to lead to errors like this; less is fine but you need to monitor & maintain your system more. — guiverc, Sep 23 '21 at 23:24
@ChanganAuto - The boot that stopped working specifies root=/dev/nvme0n1p3 (which is my SSD). The older boot, that still works specifies root=UUID=f81f27eb-c1f2-467c-a62b-fdd60b4f0592. I don't know what that means, but I guessed it might be on the hard drive. — user1759557, Sep 23 '21 at 23:53
I have added more information to the original question. @Nmath - I have not tried boot-repair. It is the next thing I plan to do, but I am trying to understand what has happened and get advice first, as I really do not want to make things worse ! — user1759557, Sep 24 '21 at 12:22
@guiverc - I did not copy the error message resulting from the upgrade: I thought it was minor, and would just go away when I freed some space. All I remember is that the problem concerned update-initramfs and matched the problem described in the link. — user1759557, Sep 24 '21 at 12:23

score 0 · Answer 1 · answered Sep 30 '21 at 17:45

Solved it ! I'll explain how for anyone encountering a similar issue. Two posts helped me solve the problem.

I booted the system using a previous kernel (if I had not had that I would have tried booting from a USB stick).

Firstly I found out how to use journalctl to view errors from the failed boot:

journalctl -b -2 -e

I added output from journalctl to my original post. You may need to change the number in order to view the correct boot. You can find the right number using:

journalctl --list-boots

The post that helped me is here

Secondly, I identified the key problem from the log as:

kernel panic - not syncing vfs unable to mount root fs on unknown-block(0 0)

This was solved by:

sudo update-initramfs -u -k 5.4.0-86-generic
sudo update-grub

Where 5.4.0-86-generic is the name of the kernel that had broken and stopped booting.

The post that helped me is this

How can I repair boot process (so that it uses my SSD)?

BEGIN /etc/grub.d/00_header

Fallback hidden-timeout code in case the timeout_style feature is

unavailable.

END /etc/grub.d/00_header

BEGIN /etc/grub.d/05_debian_theme

END /etc/grub.d/05_debian_theme

BEGIN /etc/grub.d/10_linux

END /etc/grub.d/10_linux

BEGIN /etc/grub.d/10_linux_zfs

END /etc/grub.d/10_linux_zfs

BEGIN /etc/grub.d/20_linux_xen

END /etc/grub.d/20_linux_xen

BEGIN /etc/grub.d/20_memtest86+

END /etc/grub.d/20_memtest86+

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

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

BEGIN /etc/grub.d/30_uefi-firmware

END /etc/grub.d/30_uefi-firmware

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

END /etc/grub.d/41_custom

1 Answers1