PopOS Unable to boot (Volume group not found)

**TheFu** · August 13th, 2021

To remove the swap LV, just disable the swap (swapoff), delete that LV (lvremove), then recreate a new LV (lvcreate) and format it for as swap (mkswap) and get the new device pointer - something like /dev/{vgname}/{lvname} and put that into the fstab as swap.
Remove the crypttab line with swap - or comment it out.

Finally, run swapon -a.

All this can happen while the system keeps running. The swapoff command can take 15+ minutes. Use free to see how much swap is being used.

Lastly, run update-grub.

If there are any errors about being out of storage, don't reboot. It isn't uncommon for too many kernels to be in /boot/ and eating too much storage. I don't see how that can happen without a separate /boot partition, but we see odd things all the time here.

**robo731** · August 16th, 2021

Ok, that sounds like a good plan, thanks.

I disabled the swap, but when I try to delete the LV, it says the device is in use even though free seems to indicate otherwise:

Code:

Logical volume OSs/Swap is used by another device.

I tried this suggestion next: https://askubuntu.com/a/109961/491784, but it gives a similar error:

Code:

Device /dev/mapper/OSs-Swap is still in use.

I was also confused by the output of sudo fdisk -l:

Code:

Disk /dev/nvme0n1: 238.47 GiB, 256060514304 bytes, 500118192 sectorsDisk model: SAMSUNG ************-******             
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: EB5E32A4-E0CE-49B9-9DBF-066016079B80


Device           Start       End   Sectors   Size Type
/dev/nvme0n1p1    2048   1048575   1046528   511M EFI System
/dev/nvme0n1p3 5769216 500117503 494348288 235.7G Linux LVM




Disk /dev/mapper/OSs-Swap: 12 GiB, 12884901888 bytes, 25165824 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 /dev/mapper/OSs-Pop: 100 GiB, 107374182400 bytes, 209715200 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 /dev/mapper/cryptswap: 12 GiB, 12884377600 bytes, 25164800 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

I see /dev/mapper/OSs-Swap and also /dev/mapper/cryptswap.

PopOS uses systemd so I think I'll need to do bootctl update instead of update-grub when we can reach that step.

EDIT:

I tried the other suggestion here: https://askubuntu.com/a/109961/491784 and commented out the swap in /etc/fstab and /etc/crypttab and then after rebooting, I was able to remove the volume and both entries are gone from fdisk's output.

I ran sudo update-initramfs -u and bootctl update which gave:

Code:

Skipping "/boot/efi/EFI/systemd/systemd-bootx64.efi", since a newer boot loader version exists already.
Skipping "/boot/efi/EFI/BOOT/BOOTX64.EFI", since a newer boot loader version exists already.

I still was not able to boot with the current kernel, but still can with the old one.

**robo731** · August 18th, 2021

I tried updating my system and rebooting, but no change.

When I boot and get dumped to BusyBox and try to exit, it was giving me an error similar to this:

https://www.reddit.com/r/linuxquesti...d_claims_uuid/

One of the responses here says that maybe the kernel did not include the nvme module. Do you think something like that could be the case?

When I tried running blkid, there was no output.

Maybe this would help: https://askubuntu.com/a/788802/491784

**TheFu** · August 18th, 2021

I don't have any NVMe installed in any of my systems currently. Sorry. I have an NVMe drive, but that's for a new build, plus I was careful to get a well-regarded model.

You say that you disabled swap. How? Only the swapoff command will work.
Then comment out the swap line in the fstab and the crypttab.
Then go do the partition work. I'd delete everything including /dev/nvme0n1p3, then create a 4.1G partition and format it as Linux Swap. No need for LUKS or LVM at all.
There is little reason for swap to be larger than 4.1G on a desktop. In a server, the goal should be to avoid needing **any** swap, since RAM is cheap again.

Rather they saying what happened, SHOW IT!

**robo731** · August 19th, 2021

Yes, I disabled it with swapoff and commented it out in fstab and crypttab.

Here's the output of fdisk which shows the swap is gone:

Code:

Disk /dev/nvme0n1: 238.47 GiB, 256060514304 bytes, 500118192 sectors
Disk model: SAMSUNG *********-*****              
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: *****************


Device           Start       End   Sectors   Size Type
/dev/nvme0n1p1    2048   1048575   1046528   511M EFI System
/dev/nvme0n1p3 5769216 500117503 494348288 235.7G Linux LVM




Disk /dev/mapper/OSs-Pop: 100 GiB, 107374182400 bytes, 209715200 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

And free:

Code:

              total        used        free      shared  buff/cache   available
Mem:        8005256     4547508      271284     2235296     3186464      956260
Swap:             0           0           0

If there's anything else you'd like to see, just let me know, I'll do my best to provide it.

I am thinking the issue is not related to the swap or encryption afterall.

I think we can also rule out the NVMe theory I had before as well, I ran update-initramfs in verbose mode and the output shows the nvme modules being included: https://pastebin.ubuntu.com/p/myKCRRG962/

I am thinking the issue is related to initramfs or to the update state of my machine maybe. I would like to disable the splash screen on boot and set the mode to verbose so I can see the messages when I am booting up. I sometimes see some text flash by, it might give a clue.

I wonder if trying to remove the kernel which is not working and trying to reinstall it would help.

The other thing I suspect is that the upgrade/update did not complete correctly. The "Pop Shop" shows some updates for my system:

But fails to install them with the following error:

Code:

The following packages have unmet dependencies:
  gnome-shell: Depends: gir1.2-mutter-7 (>= 3.38.4) but 3.38.3-2ubuntu0.20.10.1pop1~1614025450~20.10~5e5ece9 is to be installed
               Depends: libedataserver-1.2-26 (>= 3.33.1) but it is not installable
               Depends: libgdk-pixbuf-2.0-0 (>= 2.22.0) but it is not installable
               Depends: libmutter-7-0 (>= 3.38.4) but 3.38.3-2ubuntu0.20.10.1pop1~1614025450~20.10~5e5ece9 is to be installed

There was also some problems before I initiated the upgrade to this new kernel in Pop Shop, but I just used apt to update instead hoping to avoid the issue. Maybe this is the cause of the problem.

**robo731** · August 23rd, 2021

I did some more research in the incomplete update vein. I think this is the problem. When I run apt upgrade, it gives the following output:

Code:

The following packages have been kept back:
  fwupd-signed gir1.2-gdm-1.0 gir1.2-mutter-7 gnome-control-center
  gnome-shell-common gnome-shell-extension-prefs libglapi-mesa
  libnss-systemd linux-generic linux-headers-generic
  linux-image-5.11.0-7620-generic linux-image-generic
  linux-modules-extra-5.11.0-7620-generic linux-system76
  nautilus-extension-gnome-terminal systemd-sysv virtualbox-dkms
0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.

I think I need to run apt full-upgrade if I want to continue updating. I did a dry run of it though and I got the following output:

Code:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
  gnome-shell-extension-alt-tab-raise-first-window
  gnome-shell-extension-always-show-workspaces
  gnome-shell-extension-pop-shop-details
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  linux-generic linux-system76 pop-desktop
The following packages have been kept back:
  fwupd-signed gir1.2-gdm-1.0 gir1.2-mutter-7 gnome-control-center
  gnome-shell-common gnome-shell-extension-prefs libglapi-mesa
  libnss-systemd linux-headers-generic nautilus-extension-gnome-terminal
  systemd-sysv
The following packages will be upgraded:
  linux-image-5.11.0-7620-generic linux-image-generic
  linux-modules-extra-5.11.0-7620-generic virtualbox-dkms
WARNING: The following essential packages will be removed.
This should NOT be done unless you know exactly what you are doing!
  pop-desktop linux-system76 (due to pop-desktop)
4 upgraded, 0 newly installed, 3 to remove and 11 not upgraded.
Remv pop-desktop [1.6.0~1625267683~21.04~ac0465f]
Remv linux-system76 [5.11.0.7620.21~1624379747~20.10~3abeff8]
Remv linux-generic [5.11.0.7620.21~1624379747~20.10~3abeff8]
Inst linux-image-5.11.0-7620-generic [5.11.0-7620.21~1624379747~20.10~3abeff8] (5.11.0-7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64]) [linux-image-generic:amd64 ]
Conf linux-image-5.11.0-7620-generic (5.11.0-7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64]) [linux-image-generic:amd64 ]
Inst linux-modules-extra-5.11.0-7620-generic [5.11.0-7620.21~1624379747~20.10~3abeff8] (5.11.0-7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64]) [linux-image-generic:amd64 ]
Conf linux-modules-extra-5.11.0-7620-generic (5.11.0-7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64]) [linux-image-generic:amd64 ]
Inst linux-image-generic [5.11.0.7620.21~1624379747~20.10~3abeff8] (5.11.0.7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64])
Conf linux-image-generic (5.11.0.7620.21~1626191760~21.04~55de9c3 Pop!_OS PPA:21.04/hirsute [amd64])
Inst virtualbox-dkms [6.1.18-dfsg-5pop0~1624392638~20.10~b904788] (6.1.18-dfsg-5pop0~1624392638~21.04~b904788 Pop!_OS PPA:21.04/hirsute [amd64])
Conf virtualbox-dkms (6.1.18-dfsg-5pop0~1624392638~21.04~b904788 Pop!_OS PPA:21.04/hirsute [amd64])

I'm concerned that this combination of removals, withholding and upgrades, might result in a still incomplete state.