Ubuntu – GRUB Confuses Kernels/Initramfs of Ubuntu and Arch Linux Installation

arch linuxdual-bootgrub2initramfsUbuntu

I have a machine that used to dual-boot Ubuntu (16.04 currently) and Windows 7, with Ubuntu's GRUB as boot loader.

Now I just added Arch Linux as third OS, following the official installation instructions. I did not install GRUB from Arch because I wanted to use the one controlled by Ubuntu. The instructions contained a command mkinitcpio -p linux that probably generated some boot files which I ran as described.

Now when I try to boot Ubuntu from GRUB through its default entry, I get this unpleasant error (sorry for the screen photo):

As the output of uname -a shows, it's trying to boot the Arch kernel, but /dev/sda6 is the Ubuntu root partition.

I have to navigate to Advanced options for Ubuntu and select one of the Ubuntu, with Linux 4.4.0-* entries to be able to load Ubuntu, I couldn't find an entry that would correctly load Arch though.

Running sudo update-grub from Ubuntu ("update-grub is a stub for running grub-mkconfig -o /boot/grub/grub.cfg to generate a grub2 config file.") does not change anything. The grub-customizer tool was also useless in fixing this so far.

What causes this confusion of GRUB and how do I fix it so that each Linux version boots with the correct kernel and from the correct partition?

It looks like I stupidly installed Arch with Ubuntu's /boot mounted, so it probably placed its boot files in there.

I'm fine with erasing all the Arch related stuff to get Ubuntu's boot loader straight again and do a clean install of Arch later.

Updates (thanks to @terdon for his support in the Ask Ubuntu chat):

Here is my /boot/grub/grub.cfg.

All Linux entries seem to point at my /dev/sda6 partition, which is Ubuntu's root:

$ grep ' linux /' /boot/grub/grub.cfg
    linux /vmlinuz-linux root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro
        linux /vmlinuz-linux root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro
        linux /vmlinuz-linux root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro
        linux /vmlinuz-linux root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro init=/sbin/upstart
        linux /vmlinuz-linux root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro recovery nomodeset
        linux /vmlinuz-4.4.0-21-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro
        linux /vmlinuz-4.4.0-21-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro init=/sbin/upstart
        linux /vmlinuz-4.4.0-21-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro recovery nomodeset
        linux /vmlinuz-4.2.0-35-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro
        linux /vmlinuz-4.2.0-35-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro init=/sbin/upstart
        linux /vmlinuz-4.2.0-35-generic root=UUID=eee18451-b607-4875-8a88-c9cb6c6544c8 ro recovery nomodeset

I tried to update GRUB config from Ubuntu:

$ sudo grub-mkconfig -o /boot/grub/grub.cfg 
Generating grub configuration file ...
dpkg: warning: version 'linux' has bad syntax: version number does not start with a digit
Found linux image: /boot/vmlinuz-linux
Found initrd image: /boot/initramfs-linux.img
Found linux image: /boot/vmlinuz-4.4.0-21-generic
Found initrd image: /boot/initrd.img-4.4.0-21-generic
Found linux image: /boot/vmlinuz-4.2.0-35-generic
Found initrd image: /boot/initrd.img-4.2.0-35-generic
Found memtest86+ image: /memtest86+.elf
Found memtest86+ image: /memtest86+.bin
Found Windows 7 (loader) on /dev/sda1
Found Arch on /dev/sda8
done

I tried to reinstall GRUB to the MBR from Ubuntu:

$ sudo grub-install /dev/sda
Installing for i386-pc platform.
Installation finished. No error reported.

$ sudo grub-install --recheck /dev/sda
Installing for i386-pc platform.
Installation finished. No error reported.

Those are the installed Ubuntu kernel packages by the way, I did try to dpkg-reconfigure all of them, but without any effect on the issue:

$ dpkg -l linux-image* | grep ^ii
ii  linux-image-4.2.0-35-generic       4.2.0-35.40  amd64        Linux kernel image for version 4.2.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-21-generic       4.4.0-21.37  amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-extra-4.2.0-35-generic 4.2.0-35.40  amd64        Linux kernel extra modules for version 4.2.0 on 64 bit x86 SMP
ii  linux-image-extra-4.4.0-21-generic 4.4.0-21.37  amd64        Linux kernel extra modules for version 4.4.0 on 64 bit x86 SMP

I also tried to regenerate the Ubuntu initramfs:

$ sudo update-initramfs -u -k all
update-initramfs: Generating /boot/initrd.img-4.4.0-21-generic
update-initramfs: Generating /boot/initrd.img-4.2.0-35-generic

My partition layout:

Checked from the Ubuntu system. The labels should explain themselves.

$ lsblk -f /dev/sda
NAME    FSTYPE LABEL       UUID                                 MOUNTPOINT
sda                                                             
├─sda1  ntfs   win7-boot   90DCF3A5DCF3842E                     /win/boot
├─sda2  ntfs   windows7    482C7A572C7A3FCC                     /win/c
├─sda3  ext4   grub-boot   6dbb8633-dadd-4b5e-8d85-b0895fde9dfb /boot
├─sda5  ext4   images      81dc42c4-a161-4ccd-b704-6e5c09298943 /images
├─sda6  ext4   ubuntu-1604 eee18451-b607-4875-8a88-c9cb6c6544c8 /
├─sda7  ext4   ubuntu-home 485b3ef1-7216-4053-b25c-f656d529e8e6 /home
├─sda8  ext4   arch-root   8d281a0c-969c-44cf-ba6a-1d3c7b4be7ec 
├─sda9  ext4   arch-home   32522902-a53d-44c8-90f2-6bbf14c40f1f 
└─sda10 swap   linux-swap  8b05bd9b-bc42-46f6-8c18-50711a3c48b9 [SWAP]

My GRUB menu structure:

Advanced options for Ubuntu:

Advanced options for Arch:

My `/boot` directory:

$ ls -la /boot
total 118480
drwxr-xr-x  4 root root     4096 Apr 24 20:50 .
drwxr-xr-x 28 root root     4096 Apr 24 19:44 ..
-rw-r--r--  1 root root  1313029 Mär 16 01:45 abi-4.2.0-35-generic
-rw-r--r--  1 root root  1239577 Apr 19 00:21 abi-4.4.0-21-generic
-rw-r--r--  1 root root   184888 Mär 16 01:45 config-4.2.0-35-generic
-rw-r--r--  1 root root   189412 Apr 19 00:21 config-4.4.0-21-generic
drwxr-xr-x  6 root root     4096 Apr 26 19:58 grub
-rw-r--r--  1 root root 18598360 Apr 24 20:59 initramfs-linux-fallback.img
-rw-r--r--  1 root root  3516429 Apr 24 20:59 initramfs-linux.img
-rw-r--r--  1 root root 33642388 Apr 24 18:31 initrd.img-4.2.0-35-generic
-rw-r--r--  1 root root 36143341 Apr 24 19:51 initrd.img-4.4.0-21-generic
drwx------  2 root root    16384 Okt 28 17:43 lost+found
-rw-r--r--  1 root root   182704 Jan 28 13:44 memtest86+.bin
-rw-r--r--  1 root root   184380 Jan 28 13:44 memtest86+.elf
-rw-r--r--  1 root root   184840 Jan 28 13:44 memtest86+_multiboot.bin
-rw-------  1 root root  3745312 Mär 16 01:45 System.map-4.2.0-35-generic
-rw-------  1 root root  3853719 Apr 19 00:21 System.map-4.4.0-21-generic
-rw-------  1 root root  6829104 Mär 16 01:45 vmlinuz-4.2.0-35-generic
-rw-------  1 root root  7013968 Apr 19 00:21 vmlinuz-4.4.0-21-generic
-rw-r--r--  1 root root  4435552 Apr 14 19:20 vmlinuz-linux

The 4.4.0 and 4.2.0 kernels should be Ubuntu, Arch should have a 4.5.0 kernel. But how do I find out which file without kernel version in its name belongs to what?

My Ubuntu root directory (directories excluded):

$ ls -la / | grep ^[^d]
total 124
lrwxrwxrwx   1 root      root         32 Apr 24 19:44 initrd.img -> boot/initrd.img-4.4.0-21-generic
lrwxrwxrwx   1 root      root         32 Apr  5 17:45 initrd.img.old -> boot/initrd.img-4.2.0-35-generic
lrwxrwxrwx   1 root      root         29 Apr 24 19:44 vmlinuz -> boot/vmlinuz-4.4.0-21-generic
lrwxrwxrwx   1 root      root         29 Apr  5 17:45 vmlinuz.old -> boot/vmlinuz-4.2.0-35-generic

My Arch root directory does not contain any files or links.

Best Answer

I finally solved it by nuking the Arch partition and its boot files in my Ubuntu's /boot directory from orbit. Ubuntu is fine again now, all remaining GRUB entries are working again.

Here's a list of what I did:

Delete Arch's initramfs files:
```
sudo rm /boot/initramfs-linux*
```
Delete Arch's vmlinuz file:
```
sudo rm vmlinuz-linux
```
Format the Arch partition (/dev/sda8) using GParted
Update GRUB's configuration:
```
sudo update-grub
```
Reboot and enjoy!

Updates (thanks to @terdon for his support in the Ask Ubuntu chat):

My partition layout:

My GRUB menu structure:

My /boot directory:

My Ubuntu root directory (directories excluded):

Best Answer

Related Solutions

Initramfs Prompt – Fix ‘Can’t Read /etc/fstab’ and ‘No Init Found’

Os-prober giving wrong UUID for Arch Linux

Related Question

My `/boot` directory: