Unable to load any modules after running eclean-kernel

[anyuta1166]

Hello. I've found rather critical bug that caused my server malfunction for several hours (time needed to recompile a kernel).

Steps to reproduce:

1. Compile a kernel with genkernel.
2. Recompile the same kernel version with genkernel again (for example, I decided to recompile the kernel with different config).
3. Run eclean-kernel -n 1

After the second compilation you have the following layout:

lily ~ # eclean-kernel -l
5.17.9-gentoo-x86_64 [5.17.9-gentoo-x86_64]
- systemmap: /boot/System.map-5.17.9-gentoo-x86_64
- initramfs: /boot/initramfs-5.17.9-gentoo-x86_64.img
- vmlinuz: /boot/vmlinuz-5.17.9-gentoo-x86_64
- modules: /lib/modules/5.17.9-gentoo-x86_64
- build: /usr/src/linux-5.17.9-gentoo
- last modified: 2022-09-12 09:37:10
5.17.9-gentoo-x86_64.old [5.17.9-gentoo-x86_64]
- systemmap: /boot/System.map-5.17.9-gentoo-x86_64.old
- initramfs: /boot/initramfs-5.17.9-gentoo-x86_64.img.old
- vmlinuz: /boot/vmlinuz-5.17.9-gentoo-x86_64.old
- modules: /lib/modules/5.17.9-gentoo-x86_64
- build: /usr/src/linux-5.17.9-gentoo
- last modified: 2022-09-12 09:37:10
lily ~ # ls -l /boot /lib/modules/*
/boot:
total 56888
drwxr-xr-x 6 root root     4096 Sep 12 15:50 grub
-rw-r--r-- 1 root root 11716484 Sep 12 15:12 initramfs-5.17.9-gentoo-x86_64.img
-rw-r--r-- 1 root root 11716484 Sep 12 15:12 initramfs-5.17.9-gentoo-x86_64.img.old
-rw-r--r-- 1 root root 10798080 May 22 22:15 intel-uc.img
-rw-r--r-- 1 root root  5093296 Sep 12 12:37 System.map-5.17.9-gentoo-x86_64
-rw-r--r-- 1 root root  5093296 Sep 12 12:37 System.map-5.17.9-gentoo-x86_64.old
-rw-r--r-- 1 root root  6906112 Sep 12 12:38 vmlinuz-5.17.9-gentoo-x86_64
-rw-r--r-- 1 root root  6906112 Sep 12 12:38 vmlinuz-5.17.9-gentoo-x86_64.old

/lib/modules/5.17.9-gentoo-x86_64:
total 4724
lrwxrwxrwx  1 root root      28 May 21 22:12 build -> /usr/src/linux-5.17.9-gentoo
drwxr-xr-x 14 root root    4096 Sep 12 15:12 kernel
-rw-r--r--  1 root root 1183583 Sep 12 15:12 modules.alias
-rw-r--r--  1 root root 1153484 Sep 12 15:12 modules.alias.bin
-rw-r--r--  1 root root    7051 Sep 12 15:11 modules.builtin
-rw-r--r--  1 root root   18808 Sep 12 15:12 modules.builtin.alias.bin
-rw-r--r--  1 root root    9415 Sep 12 15:12 modules.builtin.bin
-rw-r--r--  1 root root   57485 Sep 12 15:11 modules.builtin.modinfo
-rw-r--r--  1 root root  431094 Sep 12 15:12 modules.dep
-rw-r--r--  1 root root  587075 Sep 12 15:12 modules.dep.bin
-rw-r--r--  1 root root     453 Sep 12 15:12 modules.devname
-rw-r--r--  1 root root  138549 Sep 12 15:11 modules.order
-rw-r--r--  1 root root    1144 Sep 12 15:12 modules.softdep
-rw-r--r--  1 root root  551107 Sep 12 15:12 modules.symbols
-rw-r--r--  1 root root  665591 Sep 12 15:12 modules.symbols.bin
lrwxrwxrwx  1 root root      28 Sep 12 15:11 source -> /usr/src/linux-5.17.9-gentoo

Now run eclean-kernel:

lily ~ # eclean-kernel -p -n 1
Legend:
[-] file being removed
[+] file being kept (used by other kernels)

These are the kernels which would be removed:
- 5.17.9-gentoo-x86_64.old: not referenced by bootloader (grub2)
 [-] /boot/vmlinuz-5.17.9-gentoo-x86_64.old
 [+] /usr/src/linux-5.17.9-gentoo
 [+] /lib/modules/5.17.9-gentoo-x86_64
 [-] /boot/System.map-5.17.9-gentoo-x86_64.old
 [-] /boot/initramfs-5.17.9-gentoo-x86_64.img.old
kernel-install will be called to perform prerm tasks.
Bootloader grub2 config will be updated.
lily ~ # eclean-kernel -n 1
Legend:
[-] file being removed
[x] file does not exist (anymore)
[+] file being kept (used by other kernels)

* Removing kernel 5.17.9-gentoo-x86_64.old (not referenced by bootloader (grub2))
 [-] /boot/vmlinuz-5.17.9-gentoo-x86_64.old
 [+] /usr/src/linux-5.17.9-gentoo
 [+] /lib/modules/5.17.9-gentoo-x86_64
 [-] /boot/System.map-5.17.9-gentoo-x86_64.old
 [-] /boot/initramfs-5.17.9-gentoo-x86_64.img.old
Removed 1 kernels
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-5.17.9-gentoo-x86_64
Found initrd image: /boot/intel-uc.img /boot/initramfs-5.17.9-gentoo-x86_64.img
Warning: os-prober will not be executed to detect other bootable partitions.
Systems on them will not be added to the GRUB boot configuration.
Check GRUB_DISABLE_OS_PROBER documentation entry.
done

And you end up with this:

lily ~ # eclean-kernel -l
5.17.9-gentoo-x86_64 [5.17.9-gentoo-x86_64]
- systemmap: /boot/System.map-5.17.9-gentoo-x86_64
- initramfs: /boot/initramfs-5.17.9-gentoo-x86_64.img
- vmlinuz: /boot/vmlinuz-5.17.9-gentoo-x86_64
- modules: /lib/modules/5.17.9-gentoo-x86_64
- build: /usr/src/linux-5.17.9-gentoo
- last modified: 2022-09-12 09:37:10
lily ~ # ls -l /boot /lib/modules/*
/boot:
total 33720
drwxr-xr-x 6 root root     4096 Sep 12 15:59 grub
-rw-r--r-- 1 root root 11716484 Sep 12 15:12 initramfs-5.17.9-gentoo-x86_64.img
-rw-r--r-- 1 root root 10798080 May 22 22:15 intel-uc.img
-rw-r--r-- 1 root root  5093296 Sep 12 12:37 System.map-5.17.9-gentoo-x86_64
-rw-r--r-- 1 root root  6906112 Sep 12 12:38 vmlinuz-5.17.9-gentoo-x86_64

/lib/modules/5.17.9-gentoo-x86_64:
total 208
lrwxrwxrwx  1 root root     28 May 21 22:12 build -> /usr/src/linux-5.17.9-gentoo
drwxr-xr-x 14 root root   4096 Sep 12 15:12 kernel
-rw-r--r--  1 root root   7051 Sep 12 15:11 modules.builtin
-rw-r--r--  1 root root  57485 Sep 12 15:11 modules.builtin.modinfo
-rw-r--r--  1 root root 138549 Sep 12 15:11 modules.order
lrwxrwxrwx  1 root root     28 Sep 12 15:11 source -> /usr/src/linux-5.17.9-gentoo

For some reason, eclean-kernel removed most of the /lib/modules/5.17.9-gentoo-x86_64/modules.* files, leaving only modules.builtin, modules.builtin.modinfo and modules.order.

This makes the system unable to load any modules. I've accidentally found this after a reboot - hardware attached to my server wasn't working because the modules were not loaded.

[mgorny]

Hmm, I suspect kernel-install may be actually doing this. As you can see in the output, EK doesn't intend to remove moduledir.