[SOLVED] No usb since kernel update

TheArchitect · 2015-04-03 18:57:57

Hello everyone,
I'm quite new at Arch, but I have a little experience with Linux and I usually manage to fix things by myself... but this time, I can't find any useful information!

Just some background information about my system: I use LVM on LUKS, so when I boot I have to type my password in order to unlock / and /home.

Here is my problem: when I updated the kernel (to version 3.19.2-1) and then rebooted, my keyboard was not responsive anymore (I was stuck at the password phase).
I downgraded my kernel, and everything worked fine again. Today I try to update it again, but I'm facing the same issue, yet I have more information. I haven't rebooted yet, so I can still use my keyboard (and mouse). Now the thing is when I plug a USB key, I get with dmesg:

usb 4-1: new SuperSpeed USB device number 4 using xhci_hcd

and with lsusb:

Bus 004 Device 004: ID 0781:5580 SanDisk Corp. SDCZ80 Flash Drive

but it doesn't appear in /dev/sd*.
Maybe an interesting fact: I can still mount all the disks partitions I want.

My guess is the new kernel can't take care of any of my USB peripherals, but the keyboard still works before the reboot because something is already loaded, and will only be replaced after reboot. I am not very familiar with the kernel and modules (yet)...

I would really appreciate your help!

(I'm not a native english speaker, so please forgive me for any mistake )

Last edited by TheArchitect (2025-02-11 00:25:33)

ewaller · 2015-04-03 19:06:34

I wager that /boot was not mounted when you did the upgrade.

Compare the output of uname -a and pacman -Qi linux when id does not work. If they don't match, look at the output of mount and see if the boot partition is mounted on /boot. If it isn't, the kernel is being written to the directory /boot, and is not actually making it to the boot partition.

Mount it (fix your /etc/fstab) and re-install the kernel ( pacman -S linux )

TheArchitect · 2015-04-03 19:26:43

Do you mean to try it after a reboot, chrooting if necessary?

Anyway, right now, uname -a tells me 3.18.6-1-ARCH and pacman -Qi linux gives me 3.19.2-1. Yet, /boot is mounted :

/dev/sda2 on /boot type ext2 (rw,relatime,stripe=4)

jasonwryan · 2015-04-03 19:33:58

If you are UEFI booting, make sure the ESP is mounted correctly (and if it isn't mounted at /boot, that the kernel and initrd are coipied to the correct location).

If it is an MBR boot, then /boot wasn't mounted for the upgrade.

In either case, make sure everything is mounted correctly and re-upgrade the kernel so that uname and Qi match.

TheArchitect · 2015-04-03 21:57:04

I think it's an MBR boot (I don't have a GPT table).

I'm completely lost now. I rebooted, so I can't type my password anymore to open the LUKS partition.
I chrooted in my system (with boot manually correctly mounted), reinstalled the kernel but no difference. uname -a still gives me 3.18.6-1, and both pacman -Qi linux and ls -a /lib/modules gives me 3.19.2-1.

ewaller · 2015-04-03 22:18:39

The problem remains. Your boot loader is loading an old kernel.
You think it is an MBR. That is pretty fundamental; I am curious how you cannot know for certain having installed it.

Regardless, If you could post the output of sudo fdisk -l /dev/sda and of ls -l /boot

TheArchitect · 2015-04-04 20:59:11

I simply had a doubt. It is MBR.

sudo fdisk -l /dev/sda

Disk /dev/sda: 223.6 GiB, 240057409536 bytes, 468862128 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: dos
Disk identifier: 0xd149f256

Device     Boot     Start       End   Sectors   Size Id Type
/dev/sda1            2048 245737471 245735424 117.2G  7 HPFS/NTFS/exFAT
/dev/sda2  *    245737472 246147071    409600   200M 83 Linux
/dev/sda3       246147072 468862127 222715056 106.2G 8e Linux LVM

ls -l /boot

total 38158
drwxr-xr-x 6 root     1024 Apr  3 22:45 grub
-rw-r--r-- 1 root 24704292 Apr  4  2015 initramfs-linux-fallback.img
-rw-r--r-- 1 root 10132432 Apr  4  2015 initramfs-linux.img
drwx------ 2 root    12288 Feb 24 18:04 lost+found
-rw-r--r-- 1 root  4065312 Feb  7 08:45 vmlinuz-linux

WorMzy · 2015-04-04 21:03:07

Mount your root partition and look in /boot. If there's a kernel there, run 'file /path/to/boot/vmlinuz-linux', is the version '3.18.6'?

TheArchitect · 2015-04-04 21:12:18

Nope, it's 3.19.2.

ewaller · 2015-04-04 21:14:23

It is MBR. Good, I can help I've never installed an EFI system. I was also probing to ensure we really were talking about real Arch system. Sorry about that.

Here is what is strange. The initramfs* files on boot were touched on April 4. That, I am guessing is when you did the upgrade and things went south. Why where the initrd images updated, but the kernel (vmlinuz-linux) has not been touched since February? That is hard to explain.

How did you upgrade and downgrade the kernel? Did you run mkinitcpio by hand?

Can you, after re-verifying that /dev/sda2 is mounted on boot, run pacman -Syu and let's see what happens.

I am also curious, were you to dismount /boot, then do a ls -l /boot and see if there is a kernel in there, and if it has a newer date. This is just to try to determine how this happened.

TheArchitect · 2015-04-04 21:33:07

No problem, thank you for your help

To upgrade the kernel I simply used a pacman -Syu which went fine. Is that naive?
To downgrade, pacman -U <old kernel> with <old kernel> found in /var/cache/pacman/pkg.

OK, I think here is the problem. With /dev/sda2 mounted, you saw what I have. But when I unmount it, ls -l /boot gives me

total 38132
drwxr-xr-x 6 root     4096 Apr  3 23:12 grub
-rw-r--r-- 1 root 24772172 Apr  3 23:12 initramfs-linux-fallback.img
-rw-r--r-- 1 root 10138577 Apr  3 23:12 initramfs-linux.img
drwx------ 2 root     4096 Apr  3 23:12 lost+found
-rw-r--r-- 1 root  4123472 Apr  3 23:12 vmlinuz-linux

How is that possible? What am I looking at when sda2 is not mounted? Do I have another /boot on the root partition?

jasonwryan · 2015-04-04 21:39:13

Please paste your /etc/fstab: it looks like you are mounting a second filesystem over /boot...

WorMzy · 2015-04-04 21:39:41

TheArchitect wrote:

How is that possible? What am I looking at when sda2 is not mounted? Do I have another /boot on the root partition?

You have a boot directory, that's what I was getting at with my questions.

Somehow you have the correct kernel on your root partition, and an old kernel on your boot partition. This suggests that you updated your kernel while your boot partition wasn't mounted. The initrds on the boot partition have been updated today, while you've been trying to diagnose the problem. Presumably they, too, hadn't been updated since February before today.

TheArchitect · 2015-04-04 21:48:30

/etc/fstab

# /dev/mapper/vg00-root
UUID=237e65da-fc8d-43aa-a5a5-b93bc644073b	/         	ext4      	rw,relatime,data=ordered	0 1

# /dev/mapper/vg00-home
UUID=9b7a902e-a9ac-4737-9374-49fd4a1f0316	/home     	ext4      	rw,relatime,data=ordered	0 2

# /dev/sda2
UUID=39fde28c-3f54-4ecb-b1ad-14a81ed2001d	/boot     	ext2      	rw,relatime,stripe=4	0 2

What is strange is that I'm almost certain /boot was mounted when I updated the kernel. Anyway, I just tried again, with the certainty that /boot is mounted, but vmlinuz-linux is still the old one. What am I doing wrong?

WorMzy · 2015-04-04 21:51:17

What is involved in "trying again"? Post the exact commands you're using.

TheArchitect · 2015-04-04 22:00:24

As I'm not sure about this /boot thing, here is what I did:

sudo umount /boot
pacman -U linux-3.18.6-1-x86_64.pkg.tar.xz
sudo mount /boot
pacman -U linux-3.18.6-1-x86_64.pkg.tar.xz

So here I should have everywhere the old kernel. Then:

pacman -Syu

which tells me it is installing linux-3.19.2-... and works apparently fine. But it is now even stranger; I post the output of ls -l /boot.
/boot unmounted

total 37968
drwxr-xr-x 6 root     4096 Apr  3 23:12 grub
-rw-r--r-- 1 root 24680736 Apr  4 23:46 initramfs-linux-fallback.img
-rw-r--r-- 1 root 10118642 Apr  4 23:46 initramfs-linux.img
drwx------ 2 root     4096 Apr  3 23:12 lost+found
-rw-r--r-- 1 root  4065312 Feb  7 08:45 vmlinuz-linux

/boot mounted

total 38257
drwxr-xr-x 6 root     1024 Apr  3 22:45 grub
-rw-r--r-- 1 root 24751936 Apr  4 23:46 initramfs-linux-fallback.img
-rw-r--r-- 1 root 10128557 Apr  4 23:46 initramfs-linux.img
drwx------ 2 root    12288 Feb 24 18:04 lost+found
-rw-r--r-- 1 root  4123472 Mar 18 16:22 vmlinuz-linux

jasonwryan · 2015-04-04 22:05:43

So when you explicitly unmount /boot is exposes the boot on your / (which is where the kernel was installed when /boot (sda2, presumably) was unmounted).

TheArchitect · 2015-04-04 22:09:41

OK, seems logical.

I suppose I can try to remove everything that is on the /boot of my /, and then see if I can boot, in order to check if /dev/sda2 is used or not?

ewaller · 2015-04-04 23:10:10

I think you get it, but, just for clarity sake, a mount point is nothing more than a directory where one file system gets grafted into the tree of another file system. In this case, the mountpoint is /boot. If there is nothing mounted there, then it is a run of the mill directory. When a volume is mounted there, the entire contents of that volume appear under /boot, but the stuff under /boot on the original file system are "masked" and become not visible. That there are files in the directory /boot means that the boot volume was certainly not mounted at the time those files were written.

What Jason was driving at in post #12 is there is a quirk that allows multiple volumes to be mounted at the same mount point. I think the last volume to have been mounted "wins" in this case, but I am not certain. It might be that, at some point, boot was mounted at boot, but also something else was mounted at boot.

Now, it appears that the date on your kernel on your boot partition is in March. Mine happens to be March 26, but I run testing. Yours is March 18 which seems correct since the latest stable kernel was released on the 19th.

If you reboot now, does it work?
And yes, it makes sense to unmount /boot and clean out the /boot directory.

Edit: This illustrates the point:

ewaller@odin ~ 1010 %sudo fdisk -l /dev/sda 
Disk /dev/sda: 298.1 GiB, 320072933376 bytes, 625142448 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
Disklabel type: dos
Disk identifier: 0x87b33479

Device     Boot     Start       End   Sectors   Size Id Type
/dev/sda1            2048 121778159 121776112  58.1G  7 HPFS/NTFS/exFAT
/dev/sda2       597366784 625135615  27768832  13.2G 83 Linux
/dev/sda3       121778160 597366783 475588624 226.8G  5 Extended
/dev/sda5  *    121778223 123770219   1991997 972.7M 83 Linux
/dev/sda6       123770283 131770589   8000307   3.8G 82 Linux swap / Solaris
/dev/sda7       193213818 597360959 404147142 192.7G 83 Linux
/dev/sda8       131781258 193213754  61432497  29.3G 83 Linux
/dev/sda9       131770591 131781194     10604   5.2M  1 FAT12

Partition table entries are not in disk order.
ewaller@odin ~ 1011 %mount | grep boot     
/dev/sda5 on /boot type ext2 (rw,relatime)
ewaller@odin ~ 1012 %sudo mount /dev/sda2 /boot
ewaller@odin ~ 1013 %mount | grep boot
/dev/sda5 on /boot type ext2 (rw,relatime)
/dev/sda2 on /boot type jfs (rw,relatime)
ewaller@odin ~ 1014 %ls -l /boot
total 104
drwxr-xr-x  2 root root  4096 May  5  2013 bin
drwxr-xr-x  2 root root     8 Jan  9  2013 boot
drwxr-xr-x  3 root root  4096 Jan 17 09:49 dev
drwxr-xr-x 52 root root 20480 Jan 17 09:50 etc
drwxr-xr-x  3 root root    16 Jan 26  2013 home
lrwxrwxrwx  1 root root     5 May  4  2013 lib -> lib64
drwxr-xr-x  2 root root  4096 May  4  2013 lib32
drwxr-xr-x 10 root root  4096 May  5  2013 lib64
drwxr-xr-x  2 root root     8 Jan  9  2013 media
drwxr-xr-x  2 root root     8 Jan  9  2013 mnt
drwxr-xr-x  2 root root     8 Jan  9  2013 opt
drwxr-xr-x  2 root root     1 Jan  9  2013 proc
drwx------  6 root root  4096 May 12  2013 root
drwxr-xr-x  5 root root    64 Jan 17 09:49 run
drwxr-xr-x  2 root root  4096 May  5  2013 sbin
drwxr-xr-x  2 root root     8 Jan  9  2013 sys
drwxrwxrwt  4 root root    24 Jan 17 09:50 tmp
drwxr-xr-x 14 root root  4096 Jan 26  2013 usr
drwxr-xr-x  9 root root    96 Jan 26  2013 var
ewaller@odin ~ 1015 %sudo umount /boot
ewaller@odin ~ 1016 %ls -l /boot
total 34688
-rw-r--r-- 1 root root   812808 Mar 12  2012 background.jpg
-rw-r--r-- 1 root root  5613120 May 12  2013 gentoo
drwxr-xr-x 6 root root     4096 Nov  3 12:49 grub
drwxr-xr-x 2 root root     4096 Oct  5  2013 images
-rw-r--r-- 1 root root 18309933 Mar 26 21:39 initramfs-linux-fallback.img
-rw-r--r-- 1 root root  3484023 Mar 26 21:38 initramfs-linux.img
-rw-r--r-- 1 root root   663040 Feb  9 07:42 intel-ucode.img
drwx------ 2 root root    16384 May  1  2011 lost+found
drwxr-xr-x 2 root root     4096 Oct  9  2013 memtest86+
drwxr-xr-x 2 root root     4096 Mar 26 21:40 syslinux
-rw-r--r-- 1 root root  2411172 Aug 20  2011 System.map
-rw-r--r-- 1 root root  4123600 Mar 26 06:57 vmlinuz-linux
ewaller@odin ~ 1017 %sudo umount /boot
ewaller@odin ~ 1018 %ll /boot
total 0
ewaller@odin ~ 1019 %

Last edited by ewaller (2015-04-04 23:17:36)

TheArchitect · 2015-04-05 11:31:28

It is perfectly clear, thank you.

I removed everything on the /boot of my root partition, updated the kernel: doesn't work, same discrepancy between pacman -Qi and uname -a . Then I downgraded it again, only the /boot on /dev/sda2 contains files, and... It doesn't work!

I think this means I boot on the wrong /boot but I upgrade the kernel correctly. Right? How to fix that?

dice · 2015-04-05 11:44:09

Just to be sure: you unmounted /boot cleaned the files in the directory then mounted /boot again and then installed the kernel?
If so the new kernel should definitely be on /dev/sda2. Are you aware that you need to reboot after installing the kernel. If you did not reboot the discrepancy is normal.

Arch Linux

#1 2015-04-03 18:57:57

[SOLVED] No usb since kernel update

#2 2015-04-03 19:06:34

Re: [SOLVED] No usb since kernel update

#3 2015-04-03 19:26:43

Re: [SOLVED] No usb since kernel update

#4 2015-04-03 19:33:58

Re: [SOLVED] No usb since kernel update

#5 2015-04-03 21:57:04

Re: [SOLVED] No usb since kernel update

#6 2015-04-03 22:18:39

Re: [SOLVED] No usb since kernel update

#7 2015-04-04 20:59:11

Re: [SOLVED] No usb since kernel update

#8 2015-04-04 21:03:07

Re: [SOLVED] No usb since kernel update

#9 2015-04-04 21:12:18

Re: [SOLVED] No usb since kernel update

#10 2015-04-04 21:14:23

Re: [SOLVED] No usb since kernel update

#11 2015-04-04 21:33:07

Re: [SOLVED] No usb since kernel update

#12 2015-04-04 21:39:13

Re: [SOLVED] No usb since kernel update

#13 2015-04-04 21:39:41

Re: [SOLVED] No usb since kernel update

#14 2015-04-04 21:48:30

Re: [SOLVED] No usb since kernel update

#15 2015-04-04 21:51:17

Re: [SOLVED] No usb since kernel update

#16 2015-04-04 22:00:24

Re: [SOLVED] No usb since kernel update

#17 2015-04-04 22:05:43

Re: [SOLVED] No usb since kernel update

#18 2015-04-04 22:09:41

Re: [SOLVED] No usb since kernel update

#19 2015-04-04 23:10:10

Re: [SOLVED] No usb since kernel update

#20 2015-04-05 11:31:28

Re: [SOLVED] No usb since kernel update

#21 2015-04-05 11:44:09

Re: [SOLVED] No usb since kernel update

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