System locked up during update of kernel, yum in unclean state and kernel half-installed

Deron Meranda deron.meranda at gmail.com
Sat Nov 19 22:12:45 UTC 2011


I'm running Fedora 16 and I attempted to install the most recent set
of released updates (from fedora-updates - I'm not using the testing
repo), using "yum update".

While it was installing the kernel package
(kernel-3.1.1-2.fc16.x86_64), the entire system locked up. It was
unresponsive to anything, even mouse movement or network access. There
was no disk access either from what I could tell. I left it that way
for a long time, and finally was forced to do a hard power-off.

After the reboot I'm not sure exactly what state my system is in, and
I may need some guidance to get it back up to normal. It is running
now, but I think the installed packages may be a bit mixed up.

This system does not have any history of having a hard lock-up. I have
been having a few Gnome freezing issues since F16, but the kernel and
OS has never locked up.

Output of "yum check" shows it's not clean:

at-3.1.13-5.fc16.x86_64 is a duplicate with at-3.1.13-3.fc16.x86_64
32:bind-9.8.1-4.P1.fc16.x86_64 is a duplicate with 32:bind-9.8.1-2.fc16.x86_64
32:bind-libs-9.8.1-4.P1.fc16.x86_64 is a duplicate with
32:bind-libs-9.8.1-2.fc16.x86_64
32:bind-license-9.8.1-4.P1.fc16.noarch is a duplicate with
32:bind-license-9.8.1-2.fc16.noarch
facter-1.6.2-1.fc16.noarch is a duplicate with facter-1.6.1-1.fc16.noarch
kernel-headers-3.1.1-2.fc16.x86_64 is a duplicate with
kernel-headers-3.1.1-1.fc16.x86_64
kernel-tools-3.1.1-2.fc16.x86_64 is a duplicate with
kernel-tools-3.1.1-1.fc16.x86_64
1:nfs-utils-1.2.5-3.fc16.x86_64 is a duplicate with
1:nfs-utils-1.2.5-1.fc16.x86_64
perl-IO-Socket-SSL-1.49-1.fc16.noarch is a duplicate with
perl-IO-Socket-SSL-1.45-1.fc16.noarch
setroubleshoot-plugins-3.0.17-1.fc16.noarch is a duplicate with
setroubleshoot-plugins-3.0.14-2.fc15.noarch
xfwm4-4.8.2-1.fc16.x86_64 is a duplicate with xfwm4-4.8.1-5.fc16.x86_64
Error: check all

Here's the last set of messages recorded in syslog:

Nov 19 16:27:59 beryl yum[12885]: Updated:
32:bind-license-9.8.1-4.P1.fc16.noarch
Nov 19 16:28:00 beryl yum[12885]: Updated: 32:bind-libs-9.8.1-4.P1.fc16.x86_64
Nov 19 16:28:03 beryl systemd[1]: Reloading.
Nov 19 16:28:04 beryl yum[12885]: Updated: 32:bind-9.8.1-4.P1.fc16.x86_64
Nov 19 16:28:08 beryl yum[12885]: Updated: git-1.7.7.3-1.fc16.x86_64
Nov 19 16:28:08 beryl yum[12885]: Updated: perl-Git-1.7.7.3-1.fc16.noarch
Nov 19 16:28:09 beryl yum[12885]: Updated: facter-1.6.2-1.fc16.noarch
Nov 19 16:28:12 beryl systemd[1]: Reloading.
Nov 19 16:28:12 beryl yum[12885]: Updated: puppet-2.6.12-1.fc16.noarch
Nov 19 16:28:13 beryl yum[12885]: Updated: 32:bind-chroot-9.8.1-4.P1.fc16.x86_64
Nov 19 16:28:13 beryl yum[12885]: Updated: 32:bind-utils-9.8.1-4.P1.fc16.x86_64
Nov 19 16:28:14 beryl yum[12885]: Updated:
32:bind-libs-lite-9.8.1-4.P1.fc16.x86_64
Nov 19 16:28:42 beryl yum[12885]: Installed: kernel-devel-3.1.1-2.fc16.x86_64
Nov 19 16:28:44 beryl yum[12885]: Updated: kernel-tools-3.1.1-2.fc16.x86_64
Nov 19 16:28:46 beryl yum[12885]: Updated: kernel-headers-3.1.1-2.fc16.x86_64
Nov 19 16:28:48 beryl yum[12885]: Updated: perl-IO-Socket-SSL-1.49-1.fc16.noarch
Nov 19 16:28:49 beryl yum[12885]: Updated:
setroubleshoot-plugins-3.0.17-1.fc16.noarch
Nov 19 16:28:54 beryl yum[12885]: Updated: xfwm4-4.8.2-1.fc16.x86_64
Nov 19 16:28:55 beryl systemd[1]: Reloading.
Nov 19 16:28:55 beryl systemd[1]: Reloading.
Nov 19 16:28:56 beryl yum[12885]: Updated: 1:nfs-utils-1.2.5-3.fc16.x86_64
Nov 19 16:28:57 beryl systemd[1]: Reloading.
Nov 19 16:28:57 beryl yum[12885]: Updated: at-3.1.13-5.fc16.x86_64
Nov 19 16:29:04 beryl yum[12885]: Installed: kernel-3.1.1-2.fc16.x86_64


If I check the rpm database it shows 3 kernel packages installed:

# rpm -qi kernel
Name        : kernel
Version     : 3.1.0
Release     : 7.fc16
Architecture: x86_64
...
Name        : kernel
Version     : 3.1.1
Release     : 1.fc16
Architecture: x86_64
...
Name        : kernel
Version     : 3.1.1
Release     : 2.fc16
Architecture: x86_64


After my reboot I booted with the most recent kernel that was
configured in grub, and now

cat /proc/version
Linux version 3.1.1-1.fc16.x86_64
(mockbuild at x86-06.phx2.fedoraproject.org) (gcc version 4.6.2 20111027
(Red Hat 4.6.2-1) (GCC) ) #1 SMP Fri Nov 11 21:47:56 UTC 2011


So the -2 revision must not have gotten fully installed.


What are my next steps?  If it was just a normal application package,
I'd force a yum re-install. But since this happened during a kernel
update, I don't want to risk messing my system up further.
-- 
Deron Meranda
http://deron.meranda.us/


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