[Bug 549428] [NEW] Triggers permanent high i/o load after upgrade

Wed Apr 21 09:41:53 UTC 2010

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Binary package hint: apparmor

Hi

So this is the second time this happens after an upgrade of my laptop: i run a package upgrade using aptitude, and when it's done, some background I/O is happening after completion.  This I/O never ends.  The first time this happened was on 2010/03/09 after my morning upgrade; list of packages upgraded from aptitude.log:
mar., mars  9 2010 10:32:47 +0100

IMPORTANT : ce journal ne contient que les actions demandées ; certaines actions qui
échouent à cause d'erreurs de dpkg peuvent donc ne pas être réalisées.

90 paquets vont être installés, et 2 retirés.
893ko d'espace disque vont être utilisés
===============================================================================
[SUPPRIMÉ, NON UTILISÉ] libparted-2.1-0
[SUPPRIMÉ, NON UTILISÉ] libparted1.8-12
[INSTALLÉ, DÉPENDANCES] libaio1
[INSTALLÉ, DÉPENDANCES] libparted0
[MIS A JOUR] apparmor 2.5~pre+bzr1364-0ubuntu1 -> 2.5~pre+bzr1367-0ubuntu1
[MIS A JOUR] apparmor-utils 2.5~pre+bzr1364-0ubuntu1 -> 2.5~pre+bzr1367-0ubuntu1
[MIS A JOUR] apturl 0.4.1ubuntu2 -> 0.4.1ubuntu3
[MIS A JOUR] apturl-common 0.4.1ubuntu2 -> 0.4.1ubuntu3
[MIS A JOUR] at-spi 1.29.90-0ubuntu2 -> 1.29.92-0ubuntu1
[MIS A JOUR] binutils 2.20.1-1ubuntu1 -> 2.20.1-2ubuntu1
[MIS A JOUR] binutils-doc 2.20.1-1ubuntu1 -> 2.20.1-2ubuntu1
[MIS A JOUR] binutils-static 2.20.1-1ubuntu1 -> 2.20.1-2ubuntu1
[MIS A JOUR] empathy 2.29.91.2-0ubuntu1 -> 2.29.91.2-0ubuntu2
[MIS A JOUR] empathy-common 2.29.91.2-0ubuntu1 -> 2.29.91.2-0ubuntu2
[MIS A JOUR] euca2ools 1.2-0ubuntu5 -> 1.2-0ubuntu6
[MIS A JOUR] evince 2.29.91-0ubuntu1 -> 2.29.91-0ubuntu2
[MIS A JOUR] firefox 3.6+nobinonly-0ubuntu5 -> 3.6+nobinonly-0ubuntu6
[MIS A JOUR] firefox-branding 3.6+nobinonly-0ubuntu5 -> 3.6+nobinonly-0ubuntu6
[MIS A JOUR] firefox-gnome-support 3.6+nobinonly-0ubuntu5 -> 3.6+nobinonly-0ubuntu6
[MIS A JOUR] gbrainy 1.30-1ubuntu5 -> 1.40-1ubuntu1
[MIS A JOUR] gcalctool 5.29.92~20100301.2-0ubuntu1 -> 5.29.92-0ubuntu1
[MIS A JOUR] gnome-about 1:2.29.91-0ubuntu1 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] gnome-accessibility-themes 2.29.91-0ubuntu1 -> 2.29.92-0ubuntu1
[MIS A JOUR] gnome-desktop-data 1:2.29.91-0ubuntu1 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] gnome-menus 2.29.91-0ubuntu2 -> 2.29.92-0ubuntu2
[MIS A JOUR] gnome-themes-selected 2.29.91-0ubuntu1 -> 2.29.92-0ubuntu1
[MIS A JOUR] gstreamer0.10-alsa 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gstreamer0.10-ffmpeg 0.10.9.3-1 -> 0.10.10-1
[MIS A JOUR] gstreamer0.10-gnomevfs 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gstreamer0.10-plugins-base 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gstreamer0.10-plugins-base-apps 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gstreamer0.10-plugins-ugly 0.10.13.3-1 -> 0.10.14-1
[MIS A JOUR] gstreamer0.10-tools 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gstreamer0.10-x 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] gvfs 1.5.4-0ubuntu1 -> 1.5.5-0ubuntu1
[MIS A JOUR] gvfs-backends 1.5.4-0ubuntu1 -> 1.5.5-0ubuntu1
[MIS A JOUR] gvfs-bin 1.5.4-0ubuntu1 -> 1.5.5-0ubuntu1
[MIS A JOUR] gvfs-fuse 1.5.4-0ubuntu1 -> 1.5.5-0ubuntu1
[MIS A JOUR] humanity-icon-theme 0.5.1.2 -> 0.5.1.3
[MIS A JOUR] libapparmor-perl 2.5~pre+bzr1364-0ubuntu1 -> 2.5~pre+bzr1367-0ubuntu1
[MIS A JOUR] libapparmor1 2.5~pre+bzr1364-0ubuntu1 -> 2.5~pre+bzr1367-0ubuntu1
[MIS A JOUR] libatk1.0-0 1.29.4-0ubuntu1 -> 1.29.92-0ubuntu1
[MIS A JOUR] libatk1.0-data 1.29.4-0ubuntu1 -> 1.29.92-0ubuntu1
[MIS A JOUR] libatk1.0-doc 1.29.4-0ubuntu1 -> 1.29.92-0ubuntu1
[MIS A JOUR] libatspi1.0-0 1.29.90-0ubuntu2 -> 1.29.92-0ubuntu1
[MIS A JOUR] libcap2 1:2.17-2 -> 1:2.17-2ubuntu1
[MIS A JOUR] libcap2-bin 1:2.17-2 -> 1:2.17-2ubuntu1
[MIS A JOUR] libevdocument2 2.29.91-0ubuntu1 -> 2.29.91-0ubuntu2
[MIS A JOUR] libevview2 2.29.91-0ubuntu1 -> 2.29.91-0ubuntu2
[MIS A JOUR] libglib2.0-0 2.23.4-1ubuntu1 -> 2.23.4-1ubuntu2
[MIS A JOUR] libglib2.0-data 2.23.4-1ubuntu1 -> 2.23.4-1ubuntu2
[MIS A JOUR] libglib2.0-dev 2.23.4-1ubuntu1 -> 2.23.4-1ubuntu2
[MIS A JOUR] libglib2.0-doc 2.23.4-1ubuntu1 -> 2.23.4-1ubuntu2
[MIS A JOUR] libgnome-desktop-2-17 1:2.29.91-0ubuntu1 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] libgnome-menu2 2.29.91-0ubuntu2 -> 2.29.92-0ubuntu2
[MIS A JOUR] libgstreamer-plugins-base0.10-0 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] libgstreamer0.10-0 0.10.26.3-1 -> 0.10.27-1
[MIS A JOUR] libgvfscommon0 1.5.4-0ubuntu1 -> 1.5.5-0ubuntu1
[MIS A JOUR] libnautilus-extension1 1:2.29.91-0ubuntu2 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] libsmbclient 2:3.4.6~dfsg-1ubuntu1 -> 2:3.4.6~dfsg-1ubuntu2
[MIS A JOUR] libtaglib2.0-cil 2.0.3.4+dfsg-2 -> 2.0.3.6+dfsg-1
[MIS A JOUR] libvirt-bin 0.7.5-5ubuntu10 -> 0.7.5-5ubuntu12
[MIS A JOUR] libvirt0 0.7.5-5ubuntu10 -> 0.7.5-5ubuntu12
[MIS A JOUR] libwbclient0 2:3.4.6~dfsg-1ubuntu1 -> 2:3.4.6~dfsg-1ubuntu2
[MIS A JOUR] nautilus 1:2.29.91-0ubuntu2 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] nautilus-data 1:2.29.91-0ubuntu2 -> 1:2.29.92-0ubuntu1
[MIS A JOUR] openssh-client 1:5.3p1-3ubuntu2 -> 1:5.3p1-3ubuntu3
[MIS A JOUR] openssh-server 1:5.3p1-3ubuntu2 -> 1:5.3p1-3ubuntu3
[MIS A JOUR] parted 2.1-4ubuntu1 -> 2.2-1ubuntu2
[MIS A JOUR] pidgin-libnotify 0.14-1ubuntu13 -> 0.14-1ubuntu14
[MIS A JOUR] python-gmenu 2.29.91-0ubuntu2 -> 2.29.92-0ubuntu2
[MIS A JOUR] python-gtkspell 2.25.3-4.1ubuntu1 -> 2.25.3-4.1ubuntu2
[MIS A JOUR] python-libvirt 0.7.5-5ubuntu10 -> 0.7.5-5ubuntu12
[MIS A JOUR] python-pyatspi 1.29.90-0ubuntu2 -> 1.29.92-0ubuntu1
[MIS A JOUR] qemu-arm-static 0.12.3-0ubuntu10 -> 0.12.3-0ubuntu11
[MIS A JOUR] qemu-kvm 0.12.3-0ubuntu10 -> 0.12.3-0ubuntu11
[MIS A JOUR] qemu-kvm-extras 0.12.3-0ubuntu10 -> 0.12.3-0ubuntu11
[MIS A JOUR] qemu-kvm-extras-static 0.12.3-0ubuntu10 -> 0.12.3-0ubuntu11
[MIS A JOUR] samba-common 2:3.4.6~dfsg-1ubuntu1 -> 2:3.4.6~dfsg-1ubuntu2
[MIS A JOUR] samba-common-bin 2:3.4.6~dfsg-1ubuntu1 -> 2:3.4.6~dfsg-1ubuntu2
[MIS A JOUR] simple-scan 0.9.6-1ubuntu1 -> 0.9.7-0ubuntu1
[MIS A JOUR] smbclient 2:3.4.6~dfsg-1ubuntu1 -> 2:3.4.6~dfsg-1ubuntu2
[MIS A JOUR] ssh-askpass-gnome 1:5.3p1-3ubuntu2 -> 1:5.3p1-3ubuntu3
[MIS A JOUR] telepathy-haze 0.3.3-1 -> 0.3.4-1
[MIS A JOUR] udisks 1.0.0~git20100227.36c8a4-1 -> 1.0.0~git20100305.fa313b2-1ubuntu1
[MIS A JOUR] update-manager 1:0.132.1 -> 1:0.133
[MIS A JOUR] update-manager-core 1:0.132.1 -> 1:0.133
[MIS A JOUR] vim 2:7.2.245-2ubuntu3 -> 2:7.2.330-1ubuntu2
[MIS A JOUR] vim-common 2:7.2.245-2ubuntu3 -> 2:7.2.330-1ubuntu2
[MIS A JOUR] vim-runtime 2:7.2.245-2ubuntu3 -> 2:7.2.330-1ubuntu2
[MIS A JOUR] vim-tiny 2:7.2.245-2ubuntu3 -> 2:7.2.330-1ubuntu2
[MIS A JOUR] watershed 4build1 -> 5
===============================================================================

I couldn't find the source of the I/O in top or iotop; either it was in the kernel or it was spread on many processes.
I asked for some help diagnosing it on irc:
11:47 < lool> Something is adding massive load to my laptop since the latest upgrade
11:47 < lool> I can't figure out what it is; I see one of my CPU is busy in kernel space
11:47 < lool> iotop shows nothing (nor top obviously)
11:48 < lool> I have a long list of console-kit processes though

I ended up rebooting.

This happened yesterday evening again; much shorter upgrade log:
ven., mars 26 2010 23:36:36 +0100

IMPORTANT : ce journal ne contient que les actions demandées ; certaines actions qui
échouent à cause d'erreurs de dpkg peuvent donc ne pas être réalisées.

41 paquets vont être installés, et 1 retirés.
1 122ko d'espace disque vont être utilisés
===============================================================================
[SUPPRIMÉ, NON UTILISÉ] libntfs-3g54
[INSTALLÉ, DÉPENDANCES] libntfs-3g75
[MIS A JOUR] apparmor 2.5-0ubuntu1 -> 2.5-0ubuntu2
[MIS A JOUR] apparmor-utils 2.5-0ubuntu1 -> 2.5-0ubuntu2
[MIS A JOUR] apt 0.7.25.3ubuntu3 -> 0.7.25.3ubuntu4
[MIS A JOUR] apt-transport-https 0.7.25.3ubuntu3 -> 0.7.25.3ubuntu4
[MIS A JOUR] apt-utils 0.7.25.3ubuntu3 -> 0.7.25.3ubuntu4
[MIS A JOUR] apt-xapian-index 0.22 -> 0.25
[MIS A JOUR] capplets-data 1:2.29.92-0ubuntu2 -> 1:2.29.92-0ubuntu3
[MIS A JOUR] console-setup 1.34ubuntu12 -> 1.34ubuntu13
[MIS A JOUR] gnome-control-center 1:2.29.92-0ubuntu2 -> 1:2.29.92-0ubuntu3
[MIS A JOUR] gnome-power-manager 2.29.91-0ubuntu8 -> 2.29.91-0ubuntu9
[MIS A JOUR] indicator-session 0.2.7-0ubuntu2 -> 0.2.7-0ubuntu3
[MIS A JOUR] initramfs-tools 0.92bubuntu69 -> 0.92bubuntu71
[MIS A JOUR] initramfs-tools-bin 0.92bubuntu69 -> 0.92bubuntu71
[MIS A JOUR] jockey-common 0.5.8-0ubuntu3 -> 0.5.8-0ubuntu5
[MIS A JOUR] jockey-gtk 0.5.8-0ubuntu3 -> 0.5.8-0ubuntu5
[MIS A JOUR] language-selector 0.5.3 -> 0.5.4
[MIS A JOUR] language-selector-common 0.5.3 -> 0.5.4
[MIS A JOUR] libapparmor-perl 2.5-0ubuntu1 -> 2.5-0ubuntu2
[MIS A JOUR] libapparmor1 2.5-0ubuntu1 -> 2.5-0ubuntu2
[MIS A JOUR] libgnome-window-settings1 1:2.29.92-0ubuntu2 -> 1:2.29.92-0ubuntu3
[MIS A JOUR] libssl0.9.8 0.9.8k-7ubuntu6 -> 0.9.8k-7ubuntu7
[MIS A JOUR] light-themes 0.1.5.9 -> 0.1.6.0
[MIS A JOUR] ntfs-3g 1:2009.4.4-1ubuntu5 -> 1:2010.3.6-1ubuntu1
[MIS A JOUR] openssl 0.9.8k-7ubuntu6 -> 0.9.8k-7ubuntu7
[MIS A JOUR] python-cupshelpers 1.1.17+20100217-0ubuntu6 -> 1.1.17+20100217-0ubuntu9
[MIS A JOUR] python-distutils-extra 2.18 -> 2.18bzr1
[MIS A JOUR] python-software-properties 0.75.7 -> 0.75.8
[MIS A JOUR] python-twisted-bin 9.0.0-1 -> 10.0.0-2
[MIS A JOUR] python-twisted-core 9.0.0-1 -> 10.0.0-2
[MIS A JOUR] python-twisted-names 9.0.0-1 -> 10.0.0-1
[MIS A JOUR] python-twisted-web 9.0.0-1 -> 10.0.0-1
[MIS A JOUR] python-xkit 0.4.2 -> 0.4.2.1
[MIS A JOUR] software-properties-gtk 0.75.7 -> 0.75.8
[MIS A JOUR] sudo 1.7.2p1-1ubuntu3 -> 1.7.2p1-1ubuntu4
[MIS A JOUR] synaptic 0.63.1ubuntu1 -> 0.63.1ubuntu2
[MIS A JOUR] system-config-printer-common 1.1.17+20100217-0ubuntu6 -> 1.1.17+20100217-0ubuntu9
[MIS A JOUR] system-config-printer-gnome 1.1.17+20100217-0ubuntu6 -> 1.1.17+20100217-0ubuntu9
[MIS A JOUR] system-config-printer-udev 1.1.17+20100217-0ubuntu6 -> 1.1.17+20100217-0ubuntu7
[MIS A JOUR] ubuntu-mono 0.0.10 -> 0.0.11
[MIS A JOUR] valgrind 1:3.6.0~svn20100212-0ubuntu3 -> 1:3.6.0~svn20100212-0ubuntu4
===============================================================================

Since apparmor appears in both and probably impacts kernel-ish stuff too, I figured it could be the culprit, and hence I'm filing the bug here.

I couldn't find anything in syslog, kernel.log, dmesg (just the regular
spam I get from other bugs).

I left my computer running all night, this morning I/O was still
happening at a high rate (my disk activity LED was blinking fast as if
doing lots of small I/O, my sysmon applet showed load and 100% CPU used
in the system for one of my CPUs).

The next time this happens, I'll try echo-ing to /proc/sys/vm/block_dump
to see where I/O is happening, but I wanted to report the bug as it
seems like a serious one.  I don't see anything special in my setup
which would trigger this, it's quite boring.  I have my /home on
ecryptfs and am using LVM.  The disk is a 120 GB SSD, so should have
gone through any global file scan over night.

I couldn't reproduce the bug by dpkg-reconfiguring *apparmor*, jockey*,
*ntfs*, apt-xapian-index nor by reinstalling them.

Bye,

ProblemType: Bug
ApparmorStatusOutput:
 Error: command /usr/sbin/apparmor_status failed with exit code 4: You do not have enough privilege to read the profile set.
 apparmor module is loaded.
Architecture: amd64
Date: Sat Mar 27 10:46:05 2010
DistroRelease: Ubuntu 10.04
Package: apparmor 2.5-0ubuntu2
ProcEnviron:
 LANGUAGE=fr_FR:fr:en_GB:en
 PATH=(custom, user)
 LANG=fr_FR.UTF-8
 SHELL=/bin/zsh
ProcVersionSignature: Ubuntu 2.6.32-17.26-generic 2.6.32.10+drm33.1
SourcePackage: apparmor
Uname: Linux 2.6.32-17-generic x86_64

** Affects: linux (Ubuntu)
     Importance: Undecided
         Status: New

** Tags: amd64 apport-bug lucid
-- 
Triggers permanent high i/o load after upgrade
https://bugs.launchpad.net/bugs/549428
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