Bug 111149 – Kernel 2.6.13.4 Error "scheduling while atomic: mysqld" using mysql-4.1.14 on alpha

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Thomas Cort (RETIRED) 2005-11-01 07:12:37 UTC]

This morning I was doing some work on my alpha box and noticed slowness for some
applications (screen, uptime, /etc/init.d/klive) and no response from others
(/etc/init.d/apache2, /etc/init.d/jabber, /etc/init.d/mysql). I looked at the
load averages and they kept climbing very rapidly.

$ uptime
08:07:40 up 17 days, 22:34,  3 users,  load average: 55.45, 46.99, 42.09

The system was so bogged down that I couldn't run many commands, so I just
rebooted. I checked the logs and found nothing useful in the system log or the
mysql logs. However in the kernel log I did find this:

Nov  1 05:04:53 [kernel] [5733083.383995] scheduling while atomic:
mysqld/0x00000001/6720

I'm not sure how or why it happened or if I can expect it to happen again. I
just upgraded to mysql-4.1.14 about 3 days ago and I'm not sure if that had
something to do with it. Can someone tell me if the cause of this is a kernel
bug, a mysql bug, or both?

Reproducible: Didn't try
Steps to Reproduce:
1. Unknown

Actual Results:  
System became unresponsive, forcing me to reboot.

Expected Results:  
It should have kept running smoothly without bringing my load average up to 55.45.

Portage 2.0.51.22-r3 (default-linux/alpha/2005.0, gcc-3.3.2,
glibc-2.3.4.20041102-r1, 2.6.13.4 alpha)
=================================================================
System uname: 2.6.13.4 alpha EV56
Gentoo Base System version 1.6.13
dev-lang/python:     2.3.5-r2, 2.4.2
sys-apps/sandbox:    1.2.12
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1
sys-devel/binutils:  2.15.92.0.2-r10
sys-devel/libtool:   1.5.20
virtual/os-headers:  2.6.8.1-r4
ACCEPT_KEYWORDS="alpha"
AUTOCLEAN="yes"
CBUILD="alpha-unknown-linux-gnu"
CFLAGS="-mieee -O3 -mcpu=ev4"
CHOST="alpha-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config
/var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-mieee -O3 -mcpu=ev4"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks sandbox sfperms strict"
GENTOO_MIRRORS="ftp://gentoo.risq.qc.ca/
http://mirror.arcticnetwork.ca/pub/gentoo/ http://adelie.polymtl.ca/
http://gentoo.cites.uiuc.edu/pub/gentoo/ ftp://gentoo.arcticnetwork.ca/pub/gentoo/"
LDFLAGS="-Wl,-O1"
LINGUAS="en"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.ca.gentoo.org/gentoo-portage"
USE="alpha X apache2 arts berkdb bitmap-fonts crypt cups curl eds encode esd fam
font-server foomatic foomaticdb fortran gd gdbm gif gnome gpm gstreamer gtk gtk2
imlib jabber jpeg kde libg++ libwww mad mikmod motif mozilla mp3 mpeg mysql
ncurses nls nptl nptlonly ogg oggvorbis opengl oss pam pdflib perl png postgres
python qt quicktime readline sdl spell ssl tcpd tiff truetype truetype-fonts
type1-fonts udev vorbis xml2 xmms xv zlib linguas_en userland_GNU kernel_linux
elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL

[Comment 1 Thomas Cort (RETIRED) 2005-11-01 07:18:32 UTC]

Created attachment 71870 [details]
Kernel Config 2.6.13.4

[Comment 2 Thomas Cort (RETIRED) 2005-11-01 07:20:06 UTC]

Created attachment 71871 [details]
MySQL Config File

[Comment 3 Daniel Drake (RETIRED) 2005-11-01 07:41:52 UTC]

I think there are known problems with 2.6.13 on alpha.

You should try 2.6.14 if possible, but I'm not sure if those issues are resolved
there

[Comment 4 Thomas Cort (RETIRED) 2005-11-01 08:10:14 UTC]

I just re-read the 2.6.14 changelog[1] and there are some atomic fixes for alpha
in 2.6.14, but unfortunately 2.6.14 doesn't compile on alpha[2]. However
2.6.14-git4[3] has a 2.6.14 compile fix[4]. I'll try the fix[4]; unfortunately
it will be hard to tell if it worked because I ran 2.6.13.4 for 17 days without
a problem, and I don't know how to reproduce the error. Thanks for the advice!

[1] http://kernel.org/pub/linux/kernel/v2.6/ChangeLog-2.6.14
[2] http://bugzilla.kernel.org/show_bug.cgi?id=5512
[3] http://kernel.org/pub/linux/kernel/v2.6/snapshots/patch-2.6.14-git4.log
[4] http://lkml.org/lkml/2005/10/26/43

[Comment 5 Thomas Cort (RETIRED) 2005-11-04 05:04:39 UTC]

I applied the patch[1] and got 2.6.14 to compile. However the "scheduling while
atomic" thing is happening again. See output below:

pan ~ # uptime
 07:49:27 up 2 days, 18:54,  1 user,  load average: 42.17, 42.05, 42.01

pan ~ # tail /var/log/kernel/current
Nov  4 05:25:13 [kernel] [4426177.025788] scheduling while atomic:
mysqld/0x00000001/10489

pan ~ # cat /proc/version
Linux version 2.6.14 (root@pan) (gcc version 3.3.2 20040119 (Gentoo Linux
3.3.2-r7, propolice-3.3-7)) #1 Tue Nov 1 12:05:18 EST 2005

I read the ChangeLog for 2.6.14-git7[2] and there are a lot of atomicity fixes.
I'll try that kernel[3] and report back if this happens again.

[1] http://lkml.org/lkml/2005/10/26/43
[2] http://kernel.org/pub/linux/kernel/v2.6/snapshots/patch-2.6.14-git7.log
[3] http://kernel.org/pub/linux/kernel/v2.6/snapshots/patch-2.6.14-git7.gz

[Comment 6 Thomas Cort (RETIRED) 2005-11-12 10:17:22 UTC]

I haven't gotten the 'scheduling while atomic' error in over a week. Upgrading
to the latest kernel solved the problem.