Bug 497766 – sys-boot/os-prober triggers lots of nasty kernel messages

• Product: Gentoo Linux
• Status: RESOLVED TEST-REQUEST

[Description Juergen Rose 2014-01-11 07:31:10 UTC]

Yesterday I did 'LANG=C grub2-mkconfig -o /boot/grub2/grub.cfg' from the console.
I got error messages about superblock on sda4. I was not able to redirect the error output to a file. But I found similar messages with 'dmesg'. So the standard output of grub2-mkconfig was:

Generating grub configuration file ...
Found linux image: /boot/kernel-genkernel-x86_64-3.12.7
Found initrd image: /boot/initramfs-genkernel-x86_64-3.12.7
Found linux image: /boot/kernel-genkernel-x86_64-3.12.6-gentoo
Found initrd image: /boot/initramfs-genkernel-x86_64-3.12.6-gentoo
Found linux image: /boot/kernel-genkernel-x86_64-3.12.6
Found initrd image: /boot/initramfs-genkernel-x86_64-3.12.6
Found linux image: /boot/kernel-genkernel-x86_64-3.12.5-gentoo
Found initrd image: /boot/initramfs-genkernel-x86_64-3.12.5-gentoo
Found linux image: /boot/kernel-genkernel-x86_64-3.12.5
Found initrd image: /boot/initramfs-genkernel-x86_64-3.12.5
Found linux image: /boot/kernel-genkernel-x86_64-3.11.6-gentoo
Found initrd image: /boot/initramfs-genkernel-x86_64-3.11.6-gentoo
Found linux image: /boot/kernel-genkernel-x86_64-3.11.6
Found initrd image: /boot/initramfs-genkernel-x86_64-3.11.6
Found linux image: /boot/kernel-genkernel-x86_64-3.10.10
Found initrd image: /boot/initramfs-genkernel-x86_64-3.10.10
Found linux image: /boot/kernel-genkernel-x86_64-3.10.6-rt-rt3
Found initrd image: /boot/initramfs-genkernel-x86_64-3.10.6-rt-rt3
Found Windows Recovery Environment (loader) on /dev/sda1
Found Windows Vista (loader) on /dev/sda2
done


And the last lines form dmesg were:

[42180.243133] REISERFS warning (device sda4): sh-2006 read_super_block: bread failed (dev sda4, block 64, size 1024)
[42180.244982] REISERFS warning (device sda4): sh-2021 reiserfs_fill_super: can not find reiserfs on sda4
[42180.248342] EXT3-fs (sda4): error: unable to read superblock
[42180.251648] EXT2-fs (sda4): error: unable to read superblock
[42180.260257] EXT4-fs (sda4): unable to read superblock
[42180.264108] XFS (sda4): bad magic number
[42180.266300] ffff8801243ac000: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[42180.268529] ffff8801243ac010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[42180.270744] ffff8801243ac020: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[42180.272946] ffff8801243ac030: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[42180.275127] XFS (sda4): Internal error xfs_sb_read_verify at line 637 of file fs/xfs/xfs_sb.c.  Caller 0xffffffffa0237965

[42180.279549] CPU: 0 PID: 5 Comm: kworker/0:0H Tainted: G           O 3.12.6-gentoo #1
[42180.281848] Hardware name: LENOVO 6458EG9/6458EG9, BIOS 7LETC9WW (2.29 ) 03/18/2011
[42180.284174] Workqueue: xfslogd xfs_buf_iodone_work [xfs]
[42180.286457]  0000000000000000 ffffffff8152f694 ffff880076b8a800 ffffffffa0239b09
[42180.288780]  0000027d00000000 ffffffffa0237965 ffff8800bb131c80 0000000000000016
[42180.291101]  ffff880076b8a800 ffff88013bc18600 ffffffffa02797ab ffffffffa0237965
[42180.293445] Call Trace:
[42180.295750]  [<ffffffff8152f694>] ? dump_stack+0x41/0x51
[42180.298097]  [<ffffffffa0239b09>] ? xfs_corruption_error+0x56/0x71 [xfs]
[42180.300447]  [<ffffffffa0237965>] ? xfs_buf_iodone_work+0x3a/0x65 [xfs]
[42180.302801]  [<ffffffffa02797ab>] ? xfs_sb_read_verify+0xbd/0xd2 [xfs]
[42180.305142]  [<ffffffffa0237965>] ? xfs_buf_iodone_work+0x3a/0x65 [xfs]
[42180.307470]  [<ffffffffa0237965>] ? xfs_buf_iodone_work+0x3a/0x65 [xfs]
[42180.309741]  [<ffffffff81067e68>] ? process_one_work+0x17a/0x28f
[42180.312000]  [<ffffffff81068328>] ? worker_thread+0x139/0x1de
[42180.314243]  [<ffffffff810681ef>] ? rescuer_thread+0x24f/0x24f
[42180.316473]  [<ffffffff8106c7f2>] ? kthread+0x7d/0x85
[42180.318686]  [<ffffffff81070000>] ? srcu_reschedule+0x70/0x9c
[42180.320890]  [<ffffffff8106c775>] ? __kthread_parkme+0x59/0x59
[42180.323086]  [<ffffffff815393bc>] ? ret_from_fork+0x7c/0xb0
[42180.325269]  [<ffffffff8106c775>] ? __kthread_parkme+0x59/0x59
[42180.327445] XFS (sda4): Corruption detected. Unmount and run xfs_repair
[42180.329632] XFS (sda4): SB validate failed with error 22.
[42180.337475] FAT-fs (sda4): bogus number of reserved sectors
[42180.339269] FAT-fs (sda4): Can't find a valid FAT filesystem
[42180.342419] FAT-fs (sda4): bogus number of reserved sectors
[42180.344195] FAT-fs (sda4): Can't find a valid FAT filesystem
[42180.347425] MINIX-fs: unable to read superblock


I do not understand, why grub2-mkconfig tries to detect filesystems an /dev/sda4 which is an extended partition:

fdisk -l

Disk /dev/sda: 931.5 GiB, 1000204886016 bytes, 1953525168 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: 0xa00041d8

Device    Boot     Start        End    Blocks  Id System
/dev/sda1           2048   14155249   7076601  27 Hidden NTFS WinRE
/dev/sda2       14155776  114849791  50347008   7 HPFS/NTFS/exFAT
/dev/sda3      114849792  115910081    530145  83 Linux
/dev/sda4      115910656 1953525167 918807256   5 Extended
/dev/sda5      115912704  141078527  12582912  82 Linux swap / Solaris
/dev/sda6      141080576  409516031 134217728  83 Linux
/dev/sda7      409518080 1953525167 772003544  83 Linux


Then I tried today once more 'LANG=C grub2-mkconfig -o /boot/grub2/grub.cfg' in a ssh session from an xterm window. There I could not see any error message. But if I do the command at the console I see it again. If I remember correctly I found the same behaviour some weeks ago at an other systems. Any hint is appreciated.



root@lynx:/usr/src/linux(15)# emerge --info
Portage 2.2.8 (default/linux/amd64/13.0/desktop, gcc-4.8.2, glibc-2.17, 3.12.6-gentoo x86_64)
=================================================================
System uname: Linux-3.12.6-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.2
KiB Mem:     3987136 total,     50620 free
KiB Swap:   12582908 total,  12582772 free
Timestamp of tree: Fri, 10 Jan 2014 06:00:01 +0000
ld GNU ld (GNU Binutils) 2.24
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p45-r1
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.6, 3.3.3
dev-util/cmake:           2.8.12.1-r3
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.14.1
sys-devel/binutils:       2.24-r1
sys-devel/gcc:            4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.12 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo lordvan sage-on-gentoo science sunrise x11 local g-cpan g-octave
Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage_lynx"
PORTDIR_OVERLAY="/var/lib/layman/lordvan /var/lib/layman/sage-on-gentoo /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/x11 /usr/local/portage /var/lib/cpan /var/lib/g-octave"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm syslog" DVB_CARDS="usb-wt220u" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

[Comment 1 Mike Gilbert 2014-01-11 16:21:49 UTC]

(In reply to Juergen Rose from comment #0)
> Yesterday I did 'LANG=C grub2-mkconfig -o /boot/grub2/grub.cfg' from the
> console.

Side note: Please switch to running grub2-mkconfig -o /boot/grub/grub.cfg.

/boot/grub has been the correct location since 2.00_p5107-r1. It currently contains a compatibility symlink for people (like you) who don't read their postinst messages.

[Comment 2 Mike Gilbert 2014-01-11 17:34:01 UTC]

Can you run "blkid /dev/sda4"? Maybe there is some stale data there.

[Comment 3 Mike Gilbert 2014-01-11 20:48:10 UTC]

This is not a grub problem at all; os-prober is what triggers those messages.

[Comment 4 Juergen Rose 2014-01-12 06:05:16 UTC]

(In reply to Mike Gilbert from comment #2)
> Can you run "blkid /dev/sda4"? Maybe there is some stale data there.

root@lynx:/root(1)# blkid /dev/sda4
/dev/sda4: PTTYPE="dos" PARTUUID="a00041d8-04"

[Comment 5 Juergen Rose 2014-02-10 10:53:44 UTC]

(In reply to Mike Gilbert from comment #1)
> (In reply to Juergen Rose from comment #0)
> > Yesterday I did 'LANG=C grub2-mkconfig -o /boot/grub2/grub.cfg' from the
> > console.
> 
> Side note: Please switch to running grub2-mkconfig -o /boot/grub/grub.cfg.
> 
> /boot/grub has been the correct location since 2.00_p5107-r1. It currently
> contains a compatibility symlink for people (like you) who don't read their
> postinst messag

I reemerged grub-2.02_beta2  and found only:
 * For information on how to configure GRUB2 please refer to the guide:
 *     http://wiki.gentoo.org/wiki/GRUB2_Quick_Start
and nothing special about moving from /boot/grub2 to /boot/grub.

Nevertheless I moved all files an directories from /boot/grub2/ to /boot/grub/. And I did then 'LANG=C grub2-mkconfig -o /boot/grub/grub.cfg'. The next boot hangs at:
error: file '/grub2/i386-pc/normal.mod' not found.
Entering rescue mode...

What can I do? Booting with a rescue CD and performing grub2-install?
Or can I do something form the grub rescue prompt?

Regards

[Comment 6 Juergen Rose 2014-02-10 12:35:56 UTC]

(In reply to Juergen Rose from comment #5)
...
> I reemerged grub-2.02_beta2  and found only:
>  * For information on how to configure GRUB2 please refer to the guide:
>  *     http://wiki.gentoo.org/wiki/GRUB2_Quick_Start
> and nothing special about moving from /boot/grub2 to /boot/grub.
> 
> Nevertheless I moved all files an directories from /boot/grub2/ to
> /boot/grub/. And I did then 'LANG=C grub2-mkconfig -o /boot/grub/grub.cfg'.
> The next boot hangs at:
> error: file '/grub2/i386-pc/normal.mod' not found.
> Entering rescue mode...
> 
> What can I do? Booting with a rescue CD and performing grub2-install?
> Or can I do something form the grub rescue prompt?
> 
> Regards

Booting with a rescue CD and performing grub2-install helped.

[Comment 7 Pacho Ramos 2017-02-06 16:28:52 UTC]

are you still suffering this with 1.71 or 1.73?