glibc, libc.so.6, nptl, nptlonly = problems

Message

destr0yr · Post by **destr0yr** » Tue Mar 14, 2006 5:32 am

hi. i just recently did a --sync and emerge -uDv world which seemed to upgrade glibc to 2.4. upon returning to my system, i was greated with the following error:

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grep: relocation error: grep: symbol ___guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

similar errors are returned when i run sed, vi or attempt to emerge any package. i'm a little lost what to do next and how to fix this.
/lib/libc.so.6 is symlinked to ./libc-2.4.so, running libc.so.6 returns the "Native POSIX Threads..."
Suggestions are very welcome...

troworld · Post by **troworld** » Tue Mar 14, 2006 5:40 am

No solution for you, but I'm experiencing similar problems: http://forums.gentoo.org/viewtopic-t-443049.html

destr0yr · Post by **destr0yr** » Tue Mar 14, 2006 5:50 am

troworld wrote:No solution for you, but I'm experiencing similar problems: http://forums.gentoo.org/viewtopic-t-443049.html

I'm surprised I didn't find your post... I've been sifting through the forums for the better part of three hours. Anyways...

Potentially superfluous information: My system makes no reference to /lib/tls/libc.so.6, only /lib/libc.so.6. From what I've read, this is due to the fact that I have nptlonly in my make.conf. I can't downgrade glibc because grep & sed are broken... `emerge [anypackage]` dies with similar "__guard, version GLIBC 2.3.2 not defined..." errors. I am running gcc 3.4.5-r1.

yarug · Post by **yarug** » Tue Mar 14, 2006 8:04 am

Same here:

>>> /usr/include/protocols/rwhod.h
>>> /usr/include/protocols/talkd.h
>>> /usr/include/protocols/timed.h
>>> /usr/include/protocols/routed.h
>>> /usr/include/assert.h
>>> /usr/include/shadow.h
>>> /usr/include/features.h
>>> /usr/include/limits.h
>>> /usr/include/regexp.h
>>> /usr/include/memory.h
--- /sbin/
>>> /sbin/sln
>>> /sbin/ldconfig
>>> /lib/libnss_nis.so.2 -> libnss_nis-2.4.so
>>> /lib/libm.so.6 -> libm-2.4.so
>>> /lib/libnss_files.so.2 -> libnss_files-2.4.so
>>> /lib/libresolv.so.2 -> libresolv-2.4.so
>>> /lib/libnsl.so.1 -> libnsl-2.4.so
>>> /lib/libutil.so.1 -> libutil-2.4.so
>>> /lib/libcidn.so.1 -> libcidn-2.4.so
>>> /lib/libBrokenLocale.so.1 -> libBrokenLocale-2.4.so
>>> Safely unmerging already-installed instance...
No package files given... Grabbing a set.
>>> Original instance of package unmerged safely.
[glibc-2.4] bash: relocation error: [glibc-2.4] bash: symbol __guard, version
GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
!!! FAILED postinst: 127

Lots of applications stopped working now and system is borked. emerge stopped
working as well, so I cannot go back to previous glibc version:

$ emerge =sys-libs/glibc-2.3.6-r3
Calculating dependencies... done!
>>> Emerging (1 of 1) sys-libs/glibc-2.3.6-r3 to /
[glibc-2.3.6-r3] bash: relocation error: [glibc-2.3.6-r3] bash: symbol __guard,
version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

I have a complete backup of my system a few days old, any clues as to which
files I can put back to make everything working again?

See also http://bugs.gentoo.org/show_bug.cgi?id=125868 and http://bugs.gentoo.org/show_bug.cgi?id=125909

Thanks,
Nes

chtephan · Post by **chtephan** » Tue Mar 14, 2006 8:22 am

__guard is part of the stack smash protector from IBM (the pre-gcc4 implementation). In the first version of the glibc-2.4 there was an autodetection to check whether on of your binaries needs this symbol and add in the compat version of SSP. Apparently this check was broken and you were hit by this.

Grahammm · Post by **Grahammm** » Tue Mar 14, 2006 9:02 am

I got hit by this same problem, but (at least partially) luckily it happened during the emerge of glibc2.4. So I removed '-fstack-protector' (which several bugs state is not a good idea to be using in isolation rather than part of a hardened profile) and did an 'emerge -e system' before upgrading to glibc 2.4. So, I am not (I hope) completely hosed but my system is currently about half way through an 'emerge -e world' using glibc2.4

wizard69 · Post by **wizard69** » Tue Mar 14, 2006 9:18 am

@destr0yr try remergeing xorg it helped me

nxsty · Post by **nxsty** » Tue Mar 14, 2006 11:44 am

Syncing and reemerging glibc should fix it. The old ssp compat stuff is now always on to prevent this kind of problems.

gemini91 · Post by **gemini91** » Tue Mar 14, 2006 5:03 pm

I had the same problem, synching and re-emerging glibc did not fix it. However re-emerging
xorg did.

whoracle · Post by **whoracle** » Tue Mar 14, 2006 9:34 pm

i had the same problem, glibc screwed up. i could not log in, not use 'su', not run any programs written in C. I only found one solution: reinstallation. I do really doubt I could have solved my problem by reemerging xorg.. mainly because gcc wouldnt want to work anymore.

destr0yr · Post by **destr0yr** » Wed Mar 15, 2006 1:33 am

I've nearly got this solved...

I downloaded the 2006.0 livecd, boot it, chroot into my system and had the same issues with grep, sed, et al. (not able to emerge anything). exited the chroot, built a binary of glibc-2.3.5 in the CD environment (emerge -B sys-libs/glibc), moved it to my packages dir (/mnt/gentoo/usr/portage/packages/{All,sys-libs}/glibc-2.3.5...whatever it was), jumped back into the chroot, emerged the binary which worked and now i'm in the process of rebuilding my system (emerge linux-headers && emerge -e system && emerge -e ...). I'm taking the opportunity to move to gcc 4.1 (already done) and am building a new binary for glibc 2.3.6-r3 just incase the emerge of 2.4 dies && blows things up again. i'll report back here if and when it's working.

i-right-i · Post by **i-right-i** » Wed Mar 15, 2006 5:52 pm

I had this same issue pretty much. All it did for me was break Xorg-x11. Re-emerging xorg fixed the issue. I had just finished upgrading to gcc 3.4.5 in the previous week. I am not exactly sure, but I think the case might be worse if you compile the new glibc with gcc 3.3, with the result being way more stuff is borked then x11.

Just an idea I have been mulling over....

i-right-i

destr0yr · Post by **destr0yr** » Wed Mar 15, 2006 5:59 pm

i-right-i wrote:I had this same issue pretty much. All it did for me was break Xorg-x11. Re-emerging xorg fixed the issue. I had just finished upgrading to gcc 3.4.5 in the previous week. I am not exactly sure, but I think the case might be worse if you compile the new glibc with gcc 3.3, with the result being way more stuff is borked then x11.

Just an idea I have been mulling over....

i-right-i

Did running 'grep' or 'sed' give you errors also? I did not try re-emerging xorg because everything else failed - portage, grep, sed, glibc, etc.

hmm... its interesting now, emerging glibc is taking 3+ hours whereas before it took ~ 1. Must be my ricer flags...

i-right-i · Post by **i-right-i** » Wed Mar 15, 2006 6:03 pm

No, both of those are working, rather were working fine. Only xorg was broken for me after the glibc upgrade. What version of gcc are you running when you upgraded glibc? When I upgraded gcc, I used the slow way just to make sure there we no issues by using he emerge -e system then emerge -e world method.

It looks like that may have been a wise choice at the time, even though I was complaining about how long it took at the time.

i-right-i

lyonsd · Post by **lyonsd** » Wed Mar 15, 2006 7:25 pm

I get it trying to run X:

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X: relocation error: X: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

nxsty wrote:Syncing and reemerging glibc should fix it. The old ssp compat stuff is now always on to prevent this kind of problems.

That didn't work for me.

i-right-i · Post by **i-right-i** » Wed Mar 15, 2006 8:14 pm

Yah, you need to re-emerge Xorg. That will fix it.

i-right-i

guero61 · Post by **guero61** » Wed Mar 15, 2006 9:14 pm

Great... this bit me big time. On a server I really don't want to rebuild.

I've got another server I did a 'quickpkg =sys-libs/glibc-2.3.6-r3' on, and copied it over to the /usr/portage/packages directory on the affected host (in the All directory with the appropriate symlink), but I keep getting an error "There are no packages available to satisfy =sys-libs/glibc-2.3.6-r3".

Does anyone know if there's extra metadata that's registered other than laying a binary tarball down in the packages directory? I'd really like to get this up and running again without having to build from bare-metal (emerge -e is acceptable once I've got 2.3.6 restored).

i-right-i · Post by **i-right-i** » Wed Mar 15, 2006 9:24 pm

I am still somewhat of a n00b to portage. Good with linux in general though, anyway shouldn't that be /usr/portage/distfiles and not usr/portage/packages? Sorry in advance if I am mistaken....

i-right-i

destr0yr · Post by **destr0yr** » Wed Mar 15, 2006 10:01 pm

guero61 wrote:Great... this bit me big time. On a server I really don't want to rebuild.

I've got another server I did a 'quickpkg =sys-libs/glibc-2.3.6-r3' on, and copied it over to the /usr/portage/packages directory on the affected host (in the All directory with the appropriate symlink), but I keep getting an error "There are no packages available to satisfy =sys-libs/glibc-2.3.6-r3".

Does anyone know if there's extra metadata that's registered other than laying a binary tarball down in the packages directory? I'd really like to get this up and running again without having to build from bare-metal (emerge -e is acceptable once I've got 2.3.6 restored).

Doh, I guess I should've used quickpkg rather than emerge -B... oh well.

AFAIK, it should look something like this:

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slaxor packages # pwd
/usr/portage/packages
slaxor packages # ls -al *
All:
total 14434
drwxr-xr-x 3 root root      112 Mar 15 04:36 ./
drwxr-xr-x 5 root root      120 Mar 15 01:19 ../
-rw-r--r-- 1 root root 14764588 Mar 15 04:36 glibc-2.3.6-r3.tbz2

sys-libs:
total 0
drwxr-xr-x 2 root root  88 Mar 15 04:36 ./
drwxr-xr-x 5 root root 120 Mar 15 01:19 ../
lrwxrwxrwx 1 root root  26 Mar 15 04:36 glibc-2.3.6-r3.tbz2 -> ../All/glibc-2.3.6-r3.tbz2

To emerge it, use `emerge -gK =sys-libs/glibc-2.3.6-r3'. I've also added ">=sys-libs/glibc-2.4" to my package.mask for the time being.

destr0yr · Post by **destr0yr** » Wed Mar 15, 2006 10:03 pm

i-right-i wrote:Yah, you need to re-emerge Xorg. That will fix it.

i-right-i

This error and the one I received a two different things, hence this new post. Re-emerging xorg does nothing for us

Simple xorg emerge:

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X: relocation error: X: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

Not so simple glibc fustercluck:

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grep: relocation error: grep: symbol ___guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

i-right-i · Post by **i-right-i** » Wed Mar 15, 2006 10:15 pm

It might not do anything you in particular dest0yer, but it should for the poster in which I responded that reply to.

lyonsd Posted: Wed Mar 15, 2006 2:25 pm Post subject:

--------------------------------------------------------------------------------

I get it trying to run X:

Code:
X: relocation error: X: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

i-right-i

guero61 · Post by **guero61** » Wed Mar 15, 2006 10:17 pm

/usr/portage/distfiles is the directory where all source tarballs are downloaded
/usr/portage/packages is the directory where all binary builds of packages are stored/downloaded.

Mine looked perfect (according to my refs and destr0yr's), but it still didn't work. Finally just went and did an 'emerge /usr/portage/packages/All/glibc-2.3.6-r3.tbz2' and it worked okay.

destr0yr · Post by **destr0yr** » Thu Mar 16, 2006 6:04 am

... after all that:

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# emerge
Segmentation fault

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USE="3dnow 3dnowext aac acpi bash-completion browserplugin cdparanoia cdrom dvd dvdr dvdread dxr3 fame fbcon fbdev ffmpeg font-server gimp glibc-omitfp hal ide imap ithreads javascript kdexdeltas kqemu ldap live mjpeg mmx mplayer musicbrainz network nonfsv4 nptl nptlonly nsplugin nvidia on-the-fly-crypt pam  pic real rtc sasl skey softmmu sse stream threads toolbar userlocales v4l v4l2 vcd vim-with-x visualization win32codecs xine xinerama xscreensaver -arts -eds -gnome -aio exif sqlite tcltk java xvid directfb flac xml aalib vorbis usb lcms imagemagick bzip2 svga audiofile cdr idn mng curl tiff cups spell ssl kdeenablefinal a52 bitmap-fonts truetype-fonts type1-fonts -nas -samba -apache2 -esd -xmms -mozilla"
CHOST="i686-pc-linux-gnu"
CFLAGS="-march=athlon-xp"
CFLAGS="${CFLAGS} -O2"
CFLAGS="${CFLAGS} -pipe"
CFLAGS="${CFLAGS} -fomit-frame-pointer"
CFLAGS="${CFLAGS} -ffast-math"
CFLAGS="${CFLAGS} -ftree-vectorize"
CFLAGS="${CFLAGS} -fprefetch-loop-arrays"
CFLAGS="${CFLAGS} -fno-ident"
CFLAGS="${CFLAGS} -fforce-addr"
CFLAGS="${CFLAGS} -ftracer"
CFLAGS="${CFLAGS} -falign-functions=64"
CXXFLAGS="${CFLAGS} -fvisibility-inlines-hidden"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--sort-common -s"
ACCEPT_KEYWORDS="x86 ~x86"
PORTAGE_TMPDIR=/var/tmp
PORTDIR=/usr/portage
DISTDIR=${PORTDIR}/distfiles
PKGDIR=${PORTDIR}/packages
PORT_LOGDIR=/var/log/portage
PORTDIR_OVERLAY=/usr/local/portage
GENTOO_MIRRORS="http://gentoo.osuosl.org/ http://adelie.polymtl.ca/ ftp://distro.ibiblio.org/pub/linux/distributions/gentoo/ ftp://ftp.gtlib.gatech.edu/pub/gentoo http://www.gtlib.gatech.edu/pub/gentoo http://gentoo.mirrors.tds.net/gentoo "
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
RSYNC_RETRIES="3"
RSYNC_TIMEOUT=180
MAKEOPTS="-j2"
PORTAGE_NICENESS=3
AUTOCLEAN="yes"
FEATURES="confcache sandbox ccache distlocks userpriv usersandbox parallel-fetch metadata-transfer"
CCACHE_SIZE="2G"
PORTAGE_ELOG_CLASSES="warn error log"
ALSA_CARDS="intel8x0"
CONFIG_PROTECT_MASK="/usr/X11R6/bin/startx"
INPUT_DEVICES="keyboard mouse evdev"
VIDEO_CARDS="vesa fbdev nvidia"
SEARCH_DIRS_MASK="/usr/lib32/openoffice"
EMERGE_DEFAULT_OPTS="--alphabetical"

gcc 4.1, glibc 2.3.6... strace emerge output: strace.emerge.out.txt

I see a lot of "No such file or directory" errors, not sure why or how they've decided to go poof.

lyonsd · Post by **lyonsd** » Thu Mar 16, 2006 6:05 pm

Re-emerging xorg-x11 fixed it for me.

antiflag1980 · Post by **antiflag1980** » Fri Mar 17, 2006 1:49 am

Reemerging xorg-x11 fixed xorg for me, I still have some problems, like gaim freezes when trying to send a message. I tried to re emerge gaim, with the same results, so I'm about 200 packages into an emerge -e world out of 700 packages. If xorg and gaim are broken and I just happen to find them right away some other packages somewhere are bound to be broken too, might as well get them out of the way now, rather than trying to figure out later why something is broken and have no clue why.