Issue Yum broken after 12.5 #44 (Centos 6.8)

[MarceauC]

Hi guys!

Yum appears to be broken after upgrating to microupdate #44.

All "yum" commands are returning "Segmentation fault".
After hours, I don't know how to repair that...

Any ideas ?

There's some output command:

Expand/Collapse Block: free -mh

             total       used       free     shared    buffers     cached
Mem:           15G        15G       685M        71M       557M        13G
-/+ buffers/cache:       1.5G        14G
Swap:         1.0G       310M       711M

Expand/Collapse Block: rpm -qa python\* rpm\* yum\* | sort

python-2.6.6-66.el6_8.x86_64
python-devel-2.6.6-66.el6_8.x86_64
python-dns-1.12.0-centos6.15081418.noarch
python-ethtool-0.6-5.el6.x86_64
python-iniparse-0.3.1-2.1.el6.noarch
python-iwlib-0.1-1.2.el6.x86_64
python-libs-2.6.6-66.el6_8.x86_64
python-libxml2-2.9.4-1.0.cf.rhel6.x86_64
python-pip-7.1.0-1.el6.noarch
python-pycurl-7.19.0-9.el6.x86_64
python-setuptools-0.6.10-3.el6.noarch
python-urlgrabber-3.9.1-11.el6.noarch
python-virtualenv-1.10.1-1.el6.noarch
rpm-4.8.0-55.el6.x86_64
rpmforge-release-0.3.6-1.el5.rf.i386
rpm-libs-4.8.0-55.el6.x86_64
rpm-python-4.8.0-55.el6.x86_64
yum-3.2.29-75.el6.centos.noarch
yum-plugin-fastestmirror-1.1.30-37.el6.noarch
yum-utils-1.1.30-37.el6.noarch

Expand/Collapse Block: strace yum

...
stat("/usr/lib/python2.6/site-packages/yum/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/yum/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/yum/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/yum/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/yum/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/bin/lzma", {st_mode=S_IFREG|0755, st_size=64944, ...}) = 0
open("/usr/bin/lzma.so", O_RDONLY)      = -1 ENOENT (No such file or directory)
open("/usr/bin/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/bin/lzma.py", O_RDONLY)      = -1 ENOENT (No such file or directory)
open("/usr/bin/lzma.pyc", O_RDONLY)     = -1 ENOENT (No such file or directory)
stat("/usr/lib/python2.6/site-packages/supervisor-3.3.0-py2.6.egg/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/supervisor-3.3.0-py2.6.egg/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/supervisor-3.3.0-py2.6.egg/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/supervisor-3.3.0-py2.6.egg/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/supervisor-3.3.0-py2.6.egg/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/lib/python2.6/site-packages/meld3-1.0.2-py2.6.egg/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/meld3-1.0.2-py2.6.egg/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/meld3-1.0.2-py2.6.egg/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/meld3-1.0.2-py2.6.egg/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/python2.6/site-packages/meld3-1.0.2-py2.6.egg/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/python2.6/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/python2.6/plat-linux2/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/plat-linux2/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/plat-linux2/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/plat-linux2/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/plat-linux2/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/python2.6/lib-dynload/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lib-dynload/lzma.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lib-dynload/lzmamodule.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lib-dynload/lzma.py", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/lib-dynload/lzma.pyc", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/python2.6/site-packages/lzma", 0x7fff8b829cd0) = -1 ENOENT (No such file or directory)
open("/usr/lib64/python2.6/site-packages/lzma.so", O_RDONLY) = 6
fstat(6, {st_mode=S_IFREG|0755, st_size=62648, ...}) = 0
open("/usr/lib64/python2.6/site-packages/lzma.so", O_RDONLY) = 7
read(7, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0000:\0\0\0\0\0\0"..., 832) = 832
fstat(7, {st_mode=S_IFREG|0755, st_size=62648, ...}) = 0
mmap(NULL, 2158376, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 7, 0) = 0x7f0baa1cc000
mprotect(0x7f0baa1d8000, 2093056, PROT_NONE) = 0
mmap(0x7f0baa3d7000, 16384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 7, 0xb000) = 0x7f0baa3d7000
close(7)                                = 0
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0} ---
+++ killed by SIGSEGV +++

Expand/Collapse Block: locate libz

/lib64/libz.so.1
/lib64/libz.so.1.2.3
/usr/lib64/libz.so

Expand/Collapse Block: locate libxml2

/usr/lib64/libxml2.so.2
/usr/lib64/libxml2.so.2.7.6
/usr/lib64/python2.6/site-packages/drv_libxml2.py
/usr/lib64/python2.6/site-packages/drv_libxml2.pyc
/usr/lib64/python2.6/site-packages/drv_libxml2.pyo
/usr/lib64/python2.6/site-packages/libxml2.py
/usr/lib64/python2.6/site-packages/libxml2.pyc
/usr/lib64/python2.6/site-packages/libxml2.pyo
/usr/lib64/python2.6/site-packages/libxml2mod.a
/usr/lib64/python2.6/site-packages/libxml2mod.la
/usr/lib64/python2.6/site-packages/libxml2mod.so

Expand/Collapse Block: tail /var/log/messages

Aug 27 15:53:20 ns318718 kernel: yum[16397]: segfault at 0 ip 00007fda841f79c8 sp 00007fff83c63720 error 6 in libpython2.6.so.1.0[7fda84166000+15d000]

Expand/Collapse Block: tail /var/log/yum.log

Aug 27 11:36:33 Updated: zip-3.0-1.el6_7.1.x86_64
Aug 27 11:36:34 Updated: unixODBC-2.2.14-14.el6.x86_64
Aug 27 11:36:34 Updated: yum-plugin-fastestmirror-1.1.30-37.el6.noarch
Aug 27 11:36:35 Updated: man-pages-overrides-6.8.2-1.el6.noarch
Aug 27 11:36:37 Updated: glibc-2.12-1.192.el6.i686
Aug 27 11:36:38 Updated: nss-softokn-freebl-3.14.3-23.3.el6_8.i686
Aug 27 11:37:12 Erased: libxml2-python
Aug 27 11:37:42 Erased: perl-Compress-Zlib
Aug 27 11:37:43 Erased: perl-IO-Compress-Zlib
Aug 27 11:38:11 Erased: perl-IO-Compress-Base

Expand/Collapse Block: cat /etc/yum.conf

[main]
cachedir=/var/cache/yum/$basearch/$releasever
keepcache=0
debuglevel=2
logfile=/var/log/yum.log
exactarch=1
obsoletes=1
gpgcheck=1
plugins=1
installonly_limit=5
bugtracker_url=http://bugs.centos.org/set_project.php?project_id=19&ref=http://bugs.centos.org/bug_report_page.php?category=yum
distroverpkg=centos-release

#  This is the default, if you make this bigger yum won't see if the metadata
# is newer on the remote and so you'll "gain" the bandwidth of not having to
# download the new metadata and "pay" for it by yum not having correct
# information.
#  It is esp. important, to have correct metadata, for distributions like
# Fedora which don't keep old packages around. If you don't like this checking
# interupting your command line usage, it's much better to have something
# manually check the metadata once an hour (yum-updatesd will do this).
# metadata_expire=90m

# PUT YOUR REPOS HERE OR IN separate files named file.repo
# in /etc/yum.repos.d

epel, dag and rpmforge are disabled.

Expand/Collapse Block: ls -lah /etc/yum.repos.d

-rw-r--r--  1 root root  935  6 févr.  2015 atomic.repo
-rw-r--r--  1 root root 2,0K 18 mai   21:47 CentOS-Base.repo
-rw-r--r--  1 root root  647 18 mai   21:47 CentOS-Debuginfo.repo
-rw-r--r--  1 root root  289 18 mai   21:47 CentOS-fasttrack.repo
-rw-r--r--  1 root root  630 18 mai   21:47 CentOS-Media.repo
-rw-r--r--  1 root root 6,2K 18 mai   21:47 CentOS-Vault.repo
-rw-r--r--  1 root root 1,1K 27 août  13:22 city-fan.org.repo
-rw-r--r--  1 root root  143 27 août  13:22 dag.repo
-rw-r--r--  1 root root  957 27 août  13:21 epel.repo
-rw-r--r--  1 root root 1,1K  5 nov.   2012 epel-testing.repo
-rw-r--r--  1 root root  684  8 mars   2007 mirrors-rpmforge
-rw-r--r--  1 root root  472 27 janv.  2016 nodesource-el.repo
-rw-r--r--  1 root root  379 27 août  04:05 plesk-letsencrypt.repo
-rw-r--r--  1 root root  180 25 mars  12:10 plesk-php5.4.repo
-rw-r--r--  1 root root  180 22 juil. 08:35 plesk-php5.5.repo
-rw-r--r--  1 root root  180 22 juil. 08:03 plesk-php5.6.repo
-rw-r--r--  1 root root  180 22 juil. 07:26 plesk-php7.0.repo
-rw-r--r--  1 root root  428 27 août  13:21 rpmforge.repo
-rw-r--r--  1 root root  636 27 août  04:05 tortix-common.repo

Thank you very much!