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Description of problem: yum update fails Version-Release number of selected component (if applicable): yum-rhn-plugin-0.9.1-36.el6.noarch How reproducible: always Steps to Reproduce: 1. 2. 3. Actual results: yum update Loaded plugins: product-id, rhnplugin, subscription-manager Updating certificate-based repositories. Segmentation fault (core dumped) Expected results: updates packages Additional info: Please let me know what additional files you need to help debug the problem, such as core dump or abrtd output?
I am running on a HP server with HP smartarray P400 and P800 with SAS drives. When I run "yum update", it dumped core and I saw these output from dmesg: cciss 0000:06:00.0: vpd r/w failed. This is likely a firmware bug on this device. Contact the card vendor for a firmware update. cciss 0000:17:00.0: vpd r/w failed. This is likely a firmware bug on this device. Contact the card vendor for a firmware update. yum[3445]: segfault at 3300000000 ip 00000033db134f70 sp 00007fff10843fe8 error 4 in libc-2.12.so[33db000000+197000] I have just updated the HP smartarray firmware from 5.20 to 7.22, but it didn't help at all. I disabled RHN part of yum and I was able to install package from EPEL repo earlier today, yum --enablerepo=epel install package, it worked fine. But if I enabled RHN, it core dumps every time and I saw the above message from dmesg. I also attempt to install HP-ProLiantSupportPack from HP repo for RHEL6.2, afterwards, yum update failed as well (with RHN disabled). By the way, directly using rpm, I was able to update packages without any issue, I installed new kernel, HP cciss driver, and a few other packages.
Yes, please provide cored dump. Together with exact version of yum, python, libc and output of uname -a
uname -a Linux deepthought.genomecenter.ucdavis.edu 2.6.32-220.7.1.el6.x86_64 #1 SMP Fri Feb 10 15:22:22 EST 2012 x86_64 x86_64 x86_64 GNU/Linux I have tried a few early kernels, but they all have the same issue. yum-3.2.29-22.el6.noarch python-2.6.6-29.el6.x86_64 glibc-2.12-1.47.el6_2.5.x86_64 The system was updated last Friday (3/2/12) and I added a few packages today with rpm (kernel, openssl). openssl-1.0.0-20.el6_2.2.x86_64 Please see attached coredump file (gzipped)
Created attachment 568855 [details] coredump file gzipped coredump file
A backtrace from gdb Program received signal SIGSEGV, Segmentation fault. 0x00000033db134f70 in __strncmp_ssse3 () from /lib64/libc.so.6 (gdb) backtrace #0 0x00000033db134f70 in __strncmp_ssse3 () from /lib64/libc.so.6 #1 0x000000339a25daf5 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2 #2 0x000000339a23374d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2 #3 0x000000339a237a06 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2 #4 0x000000339a24e02c in xmlSAXUserParseFile () from /usr/lib64/libxml2.so.2 #5 0x00007fffeca2db3a in yum_xml_parse_primary () from /usr/lib64/python2.6/site-packages/_sqlitecache.so #6 0x00007fffeca2fec4 in ?? () from /usr/lib64/python2.6/site-packages/_sqlitecache.so #7 0x00007fffeca3074a in ?? () from /usr/lib64/python2.6/site-packages/_sqlitecache.so #8 0x00000033de8de7f4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #9 0x00000033de8df99f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #10 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #11 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #12 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #13 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #14 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #15 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #16 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #17 0x00000033de86eac0 in ?? () from /usr/lib64/libpython2.6.so.1.0 #18 0x00000033de844043 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0 #19 0x00000033de844131 in ?? () from /usr/lib64/libpython2.6.so.1.0 #20 0x00000033de844d52 in PyObject_CallFunction () from /usr/lib64/libpython2.6.so.1.0 #21 0x00000033de8836e3 in PyObject_GenericGetAttr () from /usr/lib64/libpython2.6.so.1.0 #22 0x00000033de8daf2a in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #23 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #24 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #25 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #26 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #27 0x00000033de8df99f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #28 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #29 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #30 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 #31 0x00000033de8de8b4 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0 #32 0x00000033de8e0467 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0 ---Type <return> to continue, or q <return> to quit--- #33 0x00000033de8e0542 in PyEval_EvalCode () from /usr/lib64/libpython2.6.so.1.0 #34 0x00000033de8fb88c in ?? () from /usr/lib64/libpython2.6.so.1.0 #35 0x00000033de8fb960 in PyRun_FileExFlags () from /usr/lib64/libpython2.6.so.1.0 #36 0x00000033de8fce4c in PyRun_SimpleFileExFlags () from /usr/lib64/libpython2.6.so.1.0 #37 0x00000033de9094cf in Py_Main () from /usr/lib64/libpython2.6.so.1.0 #38 0x00000033db01ecdd in __libc_start_main () from /lib64/libc.so.6 #39 0x0000000000400649 in _start ()
I have attempted to install HP diagnostic tools hpdiag and hpsmh hpsmhd crashes as well with the similar backtrace and indicating xml failure __strncmp_ssse3 and __xmlParserInputBufferCreateFilename () Core was generated by `/opt/hp/hpsmh/sbin/smhconfig'. Program terminated with signal 11, Segmentation fault. #0 0x00000033db134f70 in __strncmp_ssse3 () from /lib64/libc.so.6 Missing separate debuginfos, use: debuginfo-install hpsmh-6.3.0-22.x86_64 (gdb) bt #0 0x00000033db134f70 in __strncmp_ssse3 () from /lib64/libc.so.6 #1 0x00007f9ecde6e5d8 in __xmlParserInputBufferCreateFilename () from /opt/hp/hpsmh/lib/libxml2.so.2 #2 0x00007f9ecde6e65a in xmlParserInputBufferCreateFilename__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #3 0x00007f9ecde46066 in xmlNewInputFromFile__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #4 0x00007f9ecde6f2b2 in xmlDefaultExternalEntityLoader () from /opt/hp/hpsmh/lib/libxml2.so.2 #5 0x00007f9ecde6ea3e in xmlLoadExternalEntity__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #6 0x00007f9ecde4a0ac in xmlCreateURLParserCtxt__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #7 0x00007f9ecde4a14b in xmlCreateFileParserCtxt__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #8 0x00007f9ecde5ea46 in xmlSAXParseFileWithData__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #9 0x00007f9ecde5eb4b in xmlSAXParseFile__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #10 0x00007f9ecde5eb80 in xmlParseFile__internal_alias () from /opt/hp/hpsmh/lib/libxml2.so.2 #11 0x0000000000409b3d in hpsmh_xml_open () #12 0x00000000004067f6 in hpsmh_config_get_value () #13 0x000000000040a695 in main () Downgrade libxml2-2.7.6-4.el6_2.4.x86_64 to libxml2-python-2.7.6-4.el6_2.1.x86_64 didn't help. It might be a glibc issue that affect this particular HP server.
Seeing /usr/lib64/libxml2.so.2 at the top I'm flipping it to libxml2
Seeing in #7: #1 0x00007f9ecde6e5d8 in __xmlParserInputBufferCreateFilename () from /opt/hp/hpsmh/lib/libxml2.so.2 I would say it's hp's packaging of libxml2, not the system one, and I won't take responsability for this. I can't even tell what version of libxml2 they bundled Now for comment #6 seems there is a problem. There is a known incompatibility of recent libxml2 with older zlib packages and hitting in that area with this kind of failures showing __xmlParserInputBufferCreateFilename and __strncmp_ssse3, but that's not supposed to happen on RHEL-6 as both packages are recent enough to completely avoid the issue ... unless there is a rogue zlib around. can you do as root: rpm -q libxml2 zlib rpm -V libxml2 zlib ldd /usr/bin/xmllint find /lib* /usr /opt -name libz.so\* -exec ls -l {} \; and report the output, thanks ! Daniel
This request was evaluated by Red Hat Product Management for inclusion in the current release of Red Hat Enterprise Linux. Because the affected component is not scheduled to be updated in the current release, Red Hat is unfortunately unable to address this request at this time. It has been proposed for the next release. If you would like it considered as an exception in the current release, please ask your support representative.
Without the informations asked in comment 9 #c9 I am left to guess that the issue is a zlib/libxml2 version mismatch, the stack trace is indicative of that very specific problem. In the absence of feedback I am closing the bug accordingly, please reopen if the informations can be provided. Daniel