Python's lxml segmentation fault on XSL transformation to remove attributes

Question

I perform the following XSL transformation a couple thousand time a day. I realized just recently that it fails on some occasions. I have a backtrace and example data.

Does anyone know how can I avoid this from happening since it crashes the whole Python application (meaning that nothing is even logged through our standard logging)? Any tip can help.

Calling fromHTML, an XSL tranformation, and a toHTML in a row will cause a glibc error, but calling them one after the other will not.

This seems to be a bug in LXML.

Python code

from lxml import etree
from lxml.html import tostring as toHTML, fromstring as fromHTML
fh = open('example.html')
data = '\n'.join(fh.readlines()
xslt_tree = etree.parse('./removeCSS.xsl')
transform_to_HTML = etree.XSLT(xslt_tree)
# The three following lines work well:
fromh = fromHTML(data)
trd = transform_to_HTML(fromh)
toh = toHTML(trd)
# The following line will cause a segmentation fault.
toHTML(transform_to_HTML(fromHTML(data)))

XSL file (removes attributes id , class and style ).

removeCSS.xsl

<xsl:stylesheet version="1.0"
    xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
    <xsl:output omit-xml-declaration="yes" indent="yes" />
    <xsl:strip-space elements="*" />

    <xsl:param name="removeAttributesNamed" select="'|class|id|style|'" />

    <xsl:template match="node()|@*" name="identity">
        <xsl:copy>
            <xsl:apply-templates select="node()|@*" />
        </xsl:copy>
    </xsl:template>

    <xsl:template match="@*">
        <xsl:if
            test="not(contains($removeAttributesNamed,concat('|', name(), '|')))">
            <xsl:call-template name="identity" />
        </xsl:if>
    </xsl:template>
</xsl:stylesheet>

Example data: example.html

<div xmlns:mml="http://www.w3.org/1998/Math/MathML">
    <p>We examined whether classifications based
        on reading performance are relevant to identify cognitively homogeneous subgroups of
        dyslexic children. Each of the 71 dyslexic participants was selected to have a mixed reading
        profile, i.e. poor irregular word and pseudo-word reading performance (accuracy and speed).
        Despite their homogeneous reading profile, the participants were found to split into four
        distinct cognitive subgroups, characterized by a single phonological disorder, a single
        visual attention span disorder, a double deficit or none of these disorders. The two
        subgroups characterized by single and contrasted cognitive disorders were found to exhibit a
        very similar reading pattern but more contrasted spelling performance (quantitative
        analysis). A qualitative analysis of the error types produced in reading and spelling
        provided some cues about the participants\' underlying cognitive deficit. The overall
        findings disqualify subtyping based on reading profiles as a classification method to
        identify cognitively homogeneous subgroups of dyslexic children. They rather show an opaque
        relationship between the cognitive underpinnings of developmental dyslexia and their
        behavioral manifestations in reading and spelling. Future neuroimaging and genetic studies
        should take this issue into account since synthesizing over cognitively heterogeneous
        children would entail potential pitfalls.</p>
</div>

Backtrace from gdb.

Program received signal SIGSEGV, Segmentation fault.
0x00007fffeeb01054 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
(gdb) backtrace
#0  0x00007fffeeb01054 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
#1  0x00007fffeeb010c1 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
#2  0x00007fffeeb010c1 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
#3  0x00007fffeeb010c1 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
#4  0x00007fffeeb010c1 in xmlFreeNodeList () from /usr/lib64/libxml2.so.2
#5  0x00007fffeeb00ec6 in xmlFreeDoc () from /usr/lib64/libxml2.so.2
#6  0x00007fffef294c4e in __pyx_pf_4lxml_5etree_9_Document___dealloc__ (__pyx_v_self=<optimized out>) at src/lxml/lxml.etree.c:35595
#7  __pyx_pw_4lxml_5etree_9_Document_1__dealloc__ (__pyx_v_self=0x2e3d6d8) at src/lxml/lxml.etree.c:35572
#8  __pyx_tp_dealloc_4lxml_5etree__Document (o=0x2e3d6d8) at src/lxml/lxml.etree.c:34187
#9  0x00007fffef2b2adf in __pyx_tp_dealloc_4lxml_5etree__Element (o=0x2e308f0) at src/lxml/lxml.etree.c:159739
#10 0x00007ffff7aebefa in ?? () from /usr/lib64/libpython2.7.so.1.0
#11 0x00007ffff7aea68b in ?? () from /usr/lib64/libpython2.7.so.1.0
#12 0x00007ffff7af5dc1 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#13 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#14 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#15 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#16 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#17 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#18 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#19 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#20 0x00007ffff7af6b55 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#21 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#22 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#23 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
---Type <return> to continue, or q <return> to quit---
#24 0x00007ffff7af6b55 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#25 0x00007ffff7af732c in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#26 0x00007ffff7af732c in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#27 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#28 0x00007ffff7b28802 in PyEval_EvalCode () from /usr/lib64/libpython2.7.so.1.0
#29 0x00007ffff7afb01b in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#30 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#31 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#32 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#33 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#34 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#35 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#36 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#37 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#38 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#39 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#40 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#41 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#42 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#43 0x00007ffff7adbdfa in ?? () from /usr/lib64/libpython2.7.so.1.0
#44 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#45 0x00007ffff7a9c0bc in ?? () from /usr/lib64/libpython2.7.so.1.0
#46 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#47 0x00007ffff7af5dae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
---Type <return> to continue, or q <return> to quit---
#48 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#49 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#50 0x00007ffff7af732c in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#51 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#52 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#53 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#54 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#55 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#56 0x00007ffff7af6b55 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#57 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#58 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#59 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#60 0x00007ffff7af6b55 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#61 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#62 0x00007ffff7adfcfb in ?? () from /usr/lib64/libpython2.7.so.1.0
#63 0x00007ffff7adaf16 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#64 0x00007ffff7af6b55 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#65 0x00007ffff7af732c in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#66 0x00007ffff7af732c in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#67 0x00007ffff7afb811 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#68 0x00007ffff7af55d3 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0
#69 0x00007ffff7afbae6 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
#70 0x00007ffff7b28802 in PyEval_EvalCode () from /usr/lib64/libpython2.7.so.1.0
#71 0x00007ffff7b34f6d in ?? () from /usr/lib64/libpython2.7.so.1.0
---Type <return> to continue, or q <return> to quit---
#72 0x00007ffff7ac3010 in PyRun_FileExFlags () from /usr/lib64/libpython2.7.so.1.0
#73 0x00007ffff7ac3bef in PyRun_SimpleFileExFlags () from /usr/lib64/libpython2.7.so.1.0
#74 0x00007ffff7acb81e in Py_Main () from /usr/lib64/libpython2.7.so.1.0
#75 0x00007ffff7482be5 in __libc_start_main () from /lib64/libc.so.6
#76 0x0000000000400791 in _start ()

Backtrace outputed from python (which I ran this time through django's manage.py shell , but the same happens without django):

*** Error in `python': free(): invalid pointer: 0x00007f9bdcaef49e ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7410f)[0x7f9be540210f]
/lib64/libc.so.6(+0x7996e)[0x7f9be540796e]
/lib64/libc.so.6(+0x7a647)[0x7f9be5408647]
/usr/lib64/libxml2.so.2(xmlFreeNodeList+0xe1)[0x7f9bdca2e121]
/usr/lib64/libxml2.so.2(xmlFreeProp+0x50)[0x7f9bdca2e2e0]
/usr/lib64/libxml2.so.2(xmlFreePropList+0x1c)[0x7f9bdca2e3ac]
/usr/lib64/libxml2.so.2(xmlFreeNodeList+0x13e)[0x7f9bdca2e17e]
/usr/lib64/libxml2.so.2(xmlFreeDoc+0xb6)[0x7f9bdca2dec6]
/home/chris/Workspace/Work/Sparrho/Web/venv/lib/python2.7/site-packages/lxml/etree.so(+0x2dc4e)[0x7f9bdd1c1c4e]
/home/chris/Workspace/Work/Sparrho/Web/venv/lib/python2.7/site-packages/lxml/etree.so(+0x4badf)[0x7f9bdd1dfadf]
/usr/lib64/libpython2.7.so.1.0(+0xbdefa)[0x7f9be5a18efa]
/home/chris/Workspace/Work/Sparrho/Web/venv/lib/python2.7/site-packages/lxml/etree.so(+0x2ca8e)[0x7f9bdd1c0a8e]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x60b)[0x7f9be5a21f6b]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f9be5a55802]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x66bb)[0x7f9be5a2801b]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(+0xb1cfb)[0x7f9be5a0ccfb]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(+0xaddfa)[0x7f9be5a08dfa]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(+0x6e0bc)[0x7f9be59c90bc]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x144e)[0x7f9be5a22dae]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x29cc)[0x7f9be5a2432c]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(+0xb1cfb)[0x7f9be5a0ccfb]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x21f5)[0x7f9be5a23b55]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(+0xb1cfb)[0x7f9be5a0ccfb]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x21f5)[0x7f9be5a23b55]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(+0xb1cfb)[0x7f9be5a0ccfb]
/usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x46)[0x7f9be5a07f16]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x21f5)[0x7f9be5a23b55]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x29cc)[0x7f9be5a2432c]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x29cc)[0x7f9be5a2432c]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x221)[0x7f9be5a28811]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xc73)[0x7f9be5a225d3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x4f6)[0x7f9be5a28ae6]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f9be5a55802]
/usr/lib64/libpython2.7.so.1.0(+0x106f6d)[0x7f9be5a61f6d]
/usr/lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x92)[0x7f9be59f0010]
/usr/lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x308)[0x7f9be59f0bef]
/usr/lib64/libpython2.7.so.1.0(Py_Main+0xc60)[0x7f9be59f881e]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9be53afbe5]
python[0x400791]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:08 10488689                           /home/chris/Workspace/Work/Sparrho/Web/venv/bin/python
00600000-00601000 r--p 00000000 08:08 10488689                           /home/chris/Workspace/Work/Sparrho/Web/venv/bin/python
00601000-00602000 rw-p 00001000 08:08 10488689                           /home/chris/Workspace/Work/Sparrho/Web/venv/bin/python
019e3000-040ac000 rw-p 00000000 00:00 0                                  [heap]
7f9bd4000000-7f9bd4021000 rw-p 00000000 00:00 0 
7f9bd4021000-7f9bd8000000 ---p 00000000 00:00 0 
7f9bda56f000-7f9bda585000 r-xp 00000000 08:06 1179659                    /lib64/libgcc_s.so.1
7f9bda585000-7f9bda784000 ---p 00016000 08:06 1179659                    /lib64/libgcc_s.so.1
7f9bda784000-7f9bda785000 r--p 00015000 08:06 1179659                    /lib64/libgcc_s.so.1
7f9bda785000-7f9bda786000 rw-p 00016000 08:06 1179659                    /lib64/libgcc_s.so.1
7f9bda786000-7f9bda7c4000 r-xp 00000000 08:06 1179681                    /lib64/libreadline.so.6.2
7f9bda7c4000-7f9bda9c4000 ---p 0003e000 08:06 1179681                    /lib64/libreadline.so.6.2
7f9bda9c4000-7f9bda9c6000 r--p 0003e000 08:06 1179681                    /lib64/libreadline.so.6.2
7f9bda9c6000-7f9bda9cc000 rw-p 00040000 08:06 1179681                    /lib64/libreadline.so.6.2
7f9bda9cc000-7f9bda9ce000 rw-p 00000000 00:00 0 
7f9bda9ce000-7f9bda9d3000 r-xp 00000000 08:06 171070                     /usr/lib64/python2.7/lib-dynload/readline.so
7f9bda9d3000-7f9bdabd2000 ---p 00005000 08:06 171070                     /usr/lib64/python2.7/lib-dynload/readline.so
7f9bdabd2000-7f9bdabd3000 r--p 00004000 08:06 171070                     /usr/lib64/python2.7/lib-dynload/readline.so
7f9bdabd3000-7f9bdabd5000 rw-p 00005000 08:06 171070                     /usr/lib64/python2.7/lib-dynload/readline.so
7f9bdabd5000-7f9bdabd6000 ---p 00000000 00:00 0 
7f9bdabd6000-7f9bdb3d6000 rw-p 00000000 00:00 0                          [stack:15690]
7f9bdb3d6000-7f9bdb3da000 r-xp 00000000 08:06 171047                     /usr/lib64/python2.7/lib-dynload/_lsprof.so
7f9bdb3da000-7f9bdb5d9000 ---p 00004000 08:06 171047                     /usr/lib64/python2.7/lib-dynload/_lsprof.so
7f9bdb5d9000-7f9bdb5da000 r--p 00003000 08:06 171047                     /usr/lib64/python2.7/lib-dynload/_lsprof.so
7f9bdb5da000-7f9bdb5db000 rw-p 00004000 08:06 171047                     /usr/lib64/python2.7/lib-dynload/_lsprof.so
7f9bdb5db000-7f9bdb606000 r-xp 00000000 08:06 1179652                    /lib64/libtinfo.so.5.9
7f9bdb606000-7f9bdb805000 ---p 0002b000 08:06 1179652                    /lib64/libtinfo.so.5.9
7f9bdb805000-7f9bdb809000 r--p 0002a000 08:06 1179652                    /lib64/libtinfo.so.5.9
7f9bdb809000-7f9bdb80e000 rw-p 0002e000 08:06 1179652                    /lib64/libtinfo.so.5.9
7f9bdb80e000-7f9bdb80f000 rw-p 00000000 00:00 0 
7f9bdb80f000-7f9bdb847000 r-xp 00000000 08:06 1179660                    /lib64/libncursesw.so.5.9
7f9bdb847000-7f9bdba46000 ---p 00038000 08:06 1179660                    /lib64/libncursesw.so.5.9
7f9bdba46000-7f9bdba47000 r--p 00037000 08:06 1179660                    /lib64/libncursesw.so.5.9
7f9bdba47000-7f9bdba48000 rw-p 00038000 08:06 1179660                    /lib64/libncursesw.so.5.9
7f9bdba48000-7f9bdba59000 r-xp 00000000 08:06 200603                     /usr/lib64/python2.7/lib-dynload/_curses.so
7f9bdba59000-7f9bdbc58000 ---p 00011000 08:06 200603                     /usr/lib64/python2.7/lib-dynload/_curses.so
7f9bdbc58000-7f9bdbc59000 r--p 00010000 08:06 200603                     /usr/lib64/python2.7/lib-dynload/_curses.so
7f9bdbc59000-7f9bdbc5b000 rw-p 00011000 08:06 200603                     /usr/lib64/python2.7/lib-dynload/_curses.so
7f9bdbc5b000-7f9bdbc5f000 r-xp 00000000 08:06 171065                     /usr/lib64/python2.7/lib-dynload/termios.so
7f9bdbc5f000-7f9bdbe5e000 ---p 00004000 08:06 171065                     /usr/lib64/python2.7/lib-dynload/termios.so
7f9bdbe5e000-7f9bdbe5f000 r--p 00003000 08:06 171065                     /usr/lib64/python2.7/lib-dynload/termios.so
7f9bdbe5f000-7f9bdbe61000 rw-p 00004000 08:06 171065                     /usr/lib64/python2.7/lib-dynload/termios.so
7f9bdbe61000-7f9bdbf10000 r-xp 00000000 08:06 140895                     /usr/lib64/libsqlite3.so.0.8.6
7f9bdbf10000-7f9bdc10f000 ---p 000af000 08:06 140895                     /usr/lib64/libsqlite3.so.0.8.6
7f9bdc10f000-7f9bdc111000 r--p 000ae000 08:06 140895                     /usr/lib64/libsqlite3.so.0.8.6
7f9bdc111000-7f9bdc114000 rw-p 000b0000 08:06 140895                     /usr/lib64/libsqlite3.so.0.8.6
7f9bdc114000-7f9bdc126000 r-xp 00000000 08:06 171069                     /usr/lib64/python2.7/lib-dynload/_sqlite3.so
7f9bdc126000-7f9bdc325000 ---p 00012000 08:06 171069                     /usr/lib64/python2.7/lib-dynload/_sqlite3.so
7f9bdc325000-7f9bdc326000 r--p 00011000 08:06 171069                     /usr/lib64/python2.7/lib-dynload/_sqlite3.so
7f9bdc326000-7f9bdc328000 rw-p 00012000 08:06 171069                     /usr/lib64/python2.7/lib-dynload/_sqlite3.so
7f9bdc328000-7f9bdc329000 rw-p 00000000 00:00 0 
7f9bdc329000-7f9bdc32d000 r-xp 00000000 08:06 140825                     /usr/lib64/libgpg-error.so.0.10.0
7f9bdc32d000-7f9bdc52c000 ---p 00004000 08:06 140825                     /usr/lib64/libgpg-error.so.0.10.0
7f9bdc52c000-7f9bdc52d000 r--p 00003000 08:06 140825                     /usr/lib64/libgpg-error.so.0.10.0
7f9bdc52d000-7f9bdc52e000 rw-p 00004000 08:06 140825                     /usr/lib64/libgpg-error.so.0.10.0
7f9bdc52e000-7f9bdc553000 r-xp 00000000 08:06 140800                     /usr/lib64/liblzma.so.5.0.5
7f9bdc553000-7f9bdc752000 ---p 00025000 08:06 140800                     /usr/lib64/liblzma.so.5.0.5
7f9bdc752000-7f9bdc753000 r--p 00024000 08:06 140800                     /usr/lib64/liblzma.so.5.0.5
7f9bdc753000-7f9bdc754000 rw-p 00025000 08:06 140800                     /usr/lib64/liblzma.so.5.0.5
7f9bdc754000-7f9bdc7d0000 r-xp 00000000 08:06 140748                     /usr/lib64/libgcrypt.so.11.8.2
7f9bdc7d0000-7f9bdc9d0000 ---p 0007c000 08:06 140748                     /usr/lib64/libgcrypt.so.11.8.2
7f9bdc9d0000-7f9bdc9d1000 r--p 0007c000 08:06 140748                     /usr/lib64/libgcrypt.so.11.8.2Aborted

Answer 1

just wanted to contribute:

"This particular bug seems to be inherent to libxml2 2.7.6 that is provided by RHEL6.2, and it's fixed in 2.7.7. It's not clear, though, why RPM version is not triggering it."

Link: https://github.com/OpenMS/OpenMS/issues/393

I had the same issue running python 2.6 and a libxml2 2.7.6. Took me 4 days to find above article and resolve my issue hehe

Best regards / Victor