Segmentation fault on xmlsec.tree.add_ids() in Python Development Mode

boom.py:

from lxml import etree

import xmlsec

template = etree.parse('sign1-res.xml').getroot()
xmlsec.tree.add_ids(template, ["ID"])

with sign-res.xml coming from the xmlsec examples.

Expected output

$ python boom.py
$

Observed output

$ PYTHONDEVMODE=1 python boom.py
Debug memory block at address p=0x5556aed07c40: API '!'
    15987178197214944733 bytes originally requested
    The 7 pad bytes at p-7 are not all FORBIDDENBYTE (0xfd):
        at p-7: 0x00 *** OUCH
        at p-6: 0x00 *** OUCH
        at p-5: 0x00 *** OUCH
        at p-4: 0x00 *** OUCH
        at p-3: 0x00 *** OUCH
        at p-2: 0x00 *** OUCH
        at p-1: 0x00 *** OUCH
    Because memory is corrupted at the start, the count of bytes requested
       may be bogus, and checking the trailing pad bytes may segfault.
    The 8 pad bytes at tail=0xddde33348cae5a1d are Fatal Python error: Segmentation fault

Current thread 0x00007fb7df1d8000 (most recent call first):
  File "boom.py", line 6 in <module>

Extension modules: lxml._elementpath, lxml.etree, xmlsec (total: 3)
Segmentation fault
$

Environment

I'm running on Ubuntu 22.04 with system python 3.10.6 and xmlsec 1.3.13.

pip list

Package            Version
------------------ -------------
blinker            1.4
chardet            4.0.0
cryptography       3.4.8
devscripts         2.22.1ubuntu1
dh-virtualenv      1.2.2
distro             1.7.0
httplib2           0.20.2
importlib-metadata 4.6.4
isodate            0.6.1
jeepney            0.7.1
keyring            23.5.0
launchpadlib       1.10.16
lazr.restfulclient 0.14.4
lazr.uri           1.0.6
lxml               4.9.2
more-itertools     8.10.0
netifaces          0.11.0
oauthlib           3.2.0
pip                22.0.2
PyGObject          3.42.1
PyJWT              2.3.0
pyparsing          2.4.7
python-apt         2.4.0+ubuntu1
python-debian      0.1.43ubuntu1
python3-saml       1.15.0
SecretStorage      3.3.1
setuptools         59.6.0
six                1.16.0
supervisor         4.2.1
VapourSynth        54
wadllib            1.3.6
wheel              0.37.1
xmlsec             1.3.13
zipp               1.0.0

apt list | grep xmlsec | grep installed

libxmlsec1-dev/jammy,now 1.2.33-1build2 amd64 [installed]
libxmlsec1-gcrypt/jammy,now 1.2.33-1build2 amd64 [installed,automatic]
libxmlsec1-gnutls/jammy,now 1.2.33-1build2 amd64 [installed,automatic]
libxmlsec1-nss/jammy,now 1.2.33-1build2 amd64 [installed,automatic]
libxmlsec1-openssl/jammy,now 1.2.33-1build2 amd64 [installed,automatic]
libxmlsec1/jammy,now 1.2.33-1build2 amd64 [installed,automatic]

I checked whether this is an lxml <-> xmlsec issue, but it is not:

$ pip install --no-binary :all: --force-reinstall lxml
$ PYTHONDEVMODE=1 python boom.py
(...)
Segmentation fault

Hello just had a similar problem with xmlsec.tree.add_ids
program crash on this line without any error message
I solve the issue by falling back to lxml==4.9.3 instead of lxml==5.1.0

Brgds JL

@jlthorel

@jlthorel You saved my life...!! 👍

This fixed a problem for me too. It was causing a SAML SSO login failure for me. Has anyone submitted a bug to lxml? Their bug tracker is here: https://launchpad.net/lxml

@jlthorel

@jlthorel You saved my life as well..! 💯

@jlthorel

@jlthorel You're a life saver!! Thank you very much!🎉🎉
I had the same problem as @downpa and my SAML login was failing because of lxml library

@jlthorel

@jlthorel thank you for saving us as well! You are the best!!!
We had issues recently with SSO on heroku where our ACS was failing. We isolated it to python3-saml validate_sign --> xmlsec xmlsec.tree.add_ids(elem, ["ID"]) ... thank you ❤️

@jlthorel

@jlthorel You saved my life!!

We had the same issue with our SAML SSO failing due to a seg fault, downgrading lxml resolved the issue

Hello just had a similar problem with xmlsec.tree.add_ids program crash on this line without any error message I solve the issue by falling back to lxml==4.9.3 instead of lxml==5.1.0

OMG, this was driving me crazy: my SAML SSO was failing most of the times, but sometimes it did work 😠 .
Downgrading xml fixed the issue :-) Thanks a lot for the tip!!!

This fixed a problem for me too. It was causing a SAML SSO login failure for me. Has anyone submitted a bug to lxml? Their bug tracker is here: https://launchpad.net/lxml

I couldn't find any bug report about this, so I just submitted one:
https://bugs.launchpad.net/lxml/+bug/2054606

Hello just had a similar problem with xmlsec.tree.add_ids program crash on this line without any error message I solve the issue by falling back to lxml==4.9.3 instead of lxml==5.1.0

Brgds JL

Thank you very much! This solution worked for me too.

This fixed a problem for me too. It was causing a SAML SSO login failure for me. Has anyone submitted a bug to lxml? Their bug tracker is here: https://launchpad.net/lxml

I couldn't find any bug report about this, so I just submitted one: https://bugs.launchpad.net/lxml/+bug/2054606

The folks at lxml closed the report.
They consider it is a third party issue (ie, that the problem lies in xmlsec).

@jonathangreen

I believe commit ee9fbd0 by @jonathangreen avoids the segfault without any error message, and emits instead an exception ("lxml & xmlsec libxml2 library version mismatch").

However, it's still not clear to me what we should do to avoid it.

@quique

Hi @quique. My comment here gives some context #316 (comment) that might be helpful.

Basically to avoid the issue, either both lxml and xmlsec should be installed from wheels, or should both be installed with --no-binary set.

The most recent release for xmlsec supplies wheels for most platforms, so updating to the most recent and making sure that it it installed from via a wheel is probably the easiest fix.

@jonathangreen

@jonathangreen Thank you for your helpful comment!

Unfortunately it seems I'm quite thick today, because I am unable to make it work.

This is what I do:

docker run -it python:3.12-slim-bookworm /bin/bash
# Place sign1-res.xml and boom.py inside the container (see the issue report by @Anthchirp )
pip install lxml --only-binary=lxml
pip install xmlsec --only-binary=xmlsec
PYTHONDEVMODE=1 python boom.py  # See it crash

If I understand it correctly, this way both lxml and xmlsec are installed from wheels, but I stil get a segmentation fault.
This is what I see:

root@d199d2820803:/# pip install lxml --only-binary=lxml
Collecting lxml
  Downloading lxml-5.2.1-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (3.4 kB)
Downloading lxml-5.2.1-cp312-cp312-manylinux_2_28_x86_64.whl (4.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 7.5 MB/s eta 0:00:00
Installing collected packages: lxml
Successfully installed lxml-5.2.1
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
root@d199d2820803:/# pip install xmlsec --only-binary=xmlsec
Collecting xmlsec
  Downloading xmlsec-1.3.14-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
Requirement already satisfied: lxml>=3.8 in /usr/local/lib/python3.12/site-packages (from xmlsec) (5.2.1)
Downloading xmlsec-1.3.14-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.9/3.9 MB 7.2 MB/s eta 0:00:00
Installing collected packages: xmlsec
Successfully installed xmlsec-1.3.14
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
root@d199d2820803:/# python boom.py 
root@d199d2820803:/# PYTHONDEVMODE=1 python boom.py
Debug memory block at address p=0x56499b02ca70: API '!'
    6873730420813529088 bytes originally requested
    The 7 pad bytes at p-7 are not all FORBIDDENBYTE (0xfd):
        at p-7: 0x00 *** OUCH
        at p-6: 0x00 *** OUCH
        at p-5: 0x00 *** OUCH
        at p-4: 0x00 *** OUCH
        at p-3: 0x00 *** OUCH
        at p-2: 0x00 *** OUCH
        at p-1: 0x00 *** OUCH
    Because memory is corrupted at the start, the count of bytes requested
       may be bogus, and checking the trailing pad bytes may segfault.
    The 8 pad bytes at tail=0x5f64bbafc965ca70 are Fatal Python error: Segmentation fault

Current thread 0x00007fb0f0a63740 (most recent call first):
  File "//boom.py", line 6 in <module>

Extension modules: lxml._elementpath, lxml.etree, xmlsec (total: 3)
Segmentation fault (core dumped)

Any hint? Thank you!

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Segmentation fault on `xmlsec.tree.add_ids()` in Python Development Mode #259

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Segmentation fault on xmlsec.tree.add_ids() in Python Development Mode #259

Description

boom.py:

Expected output

Observed output

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Anthchirp commented on Jun 15, 2023

jlthorel commented on Jan 16, 2024

wonjae-pro commented on Jan 17, 2024

downpat commented on Jan 23, 2024

MaylinJeong commented on Jan 26, 2024

rhenanbartels commented on Jan 30, 2024

jake-lester commented on Feb 2, 2024

Daviazuos commented on Feb 9, 2024

vpatov commented on Feb 12, 2024

quique commented on Feb 21, 2024

quique commented on Feb 21, 2024

andpena commented on Mar 15, 2024

quique commented on May 2, 2024

quique commented on May 2, 2024

jonathangreen commented on May 2, 2024

quique commented on May 3, 2024

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Segmentation fault on `xmlsec.tree.add_ids()` in Python Development Mode #259