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expat XML error after installation of MSS 9.2.0 #2489

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dhgkunkel opened this issue Aug 28, 2024 · 12 comments
Open

expat XML error after installation of MSS 9.2.0 #2489

dhgkunkel opened this issue Aug 28, 2024 · 12 comments
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request upstream help upstream fix needed a dependency of us needs an improvement

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@dhgkunkel
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After installation of MSS 9.2.0 (using miniforge and mamba) and starting the server, I got an error related to expat. Version 2.6.2 was of expat was installed.

I downgraded to version 2.6.1 which solved the issue.

I found similar reports here: matplotlib/matplotlib#28235

The error log when starting the server looked as follows:

[Wed Aug 28 16:54:07.192427 2024] [wsgi:info] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726, process='MSS', application=''): Loading Python script file '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.333530 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726): Failed to exec Python script file '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.333583 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726): Exception occurred processing WSGI script '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.346490 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] Traceback (most recent call last): [Wed Aug 28 16:54:07.347016 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/summer23/wsgi/wms.wsgi", line 24, i n <module> [Wed Aug 28 16:54:07.347029 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from mslib.mswms.wms import app as application [Wed Aug 28 16:54:07.347040 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/mslib/mswms/wms.py", line 56, in <module> [Wed Aug 28 16:54:07.347056 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from chameleon import PageTemplateLoader [Wed Aug 28 16:54:07.347064 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/__init__.py", line 1, in <module> [Wed Aug 28 16:54:07.347069 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from .zpt.template import PageTemplate [Wed Aug 28 16:54:07.347078 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/zpt/template.py", line 17, in <module> [Wed Aug 28 16:54:07.347082 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from ..template import BaseTemplate [Wed Aug 28 16:54:07.347089 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/template.py", line 48, in <module> [Wed Aug 28 16:54:07.347094 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from .loader import ModuleLoader [Wed Aug 28 16:54:07.347100 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/loader.py", line 9, in <module> [Wed Aug 28 16:54:07.347105 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] import pkg_resources [Wed Aug 28 16:54:07.347128 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/pkg_resources/__init__.py", line 63, in <module> [Wed Aug 28 16:54:07.347132 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] import plistlib [Wed Aug 28 16:54:07.347157 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3.11/plistlib.py", line 70, in <module> [Wed Aug 28 16:54:07.347162 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from xml.parsers.expat import ParserCreate [Wed Aug 28 16:54:07.347168 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3.11/xml/parsers/expat.py", line 4, in <module> [Wed Aug 28 16:54:07.347189 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from pyexpat import * [Wed Aug 28 16:54:07.347207 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] ImportError: /home/mss/miniforge3/envs/mssenv/lib/python3.11/lib-dynload/pyexpat.cpython-311-x86_64-linux-gnu.so: undefined symbol: XML_SetReparseDeferralEnabled

@ReimarBauer
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related python/cpython#115398

@ReimarBauer
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ReimarBauer commented Aug 30, 2024 •
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on my develop system it looks like this, mod_wsgi is used on an apache setup.

Can you show a similar output on yours?


(mssenvtest2) reimarb@infinity:~$ mamba repoquery whoneeds expat

Executing the query expat



 Name       Version Build        Depends              Channel     Subdir  
───────────────────────────────────────────────────────────────────────────
 dbus       1.13.6  h5008d03_3   expat >=2.4.2,<3.0a0 conda-forge linux-64
 fontconfig 2.14.2  h14ed4e7_0   conda-forge          linux-64

libexpat comes with python

mamba repoquery whoneeds libexpat

Executing the query libexpat



 Name   Version Build                Depends                 Channel     Subdir  
──────────────────────────────────────────────────────────────────────────────────
 python 3.11.6  hab00c5b_0_cpython   libexpat >=2.5.0,<3.0a0 conda-forge linux-64

@ReimarBauer
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in python 3.10. we have not any expat with python

@dhgkunkel
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(mssenv) mss@forecast:~$ mamba repoquery whoneeds expat

Executing the query expat



 Name       Version Build        Depends              Channel     Subdir  
───────────────────────────────────────────────────────────────────────────
 dbus       1.13.6  h5008d03_3   expat >=2.4.2,<3.0a0 conda-forge linux-64
 fontconfig 2.14.2  h14ed4e7_0   conda-forge          linux-64   

(mssenv) mss@forecast:~$ mamba repoquery whoneeds libexpat

Executing the query libexpat



 Name             Version Build                Depends                   Channel     Subdir  
──────────────────────────────────────────────────────────────────────────────────────────────
 expat            2.6.1   h59595ed_0           libexpat 2.6.1 h59595ed_0 conda-forge linux-64
 git              2.44.0  pl5321h709897a_0     conda-forge               linux-64   
 gst-plugins-base 1.22.9  h8e1006c_0           conda-forge               linux-64   
 python           3.11.8  hab00c5b_0_cpython   conda-forge               linux-64   
 qt-main          5.15.8  h5810be5_19          conda-forge               linux-64   
 qt-webengine     5.15.8  h7517aa4_5           conda-forge               linux-64

That is how it looks on my system.

@ReimarBauer
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Please can you verify when you update python to 3.11.9 (latest version) and latest version of expat that the problem exists

mamba install python==3.11.9
mamba install expat==2.6.2

@ReimarBauer
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ReimarBauer commented Aug 30, 2024 •
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and I need conda info for the report on the python-feedstock. conda-forge/python-feedstock#701

@ReimarBauer ReimarBauer mentioned this issue Aug 30, 2024
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@ReimarBauer
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This might be also related
conda-forge/python-feedstock#673

@ReimarBauer ReimarBauer added request upstream help upstream fix needed a dependency of us needs an improvement labels Aug 30, 2024
@dhgkunkel
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and I need conda info for the report on the python-feedstock. conda-forge/python-feedstock#701

(mssenv) mss@forecast:~$ conda info

     active environment : mssenv
    active env location : /home/mss/miniforge3/envs/mssenv
            shell level : 2
       user config file : /home/mss/.condarc
 populated config files : /home/mss/miniforge3/.condarc
                          /home/mss/.condarc
          conda version : 24.3.0
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=broadwell
                          __conda=24.3.0=0
                          __glibc=2.31=0
                          __linux=5.10.0=0
                          __unix=0=0
       base environment : /home/mss/miniforge3  (writable)
      conda av data dir : /home/mss/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/mss/miniforge3/pkgs
                          /home/mss/.conda/pkgs
       envs directories : /home/mss/miniforge3/envs
                          /home/mss/.conda/envs
               platform : linux-64
             user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

@dhgkunkel
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mamba install python==3.11.9
mamba install expat==2.6.2

Yeah, problem is persistent, changed back to python 3.11.8 and expat 2.6.1 ...

@ReimarBauer
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somehow the conda info seems to have a python version : 3.10.14.final.0
Did you done that differently?

@dhgkunkel
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somehow the conda info seems to have a python version : 3.10.14.final.0 Did you done that differently?

(base) mss@forecast:~$ conda info

     active environment : base
    active env location : /home/mss/miniforge3
            shell level : 1
       user config file : /home/mss/.condarc
 populated config files : /home/mss/miniforge3/.condarc
                          /home/mss/.condarc
          conda version : 24.3.0
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=broadwell
                          __conda=24.3.0=0
                          __glibc=2.31=0
                          __linux=5.10.0=0
                          __unix=0=0
       base environment : /home/mss/miniforge3  (writable)
      conda av data dir : /home/mss/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/mss/miniforge3/pkgs
                          /home/mss/.conda/pkgs
       envs directories : /home/mss/miniforge3/envs
                          /home/mss/.conda/envs
               platform : linux-64
             user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


(base) mss@forecast:~$ python --version
Python 3.10.14
(base) mss@forecast:~$ mamba activate mssenv
(mssenv) mss@forecast:~$ python --version
Python 3.11.8
(mssenv) mss@forecast:~$ conda info

     active environment : mssenv
    active env location : /home/mss/miniforge3/envs/mssenv
            shell level : 2
       user config file : /home/mss/.condarc
 populated config files : /home/mss/miniforge3/.condarc
                          /home/mss/.condarc
          conda version : 24.3.0
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=broadwell
                          __conda=24.3.0=0
                          __glibc=2.31=0
                          __linux=5.10.0=0
                          __unix=0=0
       base environment : /home/mss/miniforge3  (writable)
      conda av data dir : /home/mss/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/mss/miniforge3/pkgs
                          /home/mss/.conda/pkgs
       envs directories : /home/mss/miniforge3/envs
                          /home/mss/.conda/envs
               platform : linux-64
             user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

So it seems that conda info puts out the python version of the base installation, independent of the environment. But as you can see, in the environment python --version results in the correct version.

@ReimarBauer
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ok, thx for checking.

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