Version `CXXABI_1.3.15' not found when loading matplotlib through PythonCall

General Usage
,
1

Hi folks,

I want to call some functions from the Python package matplotlib in Julia through PythonCall.jl. However, it prompts version 'CXXABI_1.3.15' not found. Here is the error message:

julia> using PythonCall

julia> plt=pyimport("matplotlib")
ERROR: Python: ImportError: /home/.julia/juliaup/julia-1.10.10+0.x64.linux.gnu/bin/../lib/julia/libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /data/julia-depot/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/matplotlib/_c_internal_utils.cpython-312-x86_64-linux-gnu.so)

Within Python I can import matplotlib without error, but I just cannot do that in Julia. Does this mean that the libstdc++ shipped in Julia is outdated? And how to solve it?

Thank you!

2

What version of Julia are you using?

3

Hi Mosè, I tried both v1.11.6 and v1.10.10.

On another computer running v1.11.5, however, I can successfully pyimport("matplotlab").

4

I believe the problem is that the system libstdc++ on your fist machine is old, which would explain why it works on the second machine but not on the first.

5

Can you post the full output from versioninfo() and CondaPkg.resolve(force=true) in the non-working environment please, assuming you are using the default CondaPkg to install python dependencies.

6

This seems to be a conflict between Python version and Julia version. Your Python could be too new (and/or Julia too new).

Please show what this gives you:

julia> sys=pyimport("sys"); sys.version_info
Python: sys.version_info(major=3, minor=12, micro=11, releaselevel='final', serial=0)

julia> VERSION
v"1.11.6"

This works for me in Julia 1.10.10 but not in 1.11.6. If I recall, it’s because Python 3.12 changed from older and/or change in Julia.

This file works for me in 1.11 (but not if I ask for Python 3.13):
.julia/environments/v1.11/CondaPkg.toml

[deps]
# conda-forge = ""
numpy = ""
python = "==3.10" # before "" # "==3.13"
matplotlib = ""
# openssl = ">=3.3.2,<4.0a0"
7

Try something along the lines:

export LD_LIBRARY_PATH=~/.julia/conda/3/x86_64/lib:~/.julia/juliaup/

Does that help?

8

Sure. Here is the output:

julia> versioninfo()
Julia Version 1.10.10
Commit 95f30e51f41 (2025-06-27 09:51 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 64 × Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, cascadelake)
Threads: 1 default, 0 interactive, 1 GC (on 64 virtual cores)
Environment:
  LD_LIBRARY_PATH = /opt/FJSVxtclanga/tcsds-1.2.41/lib64:/home/apps/oss/mscp/lib64
  LD_LIBRARY_PATH_modshare = /opt/FJSVxtclanga/tcsds-1.2.41/lib64:1:/home/apps/oss/mscp/lib64:1
  JULIA_CONDAPKG_BACKEND = Pixi

julia> CondaPkg.resolve(force=true)
    CondaPkg Found dependencies: /home/.julia/environments/v1.10/CondaPkg.toml
    CondaPkg Found dependencies: /home/.julia/packages/PythonCall/avYrV/CondaPkg.toml
    CondaPkg Initialising pixi
             │ /home/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /home/.julia/environments/v1.10/.CondaPkg
Created /vol0004/mdt0/home/.julia/environments/v1.10/.CondaPkg/pixi.toml
    CondaPkg Wrote /home/.julia/environments/v1.10/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ libstdcxx-ng = ">=3.4,<14.0"
             │ yt = "*"
             │
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cpython*"
             │     version = ">=3.8,<4"
             │
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ update
             └ --manifest-path /home/.julia/environments/v1.10/.CondaPkg/pixi.toml
Environment: default
  + C _libgcc_mutex            0.1 conda_forge
  + C _openmp_mutex            4.5 2_gnu
  + C asttokens                3.0.0 pyhd8ed1ab_1
  + C brotli                   1.1.0 hb9d3cd8_3
  + C brotli-bin               1.1.0 hb9d3cd8_3
  + C bzip2                    1.0.8 h4bc722e_7
  + C ca-certificates          2025.8.3 hbd8a1cb_0
  + C cmyt                     2.0.2 pyhd8ed1ab_0
  + C colorama                 0.4.6 pyhd8ed1ab_1
  + C comm                     0.2.3 pyhe01879c_0
  + C contourpy                1.3.3 py312hd9148b4_1
  + C cpython                  3.12.11 py312hd8ed1ab_0
  + C cycler                   0.12.1 pyhd8ed1ab_1
  + C decorator                5.2.1 pyhd8ed1ab_0
  + C ewah-bool-utils          1.3.0 py312hcbe3ca9_0
  + C exceptiongroup           1.3.0 pyhd8ed1ab_0
  + C executing                2.2.0 pyhd8ed1ab_0
  + C fonttools                4.59.1 py312h8a5da7c_0
  + C freetype                 2.13.3 ha770c72_1
  + C gmp                      6.3.0 hac33072_2
  + C gmpy2                    2.2.1 py312h7201bc8_0
  + C ipython                  9.4.0 pyhfa0c392_0
  + C ipython_pygments_lexers  1.1.1 pyhd8ed1ab_0
  + C ipywidgets               8.1.7 pyhd8ed1ab_0
  + C jedi                     0.19.2 pyhd8ed1ab_1
  + C jupyterlab_widgets       3.0.15 pyhd8ed1ab_0
  + C kiwisolver               1.4.9 py312h0a2e395_0
  + C lcms2                    2.17 h717163a_0
  + C ld_impl_linux-64         2.44 h1423503_1
  + C lerc                     4.0.0 h0aef613_1
  + C libblas                  3.9.0 34_h59b9bed_openblas
  + C libbrotlicommon          1.1.0 hb9d3cd8_3
  + C libbrotlidec             1.1.0 hb9d3cd8_3
  + C libbrotlienc             1.1.0 hb9d3cd8_3
  + C libcblas                 3.9.0 34_he106b2a_openblas
  + C libdeflate               1.24 h86f0d12_0
  + C libexpat                 2.7.1 hecca717_0
  + C libffi                   3.4.6 h2dba641_1
  + C libfreetype              2.13.3 ha770c72_1
  + C libfreetype6             2.13.3 h48d6fc4_1
  + C libgcc                   15.1.0 h767d61c_4
  + C libgcc-ng                15.1.0 h69a702a_4
  + C libgfortran              15.1.0 h69a702a_4
  + C libgfortran5             15.1.0 hcea5267_4
  + C libgomp                  15.1.0 h767d61c_4
  + C libjpeg-turbo            3.1.0 hb9d3cd8_0
  + C liblapack                3.9.0 34_h7ac8fdf_openblas
  + C liblzma                  5.8.1 hb9d3cd8_2
  + C libnsl                   2.0.1 hb9d3cd8_1
  + C libopenblas              0.3.30 pthreads_h94d23a6_2
  + C libpng                   1.6.50 h421ea60_1
  + C libsqlite                3.50.4 h0c1763c_0
  + C libstdcxx                15.1.0 h8f9b012_4
  + C libstdcxx-ng             13.2.0 hc0a3c3a_7
  + C libtiff                  4.7.0 h8261f1e_6
  + C libuuid                  2.38.1 h0b41bf4_0
  + C libwebp-base             1.6.0 hd42ef1d_0
  + C libxcb                   1.17.0 h8a09558_0
  + C libxcrypt                4.4.36 hd590300_1
  + C libzlib                  1.3.1 hb9d3cd8_2
  + C matplotlib-base          3.10.5 py312he3d6523_0
  + C matplotlib-inline        0.1.7 pyhd8ed1ab_1
  + C more-itertools           10.7.0 pyhd8ed1ab_0
  + C mpc                      1.3.1 h24ddda3_1
  + C mpfr                     4.2.1 h90cbb55_3
  + C mpmath                   1.3.0 pyhd8ed1ab_1
  + C munkres                  1.1.4 pyhd8ed1ab_1
  + C ncurses                  6.5 h2d0b736_3
  + C numpy                    2.3.2 py312h33ff503_0
  + C openjpeg                 2.5.3 h55fea9a_1
  + C openssl                  3.5.2 h26f9b46_0
  + C packaging                25.0 pyh29332c3_1
  + C parso                    0.8.4 pyhd8ed1ab_1
  + C pexpect                  4.9.0 pyhd8ed1ab_1
  + C pickleshare              0.7.5 pyhd8ed1ab_1004
  + C pillow                   11.3.0 py312h80c1187_0
  + C prompt-toolkit           3.0.51 pyha770c72_0
  + C pthread-stubs            0.4 hb9d3cd8_1002
  + C ptyprocess               0.7.0 pyhd8ed1ab_1
  + C pure_eval                0.2.3 pyhd8ed1ab_1
  + C pygments                 2.19.2 pyhd8ed1ab_0
  + C pyparsing                3.2.3 pyhe01879c_2
  + C python                   3.12.11 h9e4cc4f_0_cpython
  + C python-dateutil          2.9.0.post0 pyhe01879c_2
  + C python_abi               3.12 8_cp312
  + C qhull                    2020.2 h434a139_5
  + C readline                 8.2 h8c095d6_2
  + C six                      1.17.0 pyhe01879c_1
  + C stack_data               0.6.3 pyhd8ed1ab_1
  + C sympy                    1.14.0 pyh2585a3b_105
  + C tk                       8.6.13 noxft_hd72426e_102
  + C tomli-w                  1.2.0 pyhd8ed1ab_0
  + C tqdm                     4.67.1 pyhd8ed1ab_1
  + C traitlets                5.14.3 pyhd8ed1ab_1
  + C typing_extensions        4.14.1 pyhe01879c_0
  + C tzdata                   2025b h78e105d_0
  + C unicodedata2             16.0.0 py312h66e93f0_0
  + C unyt                     3.0.4 pyhd8ed1ab_0
  + C wcwidth                  0.2.13 pyhd8ed1ab_1
  + C widgetsnbextension       4.0.14 pyhd8ed1ab_0
  + C xorg-libxau              1.0.12 hb9d3cd8_0
  + C xorg-libxdmcp            1.1.5 hb9d3cd8_0
  + C yt                       4.4.1 py312hf79963d_0
  + C zstd                     1.5.7 hb8e6e7a_2

I am running on the Fugaku supercomputer.

9

I am currently using Python 3.12.11 and Julia 1.10.10.

I can import numpy without error, but not for matplotlib :frowning:

julia> pyimport("numpy")
Python: <module 'numpy' from '/home/.julia/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/numpy/__init__.py'>

julia> pyimport("matplotlib")
ERROR: Python: ImportError: /vol0004/mdt0/home/.julia/juliaup/julia-1.10.10+0.x64.linux.gnu/bin/../lib/julia/libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/.julia/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/matplotlib/_c_internal_utils.cpython-312-x86_64-linux-gnu.so)
Python stacktrace:
 [1] <module>
   @ ~/.julia/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/matplotlib/cbook.py:32
 [2] <module>
   @ ~/.julia/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/matplotlib/__init__.py:161
Stacktrace:
 [1] pythrow()
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:89
 [2] errcheck
   @ ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:10 [inlined]
 [3] pyimport(m::String)
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/builtins.jl:1560
 [4] top-level scope
   @ REPL[4]:1
10

Thank you Uwe, I saw your post about installing PyPlot and tried your solution, but it is not working for my situation. It still prompts the same error.

julia> versioninfo()
Julia Version 1.10.10
Commit 95f30e51f41 (2025-06-27 09:51 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 64 × Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, cascadelake)
Threads: 1 default, 0 interactive, 1 GC (on 64 virtual cores)
Environment:
  LD_LIBRARY_PATH = /home/.julia/conda/3/x86_64/lib:/home/.julia/juliaup/
  LD_LIBRARY_PATH_modshare = /opt/FJSVxtclanga/tcsds-1.2.41/lib64:1:/home/apps/oss/mscp/lib64:1
  JULIA_CONDAPKG_BACKEND = Pixi

julia> using PythonCall

julia> pyimport("matplotlib")
ERROR: Python: ImportError: /vol0004/mdt0/home/.julia/juliaup/julia-1.10.10+0.x64.linux.gnu/bin/../lib/julia/libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/.julia/environments/v1.10/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/matplotlib/_c_internal_utils.cpython-312-x86_64-linux-gnu.so)
11

Sorry for this naive question, the error message says ImportError: /vol0004/mdt0/home/u13411/.julia/juliaup/julia-1.10.10+0.x64.linux.gnu/bin/../lib/julia/libstdc++.so.6: version 'CXXABI_1.3.15' not found, does this mean that Julia is looking for CXXABI_1.3.15 in its own libstdc++?

It is quite strange that my scripts have been working well with matplotlib well on this HPC for more than 6 months. After I updating Julia packages last Sunday, the version 'CXXABI_1.3.15' not found error appears. I really don’t know which part did I break…