Segmentation fault after installing ovito-python module

OVITO
1

Hello
I installed the ovito-python module (version 3.14.1) via PyPI on Windows 10. To check if the installation was successful, I ran the following command: python -c "import ovito".
However, I encountered the following error: Segmentation fault. I am not sure what caused this issue. It might be related to missing dependencies. Here are some of the packages currently installed in my environment:

Package                   Version
------------------------- --------------
ansi2html                 1.8.0
anyio                     4.4.0
argon2-cffi               23.1.0        
argon2-cffi-bindings      21.2.0        
arrow                     1.3.0
ase                       3.22.1
asteval                   0.9.31
asttokens                 2.2.1
async-lru                 2.0.4
attrs                     23.1.0
Babel                     2.15.0
backcall                  0.2.0
beautifulsoup4            4.12.3
biopython                 1.79
bleach                    6.1.0
certifi                   2023.7.22
cffi                      1.16.0
charset-normalizer        3.2.0
click                     8.1.6
colorama                  0.4.6
comm                      0.1.3
ConfigArgParse            1.7
contourpy                 1.0.6
cycler                    0.11.0
dash                      2.11.1
dash-core-components      2.0.0
dash-html-components      2.0.0
dash-table                5.0.0
debugpy                   1.6.7
decorator                 5.1.1
defusedxml                0.7.1
dill                      0.3.7
exceptiongroup            1.2.1
executing                 1.2.0
fastjsonschema            2.18.0
Flask                     2.2.5
fonttools                 4.38.0
fqdn                      1.5.1
future                    0.18.3
h11                       0.14.0
httpcore                  1.0.5
httpx                     0.27.0
idna                      3.4
imageio                   2.26.0
ipykernel                 6.25.0
ipython                   8.14.0
ipywidgets                8.0.7
isoduration               20.11.0
itsdangerous              2.1.2
jedi                      0.19.0
Jinja2                    3.1.2
joblib                    1.3.2
json5                     0.9.25
jsonpointer               3.0.0
jsonschema                4.18.4
jsonschema-specifications 2023.7.1
jupyter                   1.0.0
jupyter_client            8.3.0
jupyter-console           6.6.3
jupyter_core              5.3.1
jupyter-events            0.10.0
jupyter-lsp               2.2.5
jupyter_server            2.14.1
jupyter_server_terminals  0.5.3
jupyterlab                4.2.3
jupyterlab_pygments       0.3.0
jupyterlab_server         2.27.2
jupyterlab-widgets        3.0.8
kiwisolver                1.4.4
llvmlite                  0.44.0
lmfit                     1.2.2
MarkupSafe                2.1.3
matplotlib                3.8.0
matplotlib-inline         0.1.6
mistune                   3.0.2
mpi4py                    3.1.4
mpmath                    1.3.0
multiprocess              0.70.15
nbclient                  0.10.0
nbconvert                 7.16.4
nbformat                  5.7.0
nest-asyncio              1.5.7
notebook                  7.2.1
notebook_shim             0.2.4
numba                     0.61.2
numdifftools              0.9.41
numpy                     1.26.4
open3d                    0.17.0
overrides                 7.7.0
ovito                     3.14.1
packaging                 24.1
pandas                    1.5.3
pandocfilters             1.5.1
parso                     0.8.3
pickleshare               0.7.5
Pillow                    9.3.0
pip                       25.3
platformdirs              3.9.1
plotly                    5.15.0
pox                       0.3.3
ppft                      1.7.6.7
ProDy                     2.4.1
prometheus_client         0.20.0
prompt-toolkit            3.0.39
psutil                    5.9.5
pure-eval                 0.2.2
pycparser                 2.22
Pygments                  2.15.1
pyparsing                 3.0.9
pyqtgraph                 0.13.3
PySide6-Essentials        6.5.2
python-dateutil           2.8.2
python-json-logger        2.0.7
pytz                      2022.7.1
pywin32                   306
pywinpty                  2.0.13
PyYAML                    6.0.1
pyzmq                     25.1.0
qtconsole                 5.5.2
QtPy                      2.4.1
referencing               0.30.0
requests                  2.31.0
retrying                  1.3.4
rfc3339-validator         0.1.4
rfc3986-validator         0.1.1
rpds-py                   0.9.2
scikit-learn              1.3.2
scipy                     1.15.3
seaborn                   0.13.2
Send2Trash                1.8.3
setuptools                58.1.0
shiboken6                 6.5.2
six                       1.16.0
sniffio                   1.3.1
soupsieve                 2.5
stack-data                0.6.2
tcmlib                    1.4.0
tenacity                  8.2.2
terminado                 0.18.1
threadpoolctl             3.2.0
tinycss2                  1.3.0
tomli                     2.0.1
tornado                   6.3.2
traitlets                 5.9.0
traits                    6.4.1
types-python-dateutil     2.9.0.20240316
typing_extensions         4.7.1
uncertainties             3.1.7
uri-template              1.3.0
urllib3                   2.0.4
VTK                       9.1.0
wcwidth                   0.2.6
webcolors                 24.6.0
webencodings              0.5.1
websocket-client          1.8.0
Werkzeug                  2.2.3
widgetsnbextension        4.0.8

Has anyone experienced a similar problem or have any suggestions for resolving this? Thank you in advance!

2

By the way, I have also tried using ovito with Miniconda. I downloaded the ovito-3.14.1-py310h6d568f0_0.conda package from https://conda.ovito.org/win-64/ and installed it using the following command: conda install path\ovito-3.14.1-py310h6d568f0_0.conda

After installation, I ran: python -c "import ovito; print(ovito.__version__)". But I got the following error: ImportError: DLL load failed while importing ovito_bindings: cannot find modules.

Here is some environment info from conda list:

# Name                    Version                   Build  Channel
blas                      1.0                         mkl    defaults
bzip2                     1.0.8                h2bbff1b_6    defaults
ca-certificates           2025.9.9             haa95532_0    defaults
cairo                     1.18.4               he9e932c_0    defaults
certifi                   2025.10.5       py310haa95532_0    defaults
contourpy                 1.3.1           py310h214f63a_0    defaults
cycler                    0.11.0             pyhd3eb1b0_0    defaults
expat                     2.7.1                h8ddb27b_0    defaults
fontconfig                2.15.0               hd211d86_0    defaults
fonttools                 4.60.1          py310h02ab6af_0    defaults
freetype                  2.13.3               h0620614_0    defaults
graphite2                 1.3.14               hd77b12b_1    defaults
harfbuzz                  10.2.0               he2f9f60_1    defaults
icu                       73.1                 h6c2663c_0    defaults
intel-openmp              2025.0.0          haa95532_1164    defaults
jpeg                      9f                   ha349fce_0    defaults
kiwisolver                1.4.8           py310h5da7b33_0    defaults
lcms2                     2.16                 hb4a4139_0    defaults
lerc                      3.0                  hd77b12b_0    defaults
libdeflate                1.17                 h2bbff1b_1    defaults
libffi                    3.4.4                hd77b12b_1    defaults
libglib                   2.84.4               hfaec014_0    defaults
libiconv                  1.16                 h2bbff1b_3    defaults
libkrb5                   1.21.3               h885b0b7_4    defaults
libpng                    1.6.50               h46444df_0    defaults
libpq                     17.6                 h652a1e2_0    defaults
libtiff                   4.5.1                hd77b12b_0    defaults
libwebp-base              1.3.2                h3d04722_1    defaults
libxml2                   2.13.9               h6201b9f_0    defaults
libzlib                   1.3.1                h02ab6af_0    defaults
lz4-c                     1.9.4                h2bbff1b_1    defaults
m2w64-gcc-libgfortran     5.3.0                         6    defaults
m2w64-gcc-libs            5.3.0                         7    defaults
m2w64-gcc-libs-core       5.3.0                         7    defaults
m2w64-gmp                 6.1.0                         2    defaults
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    defaults
matplotlib                3.8.0           py310haa95532_0    defaults
matplotlib-base           3.8.0           py310h4ed8f06_0    defaults
mkl                       2025.0.0           h5da7b33_930    defaults
mkl-service               2.5.2           py310h0b37514_0    defaults
mkl_fft                   2.1.1           py310h300f80d_0    defaults
mkl_random                1.3.0           py310ha5e6156_0    defaults
mpi                       1.0                       msmpi    defaults
mpi4py                    3.1.4           py310hb01be7b_0    defaults
msmpi                     10.1.1               had4844c_0    defaults
msys2-conda-epoch         20160418                      1    defaults
mysql-common              9.3.0                hf582a5b_3    defaults
mysql-libs                9.3.0                hc0ebf12_3    defaults
numpy                     1.26.4          py310h12f7302_1    defaults
numpy-base                1.26.4          py310he4e2855_1    defaults
openjpeg                  2.5.2                hae555c5_0    defaults
openssl                   3.0.18               h543e019_0    defaults
ovito                     3.14.1          py310h6d568f0_0    <unknown>
packaging                 25.0            py310haa95532_1    defaults
pcre2                     10.46                h5740b90_0    defaults
pillow                    11.1.0          py310h096bfcc_0    defaults
pip                       25.2               pyhc872135_1    defaults
pixman                    0.46.4               h4043f72_0    defaults
pyparsing                 3.0.9           py310haa95532_0    defaults
pyqt                      6.9.1           py310h12ec796_0    defaults
pyqt6-sip                 13.10.2         py310h630b2a1_0    defaults
pyside6-essentials        6.6.0                    pypi_0    pypi
python                    3.10.19              h981015d_0    defaults
python-dateutil           2.9.0post0      py310haa95532_2    defaults
qtbase                    6.9.2                hd965823_2    defaults
qtdeclarative             6.9.2                h88b4c33_1    defaults
qtsvg                     6.9.2                h30ace32_1    defaults
qttools                   6.9.2                h7e7b719_1    defaults
qtwebchannel              6.9.2                heb02b0b_1    defaults
qtwebsockets              6.9.2                heb02b0b_1    defaults
setuptools                80.9.0          py310haa95532_0    defaults
shiboken6                 6.6.0                    pypi_0    pypi
sip                       6.12.0          py310h706e071_0    defaults
six                       1.17.0          py310haa95532_0    defaults
sqlite                    3.50.2               hda9a48d_1    defaults
tbb                       2022.0.0             h214f63a_0    defaults
tbb-devel                 2022.0.0             h214f63a_0    defaults
tk                        8.6.15               hf199647_0    defaults
tomli                     2.2.1           py310haa95532_0    defaults
tornado                   6.5.1           py310h827c3e9_0    defaults
traits                    6.4.3                    pypi_0    pypi
tzdata                    2025b                h04d1e81_0    defaults
ucrt                      10.0.22621.0         haa95532_0    defaults
vc                        14.3                h2df5915_10    defaults
vc14_runtime              14.44.35208         h4927774_10    defaults
vs2015_runtime            14.44.35208         ha6b5a95_10    defaults
wheel                     0.45.1          py310haa95532_0    defaults
xz                        5.6.4                h4754444_1    defaults
zlib                      1.3.1                h02ab6af_0    defaults
zstd                      1.5.7                h56299aa_0    defaults

Could you provide any hints or suggestions for resolving this issue? Thank you!

3

For the PyPI package, I couldn’t reproduce the segfault, and I am not sure if an unrelated package in your environment may interfere with the ovito package. Could you please create a fresh Python virtual environment and install just the ovito package? I would like to see if this solves the problem or not.

Regarding your attempt to set up a conda environment: You should let conda install download the ovito package with all its dependencies from our conda channel. Installing just the downloaded .conda file won’t automatically install these required dependencies. For example, the ospray_ovito and anari_ovito packages are not installed in your environment, which likely contain the missing DLLs that let the package import fail.

Please use Python 3.12 or 3.13 if possible.

4

For the PyPI case, I created a new environment and installed OVITO in it. The error disappeared, which suggests, as you mentioned, that there were conflicts in the old environment.

For the Conda case, I chose to download the package manually because installation using the command conda install --strict-channel-priority -c https://conda.ovito.org -c conda-forge ovito=3.14.1 failed. Here is a snapshot of the installation process:

(E:\documents\py313env) PS E:\documents\py313env> python -V
Python 3.13.9
(E:\documents\py313env) PS E:\documents\py313env> conda install --strict-channel-priority -c https://conda.ovito.org -c conda-forge ovito=3.14.1
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.

It seems to be related to an internet connectivity issue.

5

Update:
I was able to install ovito 3.14.1 after updating conda with the command: conda update -n base -c defaults conda. Then, I created a new conda environment and installed numpy, scipy, numba, and ovito. After installing these packages, I ran some basic tests:

  • python -c "import ovito; import numpy" ran successfully
  • python -c "import ovito; import numba"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import ovito; import numba
                  ^^^^^^^^^^^^
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\numba\__init__.py", line 73, in <module>
    from numba.core import config
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\numba\core\config.py", line 17, in <module>
    import llvmlite.binding as ll
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\llvmlite\binding\__init__.py", line 4, in <module>
    from .dylib import *
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\llvmlite\binding\dylib.py", line 1, in <module>
    from ctypes import c_void_p, c_char_p, c_bool, POINTER
  File "E:\documents\miniconda_env\py313env\Lib\ctypes\__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: DLL load failed while importing _ctypes: can not find module
  • python -c "import ovito; import scipy"
Traceback (most recent call last):
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\scipy\__init__.py", line 83, in <module>
    from scipy._lib._ccallback import LowLevelCallable
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\scipy\_lib\_ccallback.py", line 1, in <module>
    from . import _ccallback_c
  File "scipy/_lib/_ccallback_c.pyx", line 205, in init scipy._lib._ccallback_c
  File "E:\documents\miniconda_env\py313env\Lib\ctypes\__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: DLL load failed while importing _ctypes: can not find module

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import ovito; import scipy
                  ^^^^^^^^^^^^
  File "E:\documents\miniconda_env\py313env\Lib\site-packages\scipy\__init__.py", line 88, in <module>
    raise ImportError(msg) from e
ImportError: The `scipy` install you are using seems to be broken, (extension modules cannot be imported), please try reinstalling.

So, it seems there may be some incompatibility between these packages and the new version of ovito. Any suggestions on what might be causing this issue, or how to resolve it?

Thank you.

Attached:

# Name                       Version                Build                  Channel
anari_ovito                  0.15.0                 h91bfe4b_3640          https://conda.ovito.org
aom                          3.9.1                  he0c23c2_0             conda-forge
blas                         1.0                    mkl                    defaults
bzip2                        1.0.8                  h2bbff1b_6             defaults
ca-certificates              2025.10.5              h4c7d964_0             conda-forge
cairo                        1.18.4                 h5782bbf_0             conda-forge
cuda-cudart                  12.9.79                he0c23c2_0             conda-forge
cuda-cudart_win-64           12.9.79                he0c23c2_0             conda-forge
cuda-version                 12.9                   h4f385c5_3             conda-forge
dav1d                        1.2.1                  hcfcfb64_0             conda-forge
double-conversion            3.3.1                  he0c23c2_0             conda-forge
expat                        2.7.1                  h8ddb27b_0             defaults
ffmpeg                       8.0.0                  gpl_ha750ffe_706       conda-forge
font-ttf-dejavu-sans-mono    2.37                   hab24e00_0             conda-forge
font-ttf-inconsolata         3.000                  h77eed37_0             conda-forge
font-ttf-source-code-pro     2.038                  h77eed37_0             conda-forge
font-ttf-ubuntu              0.83                   h77eed37_3             conda-forge
fontconfig                   2.15.0                 h765892d_1             conda-forge
fonts-conda-ecosystem        1                      0                      conda-forge
fonts-conda-forge            1                      0                      conda-forge
freetype                     2.14.1                 h57928b3_0             conda-forge
fribidi                      1.0.16                 hfd05255_0             conda-forge
gdk-pixbuf                   2.44.4                 h1f5b9c4_0             conda-forge
glslang                      16.0.0                 h5b34520_0             conda-forge
graphite2                    1.3.14                 hac47afa_2             conda-forge
harfbuzz                     12.1.0                 h5f2951f_0             conda-forge
icc_rt                       2022.1.0               h6049295_2             defaults
icu                          75.1                   he0c23c2_0             conda-forge
intel-openmp                 2024.2.1               h57928b3_1083          conda-forge
krb5                         1.21.3                 hdf4eb48_0             conda-forge
lame                         3.100                  hcfcfb64_1003          conda-forge
lerc                         4.0.0                  h6470a55_1             conda-forge
libblas                      3.9.0                  26_win64_mkl           conda-forge
libcblas                     3.9.0                  26_win64_mkl           conda-forge
libclang13                   21.1.4                 default_ha2db4b5_0     conda-forge
libcurand                    10.3.10.19             hac47afa_1             conda-forge
libdeflate                   1.24                   h76ddb4d_0             conda-forge
libexpat                     2.7.1                  hac47afa_0             conda-forge
libffi                       3.5.2                  h52bdfb6_0             conda-forge
libfreetype                  2.14.1                 h57928b3_0             conda-forge
libfreetype6                 2.14.1                 hdbac1cb_0             conda-forge
libglib                      2.86.1                 hd9c3897_1             conda-forge
libhwloc                     2.12.1                 default_h64bd3f2_1002  conda-forge
libiconv                     1.18                   hc1393d2_2             conda-forge
libintl                      0.22.5                 h5728263_3             conda-forge
libjpeg-turbo                3.1.0                  h2466b09_0             conda-forge
liblapack                    3.9.0                  26_win64_mkl           conda-forge
libllvm20                    20.1.8                 h3aa9ab2_0             defaults
liblzma                      5.8.1                  h2466b09_2             conda-forge
liblzma-devel                5.8.1                  h2466b09_2             conda-forge
libmpdec                     4.0.0                  h827c3e9_0             defaults
libogg                       1.3.5                  h2466b09_1             conda-forge
libopus                      1.5.2                  h2466b09_0             conda-forge
libpng                       1.6.50                 h7351971_1             conda-forge
librsvg                      2.60.0                 hd5e4115_0             conda-forge
libsqlite                    3.50.4                 hf5d6505_0             conda-forge
libtiff                      4.7.1                  h550210a_0             conda-forge
libusb                       1.0.29                 h1839187_0             conda-forge
libvorbis                    1.3.7                  h5112557_2             conda-forge
libvulkan-loader             1.4.328.1              h477610d_0             conda-forge
libwebp-base                 1.6.0                  h4d5522a_0             conda-forge
libwinpthread                12.0.0.r4.gg4f2fc60ca  h57928b3_10            conda-forge
libxml2                      2.15.1                 ha29bfb0_0             conda-forge
libxml2-16                   2.15.1                 h06f855e_0             conda-forge
libxslt                      1.1.43                 h0fbe4c1_1             conda-forge
libzlib                      1.3.1                  h02ab6af_0             defaults
llvmlite                     0.45.1                 py313hd5b4e5d_0        defaults
lz4-c                        1.9.4                  h2bbff1b_1             defaults
mkl                          2024.2.2               h66d3029_15            conda-forge
mkl-service                  2.5.2                  py313haca3b5c_1        conda-forge
mkl_fft                      2.0.0                  py313h668c7ae_1        conda-forge
numba                        0.62.1                 py313h924e429_0        conda-forge
numpy                        2.3.4                  py313hce7ae62_0        conda-forge
openh264                     2.6.0                  hb17fa0b_0             conda-forge
openssl                      3.5.4                  h725018a_0             conda-forge
ospray_ovito                 3.2.1                  h8f8fb22_3640          https://conda.ovito.org
ovito                        3.14.1                 py313h1212747_0        https://conda.ovito.org
pango                        1.56.4                 h03d888a_0             conda-forge
pcre2                        10.46                  h3402e2f_0             conda-forge
pip                          25.2                   pyhc872135_1           defaults
pixman                       0.46.4                 h5112557_1             conda-forge
pyside6                      6.9.3                  py313h475ba69_1        conda-forge
python                       3.13.9                 h260b955_100_cp313     defaults
python_abi                   3.13                   1_cp313                defaults
qt6-main                     6.9.3                  ha0de62e_1             conda-forge
scipy                        1.16.3                 pypi_0                 pypi
sdl2                         2.32.56                h5112557_0             conda-forge
sdl3                         3.2.26                 h5112557_0             conda-forge
setuptools                   80.9.0                 py313haa95532_0        defaults
shaderc                      2025.4                 haa9a63f_0             conda-forge
spirv-tools                  2025.4                 h49e36cd_0             conda-forge
sqlite                       3.50.2                 hda9a48d_1             defaults
svt-av1                      3.1.2                  hac47afa_0             conda-forge
tbb                          2021.13.0              h18a62a1_3             conda-forge
tbb-devel                    2021.13.0              h4eb897c_3             conda-forge
tk                           8.6.15                 hf199647_0             defaults
traits                       7.0.2                  py313h5ea7bf4_1        conda-forge
tzdata                       2025b                  h04d1e81_0             defaults
ucrt                         10.0.22621.0           haa95532_0             defaults
vc                           14.3                   h2df5915_10            defaults
vc14_runtime                 14.44.35208            h4927774_10            defaults
visrtx_ovito                 0.13.2                 ha76d767_3640          https://conda.ovito.org
vs2015_runtime               14.44.35208            ha6b5a95_10            defaults
wheel                        0.45.1                 py313haa95532_0        defaults
x264                         1!164.3095             h8ffe710_2             conda-forge
x265                         3.5                    h2d74725_3             conda-forge
xz                           5.8.1                  h208afaa_2             conda-forge
xz-tools                     5.8.1                  h2466b09_2             conda-forge
zlib                         1.3.1                  h02ab6af_0             defaults
zstd                         1.5.7                  h56299aa_0             defaults
6

That conflict strange. It’s not something I would expect and, in fact, I can’t reproduce it on my Windows machine.

I tested an installation in one go:

conda create -n numba_test1 --strict-channel-priority -c https://conda.ovito.org -c conda-forge ovito==3.14.1 scipy numba
conda activate numba_test1
python -c "import ovito; import numba"

and also an incremental installation:

conda create -n numba_test2
conda activate numba_test2
conda install scipy numba
conda install --strict-channel-priority -c https://conda.ovito.org -c conda-forge ovito==3.14.1
python -c "import ovito; import numba"

Both worked equally well (no errors).

The _ctypes module, which fails to load in your case, is part of the Python interpreter. OVITO doesn’t use or need it. Have you checked if this problem is really related to the ovito module? I mean, does it only occur if you import ovito first?

7

Thank you for your reply.
I’ve identified the error. It turns out that there is a channel mismatch between the libffi package and other packages.
I apologize for not conducting a thorough analysis of the problem before bringing up this topic.