ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject #12
Description
Created a conda environment openmc-zpre-env. After executing ./run.sh and selecting either option except 7:
+ options=("k eigenvalue" "geometry plot" "geometry voxelplot" "neutron flux" "neutron flux 3d" "photon flux" "quit")
+ select opt in "${options[@]}"
1) k eigenvalue
2) geometry plot
3) geometry voxelplot
4) neutron flux
5) neutron flux 3d
6) photon flux
7) quit
I get the following ValueError (on the example of option 2):
+ case $opt in
+ echo 'plotting geometry...'
plotting geometry...
+ bash ./scripts/gp.sh
+ test -f ./h5m_files/zpre.h5m
+ python ./scripts/step_to_h5m_zpre.py
/home/<username>/anaconda3/envs/openmc-zpre-env/lib/python3.10/site-packages/pymoab/__init__.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import get_distribution, DistributionNotFound
Traceback (most recent call last):
File "/home/<username>/zpre/./scripts/step_to_h5m_zpre.py", line 6, in <module>
import CAD_to_OpenMC.assembly as ab
File "/home/<username>/anaconda3/envs/openmc-zpre-env/lib/python3.10/site-packages/CAD_to_OpenMC/assembly.py", line 17, in <module>
from pymoab import core, types
File "pymoab/core.pyx", line 1, in init pymoab.core
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
conda environment list of installed packages:
# packages in environment at /home/<username>/anaconda3/envs/openmc-zpre-env:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiohappyeyeballs 2.6.1 pypi_0 pypi
aiohttp 3.13.0 pypi_0 pypi
aiosignal 1.4.0 pypi_0 pypi
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-timeout 5.0.1 pypi_0 pypi
attr 2.5.2 h39aace5_0 conda-forge
attrs 25.4.0 pypi_0 pypi
brotli 1.1.0 hb03c661_4 conda-forge
brotli-bin 1.1.0 hb03c661_4 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.10.5 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cad-to-openmc 1.0.1 pypi_0 pypi
cadquery 2.6.0 pypi_0 pypi
cadquery-ocp 7.8.1.1.post1 pypi_0 pypi
casadi 3.7.2 pypi_0 pypi
contourpy 1.3.2 py310h3788b33_0 conda-forge
curl 8.14.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
dagmc 3.2.2 mpi_openmpi_py39ha06272d_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
eigen 3.4.0 h171cf75_1 conda-forge
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
executing 2.2.1 pyhd8ed1ab_0 conda-forge
ezdxf 1.4.2 pypi_0 pypi
fonttools 4.60.1 py310h3406613_0 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
frozenlist 1.8.0 pypi_0 pypi
future 1.0.0 pyhd8ed1ab_2 conda-forge
gmsh 4.14.1 pypi_0 pypi
h5py 3.8.0 mpi_openmpi_py310h14da842_0 conda-forge
hdf4 4.2.15 h501b40f_6 conda-forge
hdf5 1.12.2 mpi_openmpi_h41b9b70_1 conda-forge
idna 3.10 pypi_0 pypi
ipython 8.37.0 pyh8f84b5b_0 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.9 py310haaf941d_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.15 h7f713cb_2 conda-forge
ld_impl_linux-64 2.44 ha97dd6f_2 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libblas 3.9.0 36_h4a7cf45_openblas conda-forge
libbrotlicommon 1.1.0 hb03c661_4 conda-forge
libbrotlidec 1.1.0 hb03c661_4 conda-forge
libbrotlienc 1.1.0 hb03c661_4 conda-forge
libcap 2.76 h0b2e76d_0 conda-forge
libcblas 3.9.0 36_h0358290_openblas conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfido2 1.16.0 h5da5774_0 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 h767d61c_6 conda-forge
libgcc-ng 15.2.0 h69a702a_6 conda-forge
libgcrypt-lib 1.11.1 hb9d3cd8_0 conda-forge
libgfortran 15.2.0 h69a702a_6 conda-forge
libgfortran-ng 15.2.0 h69a702a_6 conda-forge
libgfortran5 15.2.0 hcd61629_6 conda-forge
libgomp 15.2.0 h767d61c_6 conda-forge
libgpg-error 1.55 h3f2d84a_0 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 2.1.5.1 hd590300_1 conda-forge
liblapack 3.9.0 36_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libnetcdf 4.9.1 mpi_openmpi_h81d4ffb_2 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnl 3.11.0 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_2 conda-forge
libpng 1.6.50 h421ea60_1 conda-forge
libsqlite 3.50.4 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h8f9b012_6 conda-forge
libstdcxx-ng 15.2.0 h4852527_6 conda-forge
libsystemd0 257.9 h996ca69_0 conda-forge
libtiff 4.6.0 h29866fb_1 conda-forge
libudev1 257.9 h085a93f_0 conda-forge
libuuid 2.41.2 he9a06e4_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h2cb61b6_1 conda-forge
libxslt 1.1.43 h7a3aeb2_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lxml 6.0.2 py310h93f867a_0 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
matplotlib-base 3.10.6 py310hfde16b3_1 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
metis 5.1.0 hd0bcaf9_1007 conda-forge
moab 5.4.1 mpi_openmpi_tempest_py310h6f50228_1 conda-forge
more-itertools 10.8.0 pypi_0 pypi
mpi 1.0 openmpi conda-forge
mpi4py 3.1.6 py310h2a790f2_0 conda-forge
msgpack 1.1.1 pypi_0 pypi
multidict 6.7.0 pypi_0 pypi
multimethod 1.12 pypi_0 pypi
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.4.2 pypi_0 pypi
njoy2016 2016.78 py310h0984a42_1 conda-forge
nlopt 2.9.1 pypi_0 pypi
numpy 2.2.6 pypi_0 pypi
openjpeg 2.5.2 h488ebb8_0 conda-forge
openmc 0.13.2 dagmc_mpi_openmpi_py310h956dc85_102 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssh 10.0p1 hc830a30_0 conda-forge
openssl 3.5.4 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.3 py310h0158d43_1 conda-forge
parso 0.8.5 pyhcf101f3_0 conda-forge
path 17.1.1 pypi_0 pypi
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge
pillow 10.0.1 py310h29da1c1_1 conda-forge
pip 25.2 pyh8b19718_0 conda-forge
prompt-toolkit 3.0.52 pyha770c72_0 conda-forge
propcache 0.4.0 pypi_0 pypi
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.5 pyhcf101f3_0 conda-forge
python 3.10.6 ha86cf86_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 8_cp310 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.3 pypi_0 pypi
qhull 2020.2 h434a139_5 conda-forge
rdma-core 59.0 hecca717_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
scipy 1.15.2 py310h1d65ade_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
tempest-remap 2.1.6 h05839da_2 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
trame 3.12.0 pypi_0 pypi
trame-client 3.11.1 pypi_0 pypi
trame-common 1.0.1 pypi_0 pypi
trame-server 3.6.3 pypi_0 pypi
trame-vtk 2.10.0 pypi_0 pypi
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
typish 1.9.3 pypi_0 pypi
tzdata 2025b h78e105d_0 conda-forge
ucx 1.19.0 hc93acc0_4 conda-forge
uncertainties 3.2.3 pyhd8ed1ab_0 conda-forge
unicodedata2 16.0.0 py310h7c4b9e2_1 conda-forge
unidecode 1.4.0 pypi_0 pypi
vtk 9.3.1 pypi_0 pypi
wcwidth 0.2.14 pyhd8ed1ab_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wslink 2.4.0 pypi_0 pypi
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
yarl 1.22.0 pypi_0 pypi
zlib 1.3.1 hb9d3cd8_2 conda-forge
zoltan 3.901 mpi_openmpi_hdeb57f9_1 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Workstation specs:
AMD Ryzen 7 7900X
OS:
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.3 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo```