VTK and PYVISTA errors

[KevinQian97]

Hi, I followed the instruction to prepare the env.

packages in environment at /home/kevinq/anaconda3/envs/glamr:

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
absl-py 1.3.0 py37h06a4308_0
aiohttp 3.8.3 py37h5eee18b_0
aiosignal 1.2.0 pyhd3eb1b0_0
appdirs 1.4.4 pyhd3eb1b0_0
async-timeout 4.0.2 py37h06a4308_0
asynctest 0.13.0 py_0
attrs 22.1.0 py37h06a4308_0
blas 1.0 mkl
blinker 1.4 py37h06a4308_0
brotlipy 0.7.0 py37h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.0 h5eee18b_0
ca-certificates 2022.12.7 ha878542_0 conda-forge cachetools 4.2.2 pyhd3eb1b0_0
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py37h5eee18b_3
cftime 1.6.0 py37hda87dfa_1 conda-forge charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py37h06a4308_0
cryptography 39.0.1 py37h9ce1e76_0
cudatoolkit 11.1.1 ha002fc5_10 conda-forge curl 7.88.1 h5eee18b_0
cycler 0.11.0 pypi_0 pypi expat 2.4.9 h6a678d5_0
ffmpeg 4.2.2 h20bf706_0
filterpy 1.4.5 pypi_0 pypi flit-core 3.6.0 pyhd3eb1b0_0
fonttools 4.38.0 pypi_0 pypi freetype 2.12.1 h4a9f257_0
frozenlist 1.3.3 py37h5eee18b_0
fsspec 2022.11.0 py37h06a4308_0
future 0.18.3 py37h06a4308_0
gmp 6.2.1 h295c915_3
gnutls 3.6.15 he1e5248_0
google-auth 2.6.0 pyhd3eb1b0_0
google-auth-oauthlib 0.4.1 py_2
grpcio 1.42.0 py37hce63b2e_0
h5py 2.9.0 nompi_py37hcafd542_1103 conda-forge hdf4 4.2.13 h3ca952b_2
hdf5 1.10.4 hb1b8bf9_0
icu 58.2 he6710b0_3
idna 3.4 py37h06a4308_0
imageio 2.9.0 pyhd3eb1b0_0
importlib-metadata 6.1.0 pypi_0 pypi intel-openmp 2021.4.0 h06a4308_3561
jpeg 9b h024ee3a_2
jsoncpp 0.10.6 1 conda-forge kiwisolver 1.4.4 pypi_0 pypi krb5 1.19.4 h568e23c_0
lame 3.100 h7b6447c_0
ld_impl_linux-64 2.38 h1181459_1
libcurl 7.88.1 h91b91d3_0
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.2 h6a678d5_6
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 11.2.0 h1234567_1
libidn2 2.3.2 h7f8727e_0
libnetcdf 4.6.1 h11d0813_2
libnghttp2 1.46.0 hce63b2e_0
libogg 1.3.5 h27cfd23_1
libopus 1.3.1 h7b6447c_0
libpng 1.6.39 h5eee18b_0
libprotobuf 3.20.3 he621ea3_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libtasn1 4.16.0 h27cfd23_0
libtheora 1.1.1 h7f8727e_3
libtiff 4.1.0 h2733197_1
libunistring 0.9.10 h27cfd23_0
libuv 1.44.2 h5eee18b_0
libvorbis 1.3.7 h7b6447c_0
libvpx 1.7.0 h439df22_0
libxml2 2.9.14 h74e7548_0
llvmlite 0.39.1 pypi_0 pypi lz4-c 1.8.3 he1b5a44_1001 conda-forge markdown 3.4.1 py37h06a4308_0
markupsafe 2.1.1 py37h7f8727e_0
matplotlib 3.5.3 pypi_0 pypi meshio 4.4.2 pyhd8ed1ab_0 conda-forge mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py37h7f8727e_0
mkl_fft 1.3.1 py37hd3c417c_0
mkl_random 1.2.2 py37h51133e4_0
multi-person-tracker 0.1 dev_0 multidict 6.0.2 py37h5eee18b_0
ncurses 6.4 h6a678d5_0
netcdf4 1.4.2 py37h808af73_0
nettle 3.7.3 hbbd107a_1
ninja 1.10.2 h06a4308_5
ninja-base 1.10.2 hd09550d_5
numba 0.56.4 pypi_0 pypi numpy 1.21.5 py37h6c91a56_3
numpy-base 1.21.5 py37ha15fc14_3
oauthlib 3.2.0 pyhd3eb1b0_1
olefile 0.46 py37_0
openh264 2.1.1 h4ff587b_0
openssl 1.1.1t h7f8727e_0
packaging 22.0 py37h06a4308_0
pillow 9.4.0 pypi_0 pypi pip 22.3.1 py37h06a4308_0
protobuf 3.20.3 py37h6a678d5_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycparser 2.21 pyhd3eb1b0_0
pydeprecate 0.3.0 pyhd8ed1ab_0 conda-forge pyjwt 2.4.0 py37h06a4308_0
pyopenssl 23.0.0 py37h06a4308_0
pyparsing 3.0.9 pypi_0 pypi pysocks 1.7.1 py37_1
python 3.7.16 h7a1cb2a_0
python-dateutil 2.8.2 pypi_0 pypi python_abi 3.7 2_cp37m conda-forge pytorch 1.8.0 py3.7_cuda11.1_cudnn8.0.5_0 pytorch pytorch-lightning 1.3.5 pyhd8ed1ab_0 conda-forge pyvista 0.31.3 pyhd8ed1ab_2 conda-forge pyyaml 5.4.1 py37h5e8e339_1 conda-forge readline 8.2 h5eee18b_0
requests 2.28.1 py37h06a4308_0
requests-oauthlib 1.3.0 py_0
rsa 4.7.2 pyhd3eb1b0_1
scipy 1.7.3 pypi_0 pypi scooby 0.7.1 pyhd8ed1ab_0 conda-forge setuptools 65.6.3 py37h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.1 h5eee18b_0
tbb 2021.7.0 hdb19cb5_0
tensorboard 2.6.0 py_1
tensorboard-data-server 0.6.1 py37h52d8a92_0
tensorboard-plugin-wit 1.8.1 py37h06a4308_0
tk 8.6.12 h1ccaba5_0
torchaudio 0.8.0 py37 pytorch torchmetrics 0.10.3 pyhd8ed1ab_0 conda-forge torchvision 0.9.0 py37_cu111 pytorch tqdm 4.64.1 py37h06a4308_0
transforms3d 0.4.1 pyhd8ed1ab_0 conda-forge typing-extensions 4.4.0 py37h06a4308_0
typing_extensions 4.4.0 py37h06a4308_0
urllib3 1.26.14 py37h06a4308_0
vtk 8.2.0 py37haa4764d_200
werkzeug 2.2.2 py37h06a4308_0
wheel 0.38.4 py37h06a4308_0
x264 1!157.20191217 h7b6447c_0
xz 5.2.10 h5eee18b_1
yaml 0.2.5 h7b6447c_0
yarl 1.8.1 py37h5eee18b_0
yolov3 0.1 dev_0 zipp 3.11.0 py37h06a4308_0
zlib 1.2.13 h5eee18b_0
zstd 1.4.4 h3b9ef0a_2 conda-forge

However, I keep encountering package errors and locate the problem is caused by "import pyvista"

Traceback (most recent call last): File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/vtkIOParallel.py", line 5, in from .vtkIOParallelPython import * ImportError: libjsoncpp.so.19: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/_vtk.py", line 382, in from vtk.vtkCommonKitPython import (buffer_shared, File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtk.py", line 32, in all_spec.loader.exec_module(all_m) File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/all.py", line 83, in from .vtkIOParallel import * File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/vtkIOParallel.py", line 9, in from vtkIOParallelPython import * ModuleNotFoundError: No module named 'vtkIOParallelPython'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/vtkIOParallel.py", line 5, in from .vtkIOParallelPython import * ImportError: libjsoncpp.so.19: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/init.py", line 11, in from pyvista.plotting import * File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/plotting/init.py", line 7, in from .helpers import plot, plot_arrows, plot_compare_four, plot_itk File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/plotting/helpers.py", line 7, in from pyvista.utilities import is_pyvista_dataset File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/utilities/init.py", line 2, in from .errors import (GPUInfo, Observer, Report, File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/utilities/errors.py", line 12, in from pyvista import _vtk File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/pyvista/_vtk.py", line 386, in from vtk.vtkCommonCore import (buffer_shared, File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtk.py", line 32, in all_spec.loader.exec_module(all_m) File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/all.py", line 83, in from .vtkIOParallel import * File "/home/kevinq/anaconda3/envs/glamr/lib/python3.7/site-packages/vtkmodules/vtkIOParallel.py", line 9, in from vtkIOParallelPython import * ModuleNotFoundError: No module named 'vtkIOParallelPython'

Would you mind helping me solve this? Thanks!

[HenrySomeCode]

I solved it by pip install pyvista==0.36.0. Is this worked for you?

[take2rohit]

See #41 Its resolved there