Cannot use pyvista with dolfinx

[RemDelaporteMathurin]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Hi @minrk

I created a conda env with:

conda create -n test_env
conda activate test_env
conda install -c conda-forge fenics-dolfinx mpich pyvista

As suggested in the docs.

Now when I try to run:

from dolfinx import mesh, fem, plot
from mpi4py import MPI

msh = mesh.create_unit_square(MPI.COMM_WORLD, 8, 8)

V = fem.FunctionSpace(msh, ("CG", 1))
u = fem.Function(V)

import pyvista
pyvista.OFF_SCREEN = True

pyvista.start_xvfb()

u_topology, u_cell_types, u_geometry = plot.vtk_mesh(V)
u_grid = pyvista.UnstructuredGrid(u_topology, u_cell_types, u_geometry)
u_grid.point_data["u"] = u.x.array.real
u_grid.set_active_scalars("u")
u_plotter = pyvista.Plotter()
u_plotter.add_mesh(u_grid, show_edges=False)
u_plotter.view_xy()
if not pyvista.OFF_SCREEN:
    u_plotter.show()
else:
    figure = u_plotter.screenshot("solution.png")

I obtain the following error:

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

I believe it has something to do with packages incompatibility. I've tried reinstalling anaconda from scratch, creating multiple clean environments, I always have the same issue.

Installed packages

# packages in environment at /home/remidm/miniconda3/envs/test_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiohttp                   3.8.6           py311h459d7ec_1    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.10               hd590300_0    conda-forge
aom                       3.6.1                h59595ed_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
binutils_linux-64         2.40                 hbdbef99_2    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0           py311hb755f60_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.20.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py311hb3a22ac_0    conda-forge
charset-normalizer        3.3.0              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.1           py311h9547e67_1    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hd590300_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
double-conversion         3.3.0                h59595ed_0    conda-forge
eigen                     3.4.0                h00ab1b0_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fenics-basix              0.7.0           py311h64516f0_1    conda-forge
fenics-basix-pybind11-abi 0.4.12               h64516f0_1    conda-forge
fenics-dolfinx            0.7.0           py311h6023476_101    conda-forge
fenics-ffcx               0.7.0              pyh4af843d_0    conda-forge
fenics-libbasix           0.7.0                hfdc072b_1    conda-forge
fenics-libdolfinx         0.7.0              heb7b2f8_101    conda-forge
fenics-ufcx               0.7.0                h4af843d_0    conda-forge
fenics-ufl                2023.2.0           pyhd8ed1ab_0    conda-forge
ffmpeg                    6.0.0           gpl_h334edf3_105    conda-forge
fftw                      3.3.10          mpi_mpich_h5537406_8    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                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.43.1          py311h459d7ec_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
frozenlist                1.4.0           py311h459d7ec_1    conda-forge
gcc_impl_linux-64         12.3.0               he2b93b0_2    conda-forge
gcc_linux-64              12.3.0               h76fc315_2    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.78.0               hfc55251_0    conda-forge
glib-tools                2.78.0               hfc55251_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gst-plugins-base          1.22.6               h8e1006c_2    conda-forge
gstreamer                 1.22.6               h98fc4e7_2    conda-forge
gxx_impl_linux-64         12.3.0               he2b93b0_2    conda-forge
gxx_linux-64              12.3.0               h8a814eb_2    conda-forge
harfbuzz                  8.2.1                h3d44ed6_0    conda-forge
hdf4                      4.2.15               h2a13503_7    conda-forge
hdf5                      1.14.2          mpi_mpich_ha2c2bf8_0    conda-forge
hypre                     2.28.0          mpi_mpich_h716cb5e_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
jsoncpp                   1.9.5                h4bd325d_1    conda-forge
kahip                     3.15                 hcc195ba_2    conda-forge
kahip-python              3.15            py311hcacd666_2    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_16    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py311h9547e67_1    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.15                 hb7c19ff_3    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libadios2                 2.9.1           mpi_mpich_h11b1e74_3    conda-forge
libaec                    1.1.2                h59595ed_1    conda-forge
libass                    0.17.1               h8fe9dca_1    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libboost                  1.82.0               h6fcfa73_6    conda-forge
libboost-devel            1.82.0               h00ab1b0_6    conda-forge
libboost-headers          1.82.0               ha770c72_6    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcap                    2.69                 h0f662aa_0    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libclang                  15.0.7          default_h7634d5b_3    conda-forge
libclang13                15.0.7          default_h9986a30_3    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libdrm                    2.4.114              h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.3                h59595ed_0    conda-forge
libgcc-devel_linux-64     12.3.0               h8bca6fd_2    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgcrypt                 1.10.1               h166bdaf_0    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libglu                    9.0.0             hac7e632_1003    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libgpg-error              1.47                 h71f35ed_0    conda-forge
libhwloc                  2.9.3           default_h554bfaf_1009    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libllvm15                 15.0.7               h5cf9203_3    conda-forge
libnetcdf                 4.9.2           nompi_h80fb2b6_112    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                hd590300_1    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpciaccess              0.17                 h166bdaf_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     16.0                 hfc447b1_1    conda-forge
libsanitizer              12.3.0               h0f45ef3_2    conda-forge
libsndfile                1.2.2                hc60ed4a_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  12.3.0               h8bca6fd_2    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libsystemd0               254                  h3516f8a_0    conda-forge
libtasn1                  4.19.0               h166bdaf_0    conda-forge
libtheora                 1.1.1             h7f98852_1005    conda-forge
libtiff                   4.6.0                ha9c0a0a_2    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libva                     2.20.0               hd590300_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libvpx                    1.13.1               h59595ed_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxkbcommon              1.6.0                h5d7e998_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libzip                    1.10.1               h2629f0a_3    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
loguru                    0.7.2           py311h38be061_1    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
matplotlib-base           3.8.0           py311h54ef318_2    conda-forge
metis                     5.1.0             h59595ed_1007    conda-forge
mpfr                      4.2.0                hb012696_0    conda-forge
mpg123                    1.32.3               h59595ed_0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.1.4           py311he01e52e_1    conda-forge
mpich                     4.1.2              h846660c_100    conda-forge
multidict                 6.0.4           py311h459d7ec_1    conda-forge
mumps-include             5.2.1               ha770c72_11    conda-forge
mumps-mpi                 5.2.1               h7ee95aa_11    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.33               hf1915f5_5    conda-forge
mysql-libs                8.0.33               hca2cd23_5    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
nlohmann_json             3.11.2               h27087fc_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.94                 h1d7d5a4_0    conda-forge
numpy                     1.26.0          py311h64a7726_0    conda-forge
openh264                  2.3.1                hcb278e6_2    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
parmetis                  4.0.3             h2a9763c_1005    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
petsc                     3.20.0          real_h622a54c_101    conda-forge
petsc4py                  3.20.0          real_h928380f_100    conda-forge
pillow                    10.0.1          py311ha6c5da5_2    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h59595ed_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyhd8ed1ab_4    conda-forge
proj                      9.3.0                h1d62c97_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptscotch                  6.0.9                hb499603_2    conda-forge
pugixml                   1.13                 h59595ed_1    conda-forge
pulseaudio-client         16.1                 hb77b528_5    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.6          hab00c5b_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pyvista                   0.42.3             pyhd8ed1ab_0    conda-forge
qt-main                   5.15.8              h82b777d_17    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
scalapack                 2.2.0                hd931219_1    conda-forge
scooby                    0.7.4              pyhd8ed1ab_0    conda-forge
scotch                    6.0.9                hb2e6521_2    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
slepc                     3.20.0          real_h905369a_100    conda-forge
slepc4py                  3.20.0          real_hd877bb9_100    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sqlite                    3.43.2               h2c6b66d_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
superlu                   5.2.2                h00795ac_0    conda-forge
superlu_dist              7.2.0                h25dcc4a_0    conda-forge
svt-av1                   1.7.0                h59595ed_0    conda-forge
sysroot_linux-64          2.12                he073ed8_16    conda-forge
tbb                       2021.10.0            h00ab1b0_1    conda-forge
tbb-devel                 2021.10.0            h00ab1b0_1    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.6              pyhd8ed1ab_0    conda-forge
utfcpp                    3.2.5                ha770c72_0    conda-forge
vtk                       9.2.6           qt_py311h1234567_217    conda-forge
vtk-base                  9.2.6           qt_py311h1234567_217    conda-forge
vtk-io-ffmpeg             9.2.6           qt_py311h1234567_217    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wslink                    1.12.3             pyhd8ed1ab_0    conda-forge
x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xcb-util                  0.4.0                hd590300_1    conda-forge
xcb-util-image            0.4.0                h8ee46fc_1    conda-forge
xcb-util-keysyms          0.4.0                h8ee46fc_1    conda-forge
xcb-util-renderutil       0.3.9                hd590300_1    conda-forge
xcb-util-wm               0.4.1                h8ee46fc_1    conda-forge
xkeyboard-config          2.40                 hd590300_0    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.7                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xf86vidmodeproto     2.3.1             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yarl                      1.9.2           py311h459d7ec_1    conda-forge
zeromq                    4.3.5                h59595ed_0    conda-forge
zfp                       0.5.5                h9c3ff4c_8    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Environment info

active environment : test_env
    active env location : /home/remidm/miniconda3/envs/test_env
            shell level : 2
       user config file : /home/remidm/.condarc
 populated config files : 
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=5.10.102.1=0
                          __glibc=2.35=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/remidm/miniconda3  (writable)
      conda av data dir : /home/remidm/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : 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/remidm/miniconda3/pkgs
                          /home/remidm/.conda/pkgs
       envs directories : /home/remidm/miniconda3/envs
                          /home/remidm/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.10.102.1-microsoft-standard-WSL2 ubuntu/22.04.1 glibc/2.35
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

[minrk]

I just found and fixed an -march=native in kahip, which produces this error when running osx-64 builds on osx-arm64 machines. There's a very good chance it was the same issue for you, in which case upgrading kahip would fix to the latest build would fix it.