Hi all,
conda create -n my_env
conda activate my_env
conda install -c conda-forge fenics-dolfinx mpich pyvista
as indicated in the instructions.
I obtain this error when trying to call pyvista:
[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
Generated with:
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 remember having similar issues with packages installed with a mix of pip and conda, but here everything is installed via conda.
Any idea?
I think this is a case of mixing matplotlib from pip or conda but not quite sure how to debug since it occurs even on a clean conda environment.
I tried pip uninstall matplotlib but still doesn’t work
You can use the following command at the terminal:conda env listpyvista.start_xvfb()
I think I ran into some similar issues and I was able to just delete that line and get the script to run.
I’m not well versed in ‘virtual framebuilders’ (see pyvista documentation ) but I believe this is related to running the script on a machine using virtual memory without have to show screen output. Sounds like this is more geared towards clusters, so you can do without on your own machine if you have a display output. Or you can make sure you go download libgl1-mesa-glx_xvfb
You will also need to change the line:u_topology, u_cell_types, u_geometry = plot.vtk_mesh(V)u_topology, u_cell_types, u_geometry = plot.create_vtk_mesh(V)
This is the command to show all the environment not showing the packages installed
Commenting this out didn’t help
jkrokowski:
You will also need to change the line:u_topology, u_cell_types, u_geometry = plot.vtk_mesh(V)u_topology, u_cell_types, u_geometry = plot.create_vtk_mesh(V)
This is the 0.7 syntax
sorry, I meantconda list
Not sure what you are talking about, plot.create_vtk_mesh() is the syntax I’ve been using since at least version 0.5
What system are you running this on? It looks like you are having an issue similar to this .
I completely reinstalled anaconda and only installed dolfinx via the commands suggested.an issue on the conda-forge repo for dolfinx giving all the details of my env.
Well the syntax has changed
wolfla
October 29, 2023, 10:30am
7
Hi, today I set up a jupyterhub for fenicsx via anaconda and had initially also issues with pyvista. I however got it to work after installing xvfb on the host system via:
$ sudo apt install libgl1-mesa-glx xvfb
I also installed all kinds of xvfb packages via conda - to be honest I’m not sure what got it to work eventually. But here is my conda env:
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiohttp 3.8.6 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
anyio 4.0.0 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pypi_0 pypi
async-timeout 4.0.3 pypi_0 pypi
attrs 23.1.0 pypi_0 pypi
babel 2.13.1 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pypi_0 pypi
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_13 conda-forge
bleach 6.1.0 pypi_0 pypi
blosc 1.21.5 h0f2a231_0 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.20.1 hd590300_1 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
certifi 2023.7.22 pypi_0 pypi
cffi 1.16.0 py310h2fee648_0 conda-forge
charset-normalizer 3.3.1 pypi_0 pypi
cmocean 3.0.3 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorcet 3.0.1 pypi_0 pypi
comm 0.1.4 pyhd8ed1ab_0 conda-forge
debugpy 1.8.0 py310hc6cd4ac_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pypi_0 pypi
exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
fastjsonschema 2.18.1 pypi_0 pypi
fenics-basix 0.5.1 py310hbf28c38_1 conda-forge
fenics-dolfinx 0.5.2 py310h7dda09f_102 conda-forge
fenics-ffcx 0.5.0 pyhb871ab6_1 conda-forge
fenics-libbasix 0.5.1 heb3b609_1 conda-forge
fenics-libdolfinx 0.5.2 hb062b81_102 conda-forge
fenics-ufcx 0.5.0 hb871ab6_1 conda-forge
fenics-ufl 2022.2.0 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 mpi_openmpi_h4a81ba8_8 conda-forge
fqdn 1.5.1 pypi_0 pypi
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pypi_0 pypi
frozenlist 1.4.0 pypi_0 pypi
gcc_impl_linux-64 10.4.0 h5231bdf_19 conda-forge
gcc_linux-64 10.4.0 h9215b83_13 conda-forge
glx 0.6 pypi_0 pypi
gmp 6.2.1 h58526e2_0 conda-forge
gxx_impl_linux-64 10.4.0 h5231bdf_19 conda-forge
gxx_linux-64 10.4.0 h6e491c6_13 conda-forge
hdf5 1.12.2 mpi_openmpi_h41b9b70_1 conda-forge
hypre 2.25.0 mpi_openmpi_ha709252_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.4 pypi_0 pypi
imageio 2.31.6 pypi_0 pypi
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipydatawidgets 4.3.5 pypi_0 pypi
ipykernel 6.26.0 pyhf8b6a83_0 conda-forge
ipython 8.16.1 pyh0d859eb_0 conda-forge
ipywidgets 8.1.1 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pypi_0 pypi
json5 0.9.14 pypi_0 pypi
jsonpointer 2.4 pypi_0 pypi
jsonschema 4.19.1 pypi_0 pypi
jsonschema-specifications 2023.7.1 pypi_0 pypi
jupyter-events 0.8.0 pypi_0 pypi
jupyter-lsp 2.2.0 pypi_0 pypi
jupyter-server 2.9.1 pypi_0 pypi
jupyter-server-proxy 4.1.0 pypi_0 pypi
jupyter-server-terminals 0.4.4 pypi_0 pypi
jupyter_client 8.5.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.4.0 py310hff52083_0 conda-forge
jupyterlab 4.0.7 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-server 2.25.0 pypi_0 pypi
jupyterlab-widgets 3.0.9 pypi_0 pypi
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lcms2 2.15 hb7c19ff_3 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libadios2 2.8.3 mpi_openmpi_h64021f3_5 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 19_linux64_openblas conda-forge
libcblas 3.9.0 19_linux64_openblas conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 10.4.0 hd38fd1e_19 conda-forge
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_2 conda-forge
libgfortran5 13.2.0 ha4646dd_2 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libhwloc 2.9.3 default_h554bfaf_1009 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 19_linux64_openblas conda-forge
libnghttp2 1.55.1 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsanitizer 10.4.0 h5246dfb_19 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 10.4.0 hd38fd1e_19 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.11.5 h232c23b_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mako 1.2.4 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.3 pypi_0 pypi
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pypi_0 pypi
meshio 5.3.4 pypi_0 pypi
metis 5.1.0 h59595ed_1007 conda-forge
mistune 3.0.2 pypi_0 pypi
mpfr 4.2.1 h9458935_0 conda-forge
mpi 1.0 openmpi conda-forge
mpi4py 3.1.5 py310h2a790f2_0 conda-forge
multidict 6.0.4 pypi_0 pypi
mumps-include 5.2.1 ha770c72_11 conda-forge
mumps-mpi 5.2.1 hfb3545b_11 conda-forge
nbclient 0.8.0 pypi_0 pypi
nbconvert 7.9.2 pypi_0 pypi
nbformat 5.9.2 pypi_0 pypi
ncurses 6.4 hcb278e6_0 conda-forge
nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge
nose 1.3.7 pypi_0 pypi
nose-xvfb 0.13.1 pypi_0 pypi
notebook-shim 0.2.3 pypi_0 pypi
numpy 1.26.0 py310hb13e2d6_0 conda-forge
openjpeg 2.5.0 h488ebb8_3 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.1.4 hd590300_0 conda-forge
overrides 7.4.0 pypi_0 pypi
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandocfilters 1.5.0 pypi_0 pypi
param 2.0.0 pypi_0 pypi
parmetis 4.0.3 he9a3056_1005 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
petsc 3.17.4 real_h4502189_101 conda-forge
petsc4py 3.17.4 real_h5540cce_101 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.1 pypi_0 pypi
pip 23.3.1 pyhd8ed1ab_0 conda-forge
pixman-cos6-x86_64 0.32.8 h9b0a68f_1105 conda-forge
platformdirs 3.11.0 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
pooch 1.8.0 pypi_0 pypi
prometheus-client 0.17.1 pypi_0 pypi
prompt-toolkit 3.0.39 pyha770c72_0 conda-forge
prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge
psutil 5.9.5 py310h2372a71_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptscotch 6.0.9 h0a9c416_2 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pugixml 1.11.4 h59595ed_1 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyct 0.5.0 pypi_0 pypi
pygments 2.16.1 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.7 pypi_0 pypi
pytest 7.4.3 pyhd8ed1ab_0 conda-forge
pytest-xvfb 3.0.0 pyhd8ed1ab_0 conda-forge
python 3.10.13 hd12c33a_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pypi_0 pypi
python_abi 3.10 4_cp310 conda-forge
pythreejs 2.4.2 pypi_0 pypi
pyvirtualdisplay 3.0 py310hff52083_3 conda-forge
pyvista 0.42.3 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 25.1.1 py310h795f18f_2 conda-forge
readline 8.2 h8228510_1 conda-forge
rectangle 0.4 pypi_0 pypi
referencing 0.30.2 pypi_0 pypi
requests 2.31.0 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rich 13.6.0 pypi_0 pypi
rpds-py 0.10.6 pypi_0 pypi
scalapack 2.2.0 h67de57e_1 conda-forge
scooby 0.9.2 pypi_0 pypi
scotch 6.0.9 hb2e6521_2 conda-forge
send2trash 1.8.2 pypi_0 pypi
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
simpervisor 1.0.0 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
slepc 3.17.2 real_h624bf36_100 conda-forge
slepc4py 3.17.2 real_h024a88e_101 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h9e50725_1 conda-forge
superlu 5.2.2 h00795ac_0 conda-forge
superlu_dist 7.2.0 h34f6f4d_0 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
tbb 2021.10.0 h00ab1b0_2 conda-forge
terminado 0.17.1 pypi_0 pypi
tinycss2 1.2.1 pypi_0 pypi
tk 8.6.13 h2797004_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py310h2372a71_1 conda-forge
traitlets 5.12.0 pyhd8ed1ab_0 conda-forge
traittypes 0.2.1 pypi_0 pypi
trame 3.2.8 pypi_0 pypi
trame-client 2.12.6 pypi_0 pypi
trame-components 2.2.1 pypi_0 pypi
trame-server 2.12.0 pypi_0 pypi
trame-vtk 2.5.9 pypi_0 pypi
trame-vuetify 2.3.1 pypi_0 pypi
types-python-dateutil 2.8.19.14 pypi_0 pypi
typing-extensions 4.8.0 hd8ed1ab_0 conda-forge
typing_extensions 4.8.0 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uri-template 1.3.0 pypi_0 pypi
urllib3 2.0.7 pypi_0 pypi
vtk 9.2.6 pypi_0 pypi
wcwidth 0.2.8 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.6.4 pypi_0 pypi
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pypi_0 pypi
wslink 1.12.4 pypi_0 pypi
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-x11-server-common-cos6-x86_64 1.17.4 h9b0a68f_1105 conda-forge
xorg-x11-server-xvfb-cos6-x86_64 1.17.4 h9b0a68f_1105 conda-forge
xtensor 0.24.7 h00ab1b0_0 conda-forge
xtl 0.7.5 hf52228f_0 conda-forge
xvfbwrapper 0.2.9 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.2 pypi_0 pypi
zeromq 4.3.5 h59595ed_0 conda-forge
zfp 0.5.5 h9c3ff4c_8 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Note that I use the fenicx version 0.5.2. Here is a working example of how I use it (and it works for me):
import pyvista
pyvista.start_xvfb()
pyvista.set_jupyter_backend("static") # change to "server" for interactive output
grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))
grid.point_data["c"] = c_n.x.array.real
grid.set_active_scalars("c")
plotter = pyvista.Plotter()
plotter.add_mesh(grid, clim=[0, 1], show_edges=True, show_scalar_bar=True)
plotter.view_xy()
figure = plotter.screenshot("initial.png")
if not pyvista.OFF_SCREEN:
plotter.show()
else:
figure = plotter.screenshot("initial.png")
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