Issue importing XDMF file in dolfinx

Quan · June 22, 2025, 6:24pm

Hi. I’m getting an error when importing an XDMF file. This code has worked well before (3 months ago on a fresh fenicsx installation). Now, I’ve installed fenicsx, and the import doesn’t work anymore. Here is my minimal working code, where “line_mesh_rotated.xdmf” is a simple line:

import dolfinx
from mpi4py import MPI
from dolfinx.io import XDMFFile

mesh_folder="example_files/meshes/"
mesh_filename="line_mesh_rotated.xdmf"

with XDMFFile(comm=MPI.COMM_WORLD,filename=mesh_folder+mesh_filename, file_mode="r",encoding=XDMFFile.Encoding.HDF5) as xdmf:
    domain = xdmf.read_mesh(name="Grid")

When importing MPI, I get this warning:

MPI startup(): FI_PSM3_UUID was not generated, please set it to avoid possible resources ownership conflicts between MPI processes

And the error shows up as:

TypeError                                 Traceback (most recent call last)
Cell In[1], line 8
      5 mesh_folder="example_files/meshes/"
      6 mesh_filename="line_mesh_rotated.xdmf"
----> 8 with XDMFFile(comm=MPI.COMM_WORLD,filename=mesh_folder+mesh_filename, file_mode="r",encoding=XDMFFile.Encoding.HDF5) as xdmf:
      9     domain = xdmf.read_mesh(name="Grid")

TypeError: __init__(): incompatible function arguments. The following argument types are supported:
    1. __init__(self, comm: MPICommWrapper, filename: str | os.PathLike, file_mode: str, encoding: dolfinx.cpp.io.XDMFFile.Encoding) -> None

Invoked with types: dolfinx.io.utils.XDMFFile, kwargs = { comm: Intracomm, filename: str, file_mode: str, encoding: dolfinx.cpp.io.Encoding }

Note that I’ve tried the XDMFFile function without an encoding specified, and with one specified. Thank you in advance.

dokken · June 22, 2025, 6:48pm

How did you install DOLFINx?
What is the output of mpirun --version?
Looking at google for this error message, it seems like something that occasionally happens with intel mpi: MPI startup(): FI_PSM3_UUID was not generated - Google Search

Quan · June 22, 2025, 7:06pm

I install fenicsx using the following commands:

mamba create --name fenicsx-env
mamba activate fenicsx-env
mamba install -c conda-forge fenics-dolfinx openmpi pyvista

And my mpi version is mpirun (Open MPI) 5.0.8. Also unsure if the MPI warning is relevant to the error I’m getting. Do you have a clue where this error come from?

dokken · June 22, 2025, 7:16pm

Could you try to call python3 -c "from mpi4py import MPI"? and mpirun -n 2 python3 -c "from mpi4py import MPI" and report if you get any issues with this?

I cannot reproduce the error on my system.
What is the output of conda env export?

Quan · June 22, 2025, 7:25pm

I have no issue for python3 -c "from mpi4py import MPI". For mpirun -n 2 python3 -c "from mpi4py import MPI", this is the error:

Your environment has OMPI_COMM_WORLD_SIZE=2 set, but mpi4py was built with Intel MPI.
You may be using `mpiexec` or `mpirun` from a different MPI implementation.
<frozen importlib._bootstrap>:488: RuntimeWarning: suspicious MPI execution environment
Your environment has OMPI_COMM_WORLD_SIZE=2 set, but mpi4py was built with Intel MPI.
You may be using `mpiexec` or `mpirun` from a different MPI implementation.

And my conda env export is here:

name: fenicsx-env
channels:
  - https://software.repos.intel.com/python/conda
  - https://software.repos.intel.com/python/conda/
  - conda-forge
  - nodefaults
dependencies:
  - _openmp_mutex=4.5=3_kmp_llvm
  - aiohappyeyeballs=2.6.1=pyhd8ed1ab_0
  - aiohttp=3.12.13=py313h8060acc_0
  - aiosignal=1.3.2=pyhd8ed1ab_0
  - alsa-lib=1.2.14=hb9d3cd8_0
  - anyio=4.9.0=pyh29332c3_0
  - argon2-cffi=25.1.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py313h536fd9c_5
  - arrow=1.3.0=pyhd8ed1ab_1
  - asttokens=3.0.0=pyhd8ed1ab_1
  - async-lru=2.0.5=pyh29332c3_0
  - attr=2.5.1=h166bdaf_1
  - attrs=25.3.0=pyh71513ae_0
  - babel=2.17.0=pyhd8ed1ab_0
  - beautifulsoup4=4.13.4=pyha770c72_0
  - binutils_impl_linux-64=2.43=h4bf12b8_5
  - binutils_linux-64=2.43=h4852527_5
  - bleach=6.2.0=pyh29332c3_4
  - bleach-with-css=6.2.0=h82add2a_4
  - blosc=1.21.6=he440d0b_1
  - brotli=1.1.0=hb9d3cd8_3
  - brotli-bin=1.1.0=hb9d3cd8_3
  - brotli-python=1.1.0=py313h46c70d0_3
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.34.5=hb9d3cd8_0
  - c-blosc2=2.18.0=h3122c55_0
  - ca-certificates=2025.6.15=hbd8a1cb_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.18.4=h3394656_0
  - certifi=2025.6.15=pyhd8ed1ab_0
  - cffi=1.17.1=py313hfab6e84_0
  - cftime=1.6.4=py313ha014f3b_1
  - charset-normalizer=3.4.2=pyhd8ed1ab_0
  - comm=0.2.2=pyhd8ed1ab_1
  - contourpy=1.3.2=py313h33d0bda_0
  - cycler=0.12.1=pyhd8ed1ab_1
  - cyrus-sasl=2.1.28=hd9c7081_0
  - dbus=1.16.2=h3c4dab8_0
  - debugpy=1.8.14=py313h46c70d0_0
  - decorator=5.2.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - double-conversion=3.3.1=h5888daf_0
  - exceptiongroup=1.3.0=pyhd8ed1ab_0
  - executing=2.2.0=pyhd8ed1ab_0
  - fenics-basix=0.9.0=py313h867a91d_2
  - fenics-basix-nanobind-abi=0.2.1.13=h6c05e69_2
  - fenics-dolfinx=0.9.0=py313hb1d6969_114
  - fenics-ffcx=0.9.0=pyh2e48890_0
  - fenics-libbasix=0.9.0=h7cb7ce6_2
  - fenics-libdolfinx=0.9.0=py313hb7a10ba_114
  - fenics-ufcx=0.9.0=hb7f7608_0
  - fenics-ufl=2024.2.0=pyhd8ed1ab_1
  - fftw=3.3.10=mpi_openmpi_h99e62ba_10
  - fmt=11.1.4=h07f6e7f_1
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=h77eed37_3
  - fontconfig=2.15.0=h7e30c49_1
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.58.4=py313h8060acc_0
  - fqdn=1.5.1=pyhd8ed1ab_1
  - freetype=2.13.3=ha770c72_1
  - frozenlist=1.6.0=py313h61b7b33_0
  - gcc_impl_linux-64=13.3.0=h1e990d8_2
  - gcc_linux-64=13.3.0=h6f18a23_11
  - geos=3.13.1=h97f6797_0
  - gl2ps=1.4.2=hae5d5c5_1
  - graphite2=1.3.14=h5888daf_0
  - h11=0.16.0=pyhd8ed1ab_0
  - h2=4.2.0=pyhd8ed1ab_0
  - h5py=3.14.0=nompi_py313hfaf8fd4_100
  - harfbuzz=11.2.1=h3beb420_0
  - hdf4=4.2.15=h2a13503_7
  - hdf5=1.14.6=mpi_openmpi_h39ae36c_1
  - hpack=4.1.0=pyhd8ed1ab_0
  - httpcore=1.0.9=pyh29332c3_0
  - httpx=0.28.1=pyhd8ed1ab_0
  - hyperframe=6.1.0=pyhd8ed1ab_0
  - hypre=2.32.0=mpi_openmpi_h398ea61_1
  - icu=75.1=he02047a_0
  - idna=3.10=pyhd8ed1ab_1
  - impi_rt=2021.15.0=intel_493
  - importlib-metadata=8.7.0=pyhe01879c_1
  - importlib_metadata=8.7.0=h40b2b14_1
  - importlib_resources=6.5.2=pyhd8ed1ab_0
  - ipykernel=6.29.5=pyh3099207_0
  - ipython=9.3.0=pyhfa0c392_0
  - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
  - ipywidgets=8.1.7=pyhd8ed1ab_0
  - isoduration=20.11.0=pyhd8ed1ab_1
  - jedi=0.19.2=pyhd8ed1ab_1
  - jinja2=3.1.6=pyhd8ed1ab_0
  - json5=0.12.0=pyhd8ed1ab_0
  - jsoncpp=1.9.6=hf42df4d_1
  - jsonpointer=3.0.0=py313h78bf25f_1
  - jsonschema=4.24.0=pyhd8ed1ab_0
  - jsonschema-specifications=2025.4.1=pyh29332c3_0
  - jsonschema-with-format-nongpl=4.24.0=hd8ed1ab_0
  - jupyter=1.1.1=pyhd8ed1ab_1
  - jupyter-lsp=2.2.5=pyhe01879c_2
  - jupyter_client=8.6.3=pyhd8ed1ab_1
  - jupyter_console=6.6.3=pyhd8ed1ab_1
  - jupyter_core=5.8.1=pyh31011fe_0
  - jupyter_events=0.12.0=pyh29332c3_0
  - jupyter_server=2.16.0=pyhe01879c_0
  - jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
  - jupyterlab=4.4.3=pyhd8ed1ab_0
  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
  - jupyterlab_server=2.27.3=pyhd8ed1ab_1
  - jupyterlab_widgets=3.0.15=pyhd8ed1ab_0
  - kahip=3.19=hd8b01d5_0
  - kernel-headers_linux-64=3.10.0=he073ed8_18
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.7=py313h33d0bda_0
  - krb5=1.21.3=h659f571_0
  - lcms2=2.17=h717163a_0
  - ld_impl_linux-64=2.43=h712a8e2_5
  - lerc=4.0.0=h0aef613_1
  - libadios2=2.10.2=mpi_openmpi_h566cb2a_7
  - libaec=1.1.4=h3f801dc_0
  - libamd=3.3.3=h456b2da_7100101
  - libblas=3.9.0=32_h59b9bed_openblas
  - libboost=1.86.0=h6c02f8c_3
  - libboost-devel=1.86.0=h1a2810e_3
  - libboost-headers=1.86.0=ha770c72_3
  - libbrotlicommon=1.1.0=hb9d3cd8_3
  - libbrotlidec=1.1.0=hb9d3cd8_3
  - libbrotlienc=1.1.0=hb9d3cd8_3
  - libbtf=2.3.2=hf02c80a_7100101
  - libcamd=3.3.3=hf02c80a_7100101
  - libcap=2.75=h39aace5_0
  - libcblas=3.9.0=32_he106b2a_openblas
  - libccolamd=3.3.4=hf02c80a_7100101
  - libcholmod=5.3.1=h9cf07ce_7100101
  - libclang-cpp20.1=20.1.7=default_h1df26ce_0
  - libclang13=20.1.7=default_he06ed0a_0
  - libcolamd=3.3.4=hf02c80a_7100101
  - libcups=2.3.3=hb8b1518_5
  - libcurl=8.14.1=h332b0f4_0
  - libdeflate=1.24=h86f0d12_0
  - libdrm=2.4.125=hb9d3cd8_0
  - libedit=3.1.20250104=pl5321h7949ede_0
  - libegl=1.7.0=ha4b6fd6_2
  - libev=4.33=hd590300_2
  - libevent=2.1.12=hf998b51_1
  - libexpat=2.7.0=h5888daf_0
  - libfabric=2.1.0=ha770c72_1
  - libfabric1=2.1.0=hf45584d_1
  - libffi=3.4.6=h2dba641_1
  - libfreetype=2.13.3=ha770c72_1
  - libfreetype6=2.13.3=h48d6fc4_1
  - libgcc=15.1.0=h767d61c_2
  - libgcc-devel_linux-64=13.3.0=hc03c837_102
  - libgcc-ng=15.1.0=h69a702a_2
  - libgcrypt-lib=1.11.1=hb9d3cd8_0
  - libgfortran=15.1.0=h69a702a_2
  - libgfortran-ng=15.1.0=h69a702a_2
  - libgfortran5=15.1.0=hcea5267_2
  - libgl=1.7.0=ha4b6fd6_2
  - libglib=2.84.2=h3618099_0
  - libglvnd=1.7.0=ha4b6fd6_2
  - libglx=1.7.0=ha4b6fd6_2
  - libgomp=15.1.0=h767d61c_2
  - libgpg-error=1.55=h3f2d84a_0
  - libhwloc=2.11.2=default_h0d58e46_1001
  - libiconv=1.18=h4ce23a2_1
  - libjpeg-turbo=3.1.0=hb9d3cd8_0
  - libklu=2.3.5=h95ff59c_7100101
  - liblapack=3.9.0=32_h7ac8fdf_openblas
  - libllvm20=20.1.7=he9d0ab4_0
  - liblzma=5.8.1=hb9d3cd8_2
  - libmpdec=4.0.0=hb9d3cd8_0
  - libnetcdf=4.9.2=nompi_h0134ee8_117
  - libnghttp2=1.64.0=h161d5f1_0
  - libnl=3.11.0=hb9d3cd8_0
  - libntlm=1.8=hb9d3cd8_0
  - libogg=1.3.5=hd0c01bc_1
  - libopenblas=0.3.30=openmp_hd680484_0
  - libpciaccess=0.18=hb9d3cd8_0
  - libpmix=5.0.8=h658e747_0
  - libpng=1.6.49=h943b412_0
  - libpq=17.5=h27ae623_0
  - libptscotch=7.0.6=h7e1c861_1
  - libsanitizer=13.3.0=he8ea267_2
  - libscotch=7.0.6=hd4c538f_1
  - libsodium=1.0.20=h4ab18f5_0
  - libspqr=4.3.4=h23b7119_7100101
  - libsqlite=3.50.1=hee588c1_4
  - libssh2=1.11.1=hcf80075_0
  - libstdcxx=15.1.0=h8f9b012_2
  - libstdcxx-ng=15.1.0=h4852527_2
  - libsuitesparseconfig=7.10.1=h901830b_7100101
  - libsystemd0=257.6=h4e0b6ca_0
  - libtheora=1.1.1=h4ab18f5_1006
  - libtiff=4.7.0=hf01ce69_5
  - libudev1=257.6=hbe16f8c_0
  - libumfpack=6.3.5=h873dde6_7100101
  - libuuid=2.38.1=h0b41bf4_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp-base=1.5.0=h851e524_0
  - libxcb=1.17.0=h8a09558_0
  - libxcrypt=4.4.36=hd590300_1
  - libxkbcommon=1.10.0=h65c71a3_0
  - libxml2=2.13.8=h4bc477f_0
  - libzip=1.11.2=h6991a6a_0
  - libzlib=1.3.1=hb9d3cd8_2
  - llvm-openmp=20.1.7=h024ca30_0
  - loguru=0.7.3=pyh707e725_0
  - lz4-c=1.10.0=h5888daf_1
  - markdown-it-py=3.0.0=pyhd8ed1ab_1
  - markupsafe=3.0.2=py313h8060acc_1
  - matplotlib-base=3.10.3=py313h129903b_0
  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
  - mdurl=0.1.2=pyhd8ed1ab_1
  - meshio=5.3.5=pyhd8ed1ab_0
  - metis=5.1.0=hd0bcaf9_1007
  - mistune=3.1.3=pyh29332c3_0
  - mpi=1.0=openmpi
  - mpi4py=4.0.3=py313hd42e859_101
  - msgpack-python=1.1.1=py313h33d0bda_0
  - multidict=6.5.0=py313h8060acc_0
  - mumps-include=5.7.3=hd53efc5_10
  - mumps-mpi=5.7.3=h85c5be4_10
  - munkres=1.1.4=pyhd8ed1ab_1
  - nbclient=0.10.2=pyhd8ed1ab_0
  - nbconvert-core=7.16.6=pyh29332c3_0
  - nbformat=5.10.4=pyhd8ed1ab_1
  - ncurses=6.5=h2d0b736_3
  - nest-asyncio=1.6.0=pyhd8ed1ab_1
  - netcdf4=1.7.2=nompi_py313h6d1955d_102
  - nlohmann_json=3.12.0=h3f2d84a_0
  - notebook=7.4.3=pyhd8ed1ab_0
  - notebook-shim=0.2.4=pyhd8ed1ab_1
  - numpy=2.3.0=py313h17eae1a_0
  - openjpeg=2.5.3=h5fbd93e_0
  - openldap=2.6.10=he970967_0
  - openmpi=5.0.8=h41ff47f_100
  - openssl=3.5.0=h7b32b05_1
  - overrides=7.7.0=pyhd8ed1ab_1
  - packaging=25.0=pyh29332c3_1
  - pandocfilters=1.5.0=pyhd8ed1ab_0
  - parmetis=4.0.3=h02de7a9_1007
  - parso=0.8.4=pyhd8ed1ab_1
  - pcre2=10.45=hc749103_0
  - petsc=3.23.3=real_h34abd39_0
  - petsc4py=3.23.3=np2py313h27975fa_0
  - pexpect=4.9.0=pyhd8ed1ab_1
  - pickleshare=0.7.5=pyhd8ed1ab_1004
  - pillow=11.2.1=py313h8db990d_0
  - pip=25.1.1=pyh145f28c_0
  - pixman=0.46.2=h29eaf8c_0
  - pkg-config=0.29.2=h4bc722e_1009
  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_2
  - platformdirs=4.3.8=pyhe01879c_0
  - pooch=1.8.2=pyhd8ed1ab_1
  - proj=9.6.2=h0054346_0
  - prometheus_client=0.22.1=pyhd8ed1ab_0
  - prompt-toolkit=3.0.51=pyha770c72_0
  - prompt_toolkit=3.0.51=hd8ed1ab_0
  - propcache=0.3.1=py313h8060acc_0
  - psutil=7.0.0=py313h536fd9c_0
  - pthread-stubs=0.4=hb9d3cd8_1002
  - ptyprocess=0.7.0=pyhd8ed1ab_1
  - pugixml=1.15=h3f63f65_0
  - pure_eval=0.2.3=pyhd8ed1ab_1
  - pycparser=2.22=pyh29332c3_1
  - pygments=2.19.1=pyhd8ed1ab_0
  - pyparsing=3.2.3=pyhd8ed1ab_1
  - pysocks=1.7.1=pyha55dd90_7
  - python=3.13.5=hec9711d_102_cp313
  - python-dateutil=2.9.0.post0=pyhff2d567_1
  - python-fastjsonschema=2.21.1=pyhd8ed1ab_0
  - python-json-logger=2.0.7=pyhd8ed1ab_0
  - python_abi=3.13=7_cp313
  - pytz=2025.2=pyhd8ed1ab_0
  - pyvista=0.45.2=pyhd8ed1ab_0
  - pyyaml=6.0.2=py313h8060acc_2
  - pyzmq=27.0.0=py313h8e95178_0
  - qhull=2020.2=h434a139_5
  - qt6-main=6.9.1=h0384650_0
  - rdma-core=57.0=h5888daf_0
  - readline=8.2=h8c095d6_2
  - referencing=0.36.2=pyh29332c3_0
  - requests=2.32.4=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_1
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rich=14.0.0=pyh29332c3_0
  - rpds-py=0.25.1=py313h4b2b08d_0
  - scalapack=2.2.0=h16fb9de_4
  - scipy=1.15.2=py313h86fcf2b_0
  - scooby=0.10.1=pyhd8ed1ab_0
  - send2trash=1.8.3=pyh0d859eb_1
  - setuptools=80.9.0=pyhff2d567_0
  - shapely=2.1.1=py313h576e190_0
  - six=1.17.0=pyhd8ed1ab_0
  - slepc=3.23.1=real_he36c950_0
  - slepc4py=3.23.1=np2py313hea9341d_0
  - snappy=1.2.1=h8bd8927_1
  - sniffio=1.3.1=pyhd8ed1ab_1
  - soupsieve=2.7=pyhd8ed1ab_0
  - spdlog=1.15.3=h10b92b3_0
  - sqlite=3.50.1=h9eae976_4
  - stack_data=0.6.3=pyhd8ed1ab_1
  - superlu=7.0.1=h8f6e6c4_0
  - superlu_dist=9.1.0=h3349319_0
  - sysroot_linux-64=2.17=h0157908_18
  - tbb=2022.1.0=h4ce085d_0
  - terminado=0.18.1=pyh0d859eb_0
  - tinycss2=1.4.0=pyhd8ed1ab_0
  - tk=8.6.13=noxft_hd72426e_102
  - tomli=2.2.1=pyhd8ed1ab_1
  - tornado=6.5.1=py313h536fd9c_0
  - traitlets=5.14.3=pyhd8ed1ab_1
  - types-python-dateutil=2.9.0.20250516=pyhd8ed1ab_0
  - typing-extensions=4.14.0=h32cad80_0
  - typing_extensions=4.14.0=pyhe01879c_0
  - typing_utils=0.1.0=pyhd8ed1ab_1
  - ucc=1.4.4=h2b97398_0
  - ucx=1.18.1=h1369271_0
  - uri-template=1.3.0=pyhd8ed1ab_1
  - urllib3=2.5.0=pyhd8ed1ab_0
  - utfcpp=4.0.6=h005c6e1_0
  - vtk-base=9.4.2=py313h6b6eb50_1
  - wayland=1.23.1=h3e06ad9_1
  - wcwidth=0.2.13=pyhd8ed1ab_1
  - webcolors=24.11.1=pyhd8ed1ab_0
  - webencodings=0.5.1=pyhd8ed1ab_3
  - websocket-client=1.8.0=pyhd8ed1ab_1
  - widgetsnbextension=4.0.14=pyhd8ed1ab_0
  - wslink=2.3.4=pyhd8ed1ab_0
  - xcb-util=0.4.1=h4f16b4b_2
  - xcb-util-cursor=0.1.5=hb9d3cd8_0
  - xcb-util-image=0.4.0=hb711507_2
  - xcb-util-keysyms=0.4.1=hb711507_0
  - xcb-util-renderutil=0.3.10=hb711507_0
  - xcb-util-wm=0.4.2=hb711507_0
  - xkeyboard-config=2.45=hb9d3cd8_0
  - xorg-libice=1.1.2=hb9d3cd8_0
  - xorg-libsm=1.2.6=he73a12e_0
  - xorg-libx11=1.8.12=h4f16b4b_0
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxcomposite=0.4.6=hb9d3cd8_2
  - xorg-libxcursor=1.2.3=hb9d3cd8_0
  - xorg-libxdamage=1.1.6=hb9d3cd8_0
  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
  - xorg-libxext=1.3.6=hb9d3cd8_0
  - xorg-libxfixes=6.0.1=hb9d3cd8_0
  - xorg-libxi=1.8.2=hb9d3cd8_0
  - xorg-libxrandr=1.5.4=hb9d3cd8_0
  - xorg-libxrender=0.9.12=hb9d3cd8_0
  - xorg-libxtst=1.2.5=hb9d3cd8_3
  - xorg-libxxf86vm=1.1.6=hb9d3cd8_0
  - yaml=0.2.5=h7f98852_2
  - yarl=1.20.1=py313h8060acc_0
  - zeromq=4.3.5=h3b0a872_7
  - zfp=1.0.1=h5888daf_2
  - zipp=3.23.0=pyhd8ed1ab_0
  - zlib=1.3.1=hb9d3cd8_2
  - zlib-ng=2.2.4=h7955e40_0
  - zstandard=0.23.0=py313h536fd9c_2
  - zstd=1.5.7=hb8e6e7a_2
  - pip:
      - dill==0.4.0
      - gmsh==4.13.1
      - multiprocess==0.70.18
      - pandas==2.3.0
      - pygmsh==7.1.17
      - salib==1.5.1
      - tzdata==2025.2
prefix: /projectnb/lejlab2/quan/.conda/envs/fenicsx-env

I’m currently using a computing cluster, so maybe I just have to contact an admin.

dokken · June 22, 2025, 7:28pm

Seems like the environment uses a mixture of openmpi and intelmpi.

Topic		Replies	Views
Importing mesh gives error dolfinx	12	3373	December 9, 2021
MED Salome to dolfinx: Issues with XDMF dolfinx	8	571	March 26, 2023
Cannot open .xdmf files in legacy version of fenics + latest Paraview General	10	1260	February 7, 2023
Problem for writing function with XDMFFile dolfinx	1	345	October 25, 2023
Import dolfin fail, with mpi error Legacy DOLFIN	3	69	November 5, 2024

Issue importing XDMF file in dolfinx

Related topics