# Problem with read a external mesh **URL:** \ **Category:** General\ **Created:** [July 6, 2023, 1:05pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678 "2023-07-06T13:05:53Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [July 6, 2023, 1:05pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/1 "2023-07-06T13:05:53Z")
Hi everyone. I’m trying to read a mesh generated by Ansys in FEniCSx. The mesh is in .msh. I change the format with ```auto meshio convert fluent.msh venturi_1600.xdmf ``` but when I try to open ```auto import dolfinx ##########################################################################################################3 # Read the mesh with dolfinx.io.XDMFFile(MPI.COMM_WORLD, "venturi_1600.xdmf", "r") as xdmf: domain = xdmf.read_mesh(name='Grid') ``` I obtain ```auto --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) Cell In[2], line 5 1 import dolfinx 4 with dolfinx.io.XDMFFile(MPI.COMM_WORLD, "venturi_1600.xdmf", "r") as xdmf: ----> 5 domain = xdmf.read_mesh(name='Grid') 7 tdim = domain.topology.dim 8 tree = dolfinx.geometry.BoundingBoxTree(domain, tdim) File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/utils.py:154, in XDMFFile.read_mesh(self, ghost_mode, name, xpath) 152 def read_mesh(self, ghost_mode=GhostMode.shared_facet, name="mesh", xpath="/Xdmf/Domain") -> Mesh: 153 """Read mesh data from file""" --> 154 cell_shape, cell_degree = super().read_cell_type(name, xpath) 155 cells = super().read_topology_data(name, xpath) 156 x = super().read_geometry_data(name, xpath) RuntimeError: Cannot recognise cell type. Unknown value: mixed ``` but the mesh has a unique element (Quadrilateral). I can export the mesh with different formats: ![kindmesh](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/8/87ae081d45abd6f8882d4e550d08a872506fbd12.png) The mesh is in this folder: > **[117.3 KB folder on MEGA](https://mega.nz/folder/FNVkRawI#RBuqEO9Yef7yHwqkZvNNnQ)** Does anyone has a idea to solve? Thank you so much! ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [July 6, 2023, 2:55pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/2 "2023-07-06T14:55:21Z")
See: [Can dolfinx read a GMSH file containing 1D mesh of an ellipse? - #2 by dokken](https://fenicsproject.discourse.group/t/can-dolfinx-read-a-gmsh-file-containing-1d-mesh-of-an-ellipse/9765/2) ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [July 6, 2023, 5:58pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/3 "2023-07-06T17:58:10Z")
I have tried that code with the following change: ```auto meshio.write("venturi_1600.xdmf, create_mesh, (mesh, "quadrilateral", True)) ``` and I get the next error ```auto KeyError: 'quadrilateral' ``` I find the name of elements here: [https://fenicsproject.org/olddocs/dolfinx/dev/python/generated/dolfinx.cpp.mesh.html](https://fenicsproject.org/olddocs/dolfinx/dev/python/generated/dolfinx.cpp.mesh.html) ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [July 6, 2023, 6:07pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/4 "2023-07-06T18:07:50Z")
> [@Karlosjusus](#): > > `meshio.write("venturi_1600.xdmf, create_mesh, (mesh, "quadrilateral", True))` This does not make sense, it should be: `meshio.write("venturi_1600.xdmf, create_mesh(mesh, "quad", True))` if `mesh` is a meshio mesh. See [https://github.com/nschloe/meshio/blob/0138cc8692b806b44b32d344f7961e8370121ff7/src/meshio/\_mesh.py#L14](https://github.com/nschloe/meshio/blob/0138cc8692b806b44b32d344f7961e8370121ff7/src/meshio/_mesh.py#L14) ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [July 7, 2023, 10:23am UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/5 "2023-07-07T10:23:06Z")
Thank you @dokken, but now I try ```auto def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) cell_data = mesh.get_cell_data("gmsh:physical", cell_type) points = mesh.points[:,:2] if prune_z else mesh.points out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data = {"name_to_read": [cell_data]}) return out_mesh mesh = meshio.read("fluent.msh") meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) ``` and obtain: ```auto KeyError Traceback (most recent call last) Cell In[1], line 36 32 return out_mesh 34 mesh = meshio.read("fluent.msh") ---> 36 meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) Cell In[1], line 29, in create_mesh(mesh, cell_type, prune_z) 27 def create_mesh(mesh, cell_type, prune_z=False): 28 cells = mesh.get_cells_type(cell_type) ---> 29 cell_data = mesh.get_cell_data("gmsh:physical", cell_type) 30 points = mesh.points[:,:2] if prune_z else mesh.points 31 out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data = {"name_to_read": [cell_data]}) File ~/.local/lib/python3.10/site-packages/meshio/_mesh.py:250, in Mesh.get_cell_data(self, name, cell_type) 248 def get_cell_data(self, name: str, cell_type: str): 249 return np.concatenate( --> 250 [d for c, d in zip(self.cells, self.cell_data[name]) if c.type == cell_type] 251 ) KeyError: 'gmsh:physical' ``` I try ```auto print(mesh.cell_data) ``` and obtain ```auto {} ``` ---
**Author:** ![violetus](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/violetus/32/5122_2.png) [@violetus](https://fenicsproject.discourse.group/u/violetus)\ **Post date:** [July 7, 2023, 1:33pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/6 "2023-07-07T13:33:32Z")
I think you need to remove the `cell_data` part and try like - ```auto def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) points = mesh.points[:,:2] if prune_z else mesh.points out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}) return out_mesh mesh = meshio.read("fluent.msh") meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) ``` ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 21, 2023, 8:19pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/7 "2023-08-21T20:19:29Z")
sorry for the delay. When I run it, I get this error. ```auto Warnig: py.warning:/urs/local/lib/python3.10/dist-packages/h5py/ __init__.py:36 UserWarning: h5py is running against HDF5 1.10.7 when it was bulit against 1.12.2, this may cause problems ``` and the kernel dies… I tried to install these version but I get the same error… ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 22, 2023, 4:47am UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/8 "2023-08-22T04:47:04Z")
See [The kernel appears to have died. It will restart automatically - #13 by dokken](https://fenicsproject.discourse.group/t/the-kernel-appears-to-have-died-it-will-restart-automatically/9752/13) ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 29, 2023, 5:20pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/9 "2023-08-29T17:20:04Z")
I followed the steps, uninstalled h5py and ran in terminalI followed the steps, uninstalled h5py and ran in terminal python3 -m pip install --no-binary=h5py h5py meshio and I get ```auto Defaulting to user installation because normal site-packages is not writeable Collecting h5py Using cached h5py-3.9.0.tar.gz (402 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: meshio in ./.local/lib/python3.10/site-packages (5.3.4) Requirement already satisfied: numpy>=1.17.3 in /usr/lib/python3/dist-packages (from h5py) (1.21.5) Requirement already satisfied: rich in ./.local/lib/python3.10/site-packages (from meshio) (13.3.4) Requirement already satisfied: pygments<3.0.0,>=2.13.0 in ./.local/lib/python3.10/site-packages (from rich->meshio) (2.15.0) Requirement already satisfied: markdown-it-py<3.0.0,>=2.2.0 in ./.local/lib/python3.10/site-packages (from rich->meshio) (2.2.0) Requirement already satisfied: mdurl~=0.1 in ./.local/lib/python3.10/site-packages (from markdown-it-py<3.0.0,>=2.2.0->rich->meshio) (0.1.2) Building wheels for collected packages: h5py Building wheel for h5py (pyproject.toml) ... error error: subprocess-exited-with-error × Building wheel for h5py (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [89 lines of output] running bdist_wheel running build running build_ext Error compiling Cython file: ------------------------------------------------------------ ... cdef struct err_data_t: H5E_error_t err int n cdef herr_t walk_cb(unsigned int n, const H5E_error_t *desc, void *e) nogil noexcept: ^ ------------------------------------------------------------ h5py/_errors.pyx:97:76: Syntax error in C variable declaration Loading library to get build settings and version: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so ******************************************************************************** Summary of the h5py configuration HDF5 include dirs: [ '/usr/include/hdf5/openmpi' '/usr/lib/x86_64-linux-gnu/openmpi/include' '/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi' ] HDF5 library dirs: [ '/usr/lib/x86_64-linux-gnu/hdf5/openmpi' '/usr/lib/x86_64-linux-gnu/openmpi/lib' ] HDF5 Version: (1, 10, 7) MPI Enabled: False ROS3 VFD Enabled: True DIRECT VFD Enabled: False Rebuild Required: True MS-MPI Enabled: False MS-MPI include dirs: [] MS-MPI library dirs: [] ******************************************************************************** Executing api_gen rebuild of defs Updated /tmp/pip-install-mz8ute5r/h5py_7dbb00c2e84c4528a56317c969e584e7/h5py/config.pxi Executing cythonize() [1/24] Cythonizing /tmp/pip-install-mz8ute5r/h5py_7dbb00c2e84c4528a56317c969e584e7/h5py/_conv.pyx [2/24] Cythonizing /tmp/pip-install-mz8ute5r/h5py_7dbb00c2e84c4528a56317c969e584e7/h5py/_errors.pyx Traceback (most recent call last): File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in main() File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel return _build_backend().build_wheel(wheel_directory, config_settings, File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 230, in build_wheel return self._build_with_temp_dir(['bdist_wheel'], '.whl', File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 215, in _build_with_temp_dir self.run_setup() File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 158, in run_setup exec(compile(code, __file__ , 'exec'), locals()) File "setup.py", line 68, in setup( File "/usr/lib/python3/dist-packages/setuptools/ __init__.py", line 153, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 148, in setup return run_commands(dist) File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 163, in run_commands dist.run_commands() File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 967, in run_commands self.run_command(cmd) File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command cmd_obj.run() File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 299, in run self.run_command('build') File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command cmd_obj.run() File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 986, in run_command cmd_obj.run() File "/tmp/pip-install-mz8ute5r/h5py_7dbb00c2e84c4528a56317c969e584e7/setup_build.py", line 171, in run self.extensions = cythonize(self._make_extensions(config), File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1127, in cythonize cythonize_one(*args) File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1250, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /tmp/pip-install-mz8ute5r/h5py_7dbb00c2e84c4528a56317c969e584e7/h5py/_errors.pyx [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for h5py Failed to build h5py ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects ``` ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 29, 2023, 5:27pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/10 "2023-08-29T17:27:52Z")
Could you check what cython version you have on your system, as they just released a new version 2 days ago (it might be that you need to pin it to an earlier version of cython). > **[Releases · cython/cython](https://github.com/cython/cython/releases)** > > The most widely used Python to C compiler. Contribute to cython/cython development by creating an account on GitHub. ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 29, 2023, 5:34pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/11 "2023-08-29T17:34:14Z")
I have Cython version 0.29.28 ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 29, 2023, 5:36pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/12 "2023-08-29T17:36:11Z")
What system are you running on? Can you produce an environment that reproduces this error (say with docker)? ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 29, 2023, 5:45pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/13 "2023-08-29T17:45:44Z")
I use Ubuntu 22.04.2 LTS. I have never used docker. how can I do it? ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 29, 2023, 6:35pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/14 "2023-08-29T18:35:57Z")
How did you install dolfinx? Through apt-Get? ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 29, 2023, 6:42pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/15 "2023-08-29T18:42:54Z")
with this add-apt-repository ppa:fenics-packages/fenics apt update apt install fenicsx ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 29, 2023, 7:32pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/16 "2023-08-29T19:32:26Z")
I cannot reproduce this error with a clean ubuntu system: `Dockerfile`: ```plaintext FROM ubuntu:22.04 ENV DEBIAN_FRONTEND=noninteractive RUN apt-get update && \ apt-get install -y software-properties-common && \ add-apt-repository ppa:fenics-packages/fenics && \ apt-get install -y fenicsx python3-pip RUN python3 -m pip install --no-binary=h5py h5py meshio ``` built with: ```bash docker build -t dx_meshio . ``` ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 29, 2023, 7:44pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/17 "2023-08-29T19:44:47Z")
Do you have any suggestions? I just need to transform the mesh and do the rest in my original code. ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [August 29, 2023, 8:00pm UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/18 "2023-08-29T20:00:04Z")
Its hard when I cant reproduce the error. What happens if you use the Gmsh Python interface to read the msh file and use `dolfinx.io.gmshio.read_from_msh` or `dolfinx.io.gmshio.model_to_mesh`? ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 30, 2023, 8:27am UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/19 "2023-08-30T08:27:38Z")
If I use ```auto mesh = dolfinx.io.gmshio.read_from_msh("fluent.msh", MPI.COMM_WORLD,gdim=2) ``` I get ```auto Error : 'fluent.msh', line 1: syntax error (() --------------------------------------------------------------------------- Exception Traceback (most recent call last) Cell In[4], line 27 22 import meshio 23 ##########################################################################################################3 24 25 # Read the mesh ---> 27 mesh = dolfinx.io.gmshio.read_from_msh("fluent.msh", MPI.COMM_WORLD,gdim=2) 29 def create_mesh(mesh, cell_type, prune_z=False): 30 cells = mesh.get_cells_type(cell_type) File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:306, in read_from_msh(filename, comm, rank, gdim, partitioner) 304 gmsh.initialize() 305 gmsh.model.add("Mesh from file") --> 306 gmsh.merge(filename) 307 msh = model_to_mesh(gmsh.model, comm, rank, gdim=gdim, partitioner=partitioner) 308 gmsh.finalize() File /usr/local/lib/python3.10/dist-packages/gmsh.py:354, in merge(fileName) 350 lib.gmshMerge( 351 c_char_p(fileName.encode()), 352 byref(ierr)) 353 if ierr.value != 0: --> 354 raise Exception(logger.getLastError()) Exception: 'fluent.msh', line 1: syntax error (() ``` and with ```auto mesh, cell_markers, facet_markers = dolfinx.io.gmshio.model_to_mesh("fluent.msh", MPI.COMM_WORLD, 0 ,gdim=2) ``` ```auto AttributeError Traceback (most recent call last) Cell In[7], line 27 22 import meshio 23 ##########################################################################################################3 24 25 # Read the mesh ---> 27 mesh, cell_markers, facet_markers = dolfinx.io.gmshio.model_to_mesh("fluent.msh", MPI.COMM_WORLD, 0 ,gdim=2) 29 def create_mesh(mesh, cell_type, prune_z=False): 30 cells = mesh.get_cells_type(cell_type) File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:199, in model_to_mesh(model, comm, rank, gdim, partitioner) 173 """Given a Gmsh model, take all physical entities of the highest 174 topological dimension and create the corresponding DOLFINx mesh. 175 (...) 194 if found in Gmsh model. 195 """ 197 if comm.rank == rank: 198 # Get mesh geometry and mesh topology for each element --> 199 x = extract_geometry(model) 200 topologies = extract_topology_and_markers(model) 202 # Extract Gmsh cell id, dimension of cell and number of 203 # nodes to cell for each File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:153, in extract_geometry(model, name) 149 model.setCurrent(name) 151 # Get the unique tag and coordinates for nodes 152 # in mesh --> 153 indices, points, _ = model.mesh.getNodes() 154 points = points.reshape(-1, 3) 156 # Gmsh indices starts at 1. We therefore subtract one to use 157 # zero-based numbering AttributeError: 'str' object has no attribute 'mesh' ``` ---
**Author:** ![Karlosjusus](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@Karlosjusus](https://fenicsproject.discourse.group/u/Karlosjusus)\ **Post date:** [August 31, 2023, 6:35am UTC](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678/20 "2023-08-31T06:35:42Z")
I have tried a somewhat rough solution. I have downloaded a dolfinx image for docker ```auto docker run -ti dolfinx/dolfinx:stable ``` and copied the .msh file to that container. if I use this version of the code, ```auto import dolfinx from mpi4py import MPI import numpy as np from dolfinx import geometry from dolfinx import io import meshio ##########################################################################################################3 # Read the mesh def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) cell_data = mesh.get_cell_data( "gmsh:physical", cell_type) points = mesh.points #points = mesh.points[:,:2] if prune_z else mesh.points if prune_z: points = mesh.points[:,:2] out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={"name_to_read": [cell_data]}) #out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}) return out_mesh mesh = meshio.read("fluent.msh") meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) ``` I get ```auto Traceback (most recent call last): File "/root/Venuri_fenicsx2D_m1600.py", line 33, in meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) File "/root/Venuri_fenicsx2D_m1600.py", line 22, in create_mesh cell_data = mesh.get_cell_data( "gmsh:physical", cell_type) File "/usr/local/lib/python3.10/dist-packages/meshio/_mesh.py", line 250, in get_cell_data [d for c, d in zip(self.cells, self.cell_data[name]) if c.type == cell_type] KeyError: 'gmsh:physical' ``` with this version, using a previous suggestion. ```auto import dolfinx from mpi4py import MPI from petsc4py import PETSc import numpy as np from petsc4py.PETSc import ScalarType from dolfinx import geometry from dolfinx import io import meshio ##########################################################################################################3 # Read the mesh def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) #cell_data = mesh.get_cell_data( "gmsh:physical", cell_type) points = mesh.points #points = mesh.points[:,:2] if prune_z else mesh.points if prune_z: points = mesh.points[:,:2] #out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={"name_to_read": [cell_data]}) out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}) return out_mesh mesh = meshio.read("fluent.msh") meshio.write("venturi_1600.xdmf", create_mesh(mesh,"quad", True)) ``` seems to work… But, when I open the .xdmf file with paraview nothing appears, but in information it does appear in number of points and dimensions. If I try to define a function with that mesh and open it with paraview, it appears completely empty. [Next page](https://fenicsproject.discourse.group/t/problem-with-read-a-external-mesh/11678.md?page=2)