Meshio-convert to `xdmf` from Abaqus raises version error for `h5py`

mesh
1

I am not sure if this concerns dolfin per se, but I am having trouble converting a quadrilateral mesh generated in Abaqus using meshio. I pip-installed meshio[all] but it raises a version error when writing to a xdmf file.
meshio version: 3.1.1

  • MWE:
import meshio 
mFile = meshio.read('trialMesh.inp')
pts, clls = mFile.points, mFile.cells
msh_meshio = meshio.Mesh(pts, clls)
meshio.write('trialMeshio_convert.xdmf',msh_meshio)

/usr/local/lib/python3.6/dist-packages/h5py/__init__.py:75: UserWarning: h5py is running against HDF5 1.10.0 when it was built against 1.10.4, this may cause problems
  '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple)
Traceback (most recent call last):
  File "test_quads_convert.py", line 49, in <module>
    meshio.write('trialMeshio_convert.xdmf',msh_meshio)
  File "/usr/local/lib/python3.6/dist-packages/meshio/_helpers.py", line 240, in write
    return interface.write(filename, mesh, *args, **_kwargs)
  File "/usr/local/lib/python3.6/dist-packages/meshio/_xdmf/main.py", line 465, in write
    XdmfWriter(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/meshio/_xdmf/main.py", line 275, in __init__
    self.h5_file = h5py.File(self.h5_filename, "w")
  File "/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py", line 391, in __init__
    fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, **kwds)
  File "/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py", line 108, in make_fapl
    plist.set_libver_bounds(low, high)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5p.pyx", line 1140, in h5py.h5p.PropFAID.set_libver_bounds
ValueError: Invalid high library version bound (invalid high library version bound)
2

Hi,

I was having a similar problem which I managed to resolve using the suggestions provided here: Gmsh 4.4.1 in FEniCS? Meshio
Hope it helps

Best Regards,
Kart

1 Like
3

@Kart thanks for the reference. I installed meshio without all it’s dependencies and separately installed lxml and h5py using the local HDF5 as suggested in the link above. Thanks for the pointer.

4

Do the solution still work for you people? It doesn’t work for me, I get a gigantic error message when builing h5py as posted in the link in the solution of this question. Any other remedy?

5

What is the version of meshio that you are using to generate a xdmf file? Uninstalling meshio and it’s dependencies and reinstalling it back (with lxml and h5py) should work. Can you post a MWE?

6

I had the same problem in the docker containers provided in FEnics.I used a workaround to solve this.I hope that can help in fast resolution of this.

7

@raboynics I was only able to replicate your problem when I tried installing everything on a new computer. Here is how I fixed it:

  1. First uninstall meshio and h5py using pip3 uninstall h5py and pip3 uninstall meshio
  2. Next pip3 install cython
  3. Then pip3 install --no-binary=h5py h5py --user The massive error is because of cython
  4. pip3 install meshio --user
    This should work
2 Likes
8

I too have struggled a lot with the h5py/hdf5 version mismatch problem. Eventually this helped me:
pip3 uninstall h5py
pip3 install h5py==2.10.0
I looked at the available versions of h5py at: h5py · PyPI

1 Like