gmsh et matplotlib :

pour éviter les problèmes : matplotlib 3.0 et gmsh-sdk (4.2.2.post1)

meshio :

Afin d'éviter des problèmes de compatibilité avec h5, h5py installé avec la commande : HDF5_VERSION=1.10.0 pip install --no-binary=h5py h5py.

Puis installation de meshio : pip install meshio[all].

Remember that pip installs wheels by default. To perform a custom installation with pip, you should use: $ pip install --no-binary=h5py h5py

You can also configure h5py using environment variables. This is handy when installing via pip, as you don’t have direct access to setup.py:

$ HDF5_DIR=/path/to/hdf5 pip install --no-binary=h5py h5py
$ HDF5_VERSION=X.Y.Z pip install --no-binary=h5py h5py
$ CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/path/to/parallel-hdf5 pip install --no-binary=h5py h5py

h5py Docs

Pour déterminer la version de h5 installée : dpkg -s libhdf5-dev

Sinon, avec h5py (2.9.0) sans la version adapté à l'installation HDF5 :

.../python3.6/site-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)
[...]
  File ".../python3.6/site-packages/meshio/xdmf_io/main.py", line 467, in write
    XdmfWriter(*args, **kwargs)
  File ".../python3.6/site-packages/meshio/xdmf_io/main.py", line 277, in __init__
    self.h5_file = h5py.File(self.h5_filename, "w")
  File ".../python3.6/site-packages/h5py/_hl/files.py", line 391, in __init__
    fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, **kwds)
  File ".../python3.6/site-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)