# Meshio-convert to \`xdmf\` from Abaqus raises version error for \`h5py\` **URL:** \ **Category:** mesh\ **Created:** [September 5, 2019, 5:12pm UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480 "2019-09-05T17:12:16Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![bhaveshshrimali](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bhaveshshrimali/32/124_2.png) [@bhaveshshrimali](https://fenicsproject.discourse.group/u/bhaveshshrimali)\ **Post date:** [September 5, 2019, 5:12pm UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/1 "2019-09-05T17:12:17Z")
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: ```auto 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) ``` ```auto /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 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) ``` ---
**Author:** ![Kart](https://avatars.discourse-cdn.com/v4/letter/k/87869e/32.png) [@Kart](https://fenicsproject.discourse.group/u/Kart)\ **Post date:** [September 6, 2019, 8:45am UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/2 "2019-09-06T08:45:26Z")
Hi, I was having a similar problem which I managed to resolve using the suggestions provided here: [Gmsh 4.4.1 in FEniCS? Meshio](https://fenicsproject.discourse.group/t/gmsh-4-4-1-in-fenics-meshio/1415) Hope it helps Best Regards, Kart ---
**Author:** ![bhaveshshrimali](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bhaveshshrimali/32/124_2.png) [@bhaveshshrimali](https://fenicsproject.discourse.group/u/bhaveshshrimali)\ **Post date:** [September 6, 2019, 7:21pm UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/3 "2019-09-06T19:21:21Z")
@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. ---
**Author:** ![raboynics](https://avatars.discourse-cdn.com/v4/letter/r/4bbf92/32.png) [@raboynics](https://fenicsproject.discourse.group/u/raboynics)\ **Post date:** [April 28, 2020, 9:43am UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/4 "2020-04-28T09:43:42Z")
> [@bhaveshshrimali](#): > > UserWarning: h5py is running against HDF5 1.10.0 when it was built against 1.10.4, this may cause problems 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? ---
**Author:** ![bhaveshshrimali](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bhaveshshrimali/32/124_2.png) [@bhaveshshrimali](https://fenicsproject.discourse.group/u/bhaveshshrimali)\ **Post date:** [April 28, 2020, 5:04pm UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/5 "2020-04-28T17:04:11Z")
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? ---
**Author:** ![Sambeet\_Panigrahi](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/sambeet_panigrahi/32/1259_2.png) [@Sambeet\_Panigrahi](https://fenicsproject.discourse.group/u/Sambeet_Panigrahi)\ **Post date:** [June 9, 2020, 5:27am UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/6 "2020-06-09T05:27:02Z")
I had the same problem in the docker containers provided in FEnics.I used a [workaround](https://fenicsproject.discourse.group/t/gmsh-4-4-1-in-fenics-meshio/1415/15) to solve this.I hope that can help in fast resolution of this. ---
**Author:** ![Kart](https://avatars.discourse-cdn.com/v4/letter/k/87869e/32.png) [@Kart](https://fenicsproject.discourse.group/u/Kart)\ **Post date:** [September 14, 2020, 10:42am UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/7 "2020-09-14T10:42:23Z")
@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 ---
**Author:** ![andraspap](https://avatars.discourse-cdn.com/v4/letter/a/b487fb/32.png) [@andraspap](https://fenicsproject.discourse.group/u/andraspap)\ **Post date:** [February 2, 2022, 3:09pm UTC](https://fenicsproject.discourse.group/t/meshio-convert-to-xdmf-from-abaqus-raises-version-error-for-h5py/1480/8 "2022-02-02T15:09:56Z")
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](https://pypi.org/project/h5py/#history)