Crash with h5py is running against HDF5 1.12.2 when it was built against 1.10.7

dolfinx
1

I’m trying to run the tutorial here

https://jorgensd.github.io/dolfinx-tutorial/chapter3/subdomains.html

on a modified docker – dolfinx/lab:latest

with the amendments

  RUN apt update
  RUN apt install -y python3-sympy
  RUN apt install h5utils libhdf5-mpich-dev -y
  ENV HDF5_MPI="ON"
  ENV CC=mpicc
  ENV HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
  RUN pip3 uninstall h5py meshio -y
  RUN pip3 install --force-reinstall --no-cache-dir --no-binary=h5py h5py meshio[all]

if I run this

import meshio
from dolfinx.fem import (Constant, dirichletbc, Function, FunctionSpace, assemble_scalar,
                     form, locate_dofs_geometrical, locate_dofs_topological)
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
from mpi4py import MPI
proc = MPI.COMM_WORLD.rank 
if proc == 0:
    # Read in mesh
    msh = meshio.read("mesh.msh")

    # Create and save one file for the mesh, and one file for the facets 
    triangle_mesh = create_mesh(msh, "triangle", prune_z=True)
    line_mesh = create_mesh(msh, "line", prune_z=True)
    meshio.write("mesh.xdmf", triangle_mesh)
    meshio.write("mt.xdmf", line_mesh)

python crashes with
WARNING:py.warnings:/usr/local/lib/python3.10/dist-packages/h5py/init.py:36: UserWarning: h5py is running against HDF5 1.12.2 when it was built against 1.10.7, this may cause problems
_warn(("h5py is running against HDF5 {0} when it was built against {1}, "

If I comment out the dolfinx.fem import it runs fine. If I run it twice (in jupyter) first with import commented out and then with the import it also runs fine.

Regards
Torben

2

Why are you install libhdf5 with apt? The docker image is already built with an HDF5 library.
Consider the following docker file: https://github.com/jorgensd/dolfinx-tutorial/blob/dokken/jupyterbook/docker/Dockerfile#L1-L10, which install the requirements in: https://github.com/jorgensd/dolfinx-tutorial/blob/dokken/jupyterbook/docker/requirements.txt

You could also use:

docker pull ghcr.io/jorgensd/dolfinx-tutorial:v0.5.1

which gives you an image compatible with the tutorial

3

Yes, thanks

Your dockerfile works with dolfinx/lab:v0.5.1 but with dolfinx/lab:latest

 meshio.write("mesh.xdmf", triangle_mesh)

fails with

ValueError: Compression filter "gzip" is unavailable

Google for solutions indicate that hdf5 would be built without gzip support, hence the reinstall with

RUN apt install h5utils libhdf5-mpich-dev -y

Best Regards
Torben

4

dolfinx/lab:latest is no longer a maintained image.
You should use dolfinx/lab:nightly as I fixed the gzip issue in: Enable zlib for hdf5 in docker images by jorgensd · Pull Request #2311 · FEniCS/dolfinx · GitHub

5

Thanks

I’ll just stay with 0.5.1 for now, or is “stable” a viable option?

Regards
Torben

6

I think stable will be updated whenever there is a new release. It should currently be equivalent to v0.5.1