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.. _h5pybackend:
H5PY-backend
-------------
The H5PY-backend relies on an MPI compatible build of :code:`HDF5`, which should be linked to the same MPI
implementation as DOLFINx relies on.
The DOLFINx docker images (:code:`ghcr.io/fenics/dolfinx/dolfinx:stable`) comes with an already configures MPI compatible HDF5 installation, and `h5py` can in
turn be installed with
.. code-block:: bash
HDF5_MPI="ON" HDF5_DIR="/usr/local" python3 -m pip install --no-binary=h5py h5py --no-build-isolation
If you are using `apt` on Ubuntu, this can for instance be achieved with the following commands (here using Docker).
Note that this code block does not install DOLFINx, it just illustrates how to get the correct `h5py`.
.. code-block:: dockerfile
FROM ubuntu:24.04 AS base
RUN apt-get update && apt-get install -y python3-dev python3-pip python3-venv libhdf5-mpi-dev libopenmpi-dev
ENV VIRTUAL_ENV=/test-env
ENV PATH=/test-env/bin:$PATH
RUN python3 -m venv ${VIRTUAL_ENV}
ENV HDF5_MPI="ON"
ENV HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi/
ENV C_PATH=/usr/lib/x86_64-linux-gnu/openmpi/include/:${C_PATH}
RUN python3 -m pip install setuptools cython numpy pkgconfig mpi4py
RUN CC=mpicc python3 -m pip install --no-binary=h5py h5py --no-build-isolation
.. automodule:: io4dolfinx.backends.h5py.backend
:members:
:exclude-members: read_point_data
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