Installation

For Python beginners

It can be a pain to install NumPy, HDF5, h5py, Cython and other dependencies. If you’re just starting out, by far the easiest approach is to install h5py via your package manager (apt-get or similar), or by using one of the major science-oriented Python distributions:

Installing on Windows

You will need:

  • Python 2.6 - 3.3
  • NumPy 1.6 or newer

Download the installer from http://www.h5py.org and run it. HDF5 is included.

Installing on Linux and Mac OS X

On Mac OS X, homebrew is a reliable way of getting Python, NumPy, HDF5 and other dependencies set up. It is also safe to use h5py with the OS X system Python.

You will need:

  • HDF5 1.8.4 or newer, shared library version with development headers (libhdf5-dev or similar)
  • Python 2.6 - 3.3 with development headers (python-dev or similar)
  • NumPy 1.6 or newer
  • Optionally Cython, if you want to access features introduced after HDF5 1.8.4, or Parallel HDF5.

With pip or easy_install:

$ pip install h5py

Manually, from the h5py tarball:

$ tar xzf h5py-X.Y.Z.tar.gz
$ cd h5py
$ python setup.py install

Running the test suite

With the tarball version of h5py:

$ python setup.py build
$ python setup.py test

After installing h5py:

>>> import h5py
>>> h5py.run_tests()

Custom installation

Build options can also be passed to setup.py directly. Keep in mind these options are “sticky”. They hang around between e.g. build and test invocations of h5py.

Specifying the path to HDF5:

$ python setup.py install --hdf5=/path/to/hdf5
$ python setup.py install --hdf5=default        # reset to compiler path

Manually specifying the HDF5 version (disables auto-detection):

$ python setup.py install --hdf5-version=1.8.11
$ python setup.py install --hdf5-version=default   # re-enable autodetection

You can also configure h5py using environment variables. The variable HDF5_DIR may contain the path to your installation of HDF5. The directory you provide should contain a subdirectory called lib:

$ export HDF5_DIR=/path/to/hdf5
$ pip install h5py

The variable HDF5_VERSION manually tells h5py to build against a specific version of HDF5, and disables the version auto-detection in setup.py:

$ export HDF5_VERSION=1.8.11
$ pip install h5py

Building against Parallel HDF5

If you just want to build with mpicc, and don’t care about using Parallel HDF5 features in h5py itself:

$ export CC=mpicc
$ python setup.py install

If you want access to the full Parallel HDF5 feature set in h5py (Parallel HDF5), you will have to build in MPI mode. Right now this must be done with command-line options from the h5py tarball. You will need:

  • Cython
  • A shared-library build of Parallel HDF5 (i.e. built with ./configure --enable-shared --enable-parallel).

To build in MPI mode (sticky option):

$ export CC=mpicc
$ python setup.py build --mpi

Option --mpi=no will reset to the default (serial) build setting.

See also Parallel HDF5.

Help! It didn’t work!

You may wish to check the FAQ first for common installation problems.

Then, feel free to ask the discussion group at Google Groups. There’s only one discussion group for h5py, so you’re likely to get help directly from the maintainers.