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Installing HDF5

HDF5 is a data file format specification with some opensource libraries. Matlab version 7.3 and above are supposed to store data in this format. You can load these files into Python using the h5py library.

  1. Due to an incompatibility with HDF5 1.8.5 h5py tests (and operation) will fail. Using 1.8.4 or earlier should resolve the issue. (issue 124)
  2. When installing h5py  change to super user account (su) rather than sudo because you need some environment variables to be set during the installation
Install HDF5 on your machine

Following instructions from

  1. grab the bz2 file
  3. bunzip2 hdf5-1.8.4-patch1.tar.bz2
  4. tar -xvf hdf5-1.8.4-patch1
  5. cd hdf5-1.8.4-patch1
  6. ./configure --prefix=/usr/local/hdf5
  7. make
  8. make check
  9. sudo make install
  10. make check-install
Install h5py

  1. su
  2. export HDF5_DIR=/usr/local/hdf5/
  3. export HDF5_API=18
  4. easy_install h5py
How to recover if you did use HDF 1.8.5:
  1. Download, compile and install the correct version of HDF (as above)
  2. Get rid of the h5py egg compiled against this by doing:
    sudo easy_install -m h5py to get rid of paths etc.
    rm -r /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/h5py-1.3.0-py2.6-macosx-10.3-fat.egg (or where ever your egg is, to get rid of the compiled version)
  3. reinstall
  4. run tests to be sure


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