Skip to main content

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


    Popular posts from this blog

    Python: Multiprocessing: passing multiple arguments to a function

    Write a wrapper function to unpack the arguments before calling the real function. Lambda won't work, for some strange un-Pythonic reason.

    import multiprocessing as mp def myfun(a,b): print a + b def mf_wrap(args): return myfun(*args) p = mp.Pool(4) fl = [(a,b) for a in range(3) for b in range(2)] #mf_wrap = lambda args: myfun(*args) -> this sucker, though more pythonic and compact, won't work, fl)

    Flowing text in inkscape (Poster making)

    You can flow text into arbitrary shapes in inkscape. (From a hint here).

    You simply create a text box, type your text into it, create a frame with some drawing tool, select both the text box and the frame (click and shift) and then go to text->flow into frame.


    The omnipresent anonymous asked:
    Trying to enter sentence so that text forms the number three...any ideas?
    The solution:
    Type '3' using the text toolConvert to path using object->pathSize as necessaryRemove fillUngroupType in actual text in new text boxSelect the text and the '3' pathFlow the text