Tuesday, July 27, 2010

Monday, July 26, 2010

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.

IMPORTANT:
  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 http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL

  1. grab the bz2 file
  2. ftp://ftp.hdfgroup.org/HDF5/prev-releases/hdf5-1.8.4-patch1/src/hdf5-1.8.4-patch1.tar.bz2
  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

    Wednesday, July 21, 2010

    Mac Word: Save As Screen Too Big

    Problem: The "save as" dialog box is too big for your screen and some of the options (such as new folder) and the resize corner are off screen, making things very, very, annoying.

    Solution: Hit the 'shrink' button (up arrow) to see the abbreviated version of the "save as" menu. Then press that button again (now the 'expand' button). The dialog box now will fit the screen and you drag the corner to resize the dialog to a sensible size, which it will store.

    From here.

    disown and nohup

    Problem: Need to make a running *nix process nohup
    Solution:
    CTRL+Z to suspend
    bg to background
    disown to make it effectively nohup

    From here and here and here