h5mma Code
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===============================================================================
h5mma
===============================================================================
Version 0.1
Copyright 2011 Barry Wardell and Ian Hinder
The h5mma package provides improved support for reading HDF5 files in
Mathematica. It is significantly faster, more memory efficient and crash
resilient than the built-in HDF5 reading support.
===============================================================================
Getting the package
-------------------
Binary versions of the h5mma package can be downloaded from the project
webpage:
http://sourceforge.net/p/h5mma
The latest development version will always be available from the project git
repository:
git clone git://git.code.sf.net/p/h5mma/code h5mma
Requirements
------------
Mathematica: h5mma requires Mathematica version 6 or newer. It may be possible
to get it to work with older versions, but this is not supported.
HDF5: A version of the HDF5 library providing the version 1.8 API is required
to build from source. Binary versions of the package already include HDF5.
Installation
------------
Mac OSX 10.6 (Binary):
Double-click the dmg fie. Drag the h5mma folder to "Mathematica Applications".
This will install h5mma in /Library/Mathematica/Applications.
Mac OSX (MacPorts):
sudo port install hdf5-18
make && make install
Mac OSX (Fink):
sudo apt-get install hdf5-18 szip
make && make install
Ubuntu:
The version of HDF5 provided with Ubuntu does not currently work due to a bug
in the package (http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=537414). This
will be fixed in the future. Until then, install HDF5 manually by downloading
the source package from http://www.hdfgroup.org/ftp/HDF5/current/src/,
extracting the tarball and then in the extracted directory running:
./configure --prefix=/usr/local && make && sudo make install
Now, copy the 'make.defs.example' file to 'make.defs' and edit it so that it
has the following:
HDF5DIR = /usr/local
MLINKDIR = /usr/local/Wolfram/Mathematica/8.0/SystemFiles/Links/MathLink/DeveloperKit/Linux/CompilerAdditions
INSTALLDIR = ${HOME}/.Mathematica/Applications/h5mma
You may need to adjust the MLINKDIR for your system. In particular, if your
system is 64-bit, change 'Linux' to 'Linux-x86-64'.
Finally, build and install h5mma:
make && make install
Other:
Create the file 'make.defs' using the template provided in
'make.defs.example' (this is not necessary on
login-damiana.aei.mpg.de, since that machine is configured
automatically). Edit the paths in this file to point to the
appropriate locations on your machine:
HDF5DIR: This should be the directory containing lib/libhdf5*.
MLINKDIR: This should be the directory containing mcc and mprep.
INSTALLDIR: This is optional and can be used to override the directory where
h5mma will be installed. Sensible defaults are chosen on Linux
(${HOME}/.Mathematica/Applications/h5mma) and Mac OSX
(${HOME}/Library/Mathematica/Applications/h5mma) so this will not
normally need to be set.
Once these paths have been set, build h5mma:
make
and install it by copying/moving/symlinking the h5mma directory into
$HOME/.Mathematica/Applications so that Mathematica can find it.
Usage
-----
The package may then be loaded into Mathematica using the command:
<< h5mma`
The main command provided is ImportHDF5, which mimics the behavior of Import.
Examples
--------
For example usage, see the h5mma.nb Mathematica notebook in the doc directory.
Changelog
---------
23 Mar 2011: Binary version for Mac OSX released.
4 Mar 2011: Initial version (0.1) released.
Known problems
--------------
Known bugs are recorded in the project bug tracker:
http://sourceforge.net/p/h5mma/tickets/
License
-------
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 2.1 of the License, or (at your option)
any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along
with this library; if not, write to the Free Software Foundation, Inc.,
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
Binary releases include the HDF5 library. Copyright information for this
library can be found in the file COPYING.HDF5.
Authors
-------
Barry Wardell
Ian Hinder
Max Planck Institute for Gravitational Physics / Albert Einstein Institute
Am Muehlenberg 1
14476 Potsdam
Germany
http://numrel.aei.mpg.de