Underworld

a long term geodynamics simulation platform

HDF5 Download and Installation

Why do I need HDF5?

HDF5 is better than acsii format because of it's portability, compressibility and simple usage. Thus HDF5 is the default library used for checkpointing meshes and particles.

When compiling Underworld using SCons, for versions of Underworld checked out or downloaded from 17 Feb 2009, if SCons can successfully find a version of HDF5, checkpointing will be in HDF5 format; if SCons can't find HDF5, Underworld will use the old acsii/binary formats.

If you are compiling your own copy of Underworld on a computer cluster, you may be able to load HDF5 as a module. For example, on the VPAC cluster "tango", type:

module load hdf5

Downloading and Installing HDF5 using MacPorts (mac only)

Note: If you intend to use Macports packages to install the dependencies required by Underworld and gLucifer, we recommend you use Macports for all dependencies (except PETSc). This will avoid problems of confusion between Macports-installed and default system libraries such as X11, which can cause run-time issues.

Type the following (from any directory, assuming you have MacPorts in your path):

port install hdf5

Downloading and Installing HDF5 Manually on all Flavours of Unix including Macs

These instructions apply to any Linux, Unix operating system, including macs..

The HDF5 source (serial version) can be downloaded from here (look for a file like hdf5-1.8.8.tar.gz). There are also some specific binaries available on the same page. Note for mac users: Underworld uses shared libraries on the mac, so download the source rather than a static mac binary. Compiling the source code uses shared libraries by default.

Untar and unzip the downloaded file (if you are on a mac, this may be done for you):

tar zxvf hdf5-1.8.8.tar.gz

Then navigate into the unzipped directory and type the following, where /usr/local/HDF5 is the location in which you would like to install HDF5 (root or administrator access may be required; on macs type "sudo make install" in place of the "make install" step):

./configure --prefix=/usr/local/hdf5

make

make check

make install

make check-install

Alternatively, you may be able to use a package manager to download and install HDF5. For example, in ubuntu8.10 get "libhdf5-serial-dev"

For hdf5 file utils, go here. (if you don't know what this means, then don't worry about it).

Setting up Environment Variables Manually

Add the following environment variable to your ~/.bashrc (if you are using bash) or ~/.tcshrc (if you are using tcsh), where /usr/local is the directory in which python is located:

bash:

export HDF5_DIR=/usr/local/hdf5

tcsh:

setenv HDF5_DIR /usr/local/hdf5

-- Wendy Mason - 01 November 2010
-- Patrick Sunter - 21 October 2010
-- Wendy Sharples - 21 October 2010