Installing Sedona

Getting the Code

The code is available for download on github here. Or you can clone from the command line using:

git clone git@github.com:dnkasen/sedona6.git

Installing Dependencies

[sedona] requires a C++ compiler for instalation. In addition. the following dependencies must be installed:

  • HDF5 (file formating)
  • GSL (gnu scientific library)
  • lua (scripting language used for parameter files)

[sedona] is parallelized using a hybrid of MPI and openMP. To run in parallel, you must also have installed an MPI and/or an openMP distribution.

These packages may already been installed on clusters and computing systems. If not, they can be conveniently installed using a package manager – see below for details.

If your dependencies are not installed in a standard location (e.g., usr/local/) then you will need to set the GSL_DIR, HDF5_DIR, and LUA_DIR environment variables to specify the path to the instalations. In the bash shell, for example, add to your bash.profile:

export  GSL_DIR=/base/path/of/gsl/
export HDF5_DIR=/base/path/of/hdf5/
export  LUA_DIR=/base/path/of/lua/

where the /base/path/of/xxx should be replaced with the full base path where the package is installed.

A python distribution is not required to run [sedona] itself, however it can be useful for working with input and output files (in particular the h5py package allows for easy creation and reading of hdf5 files). The [sedona] distribution comes with a python package called sedonalib that contains useful tools for generating, reading, and plotting files. The anaconda python distribution makes it relatively easy to install the needed python packages.

Installing Dependencies on a Mac

On a mac, the homebrew package manager provides a convenient way to install dependences. Type brew help to check if homebrew it is already installed on your machine. If the command is not found, it can be installed by issuing the command given on the homebrew installation page

Once installed, the necessary [sedona] dependencies can be installed with the following commands:

brew install lua
brew install gsl
brew install hdf5

If you wish to run mpi parallel jobs, you should also install mpich:

brew install mpich

If you lack a C++ compiler, you can install the gcc compiler through brew install gcc. Alternatively, mac Mac provides a C++ compiler through its Xcode tools.

Installing Dependencies on a Linux System

On Debian, Ubunto and some other linux systems, the apt package manager provides a convenient way to install dependences. If apt is installed on your machine, you can update it using:

sudo apt-get update

Root privileges are required. You can then install the necessary dependencies using:

sudo apt-get install gsl-bin
sudo apt-get -s install lua5.2
sudo apt-get install libhdf5-dev

If you wish to run mpi and openMP parallel jobs, you should also install:

sudo apt-get install  mpich
sudo apt install libomp-dev

Installing Dependencies on a Cluster

Many clusters and supercomputer centers will have some of the dependencies already installed. Use the module load

Compiling the Code

To compile [sedona], first change to the src/ directory in the [sedona] distribution, and type:

chmod +x ./install.sh

to ensure that the compile script is executable. [sedona] comes with a set of makefiles to facilitate compilation on different machines. To see a list of machines that have makefiles, type:

./install.sh help

If you see a machine name appropriate to your system, you can attempt compiling the code by typing:

./install.sh <MACHINE>

where <MACHINE> is the name of the machine.

If you don’t see a relevant Makefile for your machine, or if compilation fails, you should modify a Makefile directly. Open the makefiles/Makefile.general file and make sure that the CXX variable is set to your C++ compiler. You can also change the CXX_FLAGS variables to set the compiler flags of your choosing. You can also check that all dependent packages are installed and that the GSL_DIR, HDF5_DIR and LUA_DIR environment variables are set, as described in Installing Dependencies

Once compilation is successful, the executable file sedona6.ex will appear in the src/ directory. Copy this to the directory where you would like to run the code.