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Dynamic compilation of Zonation

These instruction describe the dynamic compilation of Zonation 3.1.11 on Ubuntu 13.04 (Raring Ringtail). Instructions have not been tested on other distributions/versions. You can copy the commands from this file or run the individual steps with the accompanied bash scripts.

You execute all steps by running:

./00-run-all

1. Install Zonation dependencies

sudo apt-get update
sudo apt-get install cmake libqt4-dev libfftw3-dev libqwt-dev libboost-all-dev libgdal-dev

Alternatively, run:

./01-deps-zig3

2. Get Zonation sources

Create a suitable download directory, fetch Zonation source code (version 3.1.11) from CBIG server, and extract the sources to the directory created:

mkdir zonation3
cd zonation3
wget http://cbig.it.helsinki.fi/files/zonation/zig3-src/zig3-3.1.11-src.tar.bz2
tar -jxvf zig3-3.1.11-src.tar.bz2

Alternatively, run:

./02-wget-zig3

3. Build Zonation

To build Zonation library (zig3lib) and Zonation CLI utility (zig3), do the following:

mkdir zonation3/build
cd zonation3/build
cmake ../src-3
make

If you have several cores available for compilation, you can pass switch -j X to make where X is the number of designated cores (e.g. make -j 4).

Alternatively, run:

./03-build-zig3

4. Make Zonation available system wide (optional)

In order to call zig3 anywhere on the system (instead of just the build-location), create a symbolic link:

sudo ln -s FULL_PATH/zonation3/build/zig3/zig3 /usr/local/bin/zig3

Replace FULL_PATH with the full path to the directory containing directory zonation3 created in step 2.

Alternatively, run:

./04-postinstall-zig3

Testing Zonation using the tutorial data

This stage is completely optional.

You can test that Zonation works by running some of the runs used in the Hunter Valley tutorial. This is not a thorough test, but it will at least give you an overview on whether Zonationis working as intended. Tutorial data and setup files are fetched using git and run using zrunner.

5. Install zrunner dependencies

First, install git:

sudo apt-get -y install git

Then, install Python packages needed by zrunner:

sudo apt-get -y install python-yaml python-pip

Alternatively, run:

./05-deps-zrunner

6. Install zrunner

zrunner is installed directly from GitHub using pip.

sudo pip install https://github.com/cbig/zrunner/archive/master.zip

Alternatively, run:

./06-install-zrunner

7. Clone Zonation tutorial using git

With git installed, clone the tutorial repository with the following command:

git clone https://github.com/cbig/zonation-tutorial.git

Alternatively, run:

./07-git-tutorial

8. Run the tutorial runs

You can run 5 basic tutorial variants defined in the configuration file tutorial_runs.yaml in this repository (note that similar file is found from within the tutorial repository as well) by using zrunner:

zrunner -l tutorial_runs.yaml

zrunner will produce an output file results_XXX.yaml in the same folder. XXX will correspond to information about your system. If everything went fine, you should see no critical errors on the screen and the yaml-file should report execution times for successful runs.