Python installation instructions for CLIDEsc¶

Note: you must be logged as an administrator (or root) on the clidesc server machine in order to install the Anaconda python distribution and configure clidesc to accept python as a climate services development language.

The Anaconda python distribution, download and installation¶

The Anaconda scientific python distribution is a completely free enterprise-ready Python distribution for large-scale data processing, predictive analytics, and scientific computing. It includes the python interpreter itself, the python standard library as well as a set of packages exposing data structures and methods for data manipulation and scientific computing and visualization. In particular it provides Numpy, Scipy, Pandas, Matplotlib (+ basemap). The full list of packages is available at:

http://docs.continuum.io/anaconda/pkgs.html

The Anaconda python distribution must be downloaded from:

http://continuum.io/downloads

For the correct version of your linux system, to know whether CLIDEsc is running on a 32 bits or 64 bits server, type

$ uname –a

in a terminal (the $ indicates the terminal prompt)

It will return either:

x86_64 (64 bits kernel)

or:

i686   (32 bits kernel)

Once copied over, make sure the anaconda installer is executable by going in the right directory (with cd) and entering (example for version 2.0.1 of Anaconda):

$ chmod +x Anaconda-2.0.1-Linux-x86.sh

or:

$ chmod +x Anaconda-2.0.1-Linux-x86_64.sh

then to launch the installer:

$ ./Anaconda.2.0.1-Linux-x86.sh

$ ./Anaconda.2.0.1-Linux-x86_64.sh

The installer will ask you a few questions, the most important is related to the installation directory: The recommended installation directory is /opt: i.e the python executable will be contained in /opt/anaconda/bin.

Once Anaconda is installed, you need to update conda (the python ‘package manager’ that comes with anaconda and allows the painless installation and update of third party modules) by entering

$ /opt/anaconda/bin/conda update conda

Then a good thing is to update the anaconda packages already installed

$ /opt/anaconda/bin/conda update anaconda

You also need to install pip to install packages from the Python Package Index.

$ conda install pip

Installation of additional libraries¶

A few other libraries need to be installed in order to make the most of the Python scientific stack:

basemap: to create static maps
vincent: to create dynamic visualisations in the browser
folium: to create dynamic maps in the browser
seaborn: to create sophisticated statistical visualisations

Basemap¶

Basemap is part of the Anaconda Python distribution and can be installed by:

$ /opt/anaconda/bin/conda install basemap

Vincent¶

vincent is to be installed using pip:

$ /opt/anaconda/bin/pip install vincent

Folium¶

folium, similarly install via pip:

$ /opt/anaconda/bin/pip install folium

Seaborn¶

seaborn is also to be installed via pip:

$ /opt/anaconda/bin/pip install seaborn

psycopg2: interface to the CLIDE database¶

The psycopg2 provides the interface to the Clide PostgreSQL database and needs to be installed separately from sources, as it is not part of the libraries available through the conda package manager.

One of the requirement is that pg_config should be in the system PATH, i.e. if you type:

$ pg_config --version

in a terminal it should return the version of PostgreSQL. If something goes wrong here, please refer to the psycopg installation documentation

psycopg2 can be installed in two ways:

The recommended way:

We make use of Dan Blanchard‘s channel for psycopg2

$ conda install -c https://conda.binstar.org/dan_blanchard psycopg2

Installing from sources:

If you want to install from sources, the psycopg2 archive (tar.gz) needs to be downloaded from The psycopg download page

Once downloaded, cd where you downloaded the psycopg2-2.5.2.tar.gz archive and enter:

$ tar –zxvf psycopg2-2.5.2.tar.gz

then:

$ cd psycop2-2.5.2

then install the module:

$ /opt/anaconda/bin/python setup.py build
$ /opt/anaconda/bin/python setup.py install