GNOME2

Project Documentation

FAQ -- Troubleshoot

GNOME (General NOAA Operational Modeling Environment) is a modeling tool developed by the National Oceanic and Atmospheric Administration (NOAA), Office of Response and Restoration (ORR), Emergency Response Division.

It is designed to support oil and other hazardous material spills in the coastal environment.

###Disclaimer: This code is under active development. Thus...

• It should not be considered an officially endorsed NOAA product.
• Output produced by this code should not be considered endorsed by NOAA.

For a supported version, please see our main web site: http://response.restoration.noaa.gov/gnome

Installation in Development Mode

Since this is development work, it might be good to create and run this in a virtual environment. Virtual env and Virtual env wrapper eases management of virtual environments.

A virtualenv is not required to run PyGnome. Depending on your access level/permissions, you may require a virtualenv if you cannot install python packages in the global site-packages.

Linux (Tested in 32-bit, raring 13.04)

For Linux use appropriate package manager (apt-get on ubuntu) to download/install binary dependencies.

Binary Dependencies

1. Python Imaging Library (PIL) requires:
   $ sudo apt-get install libjpeg-dev libfreetype6-dev zlib1g-dev

   Use apt-get to build dependencies for PIL
   $ sudo apt-get install build-dep python-imaging

   This did not build symlinks to libraries for me in /usr/lib, so had to manually create them:

       $ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libfreetype.so /usr/lib/
       $ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libjpeg.so /usr/lib/
       $ sudo ln -s /usr/lib/`uname -i`-linux-gnu/libz.so /usr/lib/
   

2. netCDF4 python module requires NetCDF libraries: libhdf5-serial-dev, libnetcdf-dev

3. The following python packages, documented in PyGnome's requirements.txt, may need to be manually installed. Binaries for Numpy and Cython can be installed using apt-get. Current binaries for these are sufficiently new: (Numpy >=1.7.0) and (Cython >= 0.17.1).

   If you use virtualenv and apt-get to install these system site packages. Remember to use the --system-site-packages option when creating a new virtualenv so the system packages are available in the virtualenv.

   Alternatively, pip install should also work. The following builds the latest packages in your virtualenv once the above dependencies are met.

        $ pip install numpy
        $ pip install cython
        $ pip install netCDF4
        $ pip install PIL
   

The remaining dependencies are python packages and can be installed using pip install -r requirements.txt
See Build PyGnome section below.

Windows 7 (32-bit, using VS-2008 express edition)

Binary Dependencies

Download and install the newest Windows executable distribution of Python 2.7 (note: we are not quite ready for Python 3.0) Make sure the distribution is named consistently with the Python environment you desire. For example, binaries ending in win32-py2.7.exe are for Python 2.7. (32-bit)

A number of the packages that GNOME depends on have very complex and brittle build processes, and depend on third-party libraries that can be a challenge to build.

Fortunately, Chris Gohlke's website contains pre-compiled binary distributions for many of these packages.

(The full list of dependent packages and their minimum versions can be found in the file GNOME2/py_gnome/requirements.txt)

Here are the binary packages required:

1. setuptools
2. pip
   At this point, we should test that pip is installed correctly - on command line invoke the following pip commands.
   These should show usage information for 'pip', and then a list of installed packages.

       $ pip
       Usage:
         pip <command> [options]
   
       Commands:
         install                     Install packages.
         ...
   

       $ pip list
       pip (1.4.1)
       setuptools (1.1.4)
   

3. numpy-MKL
4. Cython
5. Install PIL instead of Pillow
6. 32-bit 1.0.6 version of netCDF4
7. [lxml] (http://www.lfd.uci.edu/~gohlke/pythonlibs/#lxml) - required for webgnome
8. [python-cjson] (http://www.lfd.uci.edu/~gohlke/pythonlibs/#python-cjson) - required for webgnome

The remaining dependencies are python packages and can be installed using the command: pip install -r requirements.txt

See Build PyGnome section below.

Windows 7 (64-bit, using VS-2008 express edition)

Building GNOME for 64 bit Windows is similar to the 32 bit Windows build, and has similar binary dependencies. There are however some extra steps you need to perform in order to build py_gnome.

If you are not on a 64 bit Windows system, you may skip forward to the section Build PyGnome

1. Download and install the windows SDK. Here is the link that we are using:
   Microsoft Windows SDK for Windows 7 and .NET Framework 3.5 SP1

2. Start the Windows SDK command window.
   From your Windows Desktop, select:
   Start->All Programs->Microsoft Windows SDK v7.0->CMD Shell

   The title of your command window should read:
   'Microsoft Windows 7 x64 DEBUG Build Environment'

3. Inside your x64 Build Console: run the command "\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvars64.bat"
   This sets up the environment variables needed for 64 bit compilation.

4. Stay inside this Build console for all further build actions.

Build PyGnome

1. Clone the GNOME2 repository.

       $ git clone https://github.com/NOAA-ORR-ERD/GNOME2.git  
   

2. pip install all of GNOME's python package dependencies.

       $ cd GNOME2/py_gnome
       $ pip install -r requirements.txt
   

3. build the py_gnome module in develop mode first as install mode may still need some testing/work.

       $ python setup.py develop  
   

4. If this successfully completes, then run unit_tests

       $ py.test --runslow tests/unit_tests/  
   

Once all of the py_gnome unit tests pass, PyGnome is now built and ready to be put to use. You can use the gnome module inside your python scripts to build a variety of modelling scenarios.

Accessing GNOME from the Web

Scripting is of course the most featureful way to access GNOME's capabilities. However we do have a few projects in development that will allow a user to create and run GNOME models from a web browser.

If you are curious, you can check out the following projects:

• WebGnomeAPI: A web server that implements the PyGnome interface
• WebGnomeClient: A Web application for setting up and running PyGnome models

(Fair Warning: These two projects are very new, and are not claimed to implement the full capabilities of PyGnome.)