Difference between revisions of "Welcome to Geosciences Modeling Wiki"

Revision as of 10:05, 4 October 2014

Welcome to the Geosciences Modeling and Data Science Wiki.

Purpose:

Provide information on software tools available for data analysis and scientific program for projects within the field of Geosciences in general and to provide users a cenral resource for keeping notes on UIO specific aspects of running various software routines. Ideally, this site will become overtime a 'go to' location where incoming students who will be working with modeling and heavy data analysis on servers can find tips for getting started.

Make a contribution

Feel free to tackle something from the list of NeededUpdates. Essentially, the usefullness of this site is up to you. We are building this up as we go, but don't be shy. Your contributions are valuable. Please, if you are working on something and stumble... it's likely someone else may have the same problem eventually. Make a note here of your solution. 

Tools and Topics

Tools for WorkingOnServers at UiO.

Processing large datasets and running models for geosciences will likely require that you work on the command line of a server and not on your laptop. It's important to learn how to do this efficiently so that you don't feel that it restricts where you can work from. In fact, it's generally the opposite. Once you learn how to use a server well, you will find it much easier to work from anywhere! All you need is an internet connection.

In this section, we cover some tips for connecting via ssh, setting up your own laptop so it is 'as if' you are working locally, and other nice tricks for staying productive in a server-based environment.

Python

A starting point for all-things Python. Provides information on best practices, different packages that are frequently used, and other information to make using Python at NILU easier.

General Fortran Tips

Some general usage tips for coding in FORTRAN.

GNU and intel compilers are both available on our servers. We have a very limited number of licenses for intel compilers so we suggest you to use GNU compilers for all your development.

There is a default GNU compiler but it may be a quite old version. If you wish to use a newer version:

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;">          module avail gcc
</span></span>

it returns the list of available versions.

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;">          module load gcc/4.9.0
</span></span>

It loads GNU compilers 4.9.0 (both Fortran, C and C++ compilers).

Intel compilers are available by default on our UIO servers but on abel, you would need to load it:

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;">          module load intel</span></span>

Fortran materials

• Gunnar Wollan has compiled a set of documents at http://folk.uio.no/gunnarw/GEO4060/ and you can also find some of his documents at http://www.uio.no/studier/emner/matnat/geofag/GEF4510/h12/index.html

• An interesting free tutorial at http://www.fortrantutorial.com/ You can skip the installation of silverfrost compilers if you already have a Fortran compiler installed on your machine or if you are using sverdrup.uio.no

• The National Computational Infrastructure in Australia has class notes online for a Basic Fortran course (http://nf.nci.org.au/training/FortranBasic/) and an Advanced Fortran course (http://nf.nci.org.au/training/FortranAdvanced/).

• Fortran Wiki http://fortranwiki.org/fortran/show/HomePage

Getting data from ECMWF

Decriptions of how to get data in various ways from the ECMWF server.

FLEXPART Model

Information and resources for running and setting up FLEXPART. Mostly geared toward the ATMOS users.

FLEXINVERT

Bayesian inversion code for use with FLEXPART

WRF and WRF-CHEM Models

Information and resources for running and setting up WRF and WRF-CHEM.

OpenIFS ECMWF Model

Information and resources for running and setting up OpenIFS (ECMWF forecast model).

Data formats (netCDF, HDF4, HDF5, GRIB-1, GRIB-2, BUFR, etc.)

Descriptions on how to manipulate and visualize data in these different formats.

Matlab (Not open source, but extensively used)

Contributions from MATLAB users

Editing pages on the Geo-IT MediaWiki

A good starting place for markup reference can be found here: http://meta.wikimedia.org/wiki/Help:Wikitext_examples

Another point is that this wiki is using Subpages, so in places you'll see reference to a <subpages .> tag. This just means that the list of subpages will be dynamically generated in that location.

Editing Source Code

Note that for the purposes of documenting source code there are two important features:

1. use the <code> ... </code> to show some simple code snippets: def foo(): return
2. The syntax highlighting extension has been installed, so you can wrap source code examples in <syntaxhighlight> tags. This is helpful for documenting a code example and supports many languages. Usage is simple. Here's an example of how to display some 'Hello World' source code examples:

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;"><syntaxhighlight lang='python'>
# Hello World in Python
print("Hello World")
</syntaxhighlight>
<syntaxhighlight lang='csharp'>
//Hello World in C#
class HelloWorld
{
    static void Main()
    {
        System.Console.WriteLine("Hello, World!");
    }
}

</syntaxhighlight>


<syntaxhighlight lang='cpp'>
// Hello World in C++ (pre-ISO)

#include <iostream.h>

main()
{
    cout << "Hello World!" << endl;
    return 0;
}



</syntaxhighlight>

</span></span>

The above code block results in:

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;"><span class="co1"># Hello World in Python</span>
<span class="kw1">print</span><span class="br0">(</span><span class="st0">"Hello World"</span><span class="br0">)</span></span></span>

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;"><span class="co1">//Hello World in C#</span>
</span></span>

   static void Main()
{
System.Console.WriteLine("Hello, World!");
}

<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;"><span class="co1">// Hello World in C++ (pre-ISO)</span>
</span></span>

   cout << "Hello World!" << endl;
return 0;

Other Resources

Consult the User's Guide for information on using the wiki software. See Also:

• Configuration settings list
• MediaWiki FAQ
• MediaWiki release mailing list

/Reference