Difference between revisions of "Welcome to Geosciences Modeling Wiki"

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<span style="font-family:arial,helvetica,sans-serif">Welcome to the Geosciences Modeling and Data Science Wiki.</span>
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This Wiki is meant to provide a resource for those at UiO interested in working with computer modeling and data analysis in Earth Sciences.
  
== <span style="font-family:arial,helvetica,sans-serif">Purpose:</span> ==
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Content herein is generally specific to UiO, as otherwise it is recommended to make posts to [http://stackexchange.com/sites Stack Exchange] and the sites therein.
  
 +
This wiki uses 'category' tags, and below are some of the categories available. Note that in some cases, the content does not yet exist, in which case you are encouraged to edit and add information, or [https://wiki.uio.no/mn/geo/geoit/index.php/Maintainers contact one of the site maintainers] to request further information.
 +
 +
=== <span style="font-family:arial,helvetica,sans-serif">Purpose:</span> ===
 
<span style="font-family:arial,helvetica,sans-serif">Provide information on software tools available for data analysis and scientific program for projects within the field of Geosciences&nbsp;''in general''&nbsp;and to provide users a cenral resource for keeping notes on '''UIO specific''' aspects of running various software routines.&nbsp;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.</span>
 
<span style="font-family:arial,helvetica,sans-serif">Provide information on software tools available for data analysis and scientific program for projects within the field of Geosciences&nbsp;''in general''&nbsp;and to provide users a cenral resource for keeping notes on '''UIO specific''' aspects of running various software routines.&nbsp;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.</span>
  
==
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Enjoy!
  
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Editing Editing pages]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Editing Editing pages]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:How_to How to]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:How_to How to]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Style_guide Style guide]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Style_guide Style guide]
 
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data Data]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data Data]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Abbreviations_and_terminology Abbreviations_and_terminology]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data_formats Formats]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data_formats Formats]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Measurements Measurements]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Measurements Measurements]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Ordering Ordering]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Ordering Ordering]
 +
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Satellites Satellite imagery]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Re_analysis Re-analysis]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Re_analysis Re-analysis]
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Bias_correction Bias correction]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:GIS GIS]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Tools Tools]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Tools Tools]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/WorkingOnServers WorkingOnServers]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Command_line Command_line]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Software Software]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Software Software]
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:R R]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Code_Coffee Code Coffee]<br />
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:R R]<br />
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Fortran Fortran]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Fortran Fortran]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Micmac Micmac]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Micmac Micmac]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Matlab Matlab]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Matlab Matlab]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Excel Excel]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Excel Excel]
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:UioNetwork UiO network]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:UioNetwork Computing Facilities<br />]
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Svedrup Svedrup]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Login How to login?]<br />
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Wessel Wessel]<br />
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Sverdrup Sverdrup]<br />
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Moulin Moulin]
 
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Moulin Moulin]
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Abel Abel]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:geo-hiperf geo-hiperf]
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Nortur Nortur]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Abel Abel HPC]<br />
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Norstor Norstor]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Nortur Notur HPC]<br />
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:::[[Set-up your own server (IaaS)]]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Norstore Data storage (lagrinshotell, Norstore & storage for researchers)]<br />
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Models Models]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Models Models]
:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:ECMWF ECMWF]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:WRF WRF, WRF-CHEM and WRF-Hydro]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:OpenIFS OpenIFS]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:FLEXPART Flexpart]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:MITgcm MITgcm]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Cesm cesm]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Noresm noresm]<br />
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:ESysParticle ESys-Particle]
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:::[[SURFEX/Crocus]]<br />
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Field_of_study Field of study]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Field_of_study Field of study]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Hydrology Hydrology]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Hydrology Hydrology]
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Metrology Metrology]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Meteorology Meteorology]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Glaciology Glaciology]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Glaciology Glaciology]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Communication Communication]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Communication Communication]
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::[[Mail and Mailing lists|Mail and Mailing lists]]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Presentations Presentations]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Templates Templates]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Templates Templates]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Logo Logo]
 
::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Logo Logo]
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Administration Administration]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Administration Administration]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Teaching Teaching]
 
:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Teaching Teaching]
 
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Summerschools Summerschools]
== <span style="font-family:arial,helvetica,sans-serif">Make a contribution</span> ==
 
 
 
<span style="font-family:arial,helvetica,sans-serif">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&nbsp;don't be shy. Your&nbsp;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.&nbsp;</span>
 
 
 
== <span style="font-family:arial,helvetica,sans-serif">Tools and Topics</span> ==
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">Tools for [[WorkingOnServers]] at UiO.</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">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.</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">In this section, we give you an overview of UIO computing systems and how to set-up your environment (module package) and 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.</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[Python]]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">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.</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">General [[Fortran]] Tips</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Some general usage tips for coding in FORTRAN.</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">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.</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">There is a default GNU compiler but it may be a quite old version. If you wish to use a newer version:</span>
 
<pre>module avail gcc</pre>
 
it returns the list of available versions.
 
<pre>module load gcc/4.9.0</pre>
 
<span style="font-family:arial,helvetica,sans-serif">It loads GNU compilers 4.9.0 (both Fortran, C and C++ compilers).</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Intel compilers are available by default on our UIO servers but on abel, you would need to load it:</span>
 
<pre>module load intel</pre>
 
==== <span style="font-family:arial,helvetica,sans-serif">Other Fortran materials</span> ====
 
 
 
*<span style="font-family:arial,helvetica,sans-serif">Gunnar Wollan has compiled a set of documents at [http://folk.uio.no/gunnarw/GEO4060/ 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 http://www.uio.no/studier/emner/matnat/geofag/GEF4510/h12/index.html]</span>
 
 
 
*<span style="font-family:arial,helvetica,sans-serif">An interesting free tutorial at [http://www.fortrantutorial.com/ 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</span>
 
 
 
*<span style="font-family:arial,helvetica,sans-serif">The National Computational Infrastructure in Australia has class notes online for a Basic Fortran course ([http://nf.nci.org.au/training/FortranBasic/ http://nf.nci.org.au/training/FortranBasic/]) and an Advanced Fortran course ([http://nf.nci.org.au/training/FortranAdvanced/ http://nf.nci.org.au/training/FortranAdvanced/]).</span>
 
 
 
*<span style="font-family:arial,helvetica,sans-serif">Fortran Wiki [http://fortranwiki.org/fortran/show/HomePage http://fortranwiki.org/fortran/show/HomePage]</span>
 
 
 
 
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[Access to HPC resources]]</span> ===
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[FLEXPART Model]]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Information and resources for running and setting up FLEXPART. Mostly geared toward the ATMOS users.</span>
 
 
 
 
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[FLEXINVERT]]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Bayesian inversion code for use with FLEXPART</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[WRFand WRF-CHEM|WRF and WRF-CHEM Models]]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Information and resources for running and setting up WRF and WRF-CHEM.</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[OpenIFS|OpenIFS ECMWF Model]]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Information and resources for running and setting up OpenIFS (ECMWF forecast model).</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[DataFormats|Data formats ]](netCDF, HDF4, HDF5, GRIB-1, GRIB-2, BUFR, etc.)</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Descriptions on how to manipulate and visualize data in these different formats.</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">Getting data from [https://wiki.uio.no/mn/geo/geoit/index.php/ECMWF ECMWF]</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Decriptions of how to get data in various ways from the ECMWF server.</span>
 
 
 
=== <span style="font-family:arial,helvetica,sans-serif">[[Matlab]] (Not open source, but extensively used)</span> ===
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Contributions from MATLAB users</span>
 
 
 
 
 
 
 
=== [[Metview (ECMWF visualization package)]] ===
 
 
 
== <span style="font-family:arial,helvetica,sans-serif">Editing pages on the Geo-IT MediaWiki</span> ==
 
 
 
<span style="font-family:arial,helvetica,sans-serif">A good starting place for markup reference can be found here: [http://meta.wikimedia.org/wiki/Help:Wikitext_examples http://meta.wikimedia.org/wiki/Help:Wikitext_examples]</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Another point is that this wiki is using Subpages, so in places you'll see reference to a <nowiki><subpages .></nowiki> tag. This just means that the list of subpages will be dynamically generated in that location.</span>
 
 
 
==== <span style="font-family:arial,helvetica,sans-serif">Editing Source Code</span> ====
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Note that for the purposes of documenting source code there are two important features:</span>
 
 
 
#<span style="font-family:arial,helvetica,sans-serif">use the <nowiki><code> ... </code></nowiki> to show some simple code snippets: <code>def foo(): return</code></span>
 
#<span style="font-family:arial,helvetica,sans-serif">The syntax highlighting extension has been installed, so you can wrap source code examples in <nowiki><syntaxhighlight></nowiki> 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>
 
<pre><syntaxhighlight lang='python'>
 
# Hello World in Python
 
print("Hello World")
 
</syntaxhighlight>
 
 
 
</pre><pre />
 
&lt;syntaxhighlight lang='csharp'&gt; //Hello World in C# class HelloWorld {
 
 
 
    static void Main()
 
{
 
  System.Console.WriteLine("Hello, World!");
 
}
 
 
 
}
 
 
 
&lt;/syntaxhighlight&gt;
 
 
 
<br/>&lt;syntaxhighlight lang='cpp'&gt; // Hello World in C++ (pre-ISO)
 
 
 
#include &lt;iostream.h&gt;
 
 
 
main() {
 
 
 
    cout << "Hello World!" << endl;
 
return 0;
 
 
 
}
 
 
 
 
 
 
 
&lt;/syntaxhighlight&gt;
 
 
 
&lt;/span&gt;&lt;/span&gt;&lt;/span&gt;
 
 
 
<span style="font-family:arial,helvetica,sans-serif">The above code block results in:</span>
 
<div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="python source-python"><pre class="de1"><span style="font-family:arial,helvetica,sans-serif;"><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></pre></div></div><div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="csharp source-csharp"><pre class="de1"><span style="font-family:arial,helvetica,sans-serif;"><span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size:small;"><span class="co1">//Hello World in C#</span>
 
</span></span></span></pre>
 
<span style="font-family:arial,helvetica,sans-serif">&lt;span class="kw4"&gt;class&lt;/span&gt; HelloWorld &lt;span class="br0"&gt;{&lt;/span&gt;</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">  <span class="kw1">static</span> <span class="kw4">void</span> Main<span class="br0">(</span><span class="br0">)</span>
 
<span class="br0">{</span>
 
<span class="kw5">System</span><span class="sy0">.</span><span class="me1">Console</span><span class="sy0">.</span><span class="me1">WriteLine</span><span class="br0">(</span><span class="st0">"Hello, World!"</span><span class="br0">)</span><span class="sy0">;</span>
 
<span class="br0">}</span>
 
 
</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">&lt;span class="br0"&gt;}&lt;/span&gt; &nbsp; C&lt;span class="sy0"&gt;++&lt;/span&gt;</span>
 
<span style="font-family:arial,helvetica,sans-serif">Back to index</span></div></div><div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="cpp source-cpp"><pre class="de1"><span style="font-family:arial,helvetica,sans-serif;"><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></span></pre>
 
<span style="font-family:arial,helvetica,sans-serif">&nbsp; &lt;span class="co2"&gt;#include &lt;iostream.h&gt;&lt;/span&gt; &nbsp; main&lt;span class="br0"&gt;(&lt;/span&gt;&lt;span class="br0"&gt;)&lt;/span&gt; &lt;span class="br0"&gt;{&lt;/span&gt;</span>
 
 
 
<span style="font-family:arial,helvetica,sans-serif">  <span class="kw3">cout</span> <span class="sy1"><<</span> <span class="st0">"Hello World!"</span> <span class="sy1"><<</span> endl<span class="sy4">;</span>
 
<span class="kw1">return</span> <span class="nu0">0</span><span class="sy4">;</span>
 
 
</span>
 
<span style="font-family:arial,helvetica,sans-serif">&lt;span class="br0"&gt;}&lt;/span&gt;</span></div></div>
 
==== <span style="font-family:arial,helvetica,sans-serif">Other Resources</span> ====
 
 
 
<span style="font-family:arial,helvetica,sans-serif">Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. See Also:</span>
 
 
 
*<span style="font-family:arial,helvetica,sans-serif">[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]</span>
 
*<span style="font-family:arial,helvetica,sans-serif">[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]</span>
 
*<span style="font-family:arial,helvetica,sans-serif">[https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</span>
 
 
 
<br/><span style="font-family:arial,helvetica,sans-serif">[[/Reference]]</span>
 

Latest revision as of 14:48, 5 December 2017

This Wiki is meant to provide a resource for those at UiO interested in working with computer modeling and data analysis in Earth Sciences.

Content herein is generally specific to UiO, as otherwise it is recommended to make posts to Stack Exchange and the sites therein.

This wiki uses 'category' tags, and below are some of the categories available. Note that in some cases, the content does not yet exist, in which case you are encouraged to edit and add information, or contact one of the site maintainers to request further information.

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.

Enjoy!

Editing pages
How to
Style guide
Data
Abbreviations_and_terminology
Formats
Measurements
Ordering
Satellite imagery
Re-analysis
GIS
Tools
WorkingOnServers
Command_line
Software
Code Coffee
R
Fortran
Micmac
Python
Matlab
Excel
Computing Facilities
How to login?
Wessel
Sverdrup
Moulin
geo-hiperf
Abel HPC
Notur HPC
Set-up your own server (IaaS)
Data storage (lagrinshotell, Norstore & storage for researchers)
Models
WRF, WRF-CHEM and WRF-Hydro
OpenIFS
Flexpart
MITgcm
cesm
noresm
ESys-Particle
SURFEX/Crocus
Field of study
Hydrology
Meteorology
Glaciology
Communication
Mail and Mailing lists
Presentations
Templates
Logo
Climabyte
Administration
Teaching
Summerschools