Difference between revisions of "Welcome to Geosciences Modeling Wiki"

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(Added SURFEX/Crocus section where we will compile information on how to run SURFEX/Crocus on our machines)
 
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Welcome to the Geosciences Modeling and Data Science Wiki.  
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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.
  
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== Purpose: ==
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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.
  
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<span style="font-size:small;">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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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.
  
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== Make a contribution ==
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=== <span style="font-family:arial,helvetica,sans-serif">Purpose:</span> ===
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<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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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;
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Enjoy!
  
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Tools and Topics
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Editing Editing pages]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:How_to How to]
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==== Tools for [[WorkingOnServers]] at UiO. ====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Style_guide Style guide]
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data Data]
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An important resource for anyone using the servers.
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Abbreviations_and_terminology Abbreviations_and_terminology]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data_formats Formats]
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==== [[Python]] ====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Measurements Measurements]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Ordering Ordering]
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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.
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Satellites Satellite imagery]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Re_analysis Re-analysis]
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==== General [[Fortran]] Tips ====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:GIS GIS]
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Tools Tools]
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Some general usage tips for coding in FORTRAN.
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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]
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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.
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Software Software]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Code_Coffee Code Coffee]<br />
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There is a default GNU compiler but it may be a quite old version. If you wish to use a newer version:
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:R R]<br />
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<pre>          module avail gcc
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Fortran Fortran]
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</pre>
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Micmac Micmac]
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it returns the list of available versions.
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Python Python]
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<pre>          module load gcc/4.9.0
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Matlab Matlab]
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</pre>
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Excel Excel]
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It loads GNU compilers 4.9.0 (both Fortran, C and C++ compilers).
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:UioNetwork Computing Facilities<br />]
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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 />
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Intel compilers are available by default on our UIO servers but on abel, you would need to load it:
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Moulin Moulin]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:geo-hiperf geo-hiperf]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Abel Abel HPC]<br />
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<pre>          module load intel</pre>
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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 />
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===== Fortran materials =====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Models Models]
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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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*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]
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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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*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
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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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*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/]).
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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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*Fortran Wiki [http://fortranwiki.org/fortran/show/HomePage http://fortranwiki.org/fortran/show/HomePage]
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:::[[SURFEX/Crocus]]<br />
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Field_of_study Field of study]
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==== Getting data from [[ECMWF]] ====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Hydrology Hydrology]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Meteorology Meteorology]
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Decriptions of how to get data in various ways from the ECMWF server.
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Glaciology Glaciology]
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:[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]
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==== [[FLEXPART Model]] ====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Templates Templates]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Logo Logo]
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Information and resources for running and setting up FLEXPART. Mostly geared toward the ATMOS users.
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Climabyte Climabyte]
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Administration Administration]
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:[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]
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==== [[FLEXINVERT]] ====
 
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Bayesian inversion code for use with FLEXPART
 
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==== [[WRFand WRF-CHEM|WRF and WRF-CHEM Models]] ====
 
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Information and resources for running and setting up WRF and WRF-CHEM.
 
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==== [[OpenIFS|OpenIFS ECMWF Model]] ====
 
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Information and resources for running and setting up OpenIFS (ECMWF forecast model).
 
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==== [[DataFormats|Data formats ]](netCDF, HDF4, HDF5, GRIB-1, GRIB-2, BUFR, etc.) ====
 
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Descriptions on how to manipulate and visualize data in these different formats.
 
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==== [[Matlab]] (Not open source, but extensively used) ====
 
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Contributions from MATLAB users
 
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== Editing pages on the Geo-IT MediaWiki ==
 
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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]
 
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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.
 
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==== Editing Source Code ====
 
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Note that for the purposes of documenting source code there are two important features:
 
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#use the <nowiki><code> ... </code></nowiki> to show some simple code snippets: <code>def foo(): return</code>
 
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#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:
 
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<pre><syntaxhighlight lang='python'>
 
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# Hello World in Python
 
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print("Hello World")
 
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</syntaxhighlight>
 
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<syntaxhighlight lang='csharp'>
 
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//Hello World in C#
 
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class HelloWorld
 
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{
 
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    static void Main()
 
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    {
 
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        System.Console.WriteLine("Hello, World!");
 
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    }
 
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}
 
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</syntaxhighlight>
 
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<syntaxhighlight lang='cpp'>
 
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// Hello World in C++ (pre-ISO)
 
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#include <iostream.h>
 
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main()
 
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{
 
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    cout << "Hello World!" << endl;
 
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    return 0;
 
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}
 
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</syntaxhighlight>
 
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</pre>
 
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The above code block results in:
 
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<div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="python source-python"><pre class="de1"><span class="co1"># Hello World in Python</span>
 
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<span class="kw1">print</span><span class="br0">(</span><span class="st0">"Hello World"</span><span class="br0">)</span></pre></div></div><div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="csharp source-csharp"><pre class="de1"><span class="co1">//Hello World in C#</span>
 
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</pre>
 
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&lt;span class="kw4"&gt;class&lt;/span&gt; HelloWorld &lt;span class="br0"&gt;{&lt;/span&gt;
 
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    <span class="kw1">static</span> <span class="kw4">void</span> Main<span class="br0">(</span><span class="br0">)</span>
 
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<span class="br0">{</span>
 
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<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>
 
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<span class="br0">}</span>
 
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&lt;span class="br0"&gt;}&lt;/span&gt; &nbsp; C&lt;span class="sy0"&gt;++&lt;/span&gt;
 
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Back to index</div></div><div dir="ltr" class="mw-geshi mw-code mw-content-ltr"><div class="cpp source-cpp"><pre class="de1"><span class="co1">// Hello World in C++ (pre-ISO)</span>
 
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</pre>
 
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&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;
 
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    <span class="kw3">cout</span> <span class="sy1"><<</span> <span class="st0">"Hello World!"</span> <span class="sy1"><<</span> endl<span class="sy4">;</span>
 
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<span class="kw1">return</span> <span class="nu0">0</span><span class="sy4">;</span>
 
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&lt;span class="br0"&gt;}&lt;/span&gt;</div></div>
 
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==== Other Resources ====
 
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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. See Also:
 
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*[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
 
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*[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
 
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*[https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
 
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<br/>[[/Reference]]
 

Latest revision as of 15:48, 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
Retrieved from "https://wiki.uio.no/mn/geo/geoit/index.php?title=Welcome_to_Geosciences_Modeling_Wiki&oldid=1536"