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 NILU Open Source Wiki. The purpose of these pages is to provide information on software tools available for data analysis and scientific program for NILU projects. It is not exclusively meant for Open Source software, so if you have tips and tricks for other software, feel free to include it here as well.
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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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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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'''NOTE:''' While we are requiring registration, and have the pages hidden from anonymous viewers, the pages are ''public'' facing, meaning they may be visible to users outside of NILU. Please be thoughtful when posting scripts or information on the system infrastructure. [[User:Jfb|Jfb]] 12:50, 14 September 2011 (CEST)
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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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=== <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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== Some Open Source Projects and Tools at NILU==
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Enjoy!
  
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====[[FLEXPART_Model]]====
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Editing Editing pages]
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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:How_to How to]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Style_guide Style guide]
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====[[Python]]====
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Data Data]
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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/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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====Tools for [[WorkingOnServers]] at NILU.====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Measurements Measurements]
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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/Category:Ordering Ordering]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Satellites Satellite imagery]
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====General [[Fortran]] Tips====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Re_analysis Re-analysis]
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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/Category:GIS GIS]
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Tools Tools]
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====[[Matlab]] (Not open source, but extensively used)====
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::[https://wiki.uio.no/mn/geo/geoit/index.php/WorkingOnServers WorkingOnServers]
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Contributions from MATLAB users (mostly related to FLEXPART)
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Command_line Command_line]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Software Software]
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== Editing pages on the niluOS MediaWiki ==
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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 />
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A good starting place for markup reference can be found here: http://meta.wikimedia.org/wiki/Help:Wikitext_examples
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Fortran Fortran]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Micmac Micmac]
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Note that these MediaWiki pages contain a mix of RestructuredText and MediaWiki Markup. RestructuredText is a powerful markup language, and particularly useful for documenting [[Python]] code, especially when coupled with [[Python/Sphinx]] for making code documentation. However, to gain the navigation features of MediaWiki, it is recommended to use the mediawiki default markup here. Still, if you would prefer [[RestructuredTextEditing|RestructuredText]] then you can use it as well by simply placing your markup between <nowiki><rst> ... </rst></nowiki> tags.
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Python Python]
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Matlab Matlab]
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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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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Excel Excel]
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:UioNetwork Computing Facilities<br />]
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====Editing Source Code====
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Login How to login?]<br />
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Note that for the purposes of documenting source code there are two important features:
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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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# use the <nowiki><code> ... </code></nowiki> to show some simple code snippets: <code>def foo(): return</code>
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Moulin Moulin]
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# The source code extension has been installed, so you can wrap source code examples in <nowiki><source></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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:::[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><nowiki>
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Nortur Notur HPC]<br />
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<source lang='cs'>
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:::[[Set-up your own server (IaaS)]]
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//Hello World in C#
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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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class HelloWorld
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Models Models]
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{
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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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    static void Main()
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:OpenIFS OpenIFS]
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    {
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:FLEXPART Flexpart]
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        System.Console.WriteLine("Hello, World!");
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:MITgcm MITgcm]
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    }
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:::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Cesm cesm]
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}
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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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</source>
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:::[[SURFEX/Crocus]]<br />
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<source lang='cpp'>
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:[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Field_of_study Field of study]
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// Hello World in C++ (pre-ISO)
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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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#include <iostream.h>
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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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main()
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::[[Mail and Mailing lists|Mail and Mailing lists]]
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{
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Presentations Presentations]
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    cout << "Hello World!" << endl;
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Templates Templates]
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    return 0;
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::[https://wiki.uio.no/mn/geo/geoit/index.php/Category:Logo Logo]
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}
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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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</source>
 
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<source lang='py'>
 
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# Hello World in Python
 
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print("Hello World")
 
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</source>
 
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</nowiki></pre>
 
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Results in:
 
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<source lang='cs'>
 
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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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C++
 
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Back to index
 
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</source>
 
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<source 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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</source>
 
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<source lang='py'>
 
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# Hello World in Python
 
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print("Hello World")
 
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</source>
 
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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.
 
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See Also:
 
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* [[ RestructuredTextEditing ]]
 
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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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[[/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"