Software

From GHER

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* "[[Diva on web]]" Diva's web-interface
* "[[Diva on web]]" Diva's web-interface
* "[[OceanBrowser]]" A web-interface for visualizing [http://www.unidata.ucar.edu/software/netcdf/ NetCDF] files
* "[[OceanBrowser]]" A web-interface for visualizing [http://www.unidata.ucar.edu/software/netcdf/ NetCDF] files
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* [[GHER3D]] Three dimensional primitive equation model
 
=== Data assimilation ===
=== Data assimilation ===
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=== Octave/Matlab toolboxes ===
=== Octave/Matlab toolboxes ===
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* Octcdf, a [[NetCDF toolbox for Octave]]
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* [[Octave-netcdf]], a NetCDF interface for Octave
* [[loadgrib, a GRIB decoder for Octave]]
* [[loadgrib, a GRIB decoder for Octave]]
* optiminterp, [[Optimal interpolation Fortran module with Octave interface]]
* optiminterp, [[Optimal interpolation Fortran module with Octave interface]]
* [[Filtering inertia-gravity]] waves from the initial conditions of the linear shallow water equations
* [[Filtering inertia-gravity]] waves from the initial conditions of the linear shallow water equations
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=== Models ===
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* [[GHER3D]] Three dimensional primitive equation model
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=== Misc ===
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* [[Matlab/Octave scripts]]: read/write GHER format + commands for figures.
== Other tools ==
== Other tools ==
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=== Programming languages ===
=== Programming languages ===
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* [[Octave]]
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* [https://github.com/gher-ulg/Documentation/wiki/Octave Octave]: high-level interpreted language for scientific computing.
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* [[Matlab/Octave scripts]]: read/write GHER format + commands for figures.
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* [https://github.com/gher-ulg/Documentation/wiki/Python Python]: an object-oriented, multi-purpose language.
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* [[Julia]]: a language for technical computing (under construction)
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* [https://github.com/gher-ulg/Documentation/wiki/Julia Julia]: a language for technical computing (under construction).
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* [[GoogleEarth]]: nice stuffs to do in oceanography (under construction)
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* [https://github.com/gher-ulg/Documentation/wiki/JavaScript JavaScript]: dynamic programming language.
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* [[Tcl/Tk]]: a scripting language for GUIs (among others)
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* [https://github.com/gher-ulg/Documentation/wiki/R R]: statistical computing and graphic.
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* [[Tcl/Tk]]: a scripting language for GUIs (among others).
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==== Compilers ====
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=== Version control systems ===
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* [http://www.g95.org g95]: g95 has a good support for the Fortran 1995 standard
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* [https://github.com/gher-ulg/Documentation/wiki/Subversion Subversion] (SVN), a version control system
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* [http://gcc.gnu.org/wiki/GFortran gfortran]: gfortran supports OpenMP
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* [https://github.com/gher-ulg/Documentation/wiki/Git git]
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* [http://software.intel.com/en-us/articles/non-commercial-software-download/ ifort]: Intel compilers
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==== Tutorials ====
 
-
 
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*[http://perso.enstimac.fr/~gaborit/lang/CoursDeFortran/ Cours d'initiation au FORTRAN] (in French)
 
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*[http://www-teaching.physics.ox.ac.uk/Unix+Prog/hargrove/tutorial_90/ Fortran 90 Tutorial]
 
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*[http://docs.python.org/tut/ The Python Tutorial]
 
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*[http://www.cyclismo.org/tutorial/matlab/ Matlab Tutorial]
 
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*[http://enacit1.epfl.ch/cours_matlab/ Introduction à MATLAB et GNU Octave] (in French)
 
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*[https://computing.llnl.gov/tutorials/openMP/  Tutoriel OpenMP]
 
=== Editors and word processors ===
=== Editors and word processors ===
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* [[vi editor]]: a powerful linux text editor.  
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* [https://github.com/gher-ulg/Documentation/wiki/LaTeX LaTeX]: a document preparation system.
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* [[LaTeX]]: a document preparation system.
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* [http://www.docbook.org/ DocBook]: a semantic markup language for technical documentation
=== Linux ===
=== Linux ===
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* [http://modb.oce.ulg.ac.be/mediawiki/index.php/How_to_create_animation_%28Linux%29%3F Creation of animations]: creation of a movie using a series of images
* [http://modb.oce.ulg.ac.be/mediawiki/index.php/How_to_create_animation_%28Linux%29%3F Creation of animations]: creation of a movie using a series of images
* [[Debugging in LINUX/UNIX]]
* [[Debugging in LINUX/UNIX]]
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* [[Debugging in Matlab/Octave]]
* [http://tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide]
* [http://tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide]
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=== Misc ===
=== Misc ===
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* [[NetCDF format | NetCDF]]: a self-describing, machine-independent data format
 
* [[Programs for visualization | Visualization and drawing ]]
* [[Programs for visualization | Visualization and drawing ]]
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* [[Subversion]] (SVN), a version control system
 
* [[How to use OPeNDAP]]
* [[How to use OPeNDAP]]
* [[List of commands for newbies]]
* [[List of commands for newbies]]
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Useful to convert a pdf into text, when acrobat does not recognize properly the strings.
Useful to convert a pdf into text, when acrobat does not recognize properly the strings.
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* [http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/ pdftk] (pdftoolkit): perform operations on pdf documents.  
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* [[Manipulations on pdf files]]: tools that allow for modifications on pdf files.
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** Split a pdf file into multiple file
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pdftk mydoc.pdf burst
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* [https://www.dropbox.com Dropbox]: a file hosting service. The free account provides 2 Gb. It offers file synchronisation. Useful when having to share very large files, or to make a backup. For linux, the packages are available at https://www.dropbox.com/install?os=lnx, or can be downloaded through the package manager. (But remember there is also the in house service [https://edc.ulg.ac.be/merci merci]).
 +
 
 +
* [https://tricider.com Tricider]: a tool for brainstorming and votes. Submit one question and get ideas!
 +
 
 +
* [https://github.com/bartaz/impress.js/ Impress]: a javascript tool for presentations à la Prezi, but needs editing of hml5/css pages. Install on your machine if you want to be able to make presentations off-line.
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* [https://www.dropbox.com Dropbox]: a file hosting service. The free account provides 2 Gb. It offers file synchronisation. Useful when having to share very large files, or to make a backup. For linux, the packages are available at https://www.dropbox.com/install?os=lnx, or can be downloaded through the package manager.
+
* [http://www.mathjax.org/ Mathjax]: a javascript collection to be able to use Latex formulas (including definition of functions) in html pages. Note that $ $ needs to be replaced by \( \) in standard configurations. Install on your machine if you want to be able to make presentations off-line. If you want formulas font to herit styles, use something like <script type="text/javascript" src="MathJax/MathJax.js?config=TeX-AMS-MML_HTMLorMML.js"></script>

Latest revision as of 13:14, 27 June 2017

Contents

Tools developed by the GHER

This is a list of software and tools developed by the group, mainly in numerical modeling, spatial interpolation and data assimilation.

Interpolation

  • DINEOF (Data Interpolating Empirical Orthogonal Functions): a tool for removing missing data in geophysical data sets
  • DIVA (Data-Interpolating Variational Analysis): a spatial interpolation software
  • "Diva on web" Diva's web-interface
  • "OceanBrowser" A web-interface for visualizing NetCDF files

Data assimilation

Octave/Matlab toolboxes

Models

  • GHER3D Three dimensional primitive equation model

Misc

Other tools

Here are another set of tools useful in oceanography and numerical modeling.

Programming languages

  • Octave: high-level interpreted language for scientific computing.
  • Python: an object-oriented, multi-purpose language.
  • Julia: a language for technical computing (under construction).
  • JavaScript: dynamic programming language.
  • R: statistical computing and graphic.
  • Tcl/Tk: a scripting language for GUIs (among others).

Version control systems


Editors and word processors

  • LaTeX: a document preparation system.
  • DocBook: a semantic markup language for technical documentation

Linux

Remote access and desktop virtualization

Note: if keyboard problem (e.g., azerty vs. qwerty), type

setxkbmap be

(where 'be' has to be changed accordingly to your keyboard)

You may also need to type

setxkbmap -model evdev -layout be

in order to avoid unwanted keyboard behavior (ex: upward arrow launches snapshot tool)

Misc

Useful to convert a pdf into text, when acrobat does not recognize properly the strings.

  • Dropbox: a file hosting service. The free account provides 2 Gb. It offers file synchronisation. Useful when having to share very large files, or to make a backup. For linux, the packages are available at https://www.dropbox.com/install?os=lnx, or can be downloaded through the package manager. (But remember there is also the in house service merci).
  • Tricider: a tool for brainstorming and votes. Submit one question and get ideas!
  • Impress: a javascript tool for presentations à la Prezi, but needs editing of hml5/css pages. Install on your machine if you want to be able to make presentations off-line.
  • Mathjax: a javascript collection to be able to use Latex formulas (including definition of functions) in html pages. Note that $ $ needs to be replaced by \( \) in standard configurations. Install on your machine if you want to be able to make presentations off-line. If you want formulas font to herit styles, use something like <script type="text/javascript" src="MathJax/MathJax.js?config=TeX-AMS-MML_HTMLorMML.js"></script>
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