Software
From GHER
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* [https://github.com/gher-ulg/Documentation/wiki/Python Python]: an object-oriented, multi-purpose language. | * [https://github.com/gher-ulg/Documentation/wiki/Python Python]: an object-oriented, multi-purpose language. | ||
* [https://github.com/gher-ulg/Documentation/wiki/Julia Julia]: a language for technical computing (under construction). | * [https://github.com/gher-ulg/Documentation/wiki/Julia Julia]: a language for technical computing (under construction). | ||
- | * [ | + | * [https://github.com/gher-ulg/Documentation/wiki/JavaScript JavaScript]: dynamic programming language. |
* [[R]]: statistical computing and graphic. | * [[R]]: statistical computing and graphic. | ||
* [[GoogleEarth]]: nice stuffs to do in oceanography (under construction). | * [[GoogleEarth]]: nice stuffs to do in oceanography (under construction). |
Revision as of 08:28, 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
- Ocean Assimilation Kit: tool kit for ensemble and reduced-order assimilation
- Weakly Constrained Ensembles Method to create dynamically constrained ensemble perturbation for ensemble forecasts and data assimilation.
Octave/Matlab toolboxes
- Octave-netcdf, a NetCDF interface for Octave
- loadgrib, a GRIB decoder for Octave
- optiminterp, Optimal interpolation Fortran module with Octave interface
- Filtering inertia-gravity waves from the initial conditions of the linear shallow water equations
Models
- GHER3D Three dimensional primitive equation model
Misc
- Matlab/Octave scripts: read/write GHER format + commands for figures.
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.
- GoogleEarth: nice stuffs to do in oceanography (under construction).
- Tcl/Tk: a scripting language for GUIs (among others).
Version control systems
- Subversion (SVN), a version control system
Compilers
- g95: g95 has a good support for the Fortran 1995 standard
- gfortran: gfortran supports OpenMP
- ifort: Intel compilers
Tutorials
- Cours d'initiation au FORTRAN (in French)
- Fortran 90 Tutorial
- Matlab Tutorial
- Introduction à MATLAB et GNU Octave (in French)
Editors and word processors
- LaTeX: a document preparation system.
- DocBook: a semantic markup language for technical documentation
Linux
- Linux tips: useful commands for particular tasks in Linux
- Creation of animations: creation of a movie using a series of images
- Debugging in LINUX/UNIX
- Debugging in Matlab/Octave
- Advanced Bash-Scripting Guide
Remote access and desktop virtualization
- XMing: open-source alternative to x-win, remote x-windows over ssh
- NXclient: quicker than SSH, no need to have XWin, session management
- OPeNDAP How to use OPeNDAP
- Xvfb virtual X server
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
- Visualization and drawing
- How to use OPeNDAP
- List of commands for newbies
- Simple Linux Utility for Resource Management: SLURM
- Optical Character Recognition: http://www.free-ocr.com/
Useful to convert a pdf into text, when acrobat does not recognize properly the strings.
- Manipulations on pdf files: tools that allow for modifications on pdf files.
- 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>