Software

From GHER

Revision as of 08:28, 27 June 2017

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)

• Tutoriel OpenMP

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>