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.
- 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
- 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-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
- GHER3D Three dimensional primitive equation model
- Matlab/Octave scripts: read/write GHER format + commands for figures.
Here are another set of tools useful in oceanography and numerical modeling.
- Octave: high-level interpreted language for scientific computing.
- Python: an object-oriented, multi-purpose language.
- Julia: a language for technical computing (under construction).
- GoogleEarth: nice stuffs to do in oceanography (under construction).
- Tcl/Tk: a scripting language for GUIs (among others).
Version control systems
- g95: g95 has a good support for the Fortran 1995 standard
- gfortran: gfortran supports OpenMP
- ifort: Intel compilers
Editors and word processors
- vi editor: a powerful linux text editor.
- LaTeX: a document preparation system.
- DocBook: a semantic markup language for technical documentation
- 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
(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)
- NetCDF: a self-describing, machine-independent data format
- 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!