Useful links
Writing documents, building simulations & developping softwares

My repositories on Git Lab
at the University of Montpellier

I use a Git Lab environment at the University of Montpellier for the versioning and the storage of most of my numerical developments and for my tools dedicated to the writing of papers and reports (I developed a few things those past years). This Git Lab has a web interface (you will need an account; contact me). The network GLADYS owns a user group on this web development platform. You must have an account to contribute to the GLADYS developments.

WRITE-AND-CITE GLADYS templates for writing reports Written in Latex and Bibtex, this project consists of a simple folder hierarchy containing the basic materials (Latex class, Bib tex templates, figure templates) to write documents (report, paper draft) in the framework of GLADYS. The bundle contains a version of my numerical library (bibtex format) usually a bit out of date :-).
STOOCH Simple TOOls for Coastal Hydrodynamics Written in C++, Python, Bash, STOOCH consists in a set of tools dedicated to the processing of coastal hydro-morphodynamic data. It computes many parameters from the linear wave theory and other formalisms. It is partly designed with the same philosophy as that of GMT: pipe ASCII/NetCDF flows in between various tools to build a complex processing.
NLPC1 Non Linear Pelnard-Considère V1 Written in Fortran, Python, bash, NLPC1 is a small code developed to explore the behavior of the non-linear Pelnard-Considère equation which is one of the main concern of my research activity.
MEFOC Marine Eolian Farm Optimal Cartography MEFOC is a tool written in Bash/GMT (+ some extensions) to calculate the best places to deploy aeolian farms in a given domain where meteo-marine, morphology and economic informations exist in not-controlled quantity/quality.
NEMOTH NEarshore Morphodynamics by Optimal THeory The software NEMOTH computes the dynamics of various nearshore sand bars and other geomorphic patterns thanks to the point of view of the optimal theory / minimization principle.
Example of text with gladys template
example of spatial domain for NEMOTH
Example of MEFOC output
Example of nemoth output

The lines below allow you to recover the last versions of my git projects. GITDIRPROJECT represents any of the Git repository directions listed above; PROJECT is the name of the project associated to GITDIRPROJECT. In your terminal under Linux (if you are under Windows, just clear my sky please): cd [somewhere-you-want]
will extract the full source directory in [somewhere-you-want]/PROJECT. If you want to retrieve the updated git project in the current directory (the one where your shell is) you just add a dot like: cd [somewhere-you-want]
If you have already cloned your git repository on a local copy, and you just want to update it to its more recent version (from the current git branch), use instead: cd [somewhere-you-want]/PROJECT
git checkout Alternatively, use : pull command to merge branch
Previous commands allow you to retrieve the codes from the main branches in the repositories. Other possibilities exist but require a minimal understanding of Git principles. If you want to collaborate to the development or to get access to the versioning, you must get higher read/write rights. In such a case, get in touch first.

example of code with coffee
pure gimp stuff

The High Performance Computing center
at the University of Montpellier

For my more significant computational tasks, I use the Meso Center HPC@LR leaded by the University of Montpellier and hosted at CINES. I provide here practical informations relative to my activity on this cluster HPC (High Performance Computing).

Connecting HPC@LR

HPC@LR provides a new cluster called $\mathcal{M}$use (formerly $\tau$-au). The cluster can be touched with : ssh Or:
with the following alias defined in my $HOME/.profile file:
alias sshmuse='ssh'
As I use a ssh key, providing a keyword is not my concern. If you got your account on $\mathcal{M}$use but don't have a ssh key, you can do on your linux client: ssh-keygen -t rsa (If you don't have any ssh key)
You may use a passphrase. But if you set one, you'll have to write it. Then in all cases:
ssh-copy-id -i ~/.ssh/
Now,you can connect directly with the same syntax as mine above.

I wrote a tutorial about how to play with $\mathcal{M}$use. It focuses on my scientific activity, but you may easily adapt it to your own.

HPC@LR manages users and projects. Each project corresponds to a workspace with an amount of hours, some disk space and possibly several users. I have several projects hosted at HPC@LR which are:

GOL Since years, with colleagues and former students, I use to analyse coastal / beach hydrodynamics with the SIROCCO environment eventually coupled with WW3. This coupling has been first used in the Gulf of Lions (so the name GOL for the project). But SIROCCO is now used for wider applications in coastal dynamics & paleo-oceanography. In particular, with my friends Mathieu Schuster, Jeff Ghienne and Alexis Nutz, we developed the concept of Wind-driven Water Body (WWB), which are (usually) closed water bodies of intermediate to shallow water depth. In this group, I am in charge of the quantification of (paleo-)hydrodynamics in WWBs and of the reconstruction by numerical means of the paleo-forcings at the origin of the wind-driven geomorphic features that occur within the sedimentary deposits. The systematic modelling of several tens of WWBs around the world require robust computation facilities like HPC@LR.
SHOREMOTION I use several numerical tools dedicated to the modelling of shoreline and nearshore morphodynamics. One type of models is based on non-linear diffusion equations. Another category relies on optimal design / optimization. At now, their usage in real case studies or engineering do not require large numerical resources. But I project the usage of such tools for more realistic applications in the future. So I tentatively deploy the tools in an HPC environment.
METOCEAN This project is special insofar as it is not devoted to any specific place around the world nor any specific tool. It is dedicated to the manipulation of a SINGLE set of global forcings for all the other coastal projects at HPC@LR: we store, we extract and we prepare the input files for hydro-morphodynamic simulations performed in other HPC projects. The numerical effort corresponds mainly to the pre-processing (and eventually post-processing) of meteo-marine and bathymetric data. Although it is pre-processing, it is performed on HPC nodes.