Useful links
for software development and numerical modelling

gitlab logo
GLPI for HPC-LR logo
Wiki book relative
to GIT -- simple and usefull

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. This Git Lab has a web interface (you will need an account; contact me).

STOOCH Simple TOOls for Coastal Hydrodynamics
git@gitlab.info-ufr.univ-montp2.fr:gladys/STOOCH.git
Written in C++, STOOCH consists in a set of command line tools dedicated to the processing of coastal hydro-morphodynamic data. It computes many parameters from the linear wave theory and other formalisms. It is designed with the same philosophy as that of GMT: pipe ASCII/NetCDF flows in various tools to build a quite complex processing.
NLPC1 Non Linear Pelnard-Considère V1
git@gitlab.info-ufr.univ-montp2.fr:gladys/NLPC1.git
Written in Fortran, 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
git@gitlab.info-ufr.univ-montp2.fr:gladys/MEFOC.git
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
git@gitlab.info-ufr.univ-montp2.fr:gladys/NEMOTH.git
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 spatial domain for NEMOTH
Example of MEFOC output
Example of nemoth output

In the following, GITDIRPROJECT represents any of the Git repository directions listed above, and PROJECT the name of the software associated to GITDIRPROJECT. The lines below allow you to recover the last versions of my codes. In your terminal under Linux: cd [somewhere-you-want]
git clone GITDIRPROJECT
will extract the full source directory in [somewhere-you-want]/PROJECT. If you already did this and you just want to update your local copy from my current version (of the current git branch), use instead: cd [somewhere-you-want]/PROJECT
git checkout

These lines allow you to retrieve the codes. If you want to collaborate to the development, you must get writing access. Get in touch.

example of spatial domain for NEMOTH
Example of MEFOC output

The High Performance Computing center

For my heavy computational tasks, I use the Meso Center HPC@LR leaded by the University of Montpellier and hosted at CINES. I provide here some 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 bouchettef@muse-log.hpc-lr.univ-montp2.fr Or:
sshmuse
with the following alias defined in my $HOME/.profile file:
alias sshmuse='ssh bouchettef@muse-log.hpc-lr.univ-montp2.fr'
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/id_rsa.pub youraccount@muse-log.hpc-lr.univ-montp2.fr
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 With coleagues and former students, I use to analyse coastal / beach hydrodynamics with the SIROCCO environment coupled with WW3. This project is dedicated to the use of the coupling between these two models in studies performed in the Gulf of Lions (GOL).
WWB With my friends Mathieu Schuster, Jeff Ghienne, Alexis Nutz and Claude Roquin, all in Strasbourg, we developed the concept of Wind-driven Water Body (WWB). In this group, I am in charge of the the quantification of (paleo-)hydrodynamic patterns in such shallow water environments. I use the same coupling SIROCCO/WW3 as for the project GOL above.
SHOREMOTION I use several numerical tools dedicated to the modelling of shoreline and nearshore geomorphic features dynamics. One type of models is based on a non-linear Pelnard-Considère equation. Another category relies on an optimization point of view. In both cases, their usage in real case studies or engineering may require a significant amount of numerical resources.
TAIWAN The Taiwan island is one of my preferred place in the world. I develop there a long-term activity relative to nearshore water level, coastal hydrodynamics, cobbles morphodynamics, extreme events, and recently analysis of ambiant seismic noise,... This project is dedicated to all numerical simulations and data processings performed thereabout.
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 server.