Install the environnement

2.2. Install the environnement#

croco_pytools/prepro is a python toolbox for pre-processing CROCO input files.

It uses several python packages (see env.yml), as well as some Fortran scripts which have been interfaced with python through f2py and must therefore be compiled. The Fortran compilers are included in the python environment.

You just have to follow the two following step to install the whole toolbox:

  • Install the python environment

  • Compile the Fortran dependencies

2.2.1. Install the croco_pyenv environment#

A global conda environment is available for the three parts of croco_pytools in the env.yml file, located at the root of the croco_pytools directory..

You can use your favorite python environment manager (e.g. conda, mamba, micromamba, miniforge) to install the environment named croco_pyenv with this file.

Example with micromamba :

micromamba create -f env.yml
micromamba activate croco_pyenv

Example with conda :

conda env create -f env.yml
conda activate croco_pyenv

Tip

You can make available your croco_pyenv kernel for Jupyter Notebook by using the command : ipython kernel install --user --name=croco_pyenv

Note

You will have to activate the croco_pyenv environment each time you need to use the croco_pytools/prepro scripts!

2.2.2. Compile Fortran dependencies#

The required fortran and C compilers are included in the python environment, thus your first need to activate your python environment:

micromamba activate croco_pyenv

or

conda activate croco_pyenv

Launch the Fortran routines compilation:

cd prepro/Modules/tools_fort_routines
make clean
make

If successfull you should now have a file of this pattern in Modules:

toolsf.*.so

2.2.3. Notes on common errors#

You might face some errors while trying to compile fortran tools. Here is a list of what have been already encountered by some users and the associated solution.

  • ifort can raise wn error while compiling. In Modules/tools_fort_routines/Makedefs try to add --fcompiler=intelem in FFLAGS.

  • ImportError means you have missing librairies. In your terminal do nf-config --flibs and check that you have -lnetcdff -lnetcdf.

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