Building the environnement

1.3. Building the environnement#

1.3.1. Installation with conda and using the “install” script#

Note

Be sure to have conda install on your computer. If not, refer to Conda website to install it.

Note

the conda environment contains all the elements needed to compile fortran tools:

- gcc>=8.3.0
- gfortran>=8.3.0
- netcdf-fortran=4.6.0

  • Execute the installation script

    python install.py

  • Answer the question on the screen:

    Do you want to install conda environment? [y,[n]]: y
Do you want to compile fortran tools? y,[n]: y

Note

install.py automatically uses mamba package if it exists within conda. You can install it with the command:

conda install -n base --override-channels -c conda-forge mamba

If no error is raised environment installation and compilation were successful. Now you can load your conda environment:

conda activate croco_pyenv

That’s it, you are ready to use the preprocessing tools! Remind to activate this envrironment each time you want to use the preprocessing tools.

1.3.2. Installation with another python package manager (e.g. micromamba)#

Use the environment_tools.yml file provided in env

micromamba create -f env/environment_tools.yml  -c conda-forge

Activate the environment:

micromamba activate croco_pyenv

1.3.3. Fortran tools compilation (if not using the install.py)#

Only if you have not used the install.py script (first section), or if you have answer no to the question: Do you want to compile fortran tools? y,[n] when using install.py, you can compile the fortran tools following this procedure.

Activate your python environment:

conda activate croco_pyenv

Or:

micromamba activate croco_pyenv

Note

the croco_pyenv environment contains all the elements needed to compile fortran tools:

- gcc>=8.3.0
- gfortran>=8.3.0
- netcdf-fortran=4.6.0

Launch the Fortran routines compilation:

cd Modules/tools_fort_routines
make clean
make

If successfull you should now have this file in Modules:

toolsf.cpython-39-x86_64-linux-gnu.so

1.3.4. 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.