Quickstart

Prerequisites, configuration and compilation

1. To check if you have all the required software, type (in the cesam2k20 root directory)

./check_deps.sh

If you are looking for an easy way to build an environment dedicated to Cesam2k20, follow the instruction here.

2. Then, configure your Makefiles:

./configure.sh conf

• gfortran
• gfortran_adipls
• gfortran_h5
• gfortran_h5_adipls
• ifort
• ifort_adipls

3. Add the following lines to your .bashrc or equivalent:

export CESDIR="cesam_root_folder"

if [ -z ${LD_LIBRARY_PATH} ]
then
    export LD_LIBRARY_PATH="${CESDIR}/lib"
else
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${CESDIR}/lib"
fi

export PATH="$PATH:${CESDIR}/bin/"
export PATH="$PATH:${CESDIR}/vicmodels/bin/"

export aprgdir="${CESDIR}/adipack/"
export PATH="$PATH:${aprgdir}/bin/"

export cesacordir="${CESDIR}/ACOR/"
export PATH="$PATH:${cesacordir}/bin/"

4. You can now compile Cesam2k20. Type make install and you're done!

Known issues with the installation

• As Cesam2k20 uses submodules, it needs a version of gfortran > 6.0 of ifort > 16.0. Check the compiler version with:

  sudo gfortran --version
  gfortran --version

  (replace gfortran with your actual compiler). Are you calling the compiler you think you're calling ?
  
  
• If you are using Cesam2k20 on a server without root privileges, I may have a hard time installing Cesam2k20, either due to a wrong version of compiler or a wrong version of some library. MESA developers propose a package called mesa_sdk that contains everything you need (compiler, libraries, etc.) and can be installed locally. If after installation of mesa_sdk, gfortran cannot find a needed library (e.g. liblapack), please prepend the right path to the variable

  $LIBRARY_PATH

  (not $LD_LIBRARY_PATH). For instance:

  export LIBRARY_PATH="/home/username/mesasdk/math-slots/default/lib/:$LIBRARY_PATH"

Running and testing

run_cesam2k20.py model_name

• model_name.don, the input file with the parameters used;
• model_name.HR, a file containing the evolution of global quantities;
• model_name.osc, one or several files containing the internal structure of the last model or all models along the evolution.

Compile Cesam2k20 for HDF5 outputs

• You first need to have the hdf5 libraries installed. Either installed them using your usual package manager, or from source. If you choose to install it from source, here are the steps to follow for installation at location /usr/local/hdf5.

  gunzip < hdf5-X.Y.Z.tar.gz | tar xf -
  cd hdf5-X.Y.Z
  ./configure --prefix=/usr/local/hdf5 --enable-fortran2003 --enable-cxx
  make
  make check                # run test suite.
  make install
  make check-install        # verify installation.



• Once you are done, add to your .bashrc the locations of your hdf5 installation:

  export PATH_HDF5='/usr/local/hdf5'
  export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:/usr/local/hdf5/lib/'



• source your .bashrc

  source ~/.bashrc



• finally, go in the cesam2k20 repository and run

  make clean
  ./configure.sh gfortran_h5
  make

Create an environment with anaconda

1. Download anaconda here, and install it.

2. Create a cesam environment:

conda create -n cesam python=3.9.12
conda activate cesam

3. Install the python packages:

conda install -c conda-forge numpy=1.21.5 scipy=1.7.3 matplotlib traits=6.2.0 traitsui=8.0.0 h5py pyface=8.0.0 emcee corner ipython tqdm

4. Install the jupyter packages:

conda install -c conda-forge ipympl

5. Install the gfortran:

conda install -c conda-forge gfortran=12.1.0
conda install -c conda-forge binutils
conda install -c conda-forge ncurses

6. Add to your .bashrc the following lines:

export PATH_HDF5=/home/USERNAME/anaconda3/envs/cesam/
export LD_LIBRARY_PATH="/home/USERNAME/anaconda3/envs/cesam/lib:$LD_LIBRARY_PATH"

7. Source and activate:

source .bashrc
conda activate cesam

Tutorial