24. TRAINING 2019: DATARMOR specific

24.1. Getting the good environment

Warning

This is specific to DATARMOR cluster used for this training; if you are working on you own computer, follow the System Requirements and Downloading the code tutorials to download the code, and set-up your environment

An environment script has been created for this training on DATARMOR. It will load the necessary modules and set some useful paths and environment variables. Copy this croco_env.csh script and source it. If you already have a .cshrc or .tcshrc or .bashrc environment script, please copy it to .chsrc.bck to avoid overdefinitions and use only croco_env.csh during the training period.

cd $HOME
cp /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2019/croco_env.* .
source croco_env.csh

Now the $CROCO_DIR environment variable is defined and you will find useful material for this training in this directory.

24.2. Creating your work architecture

Let’s work on your WORKDIR to avoid disk space issues.

cd $work
mkdir TRAINING_2019
cd TRAINING_2019
mkdir croco
mkdir CONFIGS

cp -r $CROCO_DIR/SOURCE_CODES/CROCO/croco_git/croco croco/.
cp -r $CROCO_DIR/SOURCE_CODES/CROCO/croco_git/croco_tools croco/.

If you have followed this architecture, the following environment variables have also been placed to facilitate navigation:

  • $croco point to your croco sources: $work/TRAINING_2019/croco/croco

  • $tools point to your croco sources: $work/TRAINING_2019/croco/croco_tools

  • $confs point to your croco sources: $work/TRAINING_2019/CONFIGS

Investigate by your own the various directories.

Warning

do not modify any of the files contained in your source directories $croco and $tools to keep your source files clean; modifications should be perfomed in your configuration directories (as we will see later)

24.3. DATA FILES

Datasets for preparing surface and boundary conditions from climatological dataset can be downloaded on CROCO website. For this training you will find them in $CROCO_DIR/DATA/DATASETS_CROCOTOOLS ; otherwise see the Download tutorial.

You can also find the following global atmospheric reanalysis in $CROCO_DIR/DATA/METEOROLOGICAL_FORCINGS/:

  • ERAI

  • CFSR

And the following ocean reanalysis in $CROCO_DIR/DATA/3D_OCEAN_FORCING:

  • SODA

  • ECCO2

24.4. BASIN configuration for XIOS tutorial

cp -R /home/datawork-croco/datarmor-only/CONFIGS/TUTO20/BASIN_NO_XIOS/* $confs/BASIN
cd $confs/BASIN
Path for XIOS sources:
::

XIOS_ROOT_DIR=/home/datawork-croco/datarmor-only/SOURCE_CODES/XIOS/XIOS-2.5

24.5. SOURCES for coupling tutorial

For DATARMOR training, OASIS has already been compiled, so you can just copy the sources and compiled files
mkdir -p $work/TRAINING_2019/oasis
cp -r $CROCO_DIR/SOURCE_CODES/OASIS/OASIS3-MCT_3.0_branch_compiled $work/TRAINING_2019/oasis/OASIS3-MCT_3.0_branch

The configure file for compiling OASIS on DATARMOR, named make.datarmor can be found here

$CROCO_DIR/make.datarmor

For DATARMOR training, WRF has been compiled, and you can just copy the source and compiled files:

mkdir -p $work/TRAINING_2019/wrf
cp -r $CROCO_DIR/SOURCE_CODES/WRF/WRFV3.7.1_compiled $work/TRAINING_2019/wrf/WRFV3.7.1
A job for compilation is also provided::

$CROCO_DIR/job_compile_wrf.pbs

For DATARMOR training, WPS has been compiled, and you can just copy the source and compiled files:

cp -r $CROCO_DIR/SOURCE_CODES/WRF/WPSV3.7.1 $work/TRAINING_2019/wrf/.

For DATARMOR training, these data are avaiable in $CROCO_DIR/SOURCE_CODES/WRF/geog.

For DATARMOR training, CFSR data for WRF are available in $CROCO_DIR/DATA/METEOROLOGICAL_FORCINGS/CFSR/GLOBAL/NATIVE_format

For DATARMOR training, WW3 has been compiled, and you can just copy the source and compiled files:

mkdir -p $work/TRAINING_2019/ww3
cp -r $CROCO_DIR/SOURCE_CODES/WW3/github/WW3_compiled/* $work/TRAINING_2019/ww3/.
For DATARMOR training, TOY model files are provided here:
cp $CROCO_DIR/SOURCE_CODES/TOY/toy_compiled/toy_model $confs/Run_BENGUELA_LR_cpl/.

cp $CROCO_DIR/DATA/BENGUELA_CPL/toy_files/* $confs/Run_BENGUELA_LR_cpl/.

You should now have the following new files in your configuration directory:

  • toy_model

  • grid_wav.nc

  • TOYNAMELIST.nam

  • toy_wav.nc

An example of fulfilled namcouple is also provided in $CROCO_DIR/DATA/BENGUELA_CPL/oasis_files

Note

Documentation on PBS use on DATARMOR can be found here: https://w3z.ifremer.fr/intraric/Mon-IntraRIC/Calcul-et-donnees-scientifiques/Datarmor-Calcul-et-Donnees/Datarmor-calcul-et-programmes