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TRAINING 2019: DATARMOR specific

25. TRAINING 2019: DATARMOR specific#

25.1. 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.

25.2. 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)

25.3. 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

25.4. 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

25.5. 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

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