Docker image to run the Coastal and Regional Ocean COmmunity model - CROCO

Funded by ANID - Fondecyt Regular 1211230

Pre-requisites

• Install docker in your system. Some guidelines here.
• Create a Dockerhub account here.
• Pull the CROCO docker image:

docker pull andressepulveda/croco_oceanv1.2.1b

• Or if you use the Dockerfile type this command in the same directory where the Dockerfile is located (this will take several minutes). Change "andressepulveda/croco_ocean1.2.1b" with a name of your choice

docker build -t andressepulveda/croco_oceanv1.2.1_full .

Getting started

Working inside the container as user croco and in the /home/croco/croco-v1.2.1 directory

docker run -it --user croco -w /home/croco/croco-v1.2.1 andressepulveda/croco_oceanv1.2.1b

• Done, you're inside the docker container now. Let's run the Benguela test case.

./create_myconfig.bash
(press "Y")
cd Run/CROCO_FILES
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_grd.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_frc.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_clm.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_ini.nc
cd ..
./jobcomp
./croco croco.in

and your output files will be located in /home/croco/croco-v1.2.1/Run/CROCO_FILES

Storing input and out files outside the container

Create a local directory e.g. croco_docker and store the input files there

mkdir croco_docker
cd croco_docker
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_grd.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_frc.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_clm.nc
wget http://mosa.dgeo.udec.cl/CROCO2022/CursoBasico/Tutorial01/ArchivosIniciales/croco_ini.nc
cd ..

Now launch the container linking that local directory with the input/output directory in the container using the -v option

docker run -it -v /home/dgeo/croco_docker:/home/croco/croco-v1.2.1/Benguela/CROCO_FILES andressepulveda/croco_oceanv1.2.1c /home/croco/croco-v1.2.1/Benguela/croco /home/croco/croco-v1.2.1/Benguela/croco.in

Build your own CROCO configuration

In the /home/croco/croco-v1.2.1 directory edit the create_config.bash

nano create_config.bash

change this line to the name of your configuration, in this case "Chile"

MY_CONFIG_NAME=Chile

run the script

./create_config.bash

Press "Y" and change to the newly created "Chile" directory (the name of your configuration)

cd Chile

There you should edit crocotools_param.m, cppdefs.h, param.h, croco.in to suit you needs.

Create inputs file

If you create your container with the Dockerfile, we have added Octave v4.0.0 and octcdfv1.1.8 and all the datasets to allow the use of CROCO_TOOLS.

The following instructions will not work for the containers in DockHub

Known Errors

Before starting, fix this issues

• "oct_start.m"

Firt you need to edit "oct_start.m"

vim oct_start.m

and change

tools_path='../croco_tools/';

to

tools_path='../../croco_tools/';

-"make_clim" fails as a ";" is missing at the end of line 206 in the create_clim.m file located in

/home/croco/croco_tools/Preprocessing_tools

Initial steps

octave_cli
>oct_start
>make_grid
>make_forcing
>make_clim

Now all the input files shoul be located in the CROCO_FILES directory and the default Benguela simulation can be run by typing

./jobcomp
./croco croco.in

Bugs

Please report any bugs here.