Hands-on!

After install docker, docker-compose, subversion, git and all other packages we need (check this tutorial):

• Let's create a folder to organize the whole structure for the Docker-ROMS system (suggestion: call ROMS):

# create this folder in your home folder, but you can put this everywhere
mkdir ~/ROMS

• Inside your new folder, we will create the following structure:
  • ROMS/projects: is a shared folder between host (your computer) and the container (roms)
  • ROMS/src_code: another shared folder, but with the ROMS source code available to run
  • ROMS/docker-roms: folder containing all configuration files to run Docker containers related to ROMS
• Download ROMS source code to ROMS/src_code
• Clone docker-roms repository to ROMS/docker-roms

# access your ROMS folder
cd ~/ROMS

# to download ROMS source code replace joe_roms by your username
svn checkout --username joe_roms https://www.myroms.org/svn/src/trunk src_code

# clone docker-roms repository from github (Magnim, you don't need to to this step)
git clone https://github.com/CoastalHydrodynamicsLab/docker-roms.git

# start the container running (Magnim, you don't need to to this step)
cd docker-roms
sudo docker-compose -f docker-compose-personal.yml up -d
# José Roberto: use docker-compose-shelfwaves.yml if you are running on shelfwaves

# create your projects folder
cd ~/ROMS
mkdir -p projects/upwelling

To run the upwelling test case, we need four files that already came with the source code. In fact, there are several test cases, but the upwelling is simpler to run and test if everything is OK with your system.

I strongly recommend to do the following steps outside the ROMS container and the, with all set, we can access and run our application.

• Inside ROMS/projectsyou can create your projects' folder. In the last command we already created projects with upwelling on it.
• From your ROMS folder, copy the following files from src_code:

cd ~/ROMS
cp src_code/ROMS/External/roms_upwelling.in projects/upwelling
cp src_code/ROMS/External/varinfo.dat projects/upwelling
cp src_code/ROMS/Include/upwelling.h  projects/upwelling
cp src_code/ROMS/Bin/build_roms.sh  projects/upwelling

• Next, we must edit these copied files. This step is very important, because we must tell ROMS where your source code is located and where your application's files are, but using the container structure (which is very similar with your computer structure)

Editing build_roms.sh:

• Point MY_ROOT_DIR to ROMS source code folder by changing line #110 to:

MY_ROOT_DIR=${HOME}/roms_src

• Point the MY_PROJECT_DIR variable to your application folder by changing line #111 to:

MY_PROJECT_DIR=${PWD}

• Change line #124 to:

MY_ROMS_SRC=${MY_ROOT_DIR}

• Change line #173 to:

FORT=gfortran

• Change the following lines to be like:

#export           USE_MPI=on            # distributed-memory parallelism
#export        USE_MPIF90=on

export         USE_LARGE=on            # activate 64-bit compilation
export       USE_NETCDF4=on            # compile with NetCDF-4 library

Editing roms_upwelling.in: