CoastalApp

CoastalApp will be deprecated. Please switch to https://github.com/oceanmodeling/ufs-coastal

Contacts:

• [email protected]
• [email protected]

Introduction

CoastalApp is a modeling framework for coastal applications and regional forecasts. It consists of coupled modeling components that link the atmospheric, ocean and terrestrial realms under one common framework. CoastalApp is a flexible and portable modeling system. Flexibility means that additional modeling components can be added with ease and portability means that CoastalApp can be built and run under different computing environments and operating systems.

CoastalApp is based on the ESMF (https://earthsystemmodeling.org/) framework for building a NUOPC/NEMS coupling application that includes two types of components (a) 1-way and 2-way coupled modeling components (model source + NUOPC Cap) and (b) data components (NUOPC Cap only) that pass forcing data, as needed, via NetCDF files to the various models in CoastalApp. The application is based on its predecessor ESMF application ADC-WW3-NWM-NEMS (see Moghimi et. al) developed as part of the Coastal Act coupling project to determine wind versus water percentage losses caused by a Named Storm Event.

The models and modeling components (data components) currently supported in CoastalApp are outlined in Table 1.

Accessing the individual modeling components

• ATMESH : https://github.com/noaa-ocs-modeling/ATMESH
• PAHM : https://github.com/noaa-ocs-modeling/PaHM
• ADCIRC : https://adcirc.org/, https://github.com/adcirc/adcirc (requires registration; please send an email request to Crystal Fulcher)
• SCHISM : http://ccrm.vims.edu/schismweb/, https://github.com/schism-dev/schism
• FVCOM : http://fvcom.smast.umassd.edu/, https://github.com/FVCOM-GitHub
• BARDATA: https://github.com/noaa-ocs-modeling/BARDATA
• WW3 : https://github.com/NOAA-EMC/WW3/wiki, https://github.com/NOAA-EMC/WW3
• WW3DATA: https://github.com/noaa-ocs-modeling/WW3DATA

Downloading CoastalApp

CoastalApp is hosted in NOAA's Office of Coast Survey github modeling repository: https://github.com/noaa-ocs-modeling along with other applications and models. The source code of CoastalApp is publicly available from the GitHub repository: https://github.com/noaa-ocs-modeling/CoastalApp (binary distributions of CoastalApp are not currently available).

The application can be downloaded using the following method:

Clone the source code from GitHub:

    git clone --recurse-submodules  https://github.com/noaa-ocs-modeling/CoastalApp.git

The source will be downloaded into the target directory CoastalApp. It is assumed that all subsequent operations are taking place into the CoastalApp directory.

Most of the modeling components in the CoastalApp GitHub repository (e.g., ADCIRC, SCHISM, ...) are simply git submodules (pointers) that point to the respective repository of each model. Some models, for example ADCIRC and FVCOM, require that the user is registered with the respective model repository in order to be granted access. In case, users don't have access to a model and in order to avoid errors and permission issues during the cloning process of CoastalApp, they can exclude the particular modeling component using, for example, commands like:

• Exclude ADCIRC from cloning using one of the following commands:

  • git -c submodule."ADCIRC".update=none clone --recurse-submodules https://github.com/noaa-ocs-modeling/CoastalApp.git

    OR

  • git clone --recurse-submodules=":(exclude)ADCIRC" https://github.com/noaa-ocs-modeling/CoastalApp.git

• Exclude multiple components (ADCIRC, PAHM and SCHISM) from cloning using one of the following commands:

  • git -c submodule."ADCIRC".update=none -c submodule."PAHM".update=none -c submodule."SCHISM/schism".update=none -c submodule."SCHISM/schism-esmf".update=none clone --recurse-submodules https://github.com/noaa-ocs-modeling/CoastalApp.git

    OR

  • git clone --recurse-submodules=':(exclude)ADCIRC' --recurse-submodules=':(exclude)PAHM' --recurse-submodules=":(exclude)SCHISM/*" https://github.com/noaa-ocs-modeling/CoastalApp.git

Note: The alternative method of downloading the application by fetching the zip archive via the command:

    wget https://github.com/noaa-ocs-modeling/CoastalApp/archive/refs/heads/main.zip

will download CoastalApp but all the model component directories will be empty as these components are basically pointers to their respective repositories. Only CoastalApp's configuration and build files will be available in this case. If users are only interested on how CoastalApp is configured, they can download the archive and extract the sources in the CoastalApp directory by issuing the following commands:

    unzip -o main.zip  (the data will be extracted into the CoastalApp-main directory)

    mv CoastalApp-main CoastalApp  (move the extracted files to the CoastalApp directory)

By using the distributed version control system Git, users will be able to follow the CoastalApp development and its updates and furthermore they will be able to easily merge to new versions of the application. New Git users are invited to read some of the online guides to get familiar with vanilla Git concepts and commands:

• Basic and advanced guide with the Git Book.
• Reference guides with the Git Reference.
• GitHub reference sheets with the GitHub Reference.
• Manage your GitHub repositories with Git Using Git.

Building CoastalApp

The build infrastracture in CoastalApp uses a hybrid "Make" system based on GNU Make and CMake toolkits that manage building of the source code and the generation of executables and other non-source files of a program. Furthermore, CostalApp utilizes environment module systems like Lmod (installed in most HPC clusters) or Environment Modules.

Requirements

1. Recent version of CMake (version ≥ 3.2).
2. Recent Fortran/C/C++ compilers: The compilers tested are Intel ≥ 18, GCC ≥ 4.8 and PGI/NVidia ≥ 20.11.
3. Recent MPI implementation: The Message Passing Interface libraries tested are Intel's MPI, OpenMPI and MVAPICH.
4. Recent version of the NetCDF-4 libraries: the Network Common Data Form (NetCDF) C and Fortran libraries (usually installed in the host OS).
5. Recent version of the HDF5 libraries: the High-performance software and Data Format (HDF) libraries (usually installed in the host OS).
6. Recent version of the ESMF libraries: the Earth System Modeling Framework (version ≥ 8.1).
7. ParMETIS libraries (Optional). This library is required if building WaveWatch III (WW3 component, mandatory) or SCHISM (optional). The library is not shipped with CoastalApp and it is the user's responsibility to download the library before compiling CoastalApp. The script download_parmetis.sh in CostalApp/scripts directory is supplied for this reason.

NOTE: It is important to note that the user needs to make sure that all the libraries and CoastalApp are compiled using exactly the same compilers (and possibly versions; you cannot mix compilers and compiler versions).

Build System

To build CoastalApp the user should run the build.sh bash script (a link to the scripts/build.sh) located in the root directory of the downloaded source code. The build script accepts many options to allow the user to customize the compilation of CoastalApp. Running the script as:

    build.sh --help

will bring up a help screen as shown in Table 2 that explains the use of all available options to the script:

Installing ParMETIS (Optional)

The unstructured WW3 and SCHISM models require the use of ParMETIS/METIS libraries for domain decomposition. While, the installation of this library is mandatory for WW3 (at this point), for SCHISM is optional as the model contains an internal version of ParMETIS (the model can use either the internal or the externally built library or do not use ParMETIS at all). To ease the compilation of the library, CoastalApp supplies the script scripts/download_parmetis.sh to first download the source code of the library and then build the library by supplying the option --tp parmetis to the build script. The library source is downloaded into the CoastalApp/thirdparty_open directory. Assuming that ParMETIS is already downloaded, to build ParMETIS and WW3 run the build script as follows:

    build.sh -compiler intel -platform=hera --component ww3 --tp=parmetis

The above command will first compile ParMETIS and then will continue with the compilation of WW3 (notice that different formats can be used for the supplied options, all work the same way). ParMETIS libraries will be installed in the CoastalApp/THIRDPARTY_INSTALL direcory (this directory never gets deleted during a clean process).

In the case users want to use a pre-compiled version of ParMETIS (either in THIRDPARTY_INSTALL, or in a system-wide installation), they can run the build script as:

    PARMETISHOME=FULL_PATH_TO/CostalApp/THIRDPARTY_INSTALL build.sh -compiler intel -platform=hera --component schism

and CoastalApp will use the installed ParMETIS in CostalApp/THIRDPARTY_INSTALL. If there is a system wide installed ParMETIS, users can set the PARMETISHOME variable to point to the system's installed ParMETIS. In any case, CoastalApp tries to find the libraries in PARMETISHOME/lib and the header files in PARMETISHOME/include.

Compilation

This section contains some generic instructions of how to build CoastalApp (NEMS application). The following steps will help in building CoastalApp on a local machine (desktop or otherwise) or on a HPC cluster.

1. Make sure that CMake and the NetCDF/HDF5/ESMF libraries are in the user's PATH environment. In a Cluster/HPC system that uses the environment module system, the user should load all the required modules for CMake NetCDF, HDF5 and ESMF before building CoastalApp (this is done by setting the --platform option).

2. Run the build.sh script as:

     build.sh --compiler COMPILER --platform PLATFORM --component "LIST OF COMPONENTS" --tp parmetis (if needed) 
   

The option --component is mandatory as it is indentionally left with no default value. It is up to the user to supply the list of components to compile (at minimum one component is needed). All other options are optional and most of them have default values assigned to them (see Table 2). If the user chooses a supported platform to compile CoastalApp for, the build script will load the appropriate modulefile found in the modulefiles/ directory. In case the application needs to be built for an unsupported platform, ther user can copy one of the modulefiles/envmodules_<COMPILER>.custom files, rename it to modulefiles/envmodules_<COMPILER>.<USER'S_PLATFORM> and then modify the file according to the chosen platform's configuration.

Upon successful compilation of CoastalApp, the binaries and libraries for each component are installed into its respective <COMPONENT>_INSTALL directory (e.g., SCHISM_INSTALL). In addition, all component executables, libraries and other files are also installed (copied) into the ALLBIN_INSTALL directory. This directory never gets deleted during a complete cleanup of the compiled files and it is the user's responsibility to delete this directory (if needed). The final NEMS executable that contains all model components requested by the user is installed into the ALLBIN_INSTALL directory as two identical files: NEMS-<COMPONENT_LIST>.x and NEMS.x. As a sanity check, the user might want to check that all files were installed properly in the ALLBIN_INSTALL directory (e.g., check the file sizes).

• Example 1 Compile ATMESH and ADCIRC using the Intel compiler for the "tacc" platform:

    build.sh --compiler intel --platform tacc --component "atmesh adcirc"
  

  In this case, the build script will first load the modulefiles/envmodules_intel.tacc file and then will present to the user a list of the configured parameters, waiting for a yes/no to continue. Upon successful compilation all component executables, libraries and the NEMS*.x executables are installed in the ALLBIN_INSTALL directory.

• Example 2 Build NEMS.x for PAHM, ATMESH, ADCIRC, WW3 on "hera" using the Intel compiler:

  • First download ParMETIS (as described previously):

    Run: scripts/download_parmetis.sh

  • Next build the application:

    build.sh --compiler intel --platform hera --component "pahm atmesh adcirc ww3" --tp parmetis
    

  In this case, the build script will first load the modulefiles/envmodules_intel.hera file and then will present to the user a list of the configured parameters, waiting for a yes/no to continue. Next it will compile and install the ParMETIS/METIS libraries into the THIRDPARTY_INSTALL directory setting all the appropriate METIS environment variables. Finally it will continue with the compilations of all requested components to produce the NEMS.x executable.

• Example 3 Rebuild NEMS.x for PAHM, ATMESH, ADCIRC, WW3 on "hera" using the Intel compiler, the already installed ParMETIS and cleaning the previously compiled components (the ALLBIN_INSTALL directory is not deleted)

  • First run:

    PARMETISHOME=FULL_PATH/THIRDPARTY_INSTALL build.sh --compiler intel --platform hera --component "pahm atmesh adcirc ww3" --clean 2

    This cleans all components (see Table 2), and deletes all COMPONENT_INSTALL folders except the ALLBIN_INSTALL directory. This step is required to ensure the integrity of the subsequent build.

  • Next build the application:

    PARMETISHOME=FULL_PATH/THIRDPARTY_INSTALL build.sh --compiler intel --platform hera --component "pahm atmesh adcirc ww3"
    

• Example 4 Build NEMS.x for ATMESH and SCHISM, WW3 on "hera" using the Intel compiler, SCHISM's internal ParMETIS and accepting all parameter settings:

  build.sh --compiler intel --platform hera --component "atmesh schism" -y
  

  In this case, the build script will load the modulefiles/envmodules_intel.hera file and it will continue to the compilation without waiting for a yes/no answer.

Organization / Responsibility

NEMS application implementing ESMF / NUOPC coupling

• Saeed Moghimi (lead) - [email protected]
• Panagiotis Velissariou - [email protected]

Past Contributors:

• Zachary Burnett - [email protected]
• Andre Van der Westhuysen - [email protected]
• Beheen Trimble - [email protected]

ESMF / NUOPC Cap for the ADCIRC model

• Saeed Moghimi (lead) [email protected]
• Damrongsak Wirasaet - [email protected]
• Panagiotis Velissariou - [email protected]

Past Contributors:

• Guoming Ling - [email protected]
• Zachary Burnett - [email protected]

ESMF / NUOPC Cap for the FVCOM model

• Jianhua Qi (lead) - [email protected]
• Saeed Moghimi - [email protected]

ESMF / NUOPC Cap for the SCHISM model

• Carsten Lemmen (lead) - [email protected]
• Y. Joseph Zhang - [email protected]

ESMF / NUOPC Cap for the WW3 model

• Ali Abdolali - [email protected]

Past Contributors:

• Andre Van der Westhuysen - [email protected]

PaHM model and ESMF / NUOPC Cap for the PaHM model

• Panagiotis Velissariou (lead) - [email protected]

BARDATA data component and ESMF / NUOPC Cap for the BARDATA data component

• Panagiotis Velissariou (lead) - [email protected]

ATMESH data component and ESMF / NUOPC Cap for the ATMESH data component

• Saeed Moghimi (lead) [email protected]
• Panagiotis Velissariou - [email protected]

Past Contributors:

• Guoming Ling - [email protected]

WW3DATA data component and ESMF / NUOPC Cap for the WW3DATA data component

• Saeed Moghimi (lead) [email protected]
• Panagiotis Velissariou - [email protected]

Past Contributors:

• Guoming Ling - [email protected]

ESMF / NUOPC Cap for the NWM model

• Daniel Rosen (lead) - [email protected]
• Jason Ducker - [email protected]
• Other colleagues from NWS / OWP

Past Contributors:

• Beheen Trimble - [email protected]

Contributing

Feel free to fork this repository and create a pull request with contributions.

Adding a new platform / compiler to compilation script

The environment files are stored in the CoastalApp/modulefiles/ directory following the filename naming scheme: envmodules_<COMPILER>.<PLATFORM>

To compile CoastalApp in your own system you should create a similar file (if the system is not supported), and then run build.sh as usual to compile the application.

Collaboration

To collaborate and contribute to this repository follow below instructions:

1. Go to https://github.com/noaa-ocs-modeling/CoastalApp
2. Create a fork (click Fork on the upper right corner), and fork to your account.
3. Clone your forked repository: git clone --recursive https://github.com/<ACCOUNT>/CoastalApp
4. Edit the files locally: git status
5. Commit changes: git commit -a -m "describe what you changed"
6. Push your changes to GitHub: git push
7. Enter your GitHub username/password if asked
8. Create a pull request with descriptions of changes at: https://github.com/noaa-ocs-modeling/CoastalApp/compare/<BRANCH>...<ACCOUNT>:<BRANCH>

Citations

[1] Moghimi, S., Van der Westhuysen, A., Abdolali, A., Myers, E., Vinogradov, S., Ma, Z., Liu, F., Mehra, A., & Kurkowski, N. (2020). Development of an ESMF Based Flexible Coupling Application of ADCIRC and WAVEWATCH III for High Fidelity Coastal Inundation Studies. Journal of Marine Science and Engineering, 8(5), 308. https://doi.org/10.3390/jmse8050308

[2] Moghimi, S., Vinogradov, S., Myers, E. P., Funakoshi, Y., Van der Westhuysen, A. J., Abdolali, A., Ma, Z., & Liu, F. (2019). Development of a Flexible Coupling Interface for ADCIRC model for Coastal Inundation Studies. NOAA Technical Memorandum, NOS CS(41). https://repository.library.noaa.gov/view/noaa/20609/

[3] Moghimi, S., Westhuysen, A., Abdolali, A., Myers, E., Vinogradov, S., Ma, Z., Liu, F., Mehra, A., & Kurkowski, N. (2020). Development of a Flexible Coupling Framework for Coastal Inundation Studies. https://arxiv.org/abs/2003.12652