ROMS interface to JEDI

The following instructions should have the steps needed to implement an interface capable of running any ROMS-JEDI application, as well as the available data assimilation drivers.

To get started:

• Check out the ROMS-JEDI interface repository.

  git clone https://github.com/myroms/roms-jedi.git
  

  During configuration, the latest version of ROMS source code is downloaded from https://github.com/myroms/roms.git. The source code includes ROMS nonlinear model (NLM), perturbation tangent linear model (TLM), finite-amplitude tangent linear model (RPM), and adjoint model (ADM) kernels. For any ROMS-JEDI application, activate the JEDI C-preprocessing option when configuring ROMS header file to include the NLM, TLM, ADM kernels, and direct interface to the ROMS_initialize, ROMS_run, and ROMS_finalize driver phases.

• By default, ROMS-JEDI is configured with a coarse (54x53x30 grid points) US West Coast (WC13) application. See https://www.myroms.org/wiki/4DVar_Tutorial_Introduction for detailed information about the WC13 configuration. However, any other ROMS application can be configured by including in the ecbuild command the directives -DROMS_APP="MyAppCPP" and -DROMS_APP_DIR="MyAppDirPath".

• Make sure that you computer have installed the jedi-stack software for either gfortran or ifort containing several packages need to run the ROMS-JEDI interface. For more information, please check https://github.com/JCSDA/jedi-stack.

  In our computers at Rutgers University, the jedi-stack can be loaded by executing either:

  > module purge;  module load stack-gcc;    module list                     (gfortran compiler)
  > module purge;  module load stack-intel;  module list                     (ifort compiler)
  

  Installing the jedi-stack is not trivial and requires computer software expertise.

• We also like to define the MPIRUN environmental variable to specify the MPI executable in a particular computer (say, srun, mpirun, etc.). We need the full path for ctest to work. For example,

 setenv MPIRUN /opt/slurm/bin/srun

Notice that we specify this executable in the ecbuid command.

• Several environmental variables can be activated for verbose debugging of the building blocks for the ROMS-JEDI interface: (use 1 or true to activate and 0 or false to deactivate)

  setenv LdebugGeometry             1
  setenv LdebugAnalyticInit         1
  setenv LdebugField                1
  setenv LdebugFields               1
  setenv LdebugFieldsUtils          1
  setenv LdebugGeometry             1
  setenv LdebugLinearModel          1
  setenv LdebugLinearModel2Geovals  1
  setenv LdebugModel                1
  setenv LdebugModel2Geovals        1
  setenv LdebugTrajectory           1
  

• Before cloning the ROMS-JEDI interface, ensure that your ~/.gitconfig has the appropriate git-lfs configuration for correctly downloading WC13 input and observation NetCDF files. Otherwise, the default Unit Tests will fail. The Git LFS is a command line extension and specification for managing large files with Git. A sample of the configuration file looks like this:

  more ~/.gitconf
  
  [user]
       name = GivenName MiddleName FamilyName
       email = your@email
  [credential]
       helper = cache --timeout=7200
       helper = store --file ~/.my-credentials
  [filter "lfs"]
       clean = git-lfs clean -- %f
       smudge = git-lfs smudge -- %f
       process = git-lfs filter-process
       required = true
  

  Alternatively, you may execute git lfs pull at your location of the ROMS-JEDI interface to download a viable version of the Git LFS files for the remote repository in GitHub. Also, to add the LFS filter to your existing ~/.gitconfig automatically, you could use git lfs install.

• A GitHub credential file is helpful so we don't have to repeatedly type the long GitHubAccessToken when cloning/updating all JEDI components' source code.

  more ~/.my-credentials
  
  https://GitHubUserName:GitHubAccessToken@github.com
  

• Our strategy is to create a Bundle and build subdirectory for each application. For WC13 (default), we create Bundle_wc13 and build_wc13 below. Please follow the following steps to configure ROMS-JEDI in your computer:

  git clone https://github.com/myroms/roms-jedi.git          !> if first time in your computer
  
  cd roms-jedi                                               !> ROMS-JEDI interface directory, <interface_dir>
  mkdir Bundle_wc13
  cp bundle/.gitignore bundle/CMakeLists.txt Bundle_wc13
  mkdir build_wc13
  cd build_wc13
  
  ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DCMAKE_BUILD_TYPE=Release ../Bundle_wc13
  make -j 10
  
  cd roms-jedi                                               !> sub-directory: <interface_dir>/build_wc13/roms-jedi
  ctest -N                                                   !> lists all the Unit Tests available
  ctest -E -V get_                                           !> runs all the Unit Tests
  
  cd test/Data                                               !> sub-directory: <interface_dir>/build_wc13/roms-jedi/test/Data
                                                             !> to check the results in various sub-directories
  

• For example, if running the US East Coast DOPPIO application (240x104x40 grid points) or any other, please follow the following steps to configure ROMS-JEDI:

  cd roms-jedi                                               !> ROMS-JEDI interface directory, <interface_dir>
  mkdir Bundle_doppio
  cp bundle/.gitignore bundle/CMakeLists.txt Bundle_doppio
  mkdir build_doppio
  cd build_doppio
  
  ecbuild -DMPIEXEC_EXECUTABLE=$MPIRUN -DMPIEXEC_NUMPROC_FLAG="-n" -DMPIEXEC_NUMPROC=12 -DROMS_APP=DOPPIO -DROMS_APP_DIR=DOPPIOpath -DCMAKE_BUILD_TYPE=Release ../Bundle_doppio
  make -j 10
  
  cd roms-jedi                                               !> sub-directory: <interface_dir>/build_doppio/roms-jedi
  ctest -N                                                   !> lists all the Unit Tests available
  ctest -E -V get_                                           !> runs all the Unit Tests
  
  cd test/Data                                               !> sub-directory: <interface_dir>/build_doppio/roms-jedi/test/Data
                                                             !> to check the results in various sub-directories
  

  DOPPIOpath is a directory in your computer containing the DOPPIO configuration and input files. Use the default WC13 set up in roms-jedi/test/Applications/wc13 as an example of configuring any other ROMS application.

• If the directive -DMPIEXEC_NUMPROC is not specified, the ROMS-JEDI interface will run the Unit Test cases and data assimilation algorithms with two (2) processes by default. Because of efficiency and memory requirements, many MPI processes will be needed in larger applications.

• The ecbuild command builds by default the RelWithDebInfo (-O2 -g options) for optimized with debugging information version of JEDI and ROMS-JEDI, rendering slower execution. However for faster and optimized execution, we include the include the directive -DCMAKE_BUILD_TYPE=Release to the ecbuild command. For debugging with TotalView, we includle instead the directive -DCMAKE_BUILD_TYPE=Debug, which is much slower.

• Any ROMS application can be run in ROMS-JEDI by specifying the appropriate CPP option and necessary input files. Only WC13 is provided with the interface. However, we facilitate how to run such applications. Notice that the WC13 configuration and input files are located in roms-jedi/test/Applications/wc13. The template input YAML files are located roms-jedi/test/templates. We use a Perl script to create the application input YAML files from the templates. Please check in roms-jedi/test/Applications/wc13/testinput.