R4DVAR Tutorial

4-DVar Indirect Representer

The various files in the R4DVAR folder are needed to run the Strong/Weak constraint, 4-Dimensional Variational (4D-Var) data assimilation based on the indirect representer algorithm algorithm in the California Current System, 1/3° resolution, application (WC13).

This page is under construction

Important CPP Options

W4DVAR R4D-Var driver (observation space)
POSTERIOR_EOFS Estimate posterior analysis error
POSTERIOR_ERROR_I Estimate initial posterior analysis error
WC13 Application CPP option

Input NetCDF Files

Grid File: ../Data/wc13_grd.nc
Nonlinear Initial File: wc13_ini.nc
Forcing File 01: ../Data/coamps_wc13_lwrad_down.nc
Forcing File 02: ../Data/coamps_wc13_Pair.nc
Forcing File 03: ../Data/coamps_wc13_Qair.nc
Forcing File 04: ../Data/coamps_wc13_rain.nc
Forcing File 05: ../Data/coamps_wc13_swrad.nc
Forcing File 06: ../Data/coamps_wc13_Tair.nc
Forcing File 07: ../Data/coamps_wc13_wind.nc
Boundary File: ../Data/wc13_ecco_bry.nc

Initial Conditions STD File: ../Data/wc13_std_i.nc
Model STD File: ../Data/wc13_std_m.nc
Boundary Conditions STD File: ../Data/wc13_std_b.nc
Surface Forcing STD File: ../Data/wc13_std_f.nc
Initial Conditions Norm File: ../Data/wc13_nrm_i.nc
Model Norm File: ../Data/wc13_nrm_m.nc
Boundary Conditions Norm File: ../Data/wc13_nrm_b.nc
Surface Forcing Norm File: ../Data/wc13_nrm_f.nc
Observations File: wc13_obs.nc

Various Scripts and Include Files

build.bash bash shell script to compile application
build.sh csh Unix script to compile application
job_r4dvar.sh job configuration script
ocean_wc13.in ROMS standard input script for WC13
s4dvar.in 4D-Var standard input script template
wc13.h WC13 header with CPP options

Instructions

To run this application you need to take the following steps:

1. Customize your preferred build script and provide the appropriate values for:
   • Root directory, MY_ROOT_DIR
   • ROMS source code, MY_ROMS_SRC
   • Fortran compiler, FORT
   • MPI flags, USE_MPI and USE_MPIF90
   • Path of MPI, NetCDF, and ARPACK libraries according to the compiler. Notice that you need to provide the correct places of these libraries for your computer. If you want to ignore this section, comment out the assignment for the variable USE_MY_LIBS.
2. Notice that the most important CPP options for this application are specified in the build script instead of wc13.h:
   setenv MY_CPP_FLAGS "-DW4DVAR"
   setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DPOSTERIOR_EOFS"
   setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DPOSTERIOR_ERROR_I"
   This is to allow flexibility with different CPP options.
   
   For this to work, however, any #undef directives MUST be avoided in the header file wc13.h since it has precedence during C-preprocessing.
3. You MUST use the build script to compile.
4. Customize the ROMS input script ocean_wc13.in and specify the appropriate values for the distributed-memory partition. It is set by default to:
   NtileI == 2  ! I-direction partition
   NtileJ == 2  ! J-direction partition
   Notice that the adjoint-based algorithms can only be run in parallel using MPI. This is because of the way that the adjoint model is constructed.
5. Customize the configuration script job_r4dvar.sh and provide the appropriate place for the "substitute" Perl script:
   set SUBSTITUTE=${ROMS_ROOT}/ROMS/Bin/substitute
   This script is distributed with ROMS and it is found in the ROMS/Bin sub-directory. Alternatively, you can define ROMS_ROOT environmental variable in your .cshrc login script. For example, I have:
   setenv ROMS_ROOT /home/arango/ocean/toms/repository/trunk
6. Execute the configuration job_r4dvar.sh BEFORE running the model. It copies the required files and creates r4dvar.in input script from template s4dvar.in. This has to be done EVERY TIME that you run this application. We need a clean and fresh copy of the initial conditions and observation files since they are modified by ROMS during execution.
7. Run ROMS with data assimilation:
   mpirun -np 4 oceanM ocean_wc13.in > & log &

References

Moore, A.M., H.G. Arango, G. Broquet, B.S. Powell, J. Zavala-Garay, and A.T. Weaver, 2010: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part I: System overview, Ocean Modelling, draft.

Moore, A.M., H.G. Arango, and G. Broquet, C. Edwards, M. Veneziani, B.S. Powell, D. Foley, J. Doyle, D. Costa, and P. Robinson, 2010: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part II: Performance and application to the California Current System, Ocean Modelling, Draft.

Moore, A.M., H.G. Arango, and G. Broquet, C. Edwards, M. Veneziani, B.S. Powell, D. Foley, J. Doyle, D. Costa, and P. Robinson, 2010: The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems, Part III: Observation Impact and Observation Sensitivity in the California Current System, Ocean Modelling, Draft.