Executable to rule them all

CMakeLists.txt

@@ -36,6 +36,13 @@ option(BUILD_GDASBUNDLE "Build GDAS Bundle" ON)
 option(CLONE_JCSDADATA "Clone JCSDA test data repositories" OFF)
 option(WORKFLOW_TESTS "Include global-workflow dependent tests" OFF)
 
+# Build GDAS-managed JEDI executables
+if( BUILD_GDASBUNDLE )
+  find_package( fv3jedi REQUIRED )
+  find_package( soca REQUIRED )
+  add_subdirectory( mains )
+endif()
+
 # Install utility scripts.
 add_subdirectory(ush)
 

build.sh

@@ -126,7 +126,7 @@ set -x
 if [[ $BUILD_JCSDA == 'YES' ]]; then
   make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE
 else
-  builddirs="fv3-jedi soca iodaconv land-imsproc land-jediincr gdas-utils"
+  builddirs="gdas iodaconv land-imsproc land-jediincr gdas-utils"
   for b in $builddirs; do
     cd $b
     make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE

mains/CMakeLists.txt

@@ -0,0 +1,23 @@
+# Build the big gdas executable used for all generic JEDI applications
+# --------------------------------------------------------------------
+ecbuild_add_executable( TARGET  gdas.x
+                        SOURCES gdas.cc
+                        LIBS    fv3jedi soca
+                      )
+
+# Build the soca executables that are not OOPS-based
+# --------------------------------------------------
+ecbuild_add_executable( TARGET  gdas_soca_gridgen.x
+                        SOURCES ${CMAKE_SOURCE_DIR}/soca/src/mains/GridGen.cc
+                        LIBS    soca
+                      )
+
+ecbuild_add_executable( TARGET  gdas_soca_error_covariance_toolbox.x
+                        SOURCES ${CMAKE_SOURCE_DIR}/soca/src/mains/ErrorCovarianceToolbox.cc
+                        LIBS    soca saber
+                      )
+
+ecbuild_add_executable( TARGET  gdas_soca_setcorscales.x
+                        SOURCES ${CMAKE_SOURCE_DIR}/soca/src/mains/SetCorScales.cc
+                        LIBS    soca
+                      )

mains/gdas.cc

@@ -0,0 +1,122 @@
+// -------------------------------------------------------------------------------------------------
+
+#include <functional>
+#include <map>
+
+#include "fv3jedi/ObsLocalization/instantiateObsLocFactory.h"
+#include "fv3jedi/Utilities/Traits.h"
+
+#include "soca/Traits.h"
+
+#include "oops/generic/instantiateModelFactory.h"
+#include "saber/oops/instantiateCovarFactory.h"
+#include "ufo/instantiateObsErrorFactory.h"
+#include "ufo/instantiateObsFilterFactory.h"
+#include "ufo/ObsTraits.h"
+
+#include "oops/runs/ConvertState.h"
+#include "oops/runs/HofX4D.h"
+#include "oops/runs/LocalEnsembleDA.h"
+#include "oops/runs/Run.h"
+#include "oops/runs/Variational.h"
+
+// -------------------------------------------------------------------------------------------------
+
+template<typename Traits>
+int runApp(int argc, char** argv, const std::string traits, const std::string appName) {
+  // Create the Run object
+  oops::Run run(argc, argv);
+
+  // Instantiate oops factories
+  oops::instantiateModelFactory<Traits>();
+
+  // Instantiate saber factories
+  saber::instantiateCovarFactory<Traits>();
+
+  // Intantiate ufo factories
+  ufo::instantiateObsErrorFactory();
+  ufo::instantiateObsFilterFactory();
+
+  // Localization for ensemble DA
+  if (appName == "localensembleda") {
+    if (traits == "fv3jedi") {
+      fv3jedi::instantiateObsLocFactory();
+    } else if (traits == "soca") {
+      ufo::instantiateObsLocFactory<soca::Traits>();
+    }
+  }
+
+  // Application pointer
+  std::unique_ptr<oops::Application> app;
+
+  // Define a map from app names to lambda functions that create unique_ptr to Applications
+  std::map<std::string, std::function<std::unique_ptr<oops::Application>()>> apps;
+
+  apps["convertstate"] = []() {
+      return std::make_unique<oops::ConvertState<Traits>>();
+  };
+  apps["hofx4d"] = []() {
+      return std::make_unique<oops::HofX4D<Traits, ufo::ObsTraits>>();
+  };
+  apps["localensembleda"] = []() {
+      return std::make_unique<oops::LocalEnsembleDA<fv3jedi::Traits, ufo::ObsTraits>>();
+  };
+  apps["variational"] = []() {
+    return std::make_unique<oops::Variational<Traits, ufo::ObsTraits>>();
+  };
+
+  // Create application object and point to it
+  auto it = apps.find(appName);
+
+  // Run the application
+  return run.execute(*(it->second()));
+}
+
+// -------------------------------------------------------------------------------------------------
+
+int main(int argc,  char ** argv) {
+  // Check that the number of arguments is correct
+  // ----------------------------------------------
+  ASSERT_MSG(argc >= 3, "Usage: " + std::string(argv[0]) + " <traits> <application> <options>");
+
+  // Get traits from second argument passed to executable
+  // ----------------------------------------------------
+  std::string traits = argv[1];
+  for (char &c : traits) {c = std::tolower(c);}
+
+  // Get the application to be run
+  std::string app = argv[2];
+  for (char &c : app) {c = std::tolower(c);}
+
+  // Check that the traits are recognized
+  // ------------------------------------
+  const std::set<std::string> validTraits = {"fv3jedi", "soca"};
+  ASSERT_MSG(validTraits.find(traits) != validTraits.end(), "Traits not recognized: " + traits);
+
+  // Check that the application is recognized
+  // ----------------------------------------
+  const std::set<std::string> validApps = {
+    "convertstate",
+    "hofx4d",
+    "localensembleda",
+    "variational"
+  };
+  ASSERT_MSG(validApps.find(app) != validApps.end(), "Application not recognized: " + app);
+
+  // Remove traits and program from argc and argv
+  // --------------------------------------------
+  argv[2] = argv[0];  // Move executable name to third position
+  argv += 2;          // Move pointer up two
+  argc -= 2;          // Remove 2 from count
+
+  // Call application specific main functions
+  // ----------------------------------------
+  if (traits == "fv3jedi") {
+    fv3jedi::instantiateObsLocFactory();
+    return runApp<fv3jedi::Traits>(argc, argv, traits, app);
+  } else if (traits == "soca") {
+    return runApp<soca::Traits>(argc, argv, traits, app);
+  }
+}
+
+// -------------------------------------------------------------------------------------------------

scripts/exgdas_global_marine_analysis_bmat.sh

@@ -47,9 +47,9 @@ function clean_yaml()
 if [[ -e 'soca_gridspec.nc' ]]; then
     echo "soca_gridspc.nc already exists, skip the grid generation step"
 else
-    # Run soca_gridgen.x if the grid was not staged
+    # Run gdas_soca_gridgen.x if the grid was not staged
     # TODO (Guillaume): Should not use all pe's for the grid generation
-    $APRUN_OCNANAL $JEDI_BIN/soca_gridgen.x gridgen.yaml
+    $APRUN_OCNANAL $JEDI_BIN/gdas_soca_gridgen.x gridgen.yaml
     export err=$?; err_chk
     if [ $err -gt 0  ]; then
         exit $err
@@ -101,14 +101,14 @@ fi
 # Horizontal diffusion
 if [ ! -f "ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc" ]; then
     # Set decorrelation scales for the static B
-    $APRUN_OCNANAL $JEDI_BIN/soca_setcorscales.x soca_setcorscales.yaml
+    $APRUN_OCNANAL $JEDI_BIN/gdas_soca_setcorscales.x soca_setcorscales.yaml
     export err=$?; err_chk
     if [ $err -gt 0  ]; then
         exit $err
     fi
     # Initialize the horizontal diffusion block and normalize
     clean_yaml soca_parameters_diffusion_hz.yaml
-    $APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_toolbox.x soca_parameters_diffusion_hz.yaml
+    $APRUN_OCNANAL $JEDI_BIN/gdas_soca_error_covariance_toolbox.x soca_parameters_diffusion_hz.yaml
     export err=$?; err_chk
     if [ $err -gt 0  ]; then
         exit $err
@@ -125,7 +125,7 @@ python ${HOMEgfs}/sorc/gdas.cd/sorc/soca/tools/calc_scales.py soca_vtscales.yaml
 clean_yaml soca_parameters_diffusion_vt.yaml
 
 # Initialize the vertical diffusion block and normalize
-$APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_toolbox.x soca_parameters_diffusion_vt.yaml
+$APRUN_OCNANAL $JEDI_BIN/gdas_soca_error_covariance_toolbox.x soca_parameters_diffusion_vt.yaml
 export err=$?; err_chk
 if [ $err -gt 0  ]; then
     exit $err

scripts/exgdas_global_marine_analysis_chkpt.sh

@@ -67,8 +67,8 @@ fi
 # TODO: This should probably be in a separate j-job, that includes
 #       the mom6 incr postprocessing from above.
 
-$APRUN_OCNANAL ${JEDI_BIN}/soca_convertstate.x soca_2cice_arctic.yaml
-$APRUN_OCNANAL ${JEDI_BIN}/soca_convertstate.x soca_2cice_antarctic.yaml
+$APRUN_OCNANAL ${JEDI_BIN}/gdas.x soca convertstate soca_2cice_arctic.yaml
+$APRUN_OCNANAL ${JEDI_BIN}/gdas.x soca convertstate soca_2cice_antarctic.yaml
 export err=$?; err_chk
 
 ################################################################################

scripts/exgdas_global_marine_analysis_run.sh

@@ -41,7 +41,7 @@ function clean_yaml()
 # run the variational application
 cp var.yaml var_original.yaml
 clean_yaml var.yaml
-$APRUN_OCNANAL $JEDI_BIN/soca_var.x var.yaml
+$APRUN_OCNANAL $JEDI_BIN/gdas.x soca variational var.yaml
 export err=$?; err_chk
 
 ################################################################################

test/aero/global-workflow/config.aeroanl

@@ -18,6 +18,6 @@ export BERROR_DATE="20160630.000000"
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
+export JEDIEXE=${HOMEgfs}/exec/gdas.x
 
 echo "END: config.aeroanl"

test/atm/global-workflow/config.atmanl

@@ -28,6 +28,6 @@ export layout_y_atmanl=@LAYOUT_Y_ATMANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_var.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmanl"

test/atm/global-workflow/config.atmensanl

@@ -18,6 +18,6 @@ export layout_y_atmensanl=@LAYOUT_Y_ATMENSANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_letkf.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmensanl"

test/snow/create_bkg_ens.sh

@@ -30,7 +30,7 @@ if [[ ${DAtype} == 'letkfoi_snow' ]]; then
 
     B=30  # background error std for LETKFOI
 
-    JEDI_EXEC="fv3jedi_letkf.x"
+    JEDI_EXEC="gdas.x fv3jedi localensembleda"
 
     # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
     for ens in 001 002

test/snow/letkfoi_snowda.sh

@@ -38,7 +38,7 @@ if [[ ${DAtype} == 'letkfoi_snow' ]]; then
 
     B=30  # background error std for LETKFOI
 
-    JEDI_EXEC="fv3jedi_letkf.x"
+    JEDI_EXEC="gdas.x fv3jedi localensembleda"
 
     # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
     for ens in 001 002

ush/soca/marine_recenter.py

@@ -180,7 +180,7 @@ def run(self):
         chdir(self.runtime_config.DATA)
 
         exec_cmd_gridgen = Executable(self.config.APRUN_OCNANALECEN)
-        exec_name_gridgen = os.path.join(self.config.JEDI_BIN, 'soca_gridgen.x')
+        exec_name_gridgen = os.path.join(self.config.JEDI_BIN, 'gdas_soca_gridgen.x')
         exec_cmd_gridgen.add_default_arg(exec_name_gridgen)
         exec_cmd_gridgen.add_default_arg(self.config.gridgen_yaml)