Merge branch 'develop' into feature/move_jcb

NOAA-EMC · Jun 13, 2024 · 368c9c5 · 368c9c5
2 parents 0cda73b + 9ffce97
commit 368c9c5
Show file tree

Hide file tree

Showing 47 changed files with 1,175 additions and 703 deletions.
diff --git a/.github/workflows/norms.yaml b/.github/workflows/norms.yaml
@@ -25,4 +25,4 @@ jobs:
     - name: Run C++ linter on utils 
       run: |
         cd $GITHUB_WORKSPACE/GDASApp/utils/test/
-        ./cpplint.py --quiet --recursive $GITHUB_WORKSPACE/GDASApp/utils
+        ./cpplint.py --quiet --recursive --exclude=$GITHUB_WORKSPACE/GDASApp/utils/obsproc/rtofs/*.cc $GITHUB_WORKSPACE/GDASApp/utils
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,6 +8,8 @@ cmake_minimum_required( VERSION 3.20 FATAL_ERROR )
 find_package(ecbuild 3.5 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
 
 project(GDASApp VERSION 1.0.0 LANGUAGES C CXX Fortran )
+# include_directories(${CMAKE_SOURCE_DIR})
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
 include(GNUInstallDirs)
 enable_testing()

diff --git a/mains/gdas.cc b/mains/gdas.cc
@@ -14,6 +14,7 @@
 #include "ufo/instantiateObsFilterFactory.h"
 #include "ufo/ObsTraits.h"
 
+#include "oops/runs/ConvertToStructuredGrid.h"
 #include "oops/runs/ConvertState.h"
 #include "oops/runs/HofX4D.h"
 #include "oops/runs/LocalEnsembleDA.h"
@@ -52,6 +53,9 @@ int runApp(int argc, char** argv, const std::string traits, const std::string ap
   // 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["converttostructuredgrid"] = []() {
+      return std::make_unique<oops::ConvertToStructuredGrid<Traits>>();
+  };	
   apps["convertstate"] = []() {
       return std::make_unique<oops::ConvertState<Traits>>();
   };
@@ -96,6 +100,7 @@ int main(int argc,  char ** argv) {
   // Check that the application is recognized
   // ----------------------------------------
   const std::set<std::string> validApps = {
+    "converttostructuredgrid",
     "convertstate",
     "hofx4d",
     "localensembleda",

diff --git a/parm/aero/berror/aero_diagb.yaml.j2 b/parm/aero/berror/aero_diagb.yaml.j2
@@ -56,5 +56,5 @@ rescale: 2.0    # rescales the filtered std. dev. by "rescale"
 number of halo points: 4
 number of neighbors: 16
 simple smoothing:
-  horizontal iterations: 2
-  vertical iterations: 1
+  horizontal iterations: 0 
+  vertical iterations: 0
diff --git a/parm/aero/berror/aero_diffparm.yaml.j2 → parm/aero/berror/aero_diffusionparm.yaml.j2 b/parm/aero/berror/aero_diffparm.yaml.j2 → parm/aero/berror/aero_diffusionparm.yaml.j2
diff --git a/parm/aero/obs/config/viirs_n20_aod.yaml.j2 b/parm/aero/obs/config/viirs_n20_aod.yaml.j2
@@ -28,11 +28,18 @@
   obs filters:
     - filter: PreQC
       maxvalue: 1
+    - filter: Domain Check
+      where:
+      - variable:
+          name: latitude@MetaData
+        minvalue: -60
+        maxvalue: 60
     - filter: Bounds Check
       filter variables:
       - name: aerosolOpticalDepth
         channels: 4
       minvalue: 0
+      maxvalue: 4.9
       action:
         name: reject
     - filter: Background Check

diff --git a/parm/aero/obs/config/viirs_n21_aod.yaml.j2 b/parm/aero/obs/config/viirs_n21_aod.yaml.j2
@@ -0,0 +1,50 @@
+- obs space:
+    name: viirs_n21_aod
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: "{{ DATA }}/obs/{{ OPREFIX }}viirs_n21.{{ current_cycle | to_YMDH }}.nc4"
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{ DATA }}/diags/diag_viirs_n21_{{ current_cycle | to_YMDH }}.nc4"
+    io pool:
+      max pool size: 1
+    simulated variables: [aerosolOpticalDepth]
+    channels: 4
+  get values:
+    interpolation method: barycentric
+    time interpolation: linear
+  obs operator:
+    name: AodCRTM
+    Absorbers: [H2O,O3]
+    obs options:
+      Sensor_ID: v.viirs-m_j2
+      EndianType: little_endian
+      CoefficientPath: "{{ DATA }}/crtm/"
+      AerosolOption: aerosols_gocart_default
+  obs error:
+    covariance model: diagonal
+  obs filters:
+    - filter: PreQC
+      maxvalue: 1
+    - filter: Domain Check
+      where:
+      - variable:
+          name: latitude@MetaData
+        minvalue: -60
+        maxvalue: 60
+    - filter: Bounds Check
+      filter variables:
+      - name: aerosolOpticalDepth
+        channels: 4
+      minvalue: 0
+      maxvalue: 4.9
+      action:
+        name: reject
+    - filter: Background Check
+      channels: 4
+      threshold: 3.0
+      action:
+        name: inflate error
+        inflation factor: 3.0
diff --git a/parm/aero/obs/config/viirs_npp_aod.yaml.j2 b/parm/aero/obs/config/viirs_npp_aod.yaml.j2
@@ -28,11 +28,18 @@
   obs filters:
     - filter: PreQC
       maxvalue: 1
+    - filter: Domain Check
+      where:
+      - variable:
+          name: latitude@MetaData
+        minvalue: -60
+        maxvalue: 60
     - filter: Bounds Check
       filter variables:
       - name: aerosolOpticalDepth
         channels: 4
       minvalue: 0
+      maxvalue: 4.9
       action:
         name: reject
     - filter: Background Check

diff --git a/sorc/fv3 b/sorc/fv3
diff --git a/sorc/gsw b/sorc/gsw
diff --git a/sorc/land-imsproc b/sorc/land-imsproc
diff --git a/sorc/land-jediincr b/sorc/land-jediincr
diff --git a/test/atm/global-workflow/config.atmanl b/test/atm/global-workflow/config.atmanl
diff --git a/test/atm/global-workflow/config.atmensanl b/test/atm/global-workflow/config.atmensanl
diff --git a/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2 b/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2
@@ -19,5 +19,5 @@ atm_obsdatain_suffix: ".{{ current_cycle | to_YMDH }}.nc"
 # --------------
 test_reference_filename: {{ HOMEgfs }}/sorc/gdas.cd/test/atm/global-workflow/3dvar.ref
 test_output_filename: ./3dvar.out
-float_relative_tolerance: 1.0e-3
-float_absolute_tolerance: 1.0e-5
+test_float_relative_tolerance: 1.0e-3
+test_float_absolute_tolerance: 1.0e-5
diff --git a/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2 b/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2
@@ -24,5 +24,5 @@ atm_obsdatain_suffix: ".{{ current_cycle | to_YMDH }}.nc"
 # --------------
 test_reference_filename: {{ HOMEgfs }}/sorc/gdas.cd/test/atm/global-workflow/lgetkf.ref
 test_output_filename: ./lgetkf.out
-float_relative_tolerance: 1.0e-3
-float_absolute_tolerance: 1.0e-5
+test_float_relative_tolerance: 1.0e-3
+test_float_absolute_tolerance: 1.0e-5
diff --git a/test/atm/global-workflow/jjob_ens_final.sh b/test/atm/global-workflow/jjob_ens_final.sh
@@ -46,10 +46,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmensanlfinal-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
 fi
diff --git a/test/atm/global-workflow/jjob_ens_inc.sh b/test/atm/global-workflow/jjob_ens_inc.sh
@@ -46,10 +46,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT --job-name=atmensanlfv3inc-%j.out
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
 fi
diff --git a/test/atm/global-workflow/jjob_ens_init.sh b/test/atm/global-workflow/jjob_ens_init.sh
@@ -109,10 +109,8 @@ for imem in $(seq 1 $NMEM_ENS); do
 done
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmensanlinit-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
 fi
diff --git a/test/atm/global-workflow/jjob_ens_run.sh b/test/atm/global-workflow/jjob_ens_run.sh
@@ -49,10 +49,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --nodes=1 --ntasks=36 --account=$ACCOUNT --qos=batch --time=00:30:00 --export=ALL --wait --output=atmensanlletkf-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
 fi
diff --git a/test/atm/global-workflow/jjob_var_final.sh b/test/atm/global-workflow/jjob_var_final.sh
@@ -46,10 +46,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmanlfinal-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
 fi
diff --git a/test/atm/global-workflow/jjob_var_inc.sh b/test/atm/global-workflow/jjob_var_inc.sh
@@ -46,10 +46,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FV3_INCREMENT
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FV3_INCREMENT
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmanlfv3inc-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FV3_INCREMENT
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_FV3_INCREMENT
 fi
diff --git a/test/atm/global-workflow/jjob_var_init.sh b/test/atm/global-workflow/jjob_var_init.sh
@@ -130,10 +130,8 @@ done
 
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=1 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmanlinit-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
 fi
diff --git a/test/atm/global-workflow/jjob_var_run.sh b/test/atm/global-workflow/jjob_var_run.sh
@@ -49,10 +49,8 @@ elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
 fi
 
 # Execute j-job
-if [[ $machine = 'HERA' ]]; then
-    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_VARIATIONAL
-elif [[ $machine = 'ORION' || $machine = 'HERCULES' ]]; then
-    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_VARIATIONAL
+if [[ $machine = 'HERA' || $machine = 'ORION' || $machine = 'HERCULES' ]]; then
+    sbatch --ntasks=6 --account=$ACCOUNT --qos=batch --time=00:10:00 --export=ALL --wait --output=atmanlvar-%j.out ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_VARIATIONAL
 else
     ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_VARIATIONAL
 fi
diff --git a/test/atm/global-workflow/setup_workflow_exp.sh b/test/atm/global-workflow/setup_workflow_exp.sh
@@ -23,9 +23,6 @@ expdir=$bindir/test/atm/global-workflow/testrun/experiments
 rm -rf $comroot $expdir config
 
 # copy config.yaml to local config
-cp -r $configdir config
-cp $srcdir/test/atm/global-workflow/config.atmanl       config/
-cp $srcdir/test/atm/global-workflow/config.atmensanl    config/
 cp $srcdir/test/atm/global-workflow/config.yaml .
 
 # update paths in config.yaml
@@ -45,7 +42,7 @@ $srcdir/../../workflow/setup_expt.py gfs cycled --idate $idate  \
                        --resensatmos $resensatmos \
                        --nens $nens \
                        --pslot $pslot \
-                       --configdir $expdir/../config \
+                       --configdir $configdir \
                        --comroot $comroot \
                        --expdir $expdir \
                        --yaml $expdir/../config.yaml

diff --git a/test/soca/gw/CMakeLists.txt b/test/soca/gw/CMakeLists.txt
@@ -52,8 +52,9 @@ set(jjob_list "JGLOBAL_PREP_OCEAN_OBS"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN"
 #	      "JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT"
-              "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST"
-              "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")
+	      "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST")
+# Temporary Removal while fixing/improving vrfy task
+#              "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")
 
 set(setup "")
 foreach(jjob ${jjob_list})

diff --git a/utils/obsproc/CMakeLists.txt b/utils/obsproc/CMakeLists.txt
@@ -1,2 +1,2 @@
-# add_subdirectory(rtofs)
+add_subdirectory(rtofs)
 add_subdirectory(applications)
diff --git a/utils/obsproc/NetCDFToIodaConverter.h b/utils/obsproc/NetCDFToIodaConverter.h
@@ -49,6 +49,9 @@ namespace gdasapp {
       oops::Log::trace() << "NetCDFToIodaConverter::NetCDFToIodaConverter created." << std::endl;
     }
 
+
+
+
     // Method to write out a IODA file (writter called in destructor)
     void writeToIoda() {
       // Extract ioda variables from the provider's files
@@ -60,6 +63,8 @@ namespace gdasapp {
 
       // Read the provider's netcdf file
       gdasapp::obsproc::iodavars::IodaVars iodaVars = providerToIodaVars(inputFilenames_[myrank]);
+
+
       for (int i = myrank + comm_.size(); i < inputFilenames_.size(); i += comm_.size()) {
         iodaVars.append(providerToIodaVars(inputFilenames_[i]));
         oops::Log::info() << " appending: " << inputFilenames_[i] << std::endl;
@@ -200,6 +205,9 @@ namespace gdasapp {
       }
     }
 
+
+
+
    private:
     // Virtual method that reads the provider's netcdf file and store the relevant
     // info in a IodaVars struct