Merge branch 'develop' into feature/vrfy_manual

build.sh

@@ -71,7 +71,7 @@ while getopts "p:t:c:hvdfa" opt; do
 done
 
 case ${BUILD_TARGET} in
-  hera | orion | hercules | wcoss2 | noaacloud | gaea | gaeac6 )
+  hera | orion | hercules | wcoss2 | noaacloud | gaeac5 | gaeac6 )
     echo "Building GDASApp on $BUILD_TARGET"
     source $dir_root/ush/module-setup.sh
     module use $dir_root/modulefiles
@@ -103,14 +103,12 @@ WORKFLOW_BUILD=${WORKFLOW_BUILD:-"OFF"}
 CMAKE_OPTS+=" -DWORKFLOW_TESTS=${WORKFLOW_BUILD}"
 
 # JCSDA changed test data things, need to make a dummy CRTM directory
-if [[ $BUILD_TARGET == 'hera' ]]; then
-  if [ -d "$dir_root/bundle/fix/test-data-release/" ]; then rm -rf $dir_root/bundle/fix/test-data-release/; fi
-  if [ -d "$dir_root/bundle/test-data-release/" ]; then rm -rf $dir_root/bundle/test-data-release/; fi
-  mkdir -p $dir_root/bundle/fix/test-data-release/
-  mkdir -p $dir_root/bundle/test-data-release/
-  ln -sf $GDASAPP_TESTDATA/crtm $dir_root/bundle/fix/test-data-release/crtm
-  ln -sf $GDASAPP_TESTDATA/crtm $dir_root/bundle/test-data-release/crtm
-fi
+if [ -d "$dir_root/bundle/fix/test-data-release/" ]; then rm -rf $dir_root/bundle/fix/test-data-release/; fi
+if [ -d "$dir_root/bundle/test-data-release/" ]; then rm -rf $dir_root/bundle/test-data-release/; fi
+mkdir -p $dir_root/bundle/fix/test-data-release/
+mkdir -p $dir_root/bundle/test-data-release/
+ln -sf $GDASAPP_TESTDATA/crtm $dir_root/bundle/fix/test-data-release/crtm
+ln -sf $GDASAPP_TESTDATA/crtm $dir_root/bundle/test-data-release/crtm
 
 # Configure
 echo "Configuring ..."

mains/gdas.cc

@@ -56,7 +56,7 @@ int runApp(int argc, char** argv, const std::string traits, const std::string ap
 
   apps["converttostructuredgrid"] = []() {
       return std::make_unique<oops::ConvertToStructuredGrid<Traits>>();
-  };	
+  };
   apps["convertstate"] = []() {
       return std::make_unique<oops::ConvertState<Traits>>();
   };
@@ -67,7 +67,7 @@ int runApp(int argc, char** argv, const std::string traits, const std::string ap
       return std::make_unique<oops::HofX4D<Traits, ufo::ObsTraits>>();
   };
   apps["localensembleda"] = []() {
-      return std::make_unique<oops::LocalEnsembleDA<fv3jedi::Traits, ufo::ObsTraits>>();
+      return std::make_unique<oops::LocalEnsembleDA<Traits, ufo::ObsTraits>>();
   };
   apps["variational"] = []() {
     return std::make_unique<oops::Variational<Traits, ufo::ObsTraits>>();
@@ -106,6 +106,7 @@ int main(int argc,  char ** argv) {
   const std::set<std::string> validApps = {
     "converttostructuredgrid",
     "convertstate",
+    "ensmean",
     "hofx4d",
     "localensembleda",
     "variational"

modulefiles/GDAS/gaea.intel.lua → modulefiles/GDAS/gaeac5.intel.lua

@@ -10,8 +10,8 @@ prepend_path("MODULEPATH", '/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/u
 prepend_path("MODULEPATH", '/ncrc/proj/epic/rocoto/modulefiles')
 
 -- below two lines get us access to the spack-stack modules
-load("stack-intel/2023.1.0")
-load("stack-cray-mpich/8.1.25")
+load("stack-intel/2023.2.0")
+load("stack-cray-mpich/8.1.28")
 -- JCSDA has 'jedi-fv3-env/unified-dev', but we should load these manually as needed
 load("cmake/3.23.1")
 load("gettext/0.20.2")
@@ -44,11 +44,12 @@ load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
 load("fms/2023.04")
+load("esmf/8.5.0")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
 load("libjpeg/2.1.0")
-load("krb5/1.16.3")
+load("krb5/1.20.1")
 load("libtirpc/1.3.3")
 load("hdf/4.2.15")
 load("jedi-cmake/1.4.0")
@@ -84,9 +85,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/gpfs/f5/ufs-ard/world-shared/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data/test")
+setenv("CRTM_FIX","/gpfs/f5/nggps_emc/world-shared/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/gpfs/f5/nggps_emc/world-shared/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/gpfs/f5/nggps_emc/world-shared/GDASApp/unittestdata")
 
 whatis("Name: ".. "pkgName")
 whatis("Version: ".. "pkgVersion")

parm/aero/jcb-base.yaml.j2

@@ -0,0 +1,136 @@
+# Search path for model and obs for JCB
+# -------------------------------------
+algorithm_path: "{{PARMgfs}}/gdas/jcb-algorithms"
+app_path_algorithm: "{{PARMgfs}}/gdas/jcb-gdas/algorithm/aero"
+app_path_model: "{{PARMgfs}}/gdas/jcb-gdas/model/aero"
+app_path_observations: "{{PARMgfs}}/gdas/jcb-gdas/observations/aero"
+app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/aero"
+
+
+# Places where we deviate from the generic file name of a yaml
+# ------------------------------------------------------------
+final_increment_to_latlon_file: aero_final_increment_gaussian
+final_increment_file: aero_final_increment_cubed_sphere
+model_file: aero_model_pseudo
+initial_condition_file: aero_background  # Initial conditions for 4D apps is background
+background_error_file: "{{BERROR_YAML}}"
+
+# Assimilation standard things (not prepended with model choice)
+# ----------------------------
+window_begin: "{{ AERO_WINDOW_BEGIN | to_isotime }}"
+window_length: "{{ AERO_WINDOW_LENGTH }}"
+bound_to_include: begin
+minimizer: DRPCG
+final_diagnostics_departures: anlmob
+final_prints_frequency: PT3H
+number_of_outer_loops: 2
+analysis_variables: [mass_fraction_of_sulfate_in_air,
+                       mass_fraction_of_hydrophobic_black_carbon_in_air,
+                       mass_fraction_of_hydrophilic_black_carbon_in_air,
+                       mass_fraction_of_hydrophobic_organic_carbon_in_air,
+                       mass_fraction_of_hydrophilic_organic_carbon_in_air,
+                       mass_fraction_of_dust001_in_air, mass_fraction_of_dust002_in_air,
+                       mass_fraction_of_dust003_in_air, mass_fraction_of_dust004_in_air,
+                       mass_fraction_of_dust005_in_air, mass_fraction_of_sea_salt001_in_air,
+                       mass_fraction_of_sea_salt002_in_air, mass_fraction_of_sea_salt003_in_air,
+                       mass_fraction_of_sea_salt004_in_air]
+
+# Model things
+# ------------
+# Geometry
+aero_layout_x: {{ layout_x | default(1, true) }}
+aero_layout_y: {{ layout_y | default(1, true) }}
+aero_npx_ges: {{ npx_ges | default(49, true) }}
+aero_npy_ges: {{ npy_ges | default(49, true) }}
+aero_npz_ges: {{ npz_ges | default(127, true) }}
+aero_npx_anl: {{ npx_anl | default(49, true) }}
+aero_npy_anl: {{ npy_anl | default(49, true) }}
+aero_npz_anl: {{ npz_anl | default(127, true) }}
+aero_npx_clim_b: {{ npx_clim_b | default(49, true) }}
+aero_npy_clim_b: {{ npy_clim_b | default(49, true) }}
+aero_npz_clim_b: {{ npz_anl | default(127, true) }}
+
+aero_fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
+
+# Background
+aero_background_path: ./bkg
+aero_background_ensemble_path: ./ens/mem%mem%
+
+# Default background time is for 3D applications
+{% if DOIAU == True %}
+aero_background_time_iso: "{{ AERO_WINDOW_BEGIN | to_isotime }}"
+{% else %}
+aero_background_time_iso: "{{ current_cycle | to_isotime }}"
+{% endif %}
+aero_cycle_time_iso: "{{ current_cycle | to_isotime }}"
+aero_cycle_time_fv3: "{{ current_cycle | to_fv3time }}"
+
+# time for background error calculation for next cycle
+{% set offset_td = "+6H" | to_timedelta %}
+{% set background_time = current_cycle | add_to_datetime(offset_td) %}
+aero_background_error_time_iso:  "{{ background_time | to_isotime }}"
+aero_background_error_time_fv3: "{{ background_time | to_fv3time }}"
+
+# Background error
+aero_berror_data_directory: "{{ DATA }}/berror"
+aero_berror_diffusion_directory: "{{ DATA }}/diffusion"
+aero_standard_devation_path: ./stddev
+aero_climatological_b_path: ./clm_stddev
+aero_diagb_weight: {{ aero_diagb_weight | default(1.0, true) }}
+aero_diagb_static_rescale_factor: {{aero_staticb_rescaling_factor | default(1.0, true) }}
+aero_diagb_rescale_factor: {{aero_diagb_rescale | default(1.0, true) }}
+aero_diagb_n_halo: {{ aero_diagb_n_halo  | default(1, true)  }}
+aero_diagb_n_neighbors: {{ aero_diagb_n_neighbors | default(1, true) }}
+aero_diagb_smooth_horiz_iter: {{ aero_diagb_smooth_horiz_iter | default(1, true) }}
+aero_diagb_smooth_vert_iter: {{ aero_diagb_smooth_vert_iter | default(1, true) }}
+aero_diffusion_iter: {{ aero_diffusion_iter | default(1, true) }}
+aero_diffusion_horiz_len: {{ aero_diffusion_horiz_len  | default(1.0, true)}}
+aero_diffusion_fixed_val: {{ aero_diffusion_fixed_val  | default(1.0, true)}}
+
+# Forecasting
+aero_forecast_timestep: "{{ BKG_TSTEP }}"
+
+# Observation things
+# ------------------
+observations: all_observations
+
+crtm_coefficient_path: "{{ DATA }}/crtm/"
+
+# Naming conventions for observational files
+aero_obsdataroot_path: "{{COM_OBS}}"
+
+aero_obsdatain_path: "{{aero_obsdatain_path}}"
+aero_obsdatain_prefix: "{{OPREFIX}}"
+aero_obsdatain_suffix: ".tm00.nc"
+
+aero_obsdataout_path: "{{aero_obsdataout_path}}"
+aero_obsdataout_prefix: diag_
+aero_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
+
+# Naming conventions for bias correction files
+aero_obsbiasroot_path: "{{COM_CHEM_ANALYSIS_PREV}}"
+
+aero_obsbiasin_path: "{{DATA}}/obs/"
+aero_obsbiasin_prefix: "{{GPREFIX}}"
+aero_obsbiasin_suffix: ".satbias.nc"
+aero_obstlapsein_prefix: "{{GPREFIX}}"
+aero_obstlapsein_suffix: ".tlapse.txt"
+aero_obsbiascovin_prefix: "{{GPREFIX}}"
+aero_obsbiascovin_suffix: ".satbias_cov.nc"
+
+aero_obsbiasout_path: "{{DATA}}/bc/"
+aero_obsbiasout_prefix: "{{APREFIX}}"
+aero_obsbiasout_suffix: ".satbias.nc"
+aero_obsbiascovout_prefix: "{{APREFIX}}"
+aero_obsbiascovout_suffix: ".satbias_cov.nc"
+
+bias_files:
+  atms_n20: rad_varbc_params.tar
+  atms_npp: rad_varbc_params.tar
+  mtiasi_metop-a: rad_varbc_params.tar
+  mtiasi_metop-b: rad_varbc_params.tar
+  amsua_n19: rad_varbc_params.tar
+  ssmis_f17: rad_varbc_params.tar
+  ssmis_f18: rad_varbc_params.tar
+  cris-fsr_n20: rad_varbc_params.tar
+  cris-fsr_npp: rad_varbc_params.tar

parm/aero/jcb-prototype_3dvar.yaml.j2

@@ -0,0 +1,10 @@
+# Algorithm
+# ---------
+algorithm: 3dfgat
+
+# Observation things
+# ------------------
+observations:
+- viirs_n20_aod
+- viirs_npp_aod
+# - viirs_n21_aod

parm/atm/jcb-prototype_3dvar.yaml.j2

@@ -16,8 +16,8 @@ observations:
   - conventional_ps
   - gnssro
 #  - gpsro
-#  - mtiasi_metop-a
-#  - mtiasi_metop-b
+#  - iasi_metop-a
+#  - iasi_metop-b
 #  - ompsnp_n20
   - ompsnp_npp
 #  - ompstc_n20
@@ -29,3 +29,4 @@ observations:
 #  - satwnd.viirs_npp
 #  - scatwind_ascat_metop-a
 #  - snowcvr
+#  - abi_g16

parm/atm/jcb-prototype_lgetkf.yaml.j2

@@ -25,8 +25,8 @@ observations:
   - conventional_ps
   - gnssro
 #  - gpsro
-#  - mtiasi_metop-a
-#  - mtiasi_metop-b
+#  - iasi_metop-a
+#  - iasi_metop-b
 #  - ompsnp_n20
   - ompsnp_npp
 #  - ompstc_n20

parm/atm/jcb-prototype_lgetkf_observer.yaml.j2

@@ -25,8 +25,8 @@ observations:
   - conventional_ps
   - gnssro
 #  - gpsro
-#  - mtiasi_metop-a
-#  - mtiasi_metop-b
+#  - iasi_metop-a
+#  - iasi_metop-b
 #  - ompsnp_n20
   - ompsnp_npp
 #  - ompstc_n20

parm/atm/jcb-prototype_lgetkf_solver.yaml.j2

@@ -25,8 +25,8 @@ observations:
   - conventional_ps
   - gnssro
 #  - gpsro
-#  - mtiasi_metop-a
-#  - mtiasi_metop-b
+#  - iasi_metop-a
+#  - iasi_metop-b
 #  - ompsnp_n20
   - ompsnp_npp
 #  - ompstc_n20

parm/ioda/bufr2ioda/bufr2ioda_gsrcsr.json

@@ -0,0 +1,16 @@
+{
+  "data_format"      : "bufr_d",
+  "data_type"        : "gsrcsr",
+  "cycle_type"       : "{{ RUN }}",
+  "cycle_datetime"   : "{{ current_cycle | to_YMDH }}",
+  "dump_directory"   : "{{ DMPDIR }}",
+  "ioda_directory"   : "{{ COM_OBS }}",
+  "subsets"          : ['NC021046'],
+  "data_description" : "NC021046 ABI, GOES-16; NC021046 ABI, GOES-17,  NC021046 ABI, GOES-18", 
+  "data_provider"    : "U.S. NOAA/NESDIS",
+  "sensor_info"      : { "sensor_name": "ABI",  "sensor_full_name": "Advanced Baseline Imager",  "sensor_id": 617 },
+  "satellite_info"   : [
+                          { "satellite_name": "g16", "satellite_full_name": "GOES-16", "satellite_id": 270, "launch time": "20171119" },
+                          { "satellite_name": "g17", "satellite_full_name": "GOES-17", "satellite_id": 271, "launch time": "20180301" },
+                          { "satellite_name": "g18", "satellite_full_name": "GOES-18", "satellite_id": 272, "launch time": "20220301" } ]
+}

parm/ioda/bufr2ioda/bufr2ioda_mtiasi.yaml → parm/ioda/bufr2ioda/bufr2ioda_iasi.yaml

@@ -94,7 +94,7 @@ observations:
 
     ioda:
       backend: netcdf
-      obsdataout: "{{ COM_OBS }}/{{ RUN }}.t{{ cyc }}z.mtiasi_$(splitvar).tm00.nc" 
+      obsdataout: "{{ COM_OBS }}/{{ RUN }}.t{{ cyc }}z.iasi_$(splitvar).tm00.nc" 
 
       dimensions:
         - name: Channel

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_argo.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ ARGO profiles
+data_format: subpfl
+data_provider: U.S. NOAA
+data_type: argo
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: SUBPFL
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_bathy.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ Bathythermal profiles
+data_format: bathy
+data_provider: U.S. NOAA
+data_type: bathy
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: BATHY
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_glider.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ GLIDER profiles
+data_format: subpfl
+data_provider: U.S. NOAA
+data_type: glider
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: SUBPFL
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_tesac.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ TESAC profiles
+data_format: tesac
+data_provider: U.S. NOAA
+data_type: tesac
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: TESAC
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_xbtctd.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ XBT/XCTD profiles
+data_format: xbtctd
+data_provider: U.S. NOAA
+data_type: xbtctd
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: XBTCTD
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'

parm/ioda/bufr2ioda/bufr2ioda_insitu_surface_trkob.yaml

@@ -0,0 +1,11 @@
+cycle_datetime: '{{ current_cycle | to_YMDH }}'
+cycle_type: '{{ RUN }}'
+data_description: 6-hrly in situ TRACKOB surface
+data_format: trkob
+data_provider: U.S. NOAA
+data_type: trackob
+dump_directory: '{{ DMPDIR }}'
+ioda_directory: '{{ COM_OBS }}'
+source: NCEP data tank
+subsets: TRACKOB
+ocean_basin: '{{ OCEAN_BASIN_FILE }}'