Merge branch 'feature/rename_atm' of https://github.com/NOAA-EMC/GDASApp

into feature/rename_atm * 'feature/rename_atm' of https://github.com/NOAA-EMC/GDASApp: Feature/rtofs in situ (#1138) Updates to aerosol yaml templates (#1158) Use standard config files for jjob test and give output files better names (#1156) Temporary removal of soca_vrfy task (#1157) Fix keyword for float tolerances in jjob tests (#1154) Create template YAML for n21 aerosol obs and update obs QC in YAMLs (#1152) Changes name of rossrad file for letkf (#1151) Adds staging jinja/yaml file for letkf task (#1137)
NOAA-EMC · Jun 13, 2024 · fe5169c · fe5169c
2 parents 9a3a029 + 3d5f205
commit fe5169c
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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/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/parm/aero/obs/lists/gdas_aero.yaml.j2 b/parm/aero/obs/lists/gdas_aero.yaml.j2
@@ -2,4 +2,5 @@ observers:
 {% filter indent(width=2) %}
 {% include 'aero/obs/config/viirs_n20_aod.yaml.j2' %}
 {% include 'aero/obs/config/viirs_npp_aod.yaml.j2' %}
+{% include 'aero/obs/config/viirs_n21_aod.yaml.j2' %}
 {% endfilter %}
diff --git a/parm/soca/letkf/letkf.yaml.j2 b/parm/soca/letkf/letkf.yaml.j2
@@ -4,15 +4,15 @@ geometry:
   fields metadata: fields_metadata.yaml
 
 time window:
-  begin: &date '{{ ATM_WINDOW_BEGIN }}'
+  begin: &date '{{ WINDOW_BEGIN | to_isotime }}'
   length: PT6H 
 
 background:
   members from template:
     template:
-      date: '{{ ATM_WINDOW_MIDDLE }}'
-      ocn_filename: enkfgdas.ocean.t06z.inst.f009.nc
-      ice_filename: enkfgdas.ice.t06z.inst.f009.nc
+      date: '{{ WINDOW_MIDDLE | to_isotime }}'
+      ocn_filename: "{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"
+      ice_filename: "{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"
       read_from_file: 1
       basename: ./ens/mem%mem%
       state variables: [socn, tocn, ssh, uocn, vocn, cicen]

diff --git a/parm/soca/letkf/letkf_stage.yaml.j2 b/parm/soca/letkf/letkf_stage.yaml.j2
@@ -0,0 +1,49 @@
+######################################
+# set some variables
+######################################
+{% set gPDY = previous_cycle | to_YMD %}
+{% set gcyc = previous_cycle | strftime("%H") %}
+{% set PDY = current_cycle | to_YMD %}
+{% set cyc = current_cycle | strftime("%H") %}
+######################################
+# create working directories
+######################################
+mkdir:
+- "{{ DATA }}/Data"
+- "{{ DATA }}/obs"
+- "{{ DATA }}/INPUT"
+{% for mem in range(1, NMEM_ENS + 1) %}
+- "{{ DATA }}/ens/mem{{ '%03d' % mem }}"
+{% endfor %}
+copy:
+######################################
+# copy mom input template 
+######################################
+- ["{{ PARMgfs }}/gdas/soca/fms/input.nml", "{{ DATA }}/mom_input.nml.tmpl"]
+######################################
+# copy ensemble background files
+######################################
+{% for mem in range(1, NMEM_ENS + 1) %}
+# define variables
+# Declare a dict of search and replace terms to GDUMP on each template
+{% set tmpl_dict = {'ROTDIR':ROTDIR,
+                    'RUN': GDUMP_ENS,
+                    'YMD':gPDY,
+                    'HH':gcyc,
+                    'MEMDIR':"mem" + '%03d' % mem} %}
+
+# Replace template variables with tmpl_dict, one key at a time
+# This must be done in a namespace to overcome jinja scoping
+#  Variables set inside of a for loop are lost at the end of the loop
+#  unless they are part of a namespace
+{% set com_prev_ocn = namespace(COM_OCEAN_HISTORY_MEM = COM_OCEAN_HISTORY_TMPL) %}
+{% set com_prev_ice = namespace(COM_ICE_HISTORY_MEM = COM_ICE_HISTORY_TMPL) %}
+{% for key in tmpl_dict.keys() %}
+{% set search_term = '${' + key + '}' %}
+{% set replace_term = tmpl_dict[key] %}
+{% set com_prev_ocn.COM_OCEAN_HISTORY_MEM = com_prev_ocn.COM_OCEAN_HISTORY_MEM.replace(search_term, replace_term) %}
+{% set com_prev_ice.COM_ICE_HISTORY_MEM = com_prev_ice.COM_ICE_HISTORY_MEM.replace(search_term, replace_term) %}
+{% endfor %}
+- ["{{ com_prev_ocn.COM_OCEAN_HISTORY_MEM }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
+- ["{{ com_prev_ice.COM_ICE_HISTORY_MEM }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"]
+{% endfor %}
diff --git a/parm/soca/letkf/soca_fix_stage.yaml.j2 b/parm/soca/letkf/soca_fix_stage.yaml.j2
@@ -0,0 +1,16 @@
+######################################
+# fix files to copy
+######################################
+copy:
+- ["{{ SOCA_INPUT_FIX_DIR }}/rossrad.nc", "{{ DATA }}/rossrad.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/field_table", "{{ DATA }}/field_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/diag_table", "{{ DATA }}/diag_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/MOM_input", "{{ DATA }}/MOM_input"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/grid_spec.nc", "{{ DATA }}/INPUT/grid_spec.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/hycom1_25.nc", "{{ DATA }}/INPUT/hycom1_25.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/layer_coord25.nc", "{{ DATA }}/INPUT/layer_coord25.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_hgrid.nc", "{{ DATA }}/INPUT/ocean_hgrid.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_mosaic.nc", "{{ DATA }}/INPUT/ocean_mosaic.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_topog.nc", "{{ DATA }}/INPUT/ocean_topog.nc"]
diff --git a/sorc/fv3 b/sorc/fv3
diff --git a/sorc/gsibec b/sorc/gsibec
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 @@ atmosphere_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 @@ atmosphere_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