Completes LETKF task, adds WCDA CI test (#1287)

Completes LETKF task, adds WCDA CI test Mutually dependent on NOAA-EMC/global-workflow#2944 --------- Co-authored-by: Cory Martin <[email protected]> Co-authored-by: Guillaume Vernieres <[email protected]>
NOAA-EMC · Nov 7, 2024 · dfc871f · dfc871f
1 parent 1df1ad2
commit dfc871f
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Showing 24 changed files with 195 additions and 37 deletions.
diff --git a/mains/gdas.cc b/mains/gdas.cc
@@ -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>>();

diff --git a/parm/soca/ensda/stage_ens_mem.yaml.j2 b/parm/soca/ensda/stage_ens_mem.yaml.j2
@@ -9,8 +9,7 @@
 # create working directories
 ######################################
 mkdir:
-- "{{ DATAenspert }}/ens"
-
+    - "{{ ENSPERT_RELPATH }}/ens"
 ######################################
 # copy ensemble background files
 ######################################
@@ -22,6 +21,6 @@ copy:
                         '${YMD}':gPDY,
                         '${HH}':gcyc,
                         '${MEMDIR}':"mem" + '%03d' % mem} %}
-    - ["{{ COM_OCEAN_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATAenspert }}/ens/ocean.{{ mem }}.nc"]
-    - ["{{ COM_ICE_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATAenspert }}/ens/ice.{{ mem }}.nc"]
+    - ["{{ COM_OCEAN_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ ENSPERT_RELPATH }}/ens/ocean.{{ mem }}.nc"]
+    - ["{{ COM_ICE_HISTORY_TMPL | replace_tmpl(tmpl_dict) }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ ENSPERT_RELPATH }}/ens/ice.{{ mem }}.nc"]
 {% endfor %}
diff --git a/parm/soca/letkf/letkf.yaml.j2 b/parm/soca/letkf/letkf.yaml.j2
@@ -1,3 +1,5 @@
+{% set gcyc = previous_cycle | strftime("%H") %}
+
 geometry:
   geom_grid_file: soca_gridspec.nc
   mom6_input_nml: mom_input.nml
@@ -11,11 +13,11 @@ background:
   members from template:
     template:
       date: '{{ WINDOW_MIDDLE | to_isotime }}'
-      ocn_filename: "{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc"
-      ice_filename: "{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc"
+      ocn_filename: "ocean.%mem%.nc"
+      ice_filename: "ice.%mem%.nc"
       read_from_file: 1
-      basename: ./ens/mem%mem%
-      state variables: [socn, tocn, ssh, uocn, vocn, cicen]
+      basename: {{ ENSPERT_RELPATH }}/ens/
+      state variables: [socn, tocn, ssh, hocn, uocn, vocn, cicen]
     pattern: '%mem%'
     nmembers: {{ NMEM_ENS  }}
 
@@ -38,32 +40,31 @@ local ensemble DA:
     mult: 1.1
 
 output:
-  datadir: data_output/
+  datadir: letkf_output/
   date: *date
   exp: letkf
   type: ens
 
 output mean prior:
-  datadir: data_output/
+  datadir: letkf_output/
   date: *date
-  exp: letkf
+  exp: letkf.mean_prior
   type: fc
 
 output variance prior:
-  datadir: data_output/
+  datadir: letkf_output/
   date: *date
-  exp: letkf
+  exp: letkf.var_prior
   type: fc
 
 output variance posterior:
-  datadir: data_output/
+  datadir: letkf_output/
   date: *date
-  exp: letkf
+  exp: letkf.var_post
   type: an
 
 output increment:
-  datadir: data_output/
+  datadir: letkf_output/
   date: *date
   exp: letkf.inc
-  type: an
-
+  type: ens
diff --git a/parm/soca/letkf/letkf_save.yaml.j2 b/parm/soca/letkf/letkf_save.yaml.j2
@@ -0,0 +1,20 @@
+{% set PDY = current_cycle | to_YMD %}
+{% set cyc = current_cycle | strftime("%H") %}
+{% set timestr = WINDOW_BEGIN | to_isotime %}
+######################################
+# save letkf analysis to comout
+######################################
+
+copy:
+{% for mem in range(1, NMEM_ENS + 1) %}
+   {% set tmpl_dict = {'${ROTDIR}':ROTDIR,
+                       '${RUN}': GDUMP_ENS,
+                       '${YMD}':PDY,
+                       '${HH}':cyc,
+                       '${MEMDIR}':"mem" + '%03d' % mem} %}
+   {% set COMOUT_OCEAN_LETKF_MEM = COM_OCEAN_LETKF_TMPL | replace_tmpl(tmpl_dict) %}
+   {% set COMOUT_ICE_LETKF_MEM = COM_ICE_LETKF_TMPL | replace_tmpl(tmpl_dict) %}
+
+   - ["{{ DATA }}/letkf_output/ocn.letkf.ens.{{ mem }}.{{ timestr }}.PT3H.nc", "{{ COMOUT_OCEAN_LETKF_MEM }}/{{ GDUMP_ENS }}.ocean.t{{ cyc }}z.analysis.nc"]
+   - ["{{ DATA }}/letkf_output/ice.letkf.ens.{{ mem }}.{{ timestr }}.PT3H.nc", "{{ COMOUT_ICE_LETKF_MEM }}/{{ GDUMP_ENS }}.ice.t{{ cyc }}z.analysis.nc"]
+{% endfor %}
diff --git a/parm/soca/letkf/letkf_stage.yaml.j2 b/parm/soca/letkf/letkf_stage.yaml.j2
@@ -1,11 +1,30 @@
-######################################
-# create working directories
+{% set PDY = current_cycle | to_YMD %}
+{% set cyc = current_cycle | strftime("%H") %}
+{% set gcyc = previous_cycle | strftime("%H") %}
 ######################################
 mkdir:
-- "{{ DATA }}/Data"
+- "{{ DATA }}/letkf_output"
 - "{{ DATA }}/obs"
-copy:
+- "{{ DATA }}/diags"
+- "{{ COMOUT_OCEAN_LETKF }}"
+- "{{ COMOUT_ICE_LETKF }}"
+######################################
+# make comout directories
 ######################################
-# copy mom input template 
+{% for mem in range(1, NMEM_ENS + 1) %}
+   {% set tmpl_dict = {'${ROTDIR}':ROTDIR,
+                       '${RUN}':GDUMP_ENS,
+                       '${YMD}':PDY,
+                       '${HH}':cyc,
+                       '${MEMDIR}':"mem" + '%03d' % mem} %}
+- "{{ COM_OCEAN_LETKF_TMPL | replace_tmpl(tmpl_dict) }}"
+- "{{ COM_ICE_LETKF_TMPL | replace_tmpl(tmpl_dict) }}"
+{% endfor %}
 ######################################
+# copy mom input template and det bkg
+######################################
+copy:
 - ["{{ PARMgfs }}/gdas/soca/fms/input.nml", "{{ DATA }}/mom_input.nml.tmpl"]
+- ["{{ PARMgfs }}/gdas/soca/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
+- ["{{ COMIN_OCEAN_HISTORY_PREV }}/gdas.ocean.t{{ gcyc }}z.inst.f009.nc", "{{ DATA }}/INPUT/MOM.res.nc"]
+- ["{{ COMIN_ICE_HISTORY_PREV }}/gdas.ice.t{{ gcyc }}z.inst.f009.nc", "{{ DATA }}/INPUT/cice.res.nc"]
diff --git a/parm/soca/obs/config/adt_rads_all.yaml b/parm/soca/obs/config/adt_rads_all.yaml
@@ -17,6 +17,13 @@ obs operator:
   name: ADT
 obs error:
   covariance model: diagonal
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
 obs filters:
 - filter: Domain Check
   where:

diff --git a/parm/soca/obs/config/icec_amsr2_north.yaml b/parm/soca/obs/config/icec_amsr2_north.yaml
@@ -43,3 +43,10 @@ obs filters:
   where:
   - variable: {name: GeoVaLs/distance_from_coast}
     minvalue: 100e3
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/icec_amsr2_south.yaml b/parm/soca/obs/config/icec_amsr2_south.yaml
@@ -43,3 +43,10 @@ obs filters:
   where:
   - variable: {name: GeoVaLs/distance_from_coast}
     minvalue: 100e3
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/insitu_profile_argo.yaml b/parm/soca/obs/config/insitu_profile_argo.yaml
@@ -625,3 +625,10 @@ obs filters:
           - ObsError/salinity
           coefs:
           - 1000.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_abi_g16_l3c.yaml b/parm/soca/obs/config/sst_abi_g16_l3c.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_abi_g17_l3c.yaml b/parm/soca/obs/config/sst_abi_g17_l3c.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_ahi_h08_l3c.yaml b/parm/soca/obs/config/sst_ahi_h08_l3c.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_avhrr_ma_l3u.yaml b/parm/soca/obs/config/sst_avhrr_ma_l3u.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_avhrr_mb_l3u.yaml b/parm/soca/obs/config/sst_avhrr_mb_l3u.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_avhrr_mc_l3u.yaml b/parm/soca/obs/config/sst_avhrr_mc_l3u.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_viirs_n20_l3u.yaml b/parm/soca/obs/config/sst_viirs_n20_l3u.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/obs/config/sst_viirs_npp_l3u.yaml b/parm/soca/obs/config/sst_viirs_npp_l3u.yaml
@@ -54,3 +54,10 @@ obs filters:
         - ObsError/seaSurfaceTemperature
         coefs:
         - 1.0
+obs localizations:
+- localization method: Rossby
+  base value: 100.0e3
+  rossby mult: 1.0
+  min grid mult: 2.0
+  min value: 200.0e3
+  max value: 900.0e3
diff --git a/parm/soca/soca_ens_bkg_stage.yaml.j2 b/parm/soca/soca_ens_bkg_stage.yaml.j2
@@ -18,7 +18,7 @@ copy:
    # define variables
    # Declare a dict of search and replace terms to GDUMP on each template
    {% set tmpl_dict = {'ROTDIR':ROTDIR,
-                       'RUN': RUN,
+                       'RUN': GDUMP_ENS,
                        'YMD':gPDY,
                        'HH':gcyc,
                        'MEMDIR':"mem" + '%03d' % mem} %}
@@ -35,6 +35,6 @@ copy:
       {% set com_prev_ocn.COMIN_OCEAN_HISTORY_MEM = com_prev_ocn.COMIN_OCEAN_HISTORY_MEM.replace(search_term, replace_term) %}
       {% set com_prev_ice.COMIN_ICE_HISTORY_MEM = com_prev_ice.COMIN_ICE_HISTORY_MEM.replace(search_term, replace_term) %}
    {% endfor %}
-   - ["{{ com_prev_ocn.COMIN_OCEAN_HISTORY_MEM }}/{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATAens }}/ens/mem{{ '%03d' % mem }}/{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
-   - ["{{ com_prev_ice.COMIN_ICE_HISTORY_MEM }}/{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATAens }}/ens/mem{{ '%03d' % mem }}/{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc"]
+   - ["{{ com_prev_ocn.COMIN_OCEAN_HISTORY_MEM }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATAens }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
+   - ["{{ com_prev_ice.COMIN_ICE_HISTORY_MEM }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATAens }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"]
 {% endfor %}
diff --git a/parm/soca/soca_fix_stage_025.yaml.j2 b/parm/soca/soca_fix_stage_025.yaml.j2
@@ -1,4 +1,3 @@
-# TODO(AFE): make resolution dependent
 mkdir:
 - "{{ DATA }}/INPUT"
 ######################################

diff --git a/parm/soca/soca_fix_stage_100.yaml.j2 b/parm/soca/soca_fix_stage_100.yaml.j2
@@ -1,4 +1,3 @@
-# TODO(AFE): make resolution dependent
 mkdir:
 - "{{ DATA }}/INPUT"
 ######################################

diff --git a/parm/soca/soca_fix_stage_500.yaml.j2 b/parm/soca/soca_fix_stage_500.yaml.j2
@@ -1,4 +1,3 @@
-# TODO(AFE): make resolution dependent
 mkdir:
 - "{{ DATA }}/INPUT"
 ######################################
@@ -9,6 +8,7 @@ copy:
 - ["{{ 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 }}/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"]

diff --git a/test/gw-ci/CMakeLists.txt b/test/gw-ci/CMakeLists.txt
@@ -19,18 +19,39 @@ function(add_cycling_tests pslot YAML_PATH HOMEgfs RUNTESTS PROJECT_SOURCE_DIR T
   list(GET DATES_LIST 1 FULL_CYCLE)
 
   # stage IC's
-  message(STATUS "staging the 1/2 cycle IC's for ${test_name} ctest")
+  message(STATUS "staging the 1/2 cycle IC's for ${pslot} ctest")
   add_test(NAME ${test_name}_gdas_stage_ic_${HALF_CYCLE}
            COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdas_stage_ic ${HALF_CYCLE}"
            WORKING_DIRECTORY ${RUNTESTS})
   set_tests_properties(${test_name}_gdas_stage_ic_${HALF_CYCLE} PROPERTIES LABELS "manual")
 
+  # stage ensemble ics
+  if (letkf)
+    message(STATUS "preparing enkfgdas_stage_ic for ${pslot} ctest")
+    add_test(NAME ${test_name}_enkfgdas_stage_ic_${HALF_CYCLE}
+             COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} enkfgdas_stage_ic ${HALF_CYCLE}"
+             WORKING_DIRECTORY ${RUNTESTS})
+    set_tests_properties(${test_name}_enkfgdas_stage_ic_${HALF_CYCLE} PROPERTIES LABELS "manual")
+  endif()
+
   # 1/2 cycle gdas_fcst
   message(STATUS "preparing 1/2 cycle gdas_fcst for ${pslot} ctest")
-  add_test(NAME ${test_name}_gdas_fcst_${HALF_CYCLE}
+  add_test(NAME ${test_name}_gdas_fcst_seg0_${HALF_CYCLE}
            COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdas_fcst_seg0 ${HALF_CYCLE}"
            WORKING_DIRECTORY ${RUNTESTS})
-  set_tests_properties(${test_name}_gdas_fcst_${HALF_CYCLE} PROPERTIES LABELS "manual")
+  set_tests_properties(${test_name}_gdas_fcst_seg0_${HALF_CYCLE} PROPERTIES LABELS "manual")
+
+  # 1/2 cycle enkfgdas_fcst
+  if (letkf)
+    set(ENS_MEMS  "mem001" "mem002" "mem003")
+    foreach(ENS_MEM ${ENS_MEMS})
+      message(STATUS "preparing 1/2 cycle enkfgdas_fcst_${ENS_MEM} for ${pslot} ctest")
+        add_test(NAME ${test_name}_enkfgdas_fcst_${ENS_MEM}_${HALF_CYCLE}
+                 COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} enkfgdas_fcst_${ENS_MEM} ${HALF_CYCLE}"
+                 WORKING_DIRECTORY ${RUNTESTS})
+        set_tests_properties(${test_name}_enkfgdas_fcst_${ENS_MEM}_${HALF_CYCLE} PROPERTIES LABELS "manual")
+    endforeach()
+  endif()
 
   # Select the list of tasks to run for the full cycle
   message(STATUS "Tasks ${TASK_LIST}")
@@ -62,6 +83,24 @@ if (WORKFLOW_TESTS)
     "gdas_marineanlfinal"
     )
   add_cycling_tests(${pslot} ${YAML_PATH} ${HOMEgfs} ${RUNTESTS} ${PROJECT_SOURCE_DIR} "${TASK_LIST}")
+
+  # WCDA, low-res, ensemble da
+  # -------------
+  set(pslot "WCDA-hyb-C48mx500")
+  set(letkf TRUE)
+  set(YAML_PATH ${HOMEgfs}/ci/cases/pr/C48mx500_hybAOWCDA.yaml)
+  set(TASK_LIST
+    "gdas_prepoceanobs"
+    "gdas_marineanlletkf"
+    # TODO(AFE) waiting until these are working for hybrid
+    # "gdas_marinebmat"
+    # "gdas_marineanlinit"
+    # "gdas_marineanlvar"
+    # "gdas_marineanlchkpt"
+    # "gdas_marineanlfinal"
+    )
+  add_cycling_tests(${pslot} ${YAML_PATH} ${HOMEgfs} ${RUNTESTS} ${PROJECT_SOURCE_DIR} "${TASK_LIST}")
+  set(letkf FALSE)
 endif()
 
 option(RUN_GW_CI "Enable the global-workflow CI tests" OFF)