Merge branch 'develop' into feature/cubed_sphere_bkg

modulefiles/GDAS/hera.intel.lua

@@ -83,9 +83,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/data/test")
+setenv("CRTM_FIX","/scratch1/NCEPDEV/da/role.jedipara/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/scratch1/NCEPDEV/da/role.jedipara/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/scratch1/NCEPDEV/da/role.jedipara/GDASApp/unittestdata")
 --prepend_path("PATH","/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/intel-18.0.5.274/prod_util/1.2.2/bin")
 
 whatis("Name: ".. pkgName)

modulefiles/GDAS/hercules.intel.lua

@@ -79,9 +79,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/work2/noaa/da/cmartin/CI/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/cmartin/CI/GDASApp/data/test/")
+setenv("CRTM_FIX","/work2/noaa/da/role-da/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/work2/noaa/da/role-da/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/role-da/GDASApp/unittestdata")
 prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")
 
 execute{cmd="ulimit -s unlimited",modeA={"load"}}

modulefiles/GDAS/orion.intel.lua

@@ -79,9 +79,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/work2/noaa/da/cmartin/CI/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/cmartin/CI/GDASApp/data/test/")
+setenv("CRTM_FIX","/work2/noaa/da/role-da/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/work2/noaa/da/role-da/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/role-da/GDASApp/unittestdata")
 prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")
 
 execute{cmd="ulimit -s unlimited",modeA={"load"}}

modulefiles/GDAS/wcoss2.intel.lua

@@ -46,8 +46,8 @@ setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
 setenv("CRTM_FIX","/lfs/h2/emc/da/noscrub/emc.da/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/lfs/h2/emc/da/noscrub/emc.da/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/lfs/h2/emc/da/noscrub/emc.da/GDASApp/data/test")
+setenv("GDASAPP_TESTDATA","/lfs/h2/emc/da/noscrub/emc.da/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/lfs/h2/emc/da/noscrub/emc.da/GDASApp/unittestdata")
 
 whatis("Name: ".. pkgName)
 whatis("Version: ".. pkgVersion)

parm/aero/berror/aero_diffusionparm.yaml.j2

@@ -35,16 +35,16 @@ background error:
     saber block name: diffusion
     calibration:
       normalization:
-        iterations: {{ diff_iter }}    
+        iterations: {{ aero_diffusion_iter }}    
       groups:
       - horizontal:
-          fixed value: {{ horiz_len }} 
+          fixed value: {{ aero_diffusion_horiz_len }} 
         write:
-          filepath: "{{ DATA }}/berror/diffusion_hz" 
+          filepath: "{{ DATA }}/diffusion/diffusion_hz" 
       - vertical:
           levels: {{ npz_ges }} 
-          fixed value: {{ fixed_val }} 
+          fixed value: {{ aero_diffusion_fixed_val }} 
           as gaussian: true
         write:
-          filepath: "{{ DATA }}/berror/diffusion_hz" 
+          filepath: "{{ DATA }}/diffusion/diffusion_vt" 
 

parm/snow/jcb-base.yaml.j2

@@ -0,0 +1,137 @@
+# Search path for model and obs for JCB
+# -------------------------------------
+algorithm_path: "{{PARMgfs}}/gdas/jcb-algorithms"
+app_path_algorithm: "{{PARMgfs}}/gdas/jcb-gdas/algorithm/snow"
+app_path_model: "{{PARMgfs}}/gdas/jcb-gdas/model/snow"
+app_path_observations: "{{PARMgfs}}/gdas/jcb-gdas/observations/atmosphere"
+app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/atmosphere"
+
+
+# Places where we deviate from the generic file name of a yaml
+# ------------------------------------------------------------
+#final_increment_file: final_increment_gaussian
+final_increment_file: final_increment_cubed_sphere
+output_ensemble_increments_file: output_ensemble_increments_gaussian
+model_file: model_pseudo
+initial_condition_file: background  # Initial conditions for 4D apps is background
+
+
+# Assimilation window
+# -------------------
+window_begin: "{{ SNOW_WINDOW_BEGIN | to_isotime }}"
+window_length: "{{ SNOW_WINDOW_LENGTH }}"
+bound_to_include: begin
+
+# Default background time is for 3D applications
+{% if DOIAU %}
+{% set bkg_time_iso = SNOW_WINDOW_BEGIN | to_isotime %}
+{% set bkg_time_fv3 = SNOW_WINDOW_BEGIN | to_fv3time %}
+{% else %}
+{% set bkg_time_iso = current_cycle | to_isotime %}
+{% set bkg_time_fv3 = current_cycle | to_fv3time %}
+{% endif %}
+snow_background_time_iso: "{{ bkg_time_iso }}"
+snow_increment_time_iso: "{{ bkg_time_iso }}"
+snow_increment_time_fv3: "{{ bkg_time_fv3 }}"
+
+
+# Analysis standard things
+# ------------------------
+analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+minimizer: DRPCG
+final_diagnostics_departures: anlmob
+
+cost_type: 3D-Var
+number_of_outer_loops: 2
+
+# Model things
+# ------------
+# Geometry
+layout_x: {{ layout_x | default(1, true) }}
+layout_y: {{ layout_y | default(1, true) }}
+npx_ges: {{ npx_ges | default(49, true) }}
+npy_ges: {{ npy_ges | default(49, true) }}
+npz_ges: {{ npz_ges | default(127, true) }}
+npx_anl: {{ npx_anl | default(49, true) }}
+npy_anl: {{ npy_anl | default(49, true) }}
+npz_anl: {{ npz_anl | default(127, true) }}
+
+fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
+
+# Background
+background_path: ./bkg
+background_ensemble_path: ./ens/mem%mem%
+
+# Background error
+bump_data_directory: "{{ DATA }}/berror"
+gsibec_path: "{{ DATA }}/berror"
+number_ensemble_members: {{ NMEM_ENS | default(1, true) }}
+layout_gsib_x: {{ layout_gsib_x | default(1, true) }}
+layout_gsib_y: {{ layout_gsib_y | default(1, true) }}
+
+background_error_file: "{{BERROR_YAML}}"
+
+# Forecasting
+forecast_length: "{{ ATM_WINDOW_LENGTH }}"
+forecast_timestep: "{{ BKG_TSTEP }}"
+
+# Write final increment on Guassian grid in variational
+final_increment_prefix: "./anl/atminc."
+
+
+# Observation things
+# ------------------
+observations: all_observations
+
+crtm_coefficient_path: "{{ DATA }}/crtm/"
+
+# Naming conventions for observational files
+atm_obsdatain_path: "{{atm_obsdatain_path}}"
+atm_obsdatain_prefix: "{{OPREFIX}}"
+atm_obsdatain_suffix: ".tm00.nc"
+
+atm_obsdataout_path: "{{atm_obsdataout_path}}"
+atm_obsdataout_prefix: diag_
+atm_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
+
+# Naming conventions for bias correction files
+atm_obsbiasin_path: "{{DATA}}/obs/"
+atm_obsbiasin_prefix: "{{GPREFIX}}"
+atm_obsbiasin_suffix: ".satbias.nc"
+atm_obstlapsein_prefix: "{{GPREFIX}}"
+atm_obstlapsein_suffix: ".tlapse.txt"
+atm_obsbiascovin_prefix: "{{GPREFIX}}"
+atm_obsbiascovin_suffix: ".satbias_cov.nc"
+
+atm_obsbiasout_path: "{{DATA}}/bc/"
+atm_obsbiasout_prefix: "{{APREFIX}}"
+atm_obsbiasout_suffix: ".satbias.nc"
+atm_obsbiascovout_prefix: "{{APREFIX}}"
+atm_obsbiascovout_suffix: ".satbias_cov.nc"
+
+
+# Local Ensemble DA (LETKF)
+# -------------------------
+local_ensemble_da_solver: GETKF
+
+increment_variables: [ua,va,DZ,delp,t,ps,sphum,ice_wat,liq_wat,o3mr]
+
+# Veritcal localization for GETKF
+vl_fraction_of_retained_variance: 0.750
+vl_lengthscale: 2.1
+vl_lengthscale_units: logp
+inflation_rtps: 0.85
+inflation_rtpp: 0.0
+inflation_mult: 1.0
+
+# Driver
+driver_update_obs_config_with_geometry_info: true
+driver_save_posterior_mean: false
+driver_save_posterior_ensemble: false
+driver_save_prior_mean: false
+driver_save_posterior_mean_increment: false
+driver_save_posterior_ensemble_increments: true
+
+# Diagnostics
+ensemble_increment_prefix: "./anl/mem%{member}%/atminc."
+#posterior_output_gaussian: "./mem%{member}%/atmanl."

parm/snow/jcb-fv3jedi_land_ensrecenter.yaml.j2

@@ -0,0 +1,7 @@
+# Algorithm
+# ---------
+algorithm: fv3jedi_land_ensrecenter
+
+# Observation things
+# ------------------
+observations: []

parm/snow/letkfoi/ens_apply_incr_nml.j2

@@ -0,0 +1,10 @@
+&noahmp_snow
+  date_str = "{{ current_cycle | to_YMD }}",
+  hour_str = "{{ current_cycle | strftime('%H') }}",
+  res = {{ CASE_ENS[1:] }},
+  frac_grid = .true.,
+  rst_path = "{{ DATAROOT }}/anl/mem{{ MYMEM }}",
+  inc_path = "{{ DATAROOT }}/inc/ensmean",
+  orog_path = "{{ HOMEgfs }}/fix/orog/{{ CASE_ENS }}",
+  otype = "{{ CASE_ENS }}.mx{{ OCNRES }}_oro_data"
+/

parm/soca/letkf/letkf_stage.yaml.j2

@@ -36,14 +36,14 @@ copy:
 # 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) %}
+{% set com_prev_ocn = namespace(COMIN_OCEAN_HISTORY_MEM = COM_OCEAN_HISTORY_TMPL) %}
+{% set com_prev_ice = namespace(COMIN_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) %}
+{% 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.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"]
+- ["{{ com_prev_ocn.COMIN_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.COMIN_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 %}

scripts/exgdas_global_marine_analysis_prep.py

@@ -177,7 +177,7 @@ def parse_obs_list_file():
             ensroot = os.getenv('COM_OCEAN_HISTORY_PREV')
             ensdir = os.path.join(os.getenv('COM_OCEAN_HISTORY_PREV'), '..', '..', '..', '..', '..',
                                   f'enkf{RUN}.{PDY}', f'{gcyc}', f'mem{str(mem).zfill(3)}',
-                                  'model_data', domain, 'history')
+                                  'model', domain, 'history')
             ensdir_real = os.path.realpath(ensdir)
             f009 = f'enkfgdas.{domain}.t{gcyc}z.inst.f009.nc'
 

test/aero/global-workflow/jjob_var_init.sh

@@ -76,7 +76,7 @@ done
 
 
 # Copy model bacgkround on tiles
-dpath=gdas.$gPDY/$gcyc/model_data/atmos
+dpath=gdas.$gPDY/$gcyc/model/atmos
 COM_ATMOS_RESTART_PREV_DIRNAME=$(dirname $COM_ATMOS_RESTART_PREV)
 if [ -d $COM_ATMOS_RESTART_PREV_DIRNAME/restart ]; then
     rm -rf $COM_ATMOS_RESTART_PREV_DIRNAME/restart

test/atm/global-workflow/jjob_ens_init.sh

@@ -95,13 +95,13 @@ for imem in $(seq 1 $NMEM_ENS); do
 	COM_ATMOS_RESTART_PREV_ENS:COM_ATMOS_RESTART_TMPL
     COM_ATMOS_RESTART_PREV_DIRNAME_ENS=$(dirname $COM_ATMOS_RESTART_PREV_ENS)
 
-    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos
     target=$COM_ATMOS_RESTART_PREV_DIRNAME_ENS
     mkdir -p $target
     rm -rf $target/restart
     ln -fs $source/restart $target/
 
-    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos/history
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos/history
     target=$COM_ATMOS_HISTORY_PREV_ENS
     mkdir -p $target
     rm -rf $target/enkfgdas.t${gcyc}z.atmf006.nc

test/atm/global-workflow/jjob_var_init.sh

@@ -88,15 +88,15 @@ for file in $flist; do
 done
 
 # Link atmospheric background on gaussian grid
-dpath=gdas.$gPDY/$gcyc/model_data/atmos/history
+dpath=gdas.$gPDY/$gcyc/model/atmos/history
 mkdir -p $COM_ATMOS_HISTORY_PREV
 flist="atmf006.nc"
 for file in $flist; do
    ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${gprefix}.${file} $COM_ATMOS_HISTORY_PREV/${gprefix}.${file}
 done
 
 # Link atmospheric bacgkround on tiles
-dpath=gdas.$gPDY/$gcyc/model_data/atmos
+dpath=gdas.$gPDY/$gcyc/model/atmos
 COM_ATMOS_RESTART_PREV_DIRNAME=$(dirname $COM_ATMOS_RESTART_PREV)
 mkdir -p $COM_ATMOS_RESTART_PREV_DIRNAME
 flist="restart"
@@ -115,13 +115,13 @@ for imem in $(seq 1 $NMEM_ENS); do
 	COM_ATMOS_RESTART_PREV_ENS:COM_ATMOS_RESTART_TMPL
     COM_ATMOS_RESTART_PREV_DIRNAME_ENS=$(dirname $COM_ATMOS_RESTART_PREV_ENS)
 
-    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos
     target=$COM_ATMOS_RESTART_PREV_DIRNAME_ENS
     mkdir -p $target
     rm -rf $target/restart
     ln -fs $source/restart $target/
 
-    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos/history
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model/atmos/history
     target=$COM_ATMOS_HISTORY_PREV_ENS
     mkdir -p $target
     rm -rf $target/enkfgdas.t${gcyc}z.atmf006.nc

test/snow/apply_jedi_incr.sh

@@ -16,7 +16,7 @@ GHR=$(date +%H -d "$YY$MM$DD $HH - 6 hours")
 
 EXECDIR=$project_source_dir/build/bin
 WORKDIR=$project_binary_dir/test/snow/apply_jedi_incr
-RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model_data/atmos/restart
+RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model/atmos/restart
 INCDIR=$GDASAPP_TESTDATA/snow/C${RES}
 
 export TPATH="$GDASAPP_TESTDATA/snow/C${RES}"

test/snow/create_bkg_ens.sh

@@ -16,7 +16,7 @@ GYMD=$(date +%Y%m%d -d "$YY$MM$DD $HH - 6 hours")
 GHR=$(date +%H -d "$YY$MM$DD $HH - 6 hours")
 
 WORKDIR=$project_binary_dir/test/snow/create_jedi_ens
-RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model_data/atmos/restart
+RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model/atmos/restart
 GFSv17=NO
 DAtype=letkfoi_snow
 

test/snow/letkfoi_snowda.sh

@@ -16,7 +16,7 @@ GHR=$(date +%H -d "$YY$MM$DD $HH - 6 hours")
 
 EXECDIR=$project_source_dir/build/bin
 WORKDIR=$project_binary_dir/test/snow/letkfoi_snowda
-RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model_data/atmos/restart
+RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model/atmos/restart
 export OBSDIR=$GDASAPP_TESTDATA/snow
 
 GFSv17=${GFSv17:-"YES"}

test/snow/test_imsproc.sh

@@ -17,7 +17,7 @@ DOY=$(date +%j -d "$YY$MM$DD + 1 day")
 
 EXECDIR=$project_source_dir/build/bin
 WORKDIR=$project_binary_dir/test/snow/ims_proc
-RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model_data/atmos/restart
+RSTDIR=$GDASAPP_TESTDATA/lowres/gdas.$GYMD/$GHR/model/atmos/restart
 
 export OBSDIR=$GDASAPP_TESTDATA/snow/snow_ice_cover
 export TSTUB="oro_C${RES}.mx100"