Merge branch 'NOAA-EMC:develop' into feature/eupd_cyc

.gitmodules

@@ -77,6 +77,10 @@
   path = sorc/fms
   url = https://github.com/jcsda/fms.git
   branch = release-stable
+[submodule "sorc/jcb"]
+  path = sorc/jcb
+  url = https://github.com/noaa-emc/jcb.git
+  branch = develop
 [submodule "parm/jcb-gdas"]
   path = parm/jcb-gdas
   url = https://github.com/noaa-emc/jcb-gdas

build.sh

@@ -87,7 +87,7 @@ case ${BUILD_TARGET} in
     ;;
 esac
 
-CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA"
+CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA -DMACHINE=$BUILD_TARGET"
 
 BUILD_DIR=${BUILD_DIR:-$dir_root/build}
 if [[ $CLEAN_BUILD == 'YES' ]]; then

modulefiles/GDAS/orion.intel.lua

@@ -6,29 +6,30 @@ local pkgName    = myModuleName()
 local pkgVersion = myModuleVersion()
 local pkgNameVer = myModuleFullName()
 
-prepend_path("MODULEPATH", '/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core')
+prepend_path("MODULEPATH", '/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/unified-env-rocky9/install/modulefiles/Core')
 prepend_path("MODULEPATH", '/work2/noaa/da/python/opt/modulefiles/stack')
 
 -- below two lines get us access to the spack-stack modules
-load("stack-intel/2022.0.2")
-load("stack-intel-oneapi-mpi/2021.5.1")
+load("stack-intel/2021.9.0")
+load("stack-intel-oneapi-mpi/2021.9.0")
+--load("stack-python/3.10.8")
 -- JCSDA has 'jedi-fv3-env/unified-dev', but we should load these manually as needed
 load("cmake/3.23.1")
 load("curl/8.4.0")
 load("zlib/1.2.13")
-load("git/2.28.0")
-load("pkg-config/0.27.1")
+load("git/2.31.1")
+--load("pkg-config/0.27.1")
 load("hdf5/1.14.0")
 load("parallel-netcdf/1.12.2")
 load("netcdf-c/4.9.2")
 load("nccmp/1.9.0.1")
 load("netcdf-fortran/4.6.1")
 load("nco/5.0.6")
 load("parallelio/2.5.10")
-load("wget/1.21.3")
+load("wget/1.21.1")
 load("boost/1.83.0")
 load("bufr/12.0.1")
-load("git-lfs/2.12.0")
+load("git-lfs/3.1.2")
 load("ecbuild/3.7.2")
 load("openjpeg/2.3.1")
 load("eccodes/2.32.0")
@@ -43,7 +44,7 @@ load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
 load("libjpeg/2.1.0")
-load("krb5/1.15.1")
+load("krb5/1.20.1")
 load("libtirpc/1.3.3")
 load("hdf/4.2.15")
 load("jedi-cmake/1.4.0")
@@ -59,7 +60,7 @@ load("py-pybind11/2.11.0")
 --load("crtm/v2.4_jedi")
 load("contrib/0.1")
 load("noaatools/3.1")
-load("rocoto/1.3.3")
+load("rocoto/1.3.5")
 
 load("hpc/1.2.0")
 unload("python/3.10.13")

parm/aero/berror/aero_diffusionparm.yaml.j2

@@ -37,11 +37,11 @@ background error:
       - horizontal:
           fixed value: {{ horiz_len }} 
         write:
-          filepath: ./diffusion_hz
+          filepath: "{{ DATA }}/berror/diffusion_hz" 
       - vertical:
           levels: {{ npz_ges }} 
           fixed value: {{ fixed_val }} 
           as gaussian: true
         write:
-          filepath: ./diffusion_vt
+          filepath: "{{ DATA }}/berror/diffusion_hz" 
 

parm/aero/berror/staticb_diffusion.yaml.j2

@@ -0,0 +1,33 @@
+covariance model: SABER
+saber central block:
+  saber block name: diffusion 
+  read:
+    groups:
+    - 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]
+      horizontal:
+        filepath: "{{ DATA }}/berror/diffusion_hz"
+      vertical:
+        levels: {{ npz_ges }} 
+        filepath: "{{ DATA }}/berror/diffusion_vt" 
+saber outer blocks:
+- saber block name: StdDev
+  read:
+    model file:
+      datetime: '{{ current_cycle | to_isotime }}' 
+      set datetime on read: true
+      filetype: fms restart
+      psinfile: true
+      datapath: "{{ DATA }}/berror"
+      filename_core: '{{ current_cycle | to_fv3time }}.stddev.fv_core.res.nc'
+      filename_trcr: '{{ current_cycle | to_fv3time }}.stddev.fv_tracer.res.nc'
+      filename_cplr: '{{ current_cycle | to_fv3time }}.stddev.coupler.res'
+      date: '{{ current_cycle | to_isotime }}' 

parm/atm/jcb-base.yaml.j2

@@ -10,64 +10,56 @@ app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle
 # 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_cubed_sphere
-model_file: model_pseudo
-initial_condition_file: background  # Initial conditions for 4D apps is background
-
+final_increment_file: atmosphere_final_increment_cubed_sphere
+output_ensemble_increments_file: atmosphere_output_ensemble_increments_cubed_sphere
+model_file: atmosphere_model_pseudo
+initial_condition_file: atmosphere_background  # Initial conditions for 4D apps is background
+background_error_file: "{{BERROR_YAML}}"
 
-# Assimilation window
-# -------------------
+# Assimilation standard things (not prepended with model choice)
+# ----------------------------
 window_begin: "{{ ATM_WINDOW_BEGIN | to_isotime }}"
 window_length: "{{ ATM_WINDOW_LENGTH }}"
 bound_to_include: begin
-
-# Default background time is for 3D applications
-atm_background_time_iso: "{{ current_cycle | to_isotime }}"
-
-
-# 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
+analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 
 # 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) }}
+atmosphere_layout_x: {{ layout_x | default(1, true) }}
+atmosphere_layout_y: {{ layout_y | default(1, true) }}
+atmosphere_npx_ges: {{ npx_ges | default(49, true) }}
+atmosphere_npy_ges: {{ npy_ges | default(49, true) }}
+atmosphere_npz_ges: {{ npz_ges | default(127, true) }}
+atmosphere_npx_anl: {{ npx_anl | default(49, true) }}
+atmosphere_npy_anl: {{ npy_anl | default(49, true) }}
+atmosphere_npz_anl: {{ npz_anl | default(127, true) }}
 
-fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
+atmosphere_fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
 
 # Background
-background_path: ./bkg
-background_ensemble_path: ./ens/mem%mem%
+atmosphere_background_path: ./bkg
+atmosphere_background_ensemble_path: ./ens/mem%mem%
+
+# Default background time is for 3D applications
+atmosphere_background_time_iso: "{{ current_cycle | to_isotime }}"
 
 # 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) }}
+atmosphere_bump_data_directory: "{{ DATA }}/berror"
+atmosphere_gsibec_path: "{{ DATA }}/berror"
+atmosphere_number_ensemble_members: {{ NMEM_ENS | default(1, true) }}
+atmosphere_layout_gsib_x: {{ layout_gsib_x | default(1, true) }}
+atmosphere_layout_gsib_y: {{ layout_gsib_y | default(1, true) }}
 
-background_error_file: "{{BERROR_YAML}}"
 
 # Forecasting
-forecast_length: "{{ ATM_WINDOW_LENGTH }}"
-forecast_timestep: "{{ BKG_TSTEP }}"
+atmosphere_forecast_timestep: "{{ BKG_TSTEP }}"
 
 # Write final increment on Guassian grid in variational
-final_increment_prefix: "./anl/atminc."
+atmosphere_final_increment_prefix: "./anl/atminc."
 
 
 # Observation things
@@ -77,28 +69,28 @@ 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"
+atmosphere_obsdatain_path: "{{atm_obsdatain_path}}"
+atmosphere_obsdatain_prefix: "{{OPREFIX}}"
+atmosphere_obsdatain_suffix: ".tm00.nc"
 
-atm_obsdataout_path: "{{atm_obsdataout_path}}"
-atm_obsdataout_prefix: diag_
-atm_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
+atmosphere_obsdataout_path: "{{atm_obsdataout_path}}"
+atmosphere_obsdataout_prefix: diag_
+atmosphere_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"
+atmosphere_obsbiasin_path: "{{DATA}}/obs/"
+atmosphere_obsbiasin_prefix: "{{GPREFIX}}"
+atmosphere_obsbiasin_suffix: ".satbias.nc"
+atmosphere_obstlapsein_prefix: "{{GPREFIX}}"
+atmosphere_obstlapsein_suffix: ".tlapse.txt"
+atmosphere_obsbiascovin_prefix: "{{GPREFIX}}"
+atmosphere_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"
+atmosphere_obsbiasout_path: "{{DATA}}/bc/"
+atmosphere_obsbiasout_prefix: "{{APREFIX}}"
+atmosphere_obsbiasout_suffix: ".satbias.nc"
+atmosphere_obsbiascovout_prefix: "{{APREFIX}}"
+atmosphere_obsbiascovout_suffix: ".satbias_cov.nc"
 
 
 # Local Ensemble DA (LETKF)
@@ -124,5 +116,5 @@ 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."
+atmosphere_ensemble_increment_prefix: "./anl/mem%{member}%/atminc."
+atmosphere_posterior_output_gaussian: "./mem%{member}%/atmanl."

parm/atm/jcb-prototype_lgetkf.yaml.j2

@@ -9,7 +9,7 @@ algorithm: local_ensemble_da
 
 # Model things
 # ------------
-background_ensemble_path: ./bkg/mem%mem%
+atmosphere_background_ensemble_path: ./bkg/mem%mem%
 
 # Observation things
 # ------------------