Merge branch 'develop' into feature/multi_model_build

parm/config/gfs/config.aeroanl

@@ -7,41 +7,39 @@ echo "BEGIN: config.aeroanl"
 
 # define analysis resolution based on deterministic res
 case ${CASE} in
-  "C1152" | "C768" | "C384" | "C192")
-    CASE_ANL="C192"
+  "C1152" | "C768" | "C384")
+    CASE_ANL="C384"
     ;;
-  "C96" | "C48")
+  "C192" | "C96" | "C48")
     CASE_ANL=${CASE}
     ;;
   *)
     echo "FATAL ERROR: Aerosol DA not supported at ${CASE} resolution"
     exit 4
 esac
 export CASE_ANL
-export OBS_LIST="${PARMgfs}/gdas/aero/obs/lists/gdas_aero.yaml.j2"
+export JCB_ALGO_YAML_VAR=${PARMgfs}/gdas/aero/jcb-prototype_3dvar.yaml.j2
 export STATICB_TYPE='diffusion'
-export BERROR_YAML="${PARMgfs}/gdas/aero/berror/staticb_${STATICB_TYPE}.yaml.j2"
+export BERROR_YAML="aero_background_error_static_${STATICB_TYPE}"
 export BERROR_DATA_DIR="${FIXgfs}/gdas/aero/clim_b"
 
 export CRTM_FIX_YAML="${PARMgfs}/gdas/aero_crtm_coeff.yaml.j2"
 export JEDI_FIX_YAML="${PARMgfs}/gdas/aero_jedi_fix.yaml.j2"
 
+export JEDI_CONFIG_YAML="${PARMgfs}/gdas/aeroanl_jedi_config.yaml.j2"
+
 export AERO_STAGE_VARIATIONAL_TMPL="${PARMgfs}/gdas/aero_stage_variational.yaml.j2"
 export AERO_FINALIZE_VARIATIONAL_TMPL="${PARMgfs}/gdas/aero_finalize_variational.yaml.j2"
 
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
 export JEDIEXE="${EXECgfs}/gdas.x"
-export BMATEXE="${EXECgfs}/gdasapp_chem_diagb.x"
-export DIFFUSIONEXE="${EXECgfs}/gdas_fv3jedi_error_covariance_toolbox.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"
-  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_fgat_gfs_aero.yaml.j2"
 else
   export aero_bkg_times="6," # Trailing comma is necessary so this is treated as a list
-  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_gfs_aero.yaml.j2"
 fi
 
 echo "END: config.aeroanl"

parm/config/gfs/config.aeroanlgenb

@@ -8,9 +8,8 @@ echo "BEGIN: config.aeroanlgenb"
 # Get task specific resources
 source "${EXPDIR}/config.resources" aeroanlgenb
 
-export BMATYAML="${PARMgfs}/gdas/aero/berror/aero_diagb.yaml.j2"
-export DIFFUSIONYAML="${PARMgfs}/gdas/aero/berror/aero_diffusionparm.yaml.j2"
-export INTERPYAML="${PARMgfs}/gdas/aero/berror/aero_interp.yaml.j2"
+export JEDI_CONFIG_YAML="${PARMgfs}/gdas/aero_bmat_jedi_config.yaml.j2"
+export JCB_BASE_YAML="${PARMgfs}/gdas/aero/jcb-base.yaml.j2"
 export AERO_BMATRIX_STAGE_TMPL="${PARMgfs}/gdas/aero_stage_bmatrix_bkg.yaml.j2"
 export AERO_BMATRIX_FINALIZE_TMPL="${PARMgfs}/gdas/aero_finalize_bmatrix_bkg.yaml.j2"
 export aero_diffusion_iter=10

parm/gdas/aero_bmat_jedi_config.yaml.j2

@@ -0,0 +1,19 @@
+aero_interpbkg:
+  rundir: '{{ DATA }}'
+  exe_src: '{{ EXECgfs }}/gdas.x'
+  jedi_args: ['fv3jedi', 'convertstate']
+  mpi_cmd: '{{ APRUN_AEROANLGENB }}'
+  jcb_base_yaml: '{{ PARMgfs }}/gdas/aero/jcb-base.yaml.j2'
+  jcb_algo: aero_convert_background
+aero_diagb:
+  rundir: '{{ DATA }}'
+  exe_src: '{{ EXECgfs }}/gdasapp_chem_diagb.x'
+  mpi_cmd: '{{ APRUN_AEROANLGENB }}'
+  jcb_base_yaml: '{{ PARMgfs }}/gdas/aero/jcb-base.yaml.j2'
+  jcb_algo: aero_gen_bmatrix_diagb
+aero_diffusion:
+  rundir: '{{ DATA }}'
+  exe_src: '{{ EXECgfs }}/gdas_fv3jedi_error_covariance_toolbox.x'
+  mpi_cmd: '{{ APRUN_AEROANLGENB }}'
+  jcb_base_yaml: '{{ PARMgfs }}/gdas/aero/jcb-base.yaml.j2'
+  jcb_algo: aero_gen_bmatrix_diffusion

parm/gdas/aero_finalize_bmatrix_bkg.yaml.j2

@@ -4,9 +4,9 @@
 {% set background_time = current_cycle | add_to_datetime(offset_td) %}
 copy:
 ### copy YAMLs used
-{% set yaml_list = ['chem_diagb.yaml', 'chem_diffusion.yaml'] %}
+{% set yaml_list = ['aero_diagb.yaml', 'aero_diffusion.yaml', 'aero_interpbkg.yaml'] %}
 {% for fname in yaml_list %}
-- ["{{ DATA }}/{{ HEAD }}{{ fname }}", "{{ COMOUT_CHEM_BMAT }}/{{ HEAD }}{{ fname }}"]
+- ["{{ DATA }}/{{ fname }}", "{{ COMOUT_CHEM_BMAT }}/{{ HEAD }}{{ fname }}"]
 {% endfor %}
 ### copy stddev files to ROTDIR
 {% for tile in range(1, ntiles+1) %}

parm/gdas/aero_finalize_variational.yaml.j2

@@ -12,7 +12,7 @@ mkdir:
 - "{{ COMOUT_ATMOS_RESTART }}"
 copy:
 ## copy variational YAML to ROTDIR
-- ["{{ DATA }}/{{ APREFIX }}aerovar.yaml", "{{ COMOUT_CHEM_ANALYSIS }}/{{ APREFIX }}aerovar.yaml"]
+- ["{{ DATA }}/aeroanlvar.yaml", "{{ COMOUT_CHEM_ANALYSIS }}/{{ APREFIX }}aerovar.yaml"]
 ## copy increments
 {% for tile in range(1,ntiles+1) %}
 - ["{{ DATA }}/anl/aeroinc.{{ current_cycle | to_fv3time }}.fv_tracer.res.tile{{ tile }}.nc", "{{ COMOUT_CHEM_ANALYSIS }}/aeroinc.{{ current_cycle | to_fv3time }}.fv_tracer.res.tile{{ tile }}.nc"]

parm/gdas/aero_stage_bmatrix_bkg.yaml.j2

@@ -12,6 +12,7 @@ mkdir:
 - "{{ DATA }}/stddev"
 - "{{ DATA }}/clm_stddev"
 - "{{ DATA }}/diffusion"
+- "{{ DATA }}/rescale"
 copy:
 ######################################
 # copy deterministic background files
@@ -30,9 +31,15 @@ copy:
 - ["{{ COM_ATMOS_RESTART_TMPL | replace_tmpl(tmpl_dict) }}/{{ background_time | to_fv3time }}.{{ ftype }}.tile{{ tile }}.nc", "{{ DATA }}/bkg/{{ background_time | to_fv3time }}.{{ ftype }}.tile{{ tile }}.nc"]
   {% endfor %}
 {% endfor %}
+######################################
 # copy climatological stddev files
 ######################################
 {% for tile in range(1, ntiles+1) %}
 - ["{{ BERROR_DATA_DIR }}/stddev.fv_tracer.res.tile{{ tile }}.nc", "{{ DATA }}/clm_stddev/stddev.fv_tracer.res.tile{{ tile }}.nc"]
 {% endfor %}
-
+######################################
+# copy stddev rescaling factor files
+######################################
+{% for tile in range(1, ntiles+1) %}
+- ["{{ BERROR_DATA_DIR }}/rescale.fv_tracer.res.tile{{ tile }}.nc", "{{ DATA }}/rescale/rescale.fv_tracer.res.tile{{ tile }}.nc"]
+{% endfor %}

parm/gdas/aeroanl_jedi_config.yaml.j2

@@ -0,0 +1,7 @@
+aeroanlvar:
+  rundir: '{{ DATA }}'
+  exe_src: '{{ EXECgfs }}/gdas.x'
+  mpi_cmd: '{{ APRUN_AEROANL }}'
+  jedi_args: ['fv3jedi', 'variational']
+  jcb_base_yaml: '{{ PARMgfs }}/gdas/aero/jcb-base.yaml.j2'
+  jcb_algo_yaml: '{{ JCB_ALGO_YAML_VAR }}'

scripts/exgdas_aero_analysis_generate_bmatrix.py

@@ -18,10 +18,8 @@
     # Take configuration from environment and cast it as python dictionary
     config = cast_strdict_as_dtypedict(os.environ)
 
-    # Instantiate the aerosol variance and diffusion correlation tasks
-    AeroB = AerosolBMatrix(config)
-    AeroB.initialize()
-    AeroB.interpBackground()
-    AeroB.computeVariance()
-    AeroB.computeDiffusion()
-    AeroB.finalize()
+    # Create an instance of the AerosolBMatrix task
+    aeroBMat = AerosolBMatrix(config)
+    aeroBMat.initialize()
+    aeroBMat.execute()
+    aeroBMat.finalize()

scripts/exglobal_aero_analysis_finalize.py

@@ -21,4 +21,6 @@
 
     # Instantiate the aerosol analysis task
     AeroAnl = AerosolAnalysis(config)
+
+    # Finalize JEDI aerosol variational analysis
     AeroAnl.finalize()

scripts/exglobal_aero_analysis_initialize.py

@@ -21,4 +21,6 @@
 
     # Instantiate the aerosol analysis task
     AeroAnl = AerosolAnalysis(config)
+
+    # Initialize JEDI aerosol variational analysis
     AeroAnl.initialize()

scripts/exglobal_aero_analysis_variational.py

@@ -19,4 +19,6 @@
 
     # Instantiate the aerosol analysis task
     AeroAnl = AerosolAnalysis(config)
-    AeroAnl.variational()
+
+    # Execute JEDI variational analysis
+    AeroAnl.execute('aeroanlvar')

sorc/build_ww3prepost.sh

@@ -65,6 +65,7 @@ sed -e "s/DIST/SHRD/g" \
   -e "s/OMPH / /g" \
   -e "s/MPIT / /g" \
   -e "s/MPI / /g" \
+  -e "s/PIO / /g" \
   -e "s/B4B / /g" \
   -e "s/PDLIB / /g" \
   -e "s/SCOTCH / /g" \

sorc/link_workflow.sh

@@ -143,10 +143,10 @@ cd "${HOMEgfs}/parm/ufs" || exit 1
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .
 
 cd "${HOMEgfs}/parm/post" || exit 1
-for file in params_grib2_tbl_new nam_micro_lookup.dat; do
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${file}" .
-done
-for dir in gfs gefs sfs; do
+${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
+${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" .
+for dir in gfs gefs sfs
+do
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
 done
 for file in ice.csv ocean.csv ocnicepost.nml.jinja2; do

ush/parsing_namelists_CICE.sh

@@ -70,7 +70,8 @@ local CICE_RESTART_FORMAT="pnetcdf2"
 local CICE_DUMPFREQ="y"  # "h","d","m" or "y" for restarts at intervals of "hours", "days", "months" or "years"
 local CICE_DUMPFREQ_N=10000  # Set this to a really large value, as cice, mom6 and cmeps restart interval is controlled by ufs.configure
 local CICE_DIAGFREQ=$(( 86400 / DT_CICE ))  # frequency of diagnostic output in timesteps, recommended for 1x per day
-local CICE_HISTFREQ_N="0, 0, ${FHOUT_ICE}, 1, 1"
+local CICE_HISTFREQ_N="0, 0, ${FHOUT_ICE}, 0, 1"
+local CICE_hist_suffix="'x','x','x','x','x'"
 if [[ "${RUN}" =~ "gdas" ]]; then
   local CICE_HIST_AVG=".false., .false., .false., .false., .false."   # DA needs instantaneous
 else

ush/parsing_ufs_configure.sh

@@ -77,6 +77,16 @@ if [[ "${cplwav}" = ".true." ]]; then
   local MULTIGRID="${waveMULTIGRID}"
   local WW3_user_sets_restname="false"
 
+  local WW3_user_histname="false"
+  local WW3_historync="false"
+  local WW3_restartnc="false" 
+  local WW3_restart_from_binary="false"
+  local WW3_PIO_FORMAT="pnetcdf"
+  local WW3_PIO_IOTASKS=-99
+  local WW3_PIO_STRIDE=4
+  local WW3_PIO_REARR="box"
+  local WW3_PIO_ROOT=-99
+
 fi
 
 if [[ "${cplchm}" = ".true." ]]; then

ush/python/pygfs/__init__.py

@@ -2,7 +2,6 @@
 import os
 
 from .task.analysis import Analysis
-from .task.bmatrix import BMatrix
 from .task.aero_emissions import AerosolEmissions
 from .task.aero_analysis import AerosolAnalysis
 from .task.aero_bmatrix import AerosolBMatrix