Convert staging job to python and yaml

ci/cases/pr/C48mx500_3DVarAOWCDA.yaml

@@ -9,7 +9,7 @@ arguments:
   resdetocean: 5.0
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20240610
   idate: 2021032412
   edate: 2021032418
   nens: 0

ci/cases/pr/C96C48_hybatmDA.yaml

@@ -10,7 +10,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2021122018
   edate: 2021122106
   nens: 2

ci/cases/pr/C96C48_ufs_hybatmDA.yaml

@@ -9,7 +9,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2024022318
   edate: 2024022400
   nens: 2

ci/cases/pr/C96_atm3DVar.yaml

@@ -8,7 +8,7 @@ arguments:
   resdetatmos: 96
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2021122018
   edate: 2021122106
   nens: 0

ci/cases/pr/C96_atm3DVar_extended.yaml

@@ -8,7 +8,7 @@ arguments:
   resdetatmos: 96
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2021122018
   edate: 2021122118
   nens: 0

ci/cases/pr/C96_atmaerosnowDA.yaml

@@ -8,7 +8,7 @@ arguments:
   resdetatmos: 96
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2021122012
   edate: 2021122100
   nens: 0

docs/source/init.rst

@@ -125,14 +125,14 @@ Start date = 2021032312
    ├── enkfgdas.20210323
    │   ├── 06
    │   │   ├── mem001
-   │   │   │   └── model_data -> ../../../gdas.20210323/06/model_data
+   │   │   │   └── model -> ../../../gdas.20210323/06/model
    │   │   ├── mem002
-   │   │   │   └── model_data -> ../../../gdas.20210323/06/model_data
+   │   │   │   └── model -> ../../../gdas.20210323/06/model
    │   │   ├── mem003
-   │   │   │   └── model_data -> ../../../gdas.20210323/06/model_data
+   │   │   │   └── model -> ../../../gdas.20210323/06/model
    ...
    │   │   └── mem080
-   │   │       └── model_data -> ../../../gdas.20210323/06/model_data
+   │   │       └── model -> ../../../gdas.20210323/06/model
    │   └── 12
    │       ├── mem001
    │       │   └── analysis
@@ -153,7 +153,7 @@ Start date = 2021032312
    │                   └── gdas.t12z.ocninc.nc -> ../../../../../gdas.20210323/12/analysis/ocean/gdas.t12z.ocninc.nc
    └── gdas.20210323
        ├── 06
-       │   └── model_data
+       │   └── model
        │       ├── atmos
        │       │   └── restart
        │       │       ├── 20210323.120000.ca_data.tile1.nc

jobs/JGLOBAL_STAGE_IC

@@ -3,15 +3,16 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
 
-# Restart conditions for GFS cycle come from GDAS
-# shellcheck disable=SC2153
-rCDUMP=${RUN}
-# shellcheck disable=SC2153
-[[ ${RUN} = "gfs" ]] && export rCDUMP="gdas"
-export rCDUMP
+# Execute staging
+"${SCRgfs}/exglobal_stage_ic.py"
+err=$?
 
-# Execute the Script
-"${SCRgfs}/exglobal_stage_ic.sh"
+###############################################################
+# Check for errors and exit if any of the above failed
+if [[ "${err}" -ne 0 ]]; then
+  echo "FATAL ERROR: Unable to copy ICs to ${ROTDIR}; ABORT!"
+  exit "${err}"
+fi
 
 ##########################################
 # Remove the Temporary working directory

parm/config/gefs/config.base

@@ -38,7 +38,6 @@ export FIXugwd=${FIXgfs}/ugwd
 export PACKAGEROOT="@PACKAGEROOT@"    # TODO: set via prod_envir in Ops
 export COMROOT="@COMROOT@"    # TODO: set via prod_envir in Ops
 export COMINsyn="@COMINsyn@"
-export BASE_CPLIC="@BASE_CPLIC@"
 
 # USER specific paths
 export HOMEDIR="@HOMEDIR@"

parm/config/gefs/config.stage_ic

@@ -7,32 +7,27 @@ echo "BEGIN: config.stage_ic"
 # Get task specific resources
 source "${EXPDIR}/config.resources" stage_ic
 
-case "${CASE}" in
-  "C384")
-    export CPL_ATMIC=""
-    export CPL_ICEIC=""
-    export CPL_OCNIC=""
-    export CPL_WAVIC=""
-    export CPL_MEDIC=""
-    ;;
-  "C96")
-    export CPL_ATMIC=""
-    export CPL_ICEIC=""
-    export CPL_OCNIC=""
-    export CPL_WAVIC=""
-    export CPL_MEDIC=""
-    ;;
-  "C48")
-    export CPL_ATMIC="gefs_test"
-    export CPL_ICEIC="gefs_test"
-    export CPL_OCNIC="gefs_test"
-    export CPL_WAVIC="gefs_test"
-    export CPL_MEDIC="gefs_test"
-    ;;
-  *)
-    echo "FATAL ERROR Unrecognized resolution: ${CASE}"
-    exit 1
-    ;;
-esac
+export ICSDIR="@ICSDIR@" # User provided ICSDIR; blank if not provided
+export BASE_IC="@BASE_IC@" # Platform home for staged ICs
+
+export STAGE_IC_YAML_TMPL="${PARMgfs}/stage/master_gefs.yaml.j2"
+
+# Set ICSDIR
+
+if [[ -z "${ICSDIR}" ]] ; then
+
+  ic_ver="20240610"
+
+  if (( NMEM_ENS > 0 )) ; then
+    ensic="${CASE_ENS}"
+  fi
+
+  if [[ "${DO_OCN:-NO}" == "YES" ]] ; then
+    ocnic="mx${OCNRES}"
+  fi
+
+  export ICSDIR="${BASE_IC}/${CASE}${ensic:-}${ocnic:-}/${ic_ver}"
+
+fi
 
 echo "END: config.stage_ic"

parm/config/gfs/config.base

@@ -47,7 +47,6 @@ export PACKAGEROOT="@PACKAGEROOT@"    # TODO: set via prod_envir in Ops
 export COMROOT="@COMROOT@"    # TODO: set via prod_envir in Ops
 export COMINsyn="@COMINsyn@"
 export DMPDIR="@DMPDIR@"
-export BASE_CPLIC="@BASE_CPLIC@"
 
 # Gempak from external models
 # Default locations are to dummy locations for testing

parm/config/gfs/config.com

@@ -12,7 +12,7 @@ echo "BEGIN: config.com"
 #       declare_from_tmpl [-rx] $var1[:$tmpl1] [$var2[:$tmpl2]] [...]]
 #
 #       options:
-#           -r: Make variable read-only (same as `decalre -r`)
+#           -r: Make variable read-only (same as `declare -r`)
 #           -x: Mark variable for declare -rx (same as `declare -x`)
 #       var1, var2, etc: Variable names whose values will be generated from a template
 #                   and declared
@@ -51,12 +51,12 @@ declare -rx COM_TOP_TMPL='${ROTDIR}/${RUN}.${YMD}/${HH}'
 declare -rx COM_CONF_TMPL=${COM_BASE}'/conf'
 declare -rx COM_OBS_JEDI=${COM_BASE}'/obs_jedi'
 
-declare -rx COM_ATMOS_INPUT_TMPL=${COM_BASE}'/model_data/atmos/input'
-declare -rx COM_ATMOS_RESTART_TMPL=${COM_BASE}'/model_data/atmos/restart'
+declare -rx COM_ATMOS_INPUT_TMPL=${COM_BASE}'/model/atmos/input'
+declare -rx COM_ATMOS_RESTART_TMPL=${COM_BASE}'/model/atmos/restart'
 declare -rx COM_ATMOS_ANALYSIS_TMPL=${COM_BASE}'/analysis/atmos'
 declare -rx COM_SNOW_ANALYSIS_TMPL=${COM_BASE}'/analysis/snow'
-declare -rx COM_ATMOS_HISTORY_TMPL=${COM_BASE}'/model_data/atmos/history'
-declare -rx COM_ATMOS_MASTER_TMPL=${COM_BASE}'/model_data/atmos/master'
+declare -rx COM_ATMOS_HISTORY_TMPL=${COM_BASE}'/model/atmos/history'
+declare -rx COM_ATMOS_MASTER_TMPL=${COM_BASE}'/model/atmos/master'
 declare -rx COM_ATMOS_GRIB_TMPL=${COM_BASE}'/products/atmos/grib2'
 declare -rx COM_ATMOS_GRIB_GRID_TMPL=${COM_ATMOS_GRIB_TMPL}'/${GRID}'
 declare -rx COM_ATMOS_BUFR_TMPL=${COM_BASE}'/products/atmos/bufr'
@@ -70,17 +70,17 @@ declare -rx COM_ATMOS_RADMON_TMPL=${COM_BASE}'/products/atmos/radmon'
 declare -rx COM_ATMOS_MINMON_TMPL=${COM_BASE}'/products/atmos/minmon'
 declare -rx COM_ATMOS_WMO_TMPL=${COM_BASE}'/products/atmos/wmo'
 
-declare -rx COM_WAVE_RESTART_TMPL=${COM_BASE}'/model_data/wave/restart'
-declare -rx COM_WAVE_PREP_TMPL=${COM_BASE}'/model_data/wave/prep'
-declare -rx COM_WAVE_HISTORY_TMPL=${COM_BASE}'/model_data/wave/history'
+declare -rx COM_WAVE_RESTART_TMPL=${COM_BASE}'/model/wave/restart'
+declare -rx COM_WAVE_PREP_TMPL=${COM_BASE}'/model/wave/prep'
+declare -rx COM_WAVE_HISTORY_TMPL=${COM_BASE}'/model/wave/history'
 declare -rx COM_WAVE_GRID_TMPL=${COM_BASE}'/products/wave/gridded'
 declare -rx COM_WAVE_STATION_TMPL=${COM_BASE}'/products/wave/station'
 declare -rx COM_WAVE_GEMPAK_TMPL=${COM_BASE}'/products/wave/gempak'
 declare -rx COM_WAVE_WMO_TMPL=${COM_BASE}'/products/wave/wmo'
 
-declare -rx COM_OCEAN_HISTORY_TMPL=${COM_BASE}'/model_data/ocean/history'
-declare -rx COM_OCEAN_RESTART_TMPL=${COM_BASE}'/model_data/ocean/restart'
-declare -rx COM_OCEAN_INPUT_TMPL=${COM_BASE}'/model_data/ocean/input'
+declare -rx COM_OCEAN_HISTORY_TMPL=${COM_BASE}'/model/ocean/history'
+declare -rx COM_OCEAN_RESTART_TMPL=${COM_BASE}'/model/ocean/restart'
+declare -rx COM_OCEAN_INPUT_TMPL=${COM_BASE}'/model/ocean/input'
 declare -rx COM_OCEAN_ANALYSIS_TMPL=${COM_BASE}'/analysis/ocean'
 declare -rx COM_OCEAN_BMATRIX_TMPL=${COM_BASE}'/bmatrix/ocean'
 declare -rx COM_OCEAN_NETCDF_TMPL=${COM_BASE}'/products/ocean/netcdf'
@@ -89,14 +89,14 @@ declare -rx COM_OCEAN_GRIB_GRID_TMPL=${COM_OCEAN_GRIB_TMPL}'/${GRID}'
 
 declare -rx COM_ICE_ANALYSIS_TMPL=${COM_BASE}'/analysis/ice'
 declare -rx COM_ICE_BMATRIX_TMPL=${COM_BASE}'/bmatrix/ice'
-declare -rx COM_ICE_INPUT_TMPL=${COM_BASE}'/model_data/ice/input'
-declare -rx COM_ICE_HISTORY_TMPL=${COM_BASE}'/model_data/ice/history'
-declare -rx COM_ICE_RESTART_TMPL=${COM_BASE}'/model_data/ice/restart'
+declare -rx COM_ICE_INPUT_TMPL=${COM_BASE}'/model/ice/input'
+declare -rx COM_ICE_HISTORY_TMPL=${COM_BASE}'/model/ice/history'
+declare -rx COM_ICE_RESTART_TMPL=${COM_BASE}'/model/ice/restart'
 declare -rx COM_ICE_NETCDF_TMPL=${COM_BASE}'/products/ice/netcdf'
 declare -rx COM_ICE_GRIB_TMPL=${COM_BASE}'/products/ice/grib2'
 declare -rx COM_ICE_GRIB_GRID_TMPL=${COM_ICE_GRIB_TMPL}'/${GRID}'
 
-declare -rx COM_CHEM_HISTORY_TMPL=${COM_BASE}'/model_data/chem/history'
+declare -rx COM_CHEM_HISTORY_TMPL=${COM_BASE}'/model/chem/history'
 declare -rx COM_CHEM_ANALYSIS_TMPL=${COM_BASE}'/analysis/chem'
 
-declare -rx COM_MED_RESTART_TMPL=${COM_BASE}'/model_data/med/restart'
+declare -rx COM_MED_RESTART_TMPL=${COM_BASE}'/model/med/restart'

parm/config/gfs/config.stage_ic

@@ -7,39 +7,26 @@ echo "BEGIN: config.stage_ic"
 # Get task specific resources
 source "${EXPDIR}/config.resources" stage_ic
 
-case "${CASE}" in
-  "C48" | "C96" | "C192")
-    export CPL_ATMIC="workflow_${CASE}_refactored"
-    export CPL_ICEIC="workflow_${CASE}_refactored"
-    export CPL_OCNIC="workflow_${CASE}_refactored"
-    export CPL_WAVIC="workflow_${CASE}_refactored"
-    ;;
-  "C384")
-    export CPL_ATMIC=GEFS-NoahMP-aerosols-p8c_refactored
-    export CPL_ICEIC=CPC_refactored
-    export CPL_OCNIC=CPC3Dvar_refactored
-    export CPL_WAVIC=workflow_C384_refactored
-    ;;
-  "C768")
-    export CPL_ATMIC=HR3C768
-    export CPL_ICEIC=HR3marine
-    export CPL_OCNIC=HR3marine
-    export CPL_WAVIC=HR3marine
-    ;;
-  "C1152")
-    export CPL_ATMIC=HR3C1152
-    export CPL_ICEIC=HR3marine
-    export CPL_OCNIC=HR3marine
-    export CPL_WAVIC=HR3marine
-    ;;
-  *)
-    echo "FATAL ERROR Unrecognized resolution: ${CASE}"
-    exit 1
-    ;;
-esac
-
-if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
-  export CPL_ATMIC="GLOBAL-NEST_${CASE}"
+export ICSDIR="@ICSDIR@" # User provided ICSDIR; blank if not provided
+export BASE_IC="@BASE_IC@" # Platform home for staged ICs
+
+export STAGE_IC_YAML_TMPL="${PARMgfs}/stage/master_gfs.yaml.j2"
+
+# Set ICSDIR (if not defined)
+if [[ -z "${ICSDIR}" ]] ; then
+
+  ic_ver="20240610"
+
+  if (( NMEM_ENS > 0 )) ; then
+    ensic="${CASE_ENS}"
+  fi
+
+  if [[ "${DO_OCN:-NO}" == "YES" ]] ; then
+    ocnic="mx${OCNRES}"
+  fi
+
+  export ICSDIR="${BASE_IC}/${CASE}${ensic:-}${ocnic:-}/${ic_ver}"
+
 fi
 
 echo "END: config.stage_ic"

parm/stage/analysis.yaml.j2

@@ -0,0 +1,19 @@
+{% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM_list[0] | relpath(ROTDIR)) %}
+analysis:
+    mkdir:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
+        - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
+        {% endfor %}
+    copy:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
+        {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "radstat", "ratminc.nc"] %}
+        {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z." ~ ftype) %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.{{ ftype }}", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"]
+        {% endif %}
+        {% endfor %}
+        {% endfor %} # mem loop
+{% endif %}

parm/stage/atmosphere_cold.yaml.j2

@@ -0,0 +1,18 @@
+atmosphere_cold:
+    mkdir:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
+        - "{{ COMOUT_ATMOS_INPUT_MEM }}"
+        {% endfor %} # mem loop
+    copy:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/gfs_ctrl.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
+        {% for ftype in ["gfs_data", "sfc_data"] %}
+        {% for ntile in range(1, ntiles + 1) %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
+        {% endfor %} # ntile
+        {% endfor %} # ftype
+        {% endfor %} # mem loop

parm/stage/atmosphere_nest.yaml.j2

@@ -0,0 +1,33 @@
+atmosphere_nest:
+    {% set ntile = 7 %}
+    {% if EXP_WARM_START == True %}
+    mkdir:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
+        - "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"
+        {% endfor %} # mem loop
+    copy:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
+        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% endfor %}
+        {% endfor %} # mem loop
+    {% else %} # cold start
+    mkdir:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
+        - "{{ COMOUT_ATMOS_INPUT_MEM }}"
+        {% endfor %} # mem loop
+    copy:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
+        {% for ftype in ["gfs_data", "sfc_data"] %}
+        - ["{{ COMOUT_ATMOS_INPUT_MEM }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}/{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% endfor %}
+        {% endfor %} # mem loop
+    {% endif %}

parm/stage/atmosphere_perturbation.yaml.j2

@@ -0,0 +1,13 @@
+atmosphere_perturbation:
+    mkdir:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
+        - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
+        {% endfor %} # mem loop
+    copy:
+        {% for mem in range(first_mem, last_mem + 1) %}
+        {% set imem = mem - first_mem %}
+        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}/{{ RUN }}.t{{ current_cycle_HH }}z.atminc.nc"]
+        {% endfor %} # mem loop