Use stochastic restart patterns on rerun (NOAA-EMC#3077)

The stochastic pattern restart files were not being copied into the input directory when restarting the model after a segment/failure. These files are now copied in and the stochini flag set to `.true.` in the namelist on a rerun. The files are NOT copied in for non-rerun warm starts. Also removes the restriction that stochastic physics cannot be run on member 0, as this is desired down the line. Additional settings are added to the fcst and efcs configs to retain the current behavior. A bug was also discovered and corrected during this work. The stage, forecast, and archive job all assumed that `ca_data` tile files are always present, but these are only created when cellular automata is on. Now `ca_data` files are handled if CA is on. To implement this change, the `DO_CA` setting had to be moved from the forecast configs to base so it is available to the stage_ic and archive jobs. Resolves NOAA-EMC#2937
JessicaMeixner-NOAA · Dec 5, 2024 · bc61862 · bc61862
1 parent b22d61e
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diff --git a/.gitmodules b/.gitmodules
@@ -1,7 +1,6 @@
 [submodule "sorc/ufs_model.fd"]
   path = sorc/ufs_model.fd
   url = https://github.com/ufs-community/ufs-weather-model
-  ignore = dirty
 [submodule "sorc/wxflow"]
   path = sorc/wxflow
   url = https://github.com/NOAA-EMC/wxflow

diff --git a/parm/archive/enkf_restartb_grp.yaml.j2 b/parm/archive/enkf_restartb_grp.yaml.j2
@@ -27,8 +27,11 @@ enkf_restartb_grp:
         {% set r_dt = current_cycle | add_to_datetime(r_timedelta) %}
         {% set r_prefix = r_dt | to_YMD + "." + r_dt | strftime("%H") + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"

diff --git a/parm/archive/gdas_restartb.yaml.j2 b/parm/archive/gdas_restartb.yaml.j2
@@ -30,8 +30,11 @@ gdas_restartb:
         {% set r_HH = r_dt | strftime("%H") %}
         {% set r_prefix = r_YMD + "." + r_HH + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"

diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
@@ -287,10 +287,17 @@ export DO_MERGENSST="NO"
 export NMEM_ENS=@NMEM_ENS@
 
 # set default member number memdir for control
-# this will be overwritten for the perturbed members
+# this will be overwridden for the perturbed members
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
+# cellular automata
+if (( ENSMEM == 0 )); then
+    export DO_CA="YES"
+else
+    export DO_CA="YES"
+fi
+
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
 
 # Check if cycle is warm starting with IAU

diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
@@ -44,16 +44,18 @@ export SPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
 export SPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
-export DO_CA="YES"
 # OCN options
-export DO_OCN_SPPT="YES"
-export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
-export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
-export DO_OCN_PERT_EPBL="YES"
-export EPBL="0.8,0.4,0.2,0.08,0.04"
-export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+if (( OCNRES <= 100 )); then
+    # Ocean stochastic options not supported at 5p00
+    export DO_OCN_SPPT="YES"
+    export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
+    export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+    export DO_OCN_PERT_EPBL="YES"
+    export EPBL="0.8,0.4,0.2,0.08,0.04"
+    export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+fi
 
 if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
     export ODA_INCUPD="True"

diff --git a/parm/config/gefs/config.fcst b/parm/config/gefs/config.fcst
@@ -225,11 +225,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-export DO_SPPT=${DO_SPPT:-"NO"}
-export DO_SKEB=${DO_SKEB:-"NO"}
-export DO_SHUM=${DO_SHUM:-"NO"}
-export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-export DO_CA=${DO_CA:-"YES"}
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"

diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
@@ -460,6 +460,9 @@ export INCVARS_EFOLD="5"
 export netcdf_diag=".true."
 export binary_diag=".false."
 
+# Cellular automata
+export DO_CA="YES"
+
 # Verification options
 export DO_METP="@DO_METP@"   # Run METPLUS jobs - set METPLUS settings in config.metp
 export DO_FIT2OBS="YES"      # Run fit to observations package

diff --git a/parm/config/gfs/config.fcst b/parm/config/gfs/config.fcst
@@ -245,14 +245,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-export DO_SPPT=${DO_SPPT:-"NO"}
-export DO_SKEB=${DO_SKEB:-"NO"}
-export DO_SHUM=${DO_SHUM:-"NO"}
-export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-export DO_CA=${DO_CA:-"YES"}
-if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
-  export DO_CA="NO"  # CA does not work with nesting.
-fi
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"

diff --git a/parm/stage/atmosphere_nest.yaml.j2 b/parm/stage/atmosphere_nest.yaml.j2
@@ -11,8 +11,11 @@ atmosphere_nest:
         {% 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"] %}
+        {% for ftype in ["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"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.ca_data.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% endif %}
         {% endfor %}
         {% endfor %} # mem loop
     {% else %} # cold start

diff --git a/parm/stage/atmosphere_warm.yaml.j2 b/parm/stage/atmosphere_warm.yaml.j2
@@ -15,9 +15,12 @@ atmosphere_warm:
         {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
         {% endfor %}
-        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         {% for ntile in range(1, ntiles + 1) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% endif %}
         {% endfor %} # ntile
         {% endfor %} # ftype
         {% for ntile in range(1, ntiles + 1) %}

diff --git a/scripts/exgdas_enkf_earc.py b/scripts/exgdas_enkf_earc.py
@@ -25,7 +25,7 @@ def main():
             'lobsdiag_forenkf', 'FHMIN_ENKF', 'FHMAX_ENKF_GFS',
             'FHOUT_ENKF_GFS', 'FHMAX_ENKF', 'FHOUT_ENKF', 'ENKF_SPREAD',
             'restart_interval_enkfgdas', 'restart_interval_enkfgfs',
-            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU',
+            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU', 'DO_CA',
             'DO_CALC_INCREMENT', 'assim_freq', 'ARCH_CYC',
             'ARCH_WARMICFREQ', 'ARCH_FCSTICFREQ',
             'IAUFHRS_ENKF', 'NET']

diff --git a/scripts/exglobal_archive.py b/scripts/exglobal_archive.py
@@ -29,7 +29,7 @@ def main():
             'DOIAU', 'OCNRES', 'ICERES', 'NUM_SND_COLLECTIVES', 'FHOUT_WAV',
             'FHOUT_HF_WAV', 'FHMAX_WAV', 'FHMAX_HF_WAV', 'FHMAX_WAV_GFS',
             'restart_interval_gdas', 'restart_interval_gfs',
-            'DO_AERO_ANL', 'DO_AERO_FCST', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
+            'DO_AERO_ANL', 'DO_AERO_FCST', 'DO_CA', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
             'NMEM_ENS', 'DO_JEDIATMVAR', 'DO_VRFY_OCEANDA', 'FHMAX_FITS', 'waveGRD',
             'IAUFHRS', 'DO_FIT2OBS', 'NET', 'FHOUT_HF_GFS', 'FHMAX_HF_GFS', 'REPLAY_ICS',
             'OFFSET_START_HOUR']

diff --git a/scripts/exglobal_stage_ic.py b/scripts/exglobal_stage_ic.py
@@ -22,7 +22,7 @@ def main():
             'assim_freq', 'current_cycle', 'previous_cycle',
             'ROTDIR', 'ICSDIR', 'STAGE_IC_YAML_TMPL', 'DO_JEDIATMVAR',
             'OCNRES', 'waveGRD', 'ntiles', 'DOIAU', 'DO_JEDIOCNVAR',
-            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST',
+            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST', 'DO_CA',
             'USE_ATM_ENS_PERTURB_FILES', 'USE_OCN_ENS_PERTURB_FILES']
 
     stage_dict = AttrDict()

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -47,7 +47,19 @@ FV3_postdet() {
       || ( echo "FATAL ERROR: Unable to copy FV3 IC, ABORT!"; exit 1 )
     done
 
-    if [[ "${RERUN}" != "YES" ]]; then
+    if [[ "${RERUN}" == "YES" ]]; then
+      if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+            "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+        stochini=".true."
+        file_list=$(stoch_restarts)
+        echo "Copying stochastic restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
+        for stoch_file in $(stoch_restarts); do
+          restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${stoch_file}"
+          ${NCP} "${restart_dir}/${restart_file}" "${DATA}/INPUT/${stoch_file}" \
+          || ( echo "FATAL ERROR: Unable to copy stochastic restart, ABORT!"; exit 1 )
+        done
+      fi
+    else
       # Replace sfc_data with sfcanl_data restart files from current cycle (if found)
       local nn
       for (( nn = 1; nn <= ntiles; nn++ )); do
@@ -78,7 +90,7 @@ FV3_postdet() {
                  "${DATA}/INPUT/fv_tracer.res.tile${nn}.nc"
         done
       fi # if [[ ${use_anl_aero} == "YES" ]]; then
-    fi  # if [[ "${RERUN}" != "YES" ]]; then
+    fi  # if [[ "${RERUN}" == "YES" ]]; then
 
   fi  # if [[ "${warm_start}" == ".true." ]]; then
 

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
@@ -57,7 +57,10 @@ FV3_restarts(){
   # Create an array of FV3 restart files
   local fv3_restart_files tile_files
   fv3_restart_files=(coupler.res fv_core.res.nc)
-  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data ca_data)
+  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data)
+  if [[ ${DO_CA:-"NO"} == "YES" ]]; then
+    tile_files+=(ca_data)
+  fi
   local nn tt
   for (( nn = 1; nn <= ntiles; nn++ )); do
     for tt in "${tile_files[@]}"; do
@@ -68,6 +71,22 @@ FV3_restarts(){
   IFS=, echo "${fv3_restart_files[*]}"
 }
 
+stoch_restarts(){
+  # These only get copied for reruns
+  local stoch_restart_files
+  stoch_restart_files=(  )
+
+  if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+        "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+    stoch_restart_files+=(atm_stoch.res.nc)
+  fi
+  if [[ "${DO_OCN:-}" == "YES" && ( "${DO_OCN_SPPT:-}" == "YES" || "${DO_OCN_PERT_EPBL}" == "YES" ) ]]; then
+    stoch_restart_files+=(ocn_stoch.res.nc)
+  fi
+  # Create a comma separated string from array using IFS
+  IFS=, echo "${stoch_restart_files[*]}"
+}
+
 # shellcheck disable=SC2034
 common_predet(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for shared through model components"
@@ -377,41 +396,38 @@ FV3_predet(){
   do_sppt=".false."
   do_ca=".false."
   ISEED=0
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
-
-    if [[ "${DO_SKEB:-}" == "YES" ]]; then
-      do_skeb=".true."
-      ISEED_SKEB=$((base_seed + 1))
-    fi
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_SHUM:-}" == "YES" ]]; then
-      do_shum=".true."
-      ISEED_SHUM=$((base_seed + 2))
-    fi
+  if [[ "${DO_SKEB:-}" == "YES" ]]; then
+    do_skeb=".true."
+    ISEED_SKEB=$((base_seed + 1))
+  fi
 
-    if [[ "${DO_SPPT:-}" == "YES" ]]; then
-      do_sppt=".true."
-      ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
-    fi
+  if [[ "${DO_SHUM:-}" == "YES" ]]; then
+    do_shum=".true."
+    ISEED_SHUM=$((base_seed + 2))
+  fi
 
-    if [[ "${DO_CA:-}" == "YES" ]]; then
-      do_ca=".true."
-      ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
-    fi
+  if [[ "${DO_SPPT:-}" == "YES" ]]; then
+    do_sppt=".true."
+    ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
+  fi
 
-    if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
-      lndp_type=${lndp_type:-2}
-      ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
-      LNDP_TAU=${LNDP_TAU:-21600}
-      LNDP_SCALE=${LNDP_SCALE:-500000}
-      lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
-      lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
-      n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
-    fi
+  if [[ "${DO_CA:-}" == "YES" ]]; then
+    do_ca=".true."
+    ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
+  fi
 
-  fi  # end of ensemble member specific options
+  if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
+    lndp_type=${lndp_type:-2}
+    ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
+    LNDP_TAU=${LNDP_TAU:-21600}
+    LNDP_SCALE=${LNDP_SCALE:-500000}
+    lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
+    lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
+    n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
+  fi
 
   #--------------------------------------------------------------------------
 
@@ -680,17 +696,15 @@ MOM6_predet(){
 
   # If using stochastic parameterizations, create a seed that does not exceed the
   # largest signed integer
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
-      ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
-    fi
+  if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
+    ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
+  fi
 
-    if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
-      ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
-    fi
+  if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
+    ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
   fi
 
   # Fix files

diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
@@ -656,6 +656,7 @@ if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "$
 
     cat >> input.nml << EOF
 &nam_stochy
+  stochini=${stochini:-".false."}
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then