Merge branch 'NOAA-EMC:develop' into IASI-NG

NOAA-EMC · Nov 26, 2024 · fbf5be3 · fbf5be3
2 parents 2aa4f76 + e41eff2
commit fbf5be3
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diff --git a/ci/Jenkinsfile b/ci/Jenkinsfile
@@ -5,7 +5,7 @@ def cases = ''
 def GH = 'none'
 // Location of the custom workspaces for each machine in the CI system.  They are persitent for each iteration of the PR.
 def NodeName = [hera: 'Hera-EMC', orion: 'Orion-EMC', hercules: 'Hercules-EMC', gaea: 'Gaea']
-def custom_workspace = [hera: '/scratch1/NCEPDEV/global/CI', orion: '/work2/noaa/stmp/CI/ORION', hercules: '/work2/noaa/global/CI/HERCULES', gaea: '/gpfs/f5/epic/proj-shared/global/CI']
+def custom_workspace = [hera: '/scratch1/NCEPDEV/global/CI_dh', orion: '/work2/noaa/stmp/CI/ORION', hercules: '/work2/noaa/global/CI/HERCULES', gaea: '/gpfs/f5/epic/proj-shared/global/CI']
 def repo_url = '[email protected]:NOAA-EMC/global-workflow.git'
 def STATUS = 'Passed'
 

diff --git a/ci/cases/gfsv17/ocnanal.yaml b/ci/cases/gfsv17/ocnanal.yaml
@@ -15,6 +15,7 @@ base:
   DO_VRFY_OCEANDA: "NO"
   FHMAX_GFS: 240
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
 
 marineanl:
   SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca

diff --git a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml
@@ -3,3 +3,4 @@ defaults:
 base:
   DO_JEDISNOWDA: "YES"
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
diff --git a/ci/cases/yamls/gfs_defaults_ci.yaml b/ci/cases/yamls/gfs_defaults_ci.yaml
@@ -2,3 +2,4 @@ defaults:
   !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
diff --git a/ci/cases/yamls/gfs_extended_ci.yaml b/ci/cases/yamls/gfs_extended_ci.yaml
@@ -12,3 +12,4 @@ base:
   FCST_BREAKPOINTS: 192
   FHMAX_GFS: 384
   FHMAX_HF_GFS: 120
+  DO_TEST_MODE: "YES"
diff --git a/ci/cases/yamls/soca_gfs_defaults_ci.yaml b/ci/cases/yamls/soca_gfs_defaults_ci.yaml
@@ -3,3 +3,4 @@ defaults:
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
   DO_JEDIOCNVAR: "YES"
+  DO_TEST_MODE: "YES"
diff --git a/jobs/JGLOBAL_FORECAST b/jobs/JGLOBAL_FORECAST
@@ -77,7 +77,7 @@ if [[ "${DO_ICE}" == "YES" ]]; then
     COMIN_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 fi
 
-if [[ "${DO_AERO}" == "YES" ]]; then
+if [[ "${DO_AERO_FCST}" == "YES" ]]; then
   YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
     COMOUT_CHEM_HISTORY:COM_CHEM_HISTORY_TMPL
 fi

diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
@@ -67,7 +67,7 @@ gdas:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}oznstat"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}radstat"
             {% endif %}
-            {% if AERO_ANL_RUN == "gdas" or AERO_ANL_RUN == "both" %}
+            {% if DO_AERO_ANL %}
         - "{{ COMIN_CHEM_ANALYSIS | relpath(ROTDIR) }}/{{ head }}aerostat"
             {% endif %}
             {% if DO_PREP_OBS_AERO %}

diff --git a/parm/archive/gfs_arcdir.yaml.j2 b/parm/archive/gfs_arcdir.yaml.j2
@@ -50,7 +50,7 @@
                                     ARCDIR ~ "/snowstat." ~ RUN ~ "." ~ cycle_YMDH ~ ".tgz"]) %}
     {% endif %}
 
-    {% if AERO_ANL_RUN == RUN or AERO_ANL_RUN == "both" %}
+    {% if DO_AERO_ANL %}
         {% do det_anl_files.append([COMIN_CHEM_ANALYSIS ~ "/" ~ head ~ "aerostat",
                                     ARCDIR ~ "/aerostat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
     {% endif %}

diff --git a/parm/archive/gfsa.yaml.j2 b/parm/archive/gfsa.yaml.j2
@@ -38,7 +38,7 @@ gfsa:
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}gsistat"
         {% endif %}
-        {% if AERO_ANL_RUN == "gfs" or AERO_ANL_RUN == "both" %}
+        {% if DO_AERO_ANL %}
         - "{{ COMIN_CHEM_ANALYSIS | relpath(ROTDIR) }}/{{ head }}aerostat"
         {% endif %}
         {% if DO_PREP_OBS_AERO %}

diff --git a/parm/archive/master_gfs.yaml.j2 b/parm/archive/master_gfs.yaml.j2
@@ -33,7 +33,7 @@ datasets:
     {% endfilter %}
 {% endif %}
 
-{% if AERO_FCST_RUN == "gfs" or AERO_FCST_RUN == "both" %}
+{% if DO_AERO_FCST %}
     # Aerosol forecasts
     {% filter indent(width=4) %}
 {% include "chem.yaml.j2" %}

diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
@@ -65,6 +65,7 @@ export REALTIME="YES"
 # Experiment mode (cycled or forecast-only)
 export MODE="@MODE@" # cycled/forecast-only
 export SFS_POST="@SFS_POST@" # TODO, place holder until RUN=SFS is developed
+export DO_TEST_MODE="@DO_TEST_MODE@" # option to change configuration for automated testing
 
 ####################################################
 # DO NOT ADD MACHINE DEPENDENT STUFF BELOW THIS LINE
@@ -134,11 +135,8 @@ export DO_COUPLED="NO"
 export DO_WAVE="NO"
 export DO_OCN="NO"
 export DO_ICE="NO"
-export DO_AERO="NO"
 export DO_EXTRACTVARS="@DO_EXTRACTVARS@" # Option to process and extract a subset of products to save on disk
-export AERO_FCST_RUN="" # When to run aerosol forecast: gdas, gfs, or both
-export AERO_ANL_RUN="" # When to run aerosol analysis: gdas, gfs, or both
-export WAVE_RUN="" # When to include wave suite: gdas, gfs, or both
+export DO_AERO_FCST="NO"
 export DOBNDPNT_WAVE="NO" # The GEFS buoys file does not currently have any boundary points
 export DOIBP_WAV="NO" # Option to create point outputs from input boundary points
 export FRAC_GRID=".true."
@@ -183,14 +181,11 @@ case "${APP}" in
   ATM)
     ;;
   ATMA)
-    export DO_AERO="YES"
-    export AERO_ANL_RUN="both"
-    export AERO_FCST_RUN="gdas"
+    export DO_AERO_FCST="YES"
     ;;
   ATMW)
     export DO_COUPLED="YES"
     export DO_WAVE="YES"
-    export WAVE_RUN="both"
     ;;
   NG-GODAS)
     export DO_ATM="NO"
@@ -203,14 +198,11 @@ case "${APP}" in
     export DO_ICE="YES"
 
     if [[ "${APP}" =~ A$ ]]; then
-        export DO_AERO="YES"
-        export AERO_ANL_RUN="both"
-        export AERO_FCST_RUN="gdas"
+        export DO_AERO_FCST="YES"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
-        export WAVE_RUN="both"
     fi
     ;;
   *)
@@ -225,6 +217,7 @@ export FHMAX=9
 export FHOUT=3           # Will be changed to 1 in config.base if (DOHYBVAR set to NO and l4densvar set to false)
 export FHOUT_OCN=3
 export FHOUT_ICE=3
+export FHOUT_AERO=3
 
 # GFS cycle info
 export INTERVAL_GFS=@INTERVAL_GFS@ # Frequency of GFS forecast

diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
@@ -6,7 +6,7 @@
 echo "BEGIN: config.efcs"
 
 # Turn off components in ensemble
-# export DO_AERO="NO"
+# export DO_AERO_FCST="NO"
 # export DO_OCN="NO"
 # export DO_ICE="NO"
 # export DO_WAVE="NO"
@@ -19,7 +19,7 @@ string="--fv3 ${CASE}"
 [[ "${DO_OCN}" == "YES" ]] && string="${string} --mom6 ${OCNRES}"
 [[ "${DO_ICE}" == "YES" ]] && string="${string} --cice6 ${ICERES}"
 [[ "${DO_WAVE}" == "YES" ]] && string="${string} --ww3 ${waveGRD// /;}"
-[[ "${DO_AERO}" == "YES" ]] && string="${string} --gocart"
+[[ "${DO_AERO_FCST}" == "YES" ]] && string="${string} --gocart"
 # shellcheck disable=SC2086
 source "${EXPDIR}/config.ufs" ${string}
 

diff --git a/parm/config/gefs/config.fcst b/parm/config/gefs/config.fcst
@@ -8,24 +8,12 @@ echo "BEGIN: config.fcst"
 export USE_ESMF_THREADING="YES"  # Toggle to use ESMF-managed threading or traditional threading in UFSWM
 export COPY_FINAL_RESTARTS="NO" # Toggle to copy restarts from the end of GFS/GEFS Run (GDAS is handled seperately)
 
-# Turn off waves if not used for this RUN
-case ${WAVE_RUN} in
-  both | "${RUN/enkf}" ) ;; # Don't change
-  *) DO_WAVE="NO" ;; # Turn waves off
-esac
-
-# Turn off aerosols if not used for this RUN
-case ${AERO_FCST_RUN} in
-  both | "${RUN/enkf}" ) ;; # Don't change
-  *) DO_AERO="NO" ;; # Turn waves off
-esac
-
 # Source model specific information that is resolution dependent
 string="--fv3 ${CASE}"
 [[ "${DO_OCN}" == "YES" ]] && string="${string} --mom6 ${OCNRES}"
 [[ "${DO_ICE}" == "YES" ]] && string="${string} --cice6 ${ICERES}"
 [[ "${DO_WAVE}" == "YES" ]] && string="${string} --ww3 ${waveGRD// /;}"
-[[ "${DO_AERO}" == "YES" ]] && string="${string} --gocart"
+[[ "${DO_AERO_FCST}" == "YES" ]] && string="${string} --gocart"
 # We are counting on $string being multiple arguments
 # shellcheck disable=SC2086
 source "${EXPDIR}/config.ufs" ${string}
@@ -142,7 +130,7 @@ tbp=""
 if [[ "${progsigma}" == ".true." ]]; then tbp="_progsigma" ; fi
 
 # Radiation options
-if [[ "${DO_AERO}" == "YES" ]]; then
+if [[ "${DO_AERO_FCST}" == "YES" ]]; then
     export IAER=2011  # spectral band mapping method for aerosol optical properties
 else
     export IAER=1011    

diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
@@ -65,7 +65,7 @@ case ${step} in
     export ntasks=1
     export tasks_per_node=1
     export threads_per_task=1
-    export is_exclusive=True
+    export memory="4096M"
     ;;
 
   "waveinit")
@@ -144,7 +144,7 @@ case ${step} in
     echo "MEDIATOR using (threads, PETS) = (${MEDTHREADS}, ${MEDPETS})"
 
     CHMPETS=0; CHMTHREADS=0
-    if [[ "${DO_AERO}" == "YES" ]]; then
+    if [[ "${DO_AERO_FCST}" == "YES" ]]; then
       # GOCART shares the same grid and forecast tasks as FV3 (do not add write grid component tasks).
       (( CHMTHREADS = ATMTHREADS ))
       (( CHMPETS = FV3PETS ))

diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
@@ -21,6 +21,7 @@ base:
   HPSSARCH: "NO"
   LOCALARCH: "NO"
   SFS_POST: "NO"
+  DO_TEST_MODE: "NO"
 fcst:
   reforecast: "NO"
   FHZER: 6
@@ -31,4 +32,6 @@ stage_ic:
   USE_ATM_ENS_PERTURB_FILES: "NO"
 ocn:
   MOM6_INTERP_ICS: "NO"
-
+# config.aero has just a system-specific path to add.
+# This is handled by the setup_expt.py, but it has to be told to write to it.
+aero: {}
diff --git a/parm/config/gfs/config.anal b/parm/config/gfs/config.anal
@@ -29,6 +29,11 @@ fi
 export lobsdiag_forenkf=".false."  # anal does not need to write out jacobians
                    # set to .true. in config.eobs and config.eupd
 
+# Reduce number of iterations for testing mode
+if [[ ${DO_TEST_MODE} = "YES" ]]; then
+  export SETUP="${SETUP:-}niter(1)=5,niter(2)=5,"
+fi
+
 # Do not process the following datasets
 export GSNDBF=${GSNDBF:-/dev/null}
 export AMSREBF=${AMSREBF:-/dev/null}

diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
@@ -88,6 +88,7 @@ export REALTIME="YES"
 
 # Experiment mode (cycled or forecast-only)
 export MODE="@MODE@" # cycled/forecast-only
+export DO_TEST_MODE="@DO_TEST_MODE@" # option to change configuration for automated testing
 
 ####################################################
 # DO NOT ADD MACHINE DEPENDENT STUFF BELOW THIS LINE
@@ -159,6 +160,7 @@ export APP=@APP@
 
 shopt -s extglob
 # Adjust APP based on RUN
+# If a component (WAVES, etc) needs to be turned off by RUN, set it here
 case "${RUN}" in
     enkf*) # Turn off aerosols and waves
         APP="${APP/%+([WA])}"
@@ -174,11 +176,12 @@ export DO_COUPLED="NO"
 export DO_WAVE="NO"
 export DO_OCN="NO"
 export DO_ICE="NO"
-export DO_AERO="NO"
+DO_AERO="NO"
 export DO_PREP_OBS_AERO="NO"
-export AERO_FCST_RUN="" # When to run aerosol forecast: gdas, gfs, or both
-export AERO_ANL_RUN="" # When to run aerosol analysis: gdas, gfs, or both
-export WAVE_RUN="" # When to include wave suite: gdas, gfs, or both
+aero_fcst_runs="gdas" # When to run aerosol forecast: gdas, gfs, or both
+aero_anl_runs="gdas gfs" # When to run aerosol analysis: gdas, gfs, or both
+export DO_AERO_FCST="NO"
+export DO_AERO_ANL="NO"
 export DOBNDPNT_WAVE="NO"
 export DOIBP_WAV="NO" # Option to create point outputs from input boundary points
 export FRAC_GRID=".true."
@@ -220,22 +223,19 @@ case "${CASE}" in
         ;;
     *)
         echo "FATAL ERROR: Unrecognized CASE ${CASE}, ABORT!"
-        exit 1
+        exit 2
         ;;
 esac
 
 case "${APP}" in
   ATM)
     ;;
   ATMA)
-    export DO_AERO="YES"
-    export AERO_ANL_RUN="both"
-    export AERO_FCST_RUN="gdas"
+    DO_AERO="YES"
     ;;
   ATMW)
     export DO_COUPLED="YES"
     export DO_WAVE="YES"
-    export WAVE_RUN="both"
     ;;
   NG-GODAS)
     export DO_ATM="NO"
@@ -248,22 +248,29 @@ case "${APP}" in
     export DO_ICE="YES"
 
     if [[ "${APP}" =~ A$ ]]; then
-        export DO_AERO="YES"
-        export AERO_ANL_RUN="both"
-        export AERO_FCST_RUN="gdas"
+        DO_AERO="YES"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
-        export WAVE_RUN="both"
     fi
     ;;
   *)
-    echo "Unrecognized APP: '${APP}'"
-    exit 2
+    echo "FATAL ERROR: Unrecognized APP: '${APP}'"
+    exit 3
     ;;
 esac
 
+# Aerosol forecasts and analyses may be RUN-dependent
+if [[ "${DO_AERO}" == "YES" ]]; then
+  if [[ ${aero_anl_runs} =~ ${RUN} ]]; then
+    export DO_AERO_ANL="YES"
+  fi
+  if [[ ${aero_fcst_runs} =~ ${RUN} ]]; then
+    export DO_AERO_FCST="YES"
+  fi
+fi
+
 # Surface cycle update frequency
 if [[ "${RUN}" =~ "gdas" ]] ; then
    export FHCYC=1
@@ -278,6 +285,7 @@ export FHMAX=9
 export FHOUT=3           # Will be changed to 1 in config.base if (DOHYBVAR set to NO and l4densvar set to false)
 export FHOUT_OCN=3
 export FHOUT_ICE=3
+export FHOUT_AERO=3
 
 # Cycle to run EnKF  (set to BOTH for both gfs and gdas)
 export EUPD_CYC="@EUPD_CYC@"
@@ -461,8 +469,8 @@ export FHMAX_FITS=132
 export HPSSARCH="@HPSSARCH@"        # save data to HPSS archive
 export LOCALARCH="@LOCALARCH@"        # save data to local archive
 if [[ ${HPSSARCH} = "YES" ]] && [[ ${LOCALARCH} = "YES" ]]; then
-   echo "Both HPSS and local archiving selected.  Please choose one or the other."
-   exit 3
+   echo "FATAL ERROR: Both HPSS and local archiving selected.  Please choose one or the other."
+   exit 4
 fi
 export ARCH_CYC=00           # Archive data at this cycle for warm_start capability
 export ARCH_WARMICFREQ=4     # Archive frequency in days for warm_start capability

diff --git a/parm/config/gfs/config.efcs b/parm/config/gfs/config.efcs
@@ -13,7 +13,7 @@ string="--fv3 ${CASE}"
 [[ "${DO_OCN}" == "YES" ]] && string="${string} --mom6 ${OCNRES}"
 [[ "${DO_ICE}" == "YES" ]] && string="${string} --cice6 ${ICERES}"
 [[ "${DO_WAVE}" == "YES" ]] && string="${string} --ww3 ${waveGRD// /;}"
-[[ "${DO_AERO}" == "YES" ]] && string="${string} --gocart"
+[[ "${DO_AERO_FCST}" == "YES" ]] && string="${string} --gocart"
 # We are counting on $string being multiple arguments
 # shellcheck disable=SC2086
 source "${EXPDIR}/config.ufs" ${string}

diff --git a/parm/config/gfs/config.fcst b/parm/config/gfs/config.fcst
@@ -8,24 +8,12 @@ echo "BEGIN: config.fcst"
 export USE_ESMF_THREADING="YES"  # Toggle to use ESMF-managed threading or traditional threading in UFSWM
 export COPY_FINAL_RESTARTS="NO" # Toggle to copy restarts from the end of GFS/GEFS Run (GDAS is handled seperately)
 
-# Turn off waves if not used for this RUN
-case ${WAVE_RUN} in
-  both | "${RUN/enkf}" ) ;; # Don't change
-  *) DO_WAVE="NO" ;; # Turn waves off
-esac
-
-# Turn off aerosols if not used for this RUN
-case ${AERO_FCST_RUN} in
-  both | "${RUN/enkf}" ) ;; # Don't change
-  *) DO_AERO="NO" ;; # Turn aerosols off
-esac
-
 # Source model specific information that is resolution dependent
 string="--fv3 ${CASE}"
 [[ "${DO_OCN}" == "YES" ]] && string="${string} --mom6 ${OCNRES}"
 [[ "${DO_ICE}" == "YES" ]] && string="${string} --cice6 ${ICERES}"
 [[ "${DO_WAVE}" == "YES" ]] && string="${string} --ww3 ${waveGRD// /;}"
-[[ "${DO_AERO}" == "YES" ]] && string="${string} --gocart"
+[[ "${DO_AERO_FCST}" == "YES" ]] && string="${string} --gocart"
 # We are counting on $string being multiple arguments
 # shellcheck disable=SC2086
 source "${EXPDIR}/config.ufs" ${string}
@@ -157,7 +145,7 @@ tbp=""
 if [[ "${progsigma}" == ".true." ]]; then tbp="_progsigma" ; fi
 
 # Radiation options
-if [[ "${DO_AERO}" == "YES" ]]; then
+if [[ "${DO_AERO_FCST}" == "YES" ]]; then
     export IAER=2011  # spectral band mapping method for aerosol optical properties
 else
     export IAER=1011