Merge branch 'develop' into feature/jgdas_enkf_select_obs_com_in_out

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'
 

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

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 DO_AERO and (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 %}

parm/archive/gfs_arcdir.yaml.j2

@@ -50,7 +50,7 @@
                                     ARCDIR ~ "/snowstat." ~ RUN ~ "." ~ cycle_YMDH ~ ".tgz"]) %}
     {% endif %}
 
-    {% if DO_AERO and (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 %}

parm/archive/gfsa.yaml.j2

@@ -38,7 +38,7 @@ gfsa:
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}gsistat"
         {% endif %}
-        {% if DO_AERO and (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 %}

parm/archive/master_gfs.yaml.j2

@@ -33,7 +33,7 @@ datasets:
     {% endfilter %}
 {% endif %}
 
-{% if DO_AERO and (AERO_FCST_RUN == "gfs" or AERO_FCST_RUN == "both") %}
+{% if DO_AERO_FCST %}
     # Aerosol forecasts
     {% filter indent(width=4) %}
 {% include "chem.yaml.j2" %}

parm/config/gefs/config.base

@@ -135,10 +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="gefs" # When to run aerosol forecast: gdas, gfs, or both
-export WAVE_RUN="gefs" # 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."
@@ -183,7 +181,7 @@ case "${APP}" in
   ATM)
     ;;
   ATMA)
-    export DO_AERO="YES"
+    export DO_AERO_FCST="YES"
     ;;
   ATMW)
     export DO_COUPLED="YES"
@@ -200,7 +198,7 @@ case "${APP}" in
     export DO_ICE="YES"
 
     if [[ "${APP}" =~ A$ ]]; then
-        export DO_AERO="YES"
+        export DO_AERO_FCST="YES"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then

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}
 

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    

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 ))

parm/config/gfs/config.base

@@ -160,6 +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])}"
@@ -175,11 +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="gdas" # When to run aerosol forecast: gdas, gfs, or both
-export AERO_ANL_RUN="both" # When to run aerosol analysis: gdas, gfs, or both
-export WAVE_RUN="both" # 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."
@@ -221,15 +223,15 @@ case "${CASE}" in
         ;;
     *)
         echo "FATAL ERROR: Unrecognized CASE ${CASE}, ABORT!"
-        exit 1
+        exit 2
         ;;
 esac
 
 case "${APP}" in
   ATM)
     ;;
   ATMA)
-    export DO_AERO="YES"
+    DO_AERO="YES"
     ;;
   ATMW)
     export DO_COUPLED="YES"
@@ -246,19 +248,29 @@ case "${APP}" in
     export DO_ICE="YES"
 
     if [[ "${APP}" =~ A$ ]]; then
-        export DO_AERO="YES"
+        DO_AERO="YES"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
     fi
     ;;
   *)
-    echo "Unrecognized APP: '${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
@@ -457,8 +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

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}

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    

parm/config/gfs/config.resources

@@ -809,7 +809,7 @@ 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 ))
@@ -1036,7 +1036,7 @@ case ${step} in
     ntasks=1
     tasks_per_node=1
     threads_per_task=1
-    export is_exclusive=True
+    memory="4096M"
     ;;
 
   "atmensanlinit")

scripts/exglobal_archive.py

@@ -3,7 +3,7 @@
 import os
 
 from pygfs.task.archive import Archive
-from wxflow import AttrDict, Logger, cast_strdict_as_dtypedict, chdir, logit
+from wxflow import AttrDict, Logger, cast_strdict_as_dtypedict, logit
 
 # initialize root logger
 logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=True)
@@ -19,7 +19,7 @@ def main():
 
     # Pull out all the configuration keys needed to run the rest of archive steps
     keys = ['ATARDIR', 'current_cycle', 'FHMIN', 'FHMAX', 'FHOUT', 'RUN', 'PDY',
-            'DO_VERFRAD', 'DO_VMINMON', 'DO_VERFOZN', 'DO_ICE', 'DO_AERO', 'DO_PREP_OBS_AERO',
+            'DO_VERFRAD', 'DO_VMINMON', 'DO_VERFOZN', 'DO_ICE', 'DO_PREP_OBS_AERO',
             'PARMgfs', 'DO_OCN', 'DO_WAVE', 'WRITE_DOPOST', 'PSLOT', 'HPSSARCH', 'DO_MOS',
             'DO_JEDISNOWDA', 'LOCALARCH', 'REALTIME', 'ROTDIR', 'ARCH_WARMICFREQ',
             'ARCH_FCSTICFREQ', 'ARCH_CYC', 'assim_freq', 'ARCDIR', 'SDATE',
@@ -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',
-            'AERO_ANL_RUN', 'AERO_FCST_RUN', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
+            'DO_AERO_ANL', 'DO_AERO_FCST', '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']

ush/python/pygfs/task/archive.py

@@ -50,7 +50,7 @@ def configure(self, arch_dict: Dict[str, Any]) -> (Dict[str, Any], List[Dict[str
         Parameters
         ----------
         arch_dict : Dict[str, Any]
-            Task specific keys, e.g. runtime options (DO_AERO, DO_ICE, etc)
+            Task specific keys, e.g. runtime options (DO_AERO_FCST, DO_ICE, etc)
 
         Return
         ------