[develop] Add smoke and dust capability

Externals_smoke_dust.cfg

@@ -0,0 +1,29 @@
+[ufs_utils]
+protocol = git
+repo_url = https://github.com/ufs-community/UFS_UTILS
+# Specify either a branch name or a hash but not both.
+#branch = develop
+hash = 33cc663
+local_path = sorc/UFS_UTILS
+required = True
+
+[ufs-weather-model]
+protocol = git
+repo_url = https://github.com/ufs-community/ufs-weather-model
+# Specify either a branch name or a hash but not both.
+#branch = production/RRFS.v1
+hash = ce43a6f
+local_path = sorc/ufs-weather-model
+required = True
+
+[UPP]
+protocol = git
+repo_url = https://github.com/NOAA-EMC/UPP
+# Specify either a branch name or a hash but not both.
+#branch = develop
+hash = fc85241
+local_path = sorc/UPP
+required = True
+
+[externals_description]
+schema_version = 1.0.0

devbuild.sh

@@ -15,7 +15,7 @@ OPTIONS
       compiler to use; default depends on platform
       (e.g. intel | gnu | cray | gccgfortran)
   -a, --app=APPLICATION
-      weather model application to build; for example, ATMAQ for Online-CMAQ
+      weather model application to build; for example, ATMAQ for SRW-AQM
       (e.g. ATM | ATMAQ | ATMW | S2S | S2SW)
   --ccpp="CCPP_SUITE1,CCPP_SUITE2..."
       CCPP suites (CCPP_SUITES) to include in build; delimited with ','
@@ -50,6 +50,8 @@ OPTIONS
       number of build jobs; defaults to 4
   --use-sub-modules
       Use sub-component modules instead of top-level level SRW modules
+  --smoke
+      Build the app for Smoke and Dust (with production branch)
   -v, --verbose
       build with verbose output
 
@@ -82,6 +84,7 @@ Settings:
   DISABLE_OPTIONS=${DISABLE_OPTIONS}
   REMOVE=${REMOVE}
   CONTINUE=${CONTINUE}
+  SMOKE=${SMOKE}
   BUILD_TYPE=${BUILD_TYPE}
   BUILD_JOBS=${BUILD_JOBS}
   VERBOSE=${VERBOSE}
@@ -114,6 +117,7 @@ BUILD_TYPE="RELEASE"
 BUILD_JOBS=4
 REMOVE=false
 CONTINUE=false
+SMOKE=false
 VERBOSE=false
 
 # Turn off all apps to build and choose default later
@@ -160,6 +164,7 @@ while :; do
     --clean) CLEAN=true ;;
     --build) BUILD=true ;;
     --move) MOVE=true ;;
+    --smoke) SMOKE=true ;;
     --build-dir=?*) BUILD_DIR=${1#*=} ;;
     --build-dir|--build-dir=) usage_error "$1 requires argument." ;;
     --install-dir=?*) INSTALL_DIR=${1#*=} ;;
@@ -314,7 +319,11 @@ if [ -f ${RUN_VERSION_FILE} ]; then
 fi
 
 # set MODULE_FILE for this platform/compiler combination
-MODULE_FILE="build_${PLATFORM}_${COMPILER}"
+if [ "${SMOKE}" = true ]; then
+  MODULE_FILE="build_${PLATFORM}_${COMPILER}_prod"
+else
+  MODULE_FILE="build_${PLATFORM}_${COMPILER}"
+fi
 if [ ! -f "${SRW_DIR}/modulefiles/${MODULE_FILE}.lua" ]; then
   printf "ERROR: module file does not exist for platform/compiler\n" >&2
   printf "  MODULE_FILE=${MODULE_FILE}\n" >&2

environment.yml

@@ -6,3 +6,10 @@ dependencies:
   - pylint=2.17*
   - pytest=7.2*
   - uwtools=2.3*
+  - esmpy=8.6.*
+  - netcdf4=1.6.*
+  - numpy=1.23.*
+  - pandas=1.5.*
+  - scipy=1.10.*
+  - xarray=2022.11.*
+

jobs/JREGIONAL_MAKE_ICS

@@ -34,7 +34,7 @@
 #-----------------------------------------------------------------------
 #
 . $USHdir/source_util_funcs.sh
-for sect in user nco workflow ; do
+for sect in user nco workflow cpl_aqm_parm smoke_dust_parm ; do
   source_yaml ${GLOBAL_VAR_DEFNS_FP} ${sect}
 done
 . $USHdir/job_preamble.sh
@@ -103,6 +103,9 @@ if [ $RUN_ENVIR = "community" ]; then
   mkdir -p $DATA
   cd $DATA
 fi
+if [ $(boolify "${CPL_AQM}") = "TRUE" ] || [ $(boolify "${DO_SMOKE_DUST}") = "TRUE" ]; then
+  mkdir -p ${DATA_SHARE}
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_MAKE_LBCS

@@ -32,7 +32,7 @@
 #-----------------------------------------------------------------------
 #
 . $USHdir/source_util_funcs.sh
-for sect in user nco workflow ; do
+for sect in user nco workflow cpl_aqm_parm smoke_dust_parm ; do
   source_yaml ${GLOBAL_VAR_DEFNS_FP} ${sect}
 done
 . $USHdir/job_preamble.sh
@@ -100,6 +100,9 @@ if [ "${RUN_ENVIR}" = "community" ]; then
   mkdir -p $DATA
   cd $DATA
 fi
+if [ $(boolify "${CPL_AQM}") = "TRUE" ] || [ $(boolify "${DO_SMOKE_DUST}") = "TRUE" ]; then
+  mkdir -p ${DATA_SHARE}
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JSRW_AQM_ICS

@@ -105,10 +105,10 @@ export RUN="${RUN:-${RUN_default}}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver})}"
   export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}}"
   export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
 fi
 
@@ -140,20 +140,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# Set the name of and create the directory in which the output from this
-# script will be placed (if it doesn't already exist).
-#
-#-----------------------------------------------------------------------
-#
-if [ $RUN_ENVIR = "nco" ]; then
-  export INPUT_DATA="${COMIN}"
-else
-  export INPUT_DATA="${COMIN}${SLASH_ENSMEM_SUBDIR}/INPUT"
-fi
-mkdir -p "${INPUT_DATA}"
-#
-#-----------------------------------------------------------------------
-#
 # Call the ex-script for this J-job.
 #
 #-----------------------------------------------------------------------

jobs/JSRW_AQM_LBCS

@@ -142,20 +142,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# Set the name of and create the directory in which the output from this
-# script will be placed (if it doesn't already exist).
-#
-#-----------------------------------------------------------------------
-#
-if [ $RUN_ENVIR = "nco" ]; then
-  export INPUT_DATA="${COMIN}"
-else
-  export INPUT_DATA="${EXPTDIR}/${PDY}${cyc}${SLASH_ENSMEM_SUBDIR}/INPUT"
-fi
-mkdir -p "${INPUT_DATA}"
-#
-#-----------------------------------------------------------------------
-#
 # Call the ex-script for this J-job.
 #
 #-----------------------------------------------------------------------

jobs/JSRW_FORECAST

@@ -0,0 +1,184 @@
+#!/usr/bin/env bash
+
+#
+#-----------------------------------------------------------------------
+#
+# The J-Job that runs the forecast
+#
+#-----------------------------------------------------------------------
+#
+date
+export PS4='+ $SECONDS + '
+set -xue
+#
+#-----------------------------------------------------------------------
+#
+# Set the NCO standard environment variables (Table 1, pp.4)
+#
+#-----------------------------------------------------------------------
+#
+export USHsrw="${HOMEdir}/ush"
+export EXECsrw="${HOMEdir}/exec"
+export PARMsrw="${HOMEdir}/parm"
+export SCRIPTSsrw="${HOMEdir}/scripts"
+#
+#-----------------------------------------------------------------------
+#
+# Source the variable definitions file and the bash utility functions.
+#
+#-----------------------------------------------------------------------
+#
+export USHdir="${USHsrw}"  # should be removed later
+. ${USHsrw}/source_util_funcs.sh
+#
+#-----------------------------------------------------------------------
+#
+# Run-time environment variables:
+#
+#    CDATE
+#    COMIN
+#    DATA
+#    GLOBAL_VAR_DEFNS_FP
+#    SLASH_ENSMEM_SUBDIR
+#
+# Experiment variables
+#
+#  user:
+#    SCRIPTSdir
+#    USHdir
+#
+#-----------------------------------------------------------------------
+#
+for sect in user nco platform workflow global ; do
+  source_yaml ${GLOBAL_VAR_DEFNS_FP} ${sect}
+done
+#
+#-----------------------------------------------------------------------
+#
+# Get the full path to the file in which this script/function is located 
+# (scrfunc_fp), the name of that file (scrfunc_fn), and the directory in
+# which the file is located (scrfunc_dir).
+#
+#-----------------------------------------------------------------------
+#
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
+scrfunc_fn=$( basename "${scrfunc_fp}" )
+scrfunc_dir=$( dirname "${scrfunc_fp}" )
+#
+#-----------------------------------------------------------------------
+#
+# Print message indicating entry into script.
+#
+#-----------------------------------------------------------------------
+#
+print_info_msg "
+========================================================================
+Entering script:  \"${scrfunc_fn}\"
+In directory:     \"${scrfunc_dir}\"
+
+This is the J-job script for the task that runs a forecast with FV3 for
+the specified cycle.
+========================================================================"
+#
+#-----------------------------------------------------------------------
+#
+# Define job and jobid by default for rocoto
+#
+#-----------------------------------------------------------------------
+#
+WORKFLOW_MANAGER="${WORKFLOW_MANAGER:-rocoto}"
+if [ "${WORKFLOW_MANAGER}" = "rocoto" ]; then
+  if [ "${SCHED}" = "slurm" ]; then
+    job=${SLURM_JOB_NAME}
+    pid=${SLURM_JOB_ID}
+  elif [ "${SCHED}" = "pbspro" ]; then
+    job=${PBS_JOBNAME}
+    pid=${PBS_JOBID}
+  else
+    job="task"
+    pid=$$
+  fi
+  jobid="${job}.${PDY}${cyc}.${pid}"
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Create a temp working directory (DATA) and cd into it.
+#
+#-----------------------------------------------------------------------
+#
+export DATA="${DATA:-${DATAROOT}/${jobid}}"
+mkdir -p $DATA
+cd $DATA
+#
+#-----------------------------------------------------------------------
+#
+# Define NCO environment variables and set COM type definitions.
+#
+#-----------------------------------------------------------------------
+#
+export NET="${NET:-${NET_default}}"
+export RUN="${RUN:-${RUN_default}}"
+
+[[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
+if [ "${MACHINE}" = "WCOSS2" ]; then
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+else
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+fi
+
+mkdir -p ${COMOUT}
+
+# Create a teomporary share directory for RAVE interpolated data files
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+mkdir -p ${DATA_SHARE}
+
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+#
+#-----------------------------------------------------------------------
+#
+# Set sub-cycle and ensemble member names in file/diectory names
+#
+#-----------------------------------------------------------------------
+#
+if [ ${subcyc} -ne 0 ]; then
+  export cycle="t${cyc}${subcyc}z"
+fi
+if [ $(boolify "${DO_ENSEMBLE}") = "TRUE" ] && [ ! -z ${ENSMEM_INDX} ]; then
+  export dot_ensmem=".mem${ENSMEM_INDX}"
+else
+  export dot_ensmem=
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Call the ex-script for this J-job.
+#
+#-----------------------------------------------------------------------
+#
+export pgmout="${DATA}/OUTPUT.$$"
+env
+
+${SCRIPTSsrw}/exsrw_forecast.sh
+export err=$?; err_chk
+
+if [ -e "$pgmout" ]; then
+  cat $pgmout
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Whether or not working directory DATA should be kept.
+#
+#-----------------------------------------------------------------------
+#
+if [ "${KEEPDATA}" = "NO" ]; then
+  rm -rf ${DATA}
+fi
+date
+