update UFS-DA atm ens components to python g-w (NOAA-EMC#1313)

env/HERA.env

@@ -5,7 +5,7 @@ if [[ $# -ne 1 ]]; then
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
     echo "atmanalrun atmensanalrun"
-    echo "atmanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -83,6 +83,16 @@ elif [[ "${step}" = "atmanlrun" ]]; then
     [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
     export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
+elif [[ "${step}" = "atmensanlrun" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+
+    nth_max=$((npe_node_max / npe_node_atmensanlrun))
+
+    export NTHREADS_ATMENSANL=${nth_atmensanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMENSANL} -gt ${nth_max} ]] && export NTHREADS_ATMENSANL=${nth_max}
+    export APRUN_ATMENSANL="${launcher} -n ${npe_atmensanlrun}"
+
 elif [[ "${step}" = "aeroanlrun" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE

@@ -0,0 +1,62 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlfinal" -c "base atmensanl atmensanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/chem"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/chem"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMENSFINALPY:-${HOMEgfs}/scripts/exglobal_atmens_analysis_finalize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0

jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE

@@ -0,0 +1,55 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlinit" -c "base atmensanl atmensanlinit"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+export gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP_OBS}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMENSINITPY:-${HOMEgfs}/scripts/exglobal_atmens_analysis_initialize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/JGLOBAL_ATMENS_ANALYSIS_RUN

@@ -0,0 +1,56 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlrun" -c "base atmensanl atmensanlrun"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/chem"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/chem"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASATMENSRUNSH:-${HOMEgfs}/scripts/exglobal_atmens_analysis_run.sh}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/rocoto/atmensanlfinal.sh

@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmensanlfinal"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE"
+status=$?
+exit "${status}"

jobs/rocoto/atmensanlinit.sh

@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmensanlinit"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE"
+status=$?
+exit "${status}"

jobs/rocoto/atmensanlrun.sh

@@ -0,0 +1,18 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="atmensanlrun"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_RUN"
+status=$?
+exit "${status}"

parm/config/config.atmensanl

@@ -0,0 +1,31 @@
+#!/bin/bash -x
+
+########## config.atmanal ##########
+# configuration common to all atm analysis tasks
+
+echo "BEGIN: config.atmanal"
+
+export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
+export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype.yaml
+export ATMVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
+export STATICB_TYPE="identity"
+export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/berror/staticb_${STATICB_TYPE}.yaml
+export FV3JEDI_FIX=${HOMEgfs}/fix/gdas
+export R2D2_OBS_DB='ufsda_test'
+export R2D2_OBS_DUMP='oper_gdas'
+export R2D2_OBS_SRC='ncdiag'
+export R2D2_BC_SRC='gsi'
+export R2D2_BC_DUMP='oper_gdas'
+export R2D2_ARCH_DB='local'
+export INTERP_METHOD='barycentric'
+
+export layout_x=1
+export layout_y=1
+
+export io_layout_x=1
+export io_layout_y=1
+
+export JEDIVAREXE=${HOMEgfs}/exec/fv3jedi_var.x
+export CRTM_VER="2.3.0"
+
+echo "END: config.atmanal"

parm/config/config.atmensanlfinal

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmanlfinal ##########
+# Post Atm Analysis specific
+
+echo "BEGIN: config.atmanlfinal"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanlfinal
+echo "END: config.atmanlfinal"

parm/config/config.atmensanlinit

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmanlinit ##########
+# Pre Atm Analysis specific
+
+echo "BEGIN: config.atmanlinit"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanlinit
+echo "END: config.atmanlinit"

parm/config/config.atmensanlrun

@@ -0,0 +1,11 @@
+#!/bin/bash -x
+
+########## config.atmanlrun ##########
+# Atmsol Analysis specific
+
+echo "BEGIN: config.atmanlrun"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanlrun
+
+echo "END: config.atmanlrun"