Add initial land DA cycling scripts (#1351)

This PR adds rocoto jobs, jjobs, config files and updates to the machine.env to enable land-da cycling capability.
NOAA-EMC · Apr 24, 2023 · 2e88dbf · 2e88dbf
1 parent f159d39
commit 2e88dbf
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Showing 19 changed files with 354 additions and 6 deletions.
diff --git a/env/CONTAINER.env b/env/CONTAINER.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"

diff --git a/env/HERA.env b/env/HERA.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -74,6 +74,14 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
     export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
 
+elif [[ "${step}" = "landanlrun" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_landanlrun))
+
+    export NTHREADS_LANDANL=${nth_landanlrun:-${nth_max}}
+    [[ ${NTHREADS_LANDANL} -gt ${nth_max} ]] && export NTHREADS_LANDANL=${nth_max}
+    export APRUN_LANDANL="${launcher} -n ${npe_landanlrun}"
+
 elif [[ "${step}" = "ocnanalbmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"

diff --git a/env/JET.env b/env/JET.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -73,6 +73,14 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
     export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
 
+elif [[ "${step}" = "landanlrun" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_landanlrun))
+
+    export NTHREADS_LANDANL=${nth_landanlrun:-${nth_max}}
+    [[ ${NTHREADS_LANDANL} -gt ${nth_max} ]] && export NTHREADS_LANDANL=${nth_max}
+    export APRUN_LANDANL="${launcher} -n ${npe_landanlrun}"
+
 elif [[ "${step}" = "ocnanalbmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

diff --git a/env/ORION.env b/env/ORION.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -74,6 +74,14 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
     export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
 
+elif [[ "${step}" = "landanlrun" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_landanlrun))
+
+    export NTHREADS_LANDANL=${nth_landanlrun:-${nth_max}}
+    [[ ${NTHREADS_LANDANL} -gt ${nth_max} ]] && export NTHREADS_LANDANL=${nth_max}
+    export APRUN_LANDANL="${launcher} -n ${npe_landanlrun}"
+
 elif [[ "${step}" = "ocnanalbmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

diff --git a/env/S4.env b/env/S4.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -72,6 +72,14 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
     export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
 
+elif [[ "${step}" = "landanlrun" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_landanlrun))
+
+    export NTHREADS_LANDANL=${nth_landanlrun:-${nth_max}}
+    [[ ${NTHREADS_LANDANL} -gt ${nth_max} ]] && export NTHREADS_LANDANL=${nth_max}
+    export APRUN_LANDANL="${launcher} -n ${npe_landanlrun}"
+
 elif [[ "${step}" = "ocnanalbmat" ]]; then
      echo "WARNING: ${step} is not enabled on S4!"
 

diff --git a/env/WCOSS2.env b/env/WCOSS2.env
@@ -4,7 +4,7 @@ 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 "atmanlrun atmensanlrun aeroanlrun"
+    echo "atmanlrun atmensanlrun aeroanlrun landanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen esfc efcs epos"
     echo "postsnd awips gempak"
@@ -61,6 +61,14 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
     [[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
     export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"
 
+elif [[ "${step}" = "landanlrun" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_landanlrun))
+
+    export NTHREADS_LANDANL=${nth_landanlrun:-${nth_max}}
+    [[ ${NTHREADS_LANDANL} -gt ${nth_max} ]] && export NTHREADS_LANDANL=${nth_max}
+    export APRUN_LANDANL="${launcher} -n ${npe_landanlrun}"
+
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 
     export OMP_PLACES=cores

diff --git a/jobs/JGLOBAL_LAND_ANALYSIS_FINALIZE b/jobs/JGLOBAL_LAND_ANALYSIS_FINALIZE
@@ -0,0 +1,50 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "landanlfinal" -c "base landanl landanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASLANDFINALPY:-${HOMEgfs}/scripts/exglobal_land_analysis_finalize.py}
+${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}" || ( echo "FATAL ERROR: ${DATAROOT} does not exist, ABORT!"; exit 1 )
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0
diff --git a/jobs/JGLOBAL_LAND_ANALYSIS_INITIALIZE b/jobs/JGLOBAL_LAND_ANALYSIS_INITIALIZE
@@ -0,0 +1,43 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "landanlinit" -c "base landanl landanlinit"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASLANDINITPY:-${HOMEgfs}/scripts/exglobal_land_analysis_initialize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/JGLOBAL_LAND_ANALYSIS_RUN b/jobs/JGLOBAL_LAND_ANALYSIS_RUN
@@ -0,0 +1,44 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "landanlrun" -c "base landanl landanlrun"
+
+##############################################
+# Set variables used in the script
+##############################################
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+GDUMP="gdas"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${GDATE:0:8}/${GDATE:8:2}/atmos"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASLANDRUNSH:-${HOMEgfs}/scripts/exglobal_land_analysis_run.sh}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/rocoto/landanlfinal.sh b/jobs/rocoto/landanlfinal.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="landanlfinal"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_LAND_ANALYSIS_FINALIZE"
+status=$?
+exit "${status}"
diff --git a/jobs/rocoto/landanlinit.sh b/jobs/rocoto/landanlinit.sh
@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="landanlinit"
+export jobid="${job}.$$"
+
+###############################################################
+# 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_LAND_ANALYSIS_INITIALIZE"
+status=$?
+exit "${status}"
diff --git a/jobs/rocoto/landanlrun.sh b/jobs/rocoto/landanlrun.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="landanlrun"
+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_LAND_ANALYSIS_RUN"
+status=$?
+exit "${status}"
diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
@@ -311,6 +311,7 @@ export imp_physics=@IMP_PHYSICS@
 export DO_JEDIVAR="NO"
 export DO_JEDIENS="NO"
 export DO_JEDIOCNVAR="NO"
+export DO_JEDILANDDA="NO"
 export DO_MERGENSST="NO"
 
 # Hybrid related

diff --git a/parm/config/config.landanl b/parm/config/config.landanl
@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+########## config.landanl ##########
+# configuration common to all land analysis tasks
+
+echo "BEGIN: config.landanl"
+
+obs_list_name=gdas_land_adpsfc_only.yaml
+if [[ "${cyc}" == "18" ]]; then
+    obs_list_name=gdas_land_prototype.yaml
+fi
+
+export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/land/obs/config/
+export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/land/obs/lists/${obs_list_name}
+export LANDVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/land/letkfoi/letkfoi.yaml
+export FV3JEDI_FIX=${HOMEgfs}/fix/gdas
+
+export io_layout_x=@IO_LAYOUT_X@
+export io_layout_y=@IO_LAYOUT_Y@
+
+export JEDIEXE=${HOMEgfs}/exec/fv3jedi_letkf.x
+
+echo "END: config.landanl"
diff --git a/parm/config/config.landanlfinal b/parm/config/config.landanlfinal
@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.landanlfinal ##########
+# Post Land Analysis specific
+
+echo "BEGIN: config.landanlfinal"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" landanlfinal
+echo "END: config.landanlfinal"
diff --git a/parm/config/config.landanlinit b/parm/config/config.landanlinit
@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.landanlinit ##########
+# Pre Land Analysis specific
+
+echo "BEGIN: config.landanlinit"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" landanlinit
+echo "END: config.landanlinit"