Add GLDAS scripts & fix GLDAS job (#1018)

Absorb GLDAS scripts into global-workflow and fix GLDAS job by updating scripts to use new GLDAS fix file set.

* Remove GLDAS scripts from .gitignore
* Remove GLDAS script symlinks from link_workflow.sh
* Add GLDAS scripts to global-workflow
* Updates to GLDAS scripts, includes converting GLDAS script to replace machine checks with CFP variables
* Address linter warnings and remove obsolete platforms

Refs #622 #1014

.gitignore

@@ -135,7 +135,6 @@ sorc/wafs_setmissing.fd
 # Ignore scripts from externals
 #------------------------------
 # jobs symlinks
-jobs/JGDAS_ATMOS_GLDAS
 jobs/JGFS_ATMOS_WAFS
 jobs/JGFS_ATMOS_WAFS_BLENDING
 jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
@@ -144,7 +143,6 @@ jobs/JGFS_ATMOS_WAFS_GRIB2
 jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
 # scripts symlinks
 scripts/exemcsfc_global_sfc_prep.sh
-scripts/exgdas_atmos_gldas.sh
 scripts/exgfs_atmos_wafs_blending.sh
 scripts/exgfs_atmos_wafs_blending_0p25.sh
 scripts/exgfs_atmos_wafs_gcip.sh
@@ -160,12 +158,6 @@ ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_filter_topo.sh
 ush/fv3gfs_make_grid.sh
 ush/fv3gfs_make_orog.sh
-ush/gldas_archive.sh
-ush/gldas_forcing.sh
-ush/gldas_get_data.sh
-ush/gldas_liscrd.sh
-ush/gldas_post.sh
-ush/gldas_process_data.sh
 ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh

env/HERA.env

@@ -125,6 +125,9 @@ elif [ $step = "sfcanl" ]; then
 
 elif [ $step = "gldas" ]; then
 
+    export USE_CFP="YES"
+    export CFP_MP="YES"
+
     nth_max=$(($npe_node_max / $npe_node_gldas))
 
     export NTHREADS_GLDAS=${nth_gldas:-$nth_max}

env/ORION.env

@@ -123,6 +123,8 @@ elif [ $step = "sfcanl" ]; then
 
 elif [ $step = "gldas" ]; then
 
+    export USE_CFP="NO"
+
     nth_max=$(($npe_node_max / $npe_node_gldas))
 
     export NTHREADS_GLDAS=${nth_gldas:-$nth_max}

jobs/JGDAS_ATMOS_GLDAS

@@ -0,0 +1,136 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs:?}/ush/preamble.sh"
+
+export RUN_ENVIR=${RUN_ENVIR:-"nco"}
+
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+configs="base gldas"
+config_path=${EXPDIR:-${NWROOT}/gfs.${gfs_ver}/parm/config}
+for config in ${configs}; do
+    # shellcheck disable=SC1090-SC1091
+    . "${config_path}/config.${config}"
+    # shellcheck disable=
+    status=$?
+    [[ ${status} -ne 0 ]] && exit "${status}"
+done
+
+
+if [[ "${cyc:?}" -ne "${gldas_cyc:?}" ]]; then
+    echo "GLDAS only runs for ${gldas_cyc} cycle; Skip GLDAS step for cycle ${cyc}"
+    exit 0
+fi
+
+gldas_spinup_hours=${gldas_spinup_hours-:72}
+xtime=$((gldas_spinup_hours+12))
+if [[ "${CDATE}" -le "$(${NDATE:?} +"${xtime}" "${SDATE:?}")" ]]; then
+    echo "GLDAS needs fluxes as forcing from cycles in previous ${xtime} hours"
+    echo "starting from ${SDATE}. This gldas cycle is skipped"
+    exit 0
+fi
+
+##########################################
+# Source machine runtime environment
+##########################################
+# shellcheck disable=SC1090-SC1091
+. "${HOMEgfs}/env/${machine:?}.env" gldas
+# shellcheck disable=
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
+##############################################
+# Obtain unique process id (pid) and make temp directory
+##############################################
+export pid=${pid:-$$}
+export outid=${outid:-"LL${job}"}
+
+export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+mkdir -p "${DATA}"
+cd "${DATA}" || exit 1
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+# shellcheck disable=SC1091
+. ./PDY
+# shellcheck disable=
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
+##############################################
+# Set variables used in the exglobal script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gdas"}}
+export COMPONENT=${COMPONENT:-atmos}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+export gldas_ver=${gldas_ver:-v2.3.0}
+export HOMEgldas=${HOMEgldas:-${HOMEgfs}}
+export FIXgldas=${FIXgldas:-${HOMEgldas}/fix/fix_gldas}
+export PARMgldas=${PARMgldas:-${HOMEgldas}/parm/gldas}
+export EXECgldas=${EXECgldas:-${HOMEgldas}/exec}
+export USHgldas=${USHgldas:-${HOMEgldas}/ush}
+export PARA_CONFIG=${HOMEgfs}/parm/config/config.gldas
+
+if [[ "${RUN_ENVIR}" = "nco" ]]; then
+    export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+    export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+else
+    export COMIN="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
+    export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
+fi
+if [[ ! -d ${COMOUT} ]]; then
+    mkdir -p "${COMOUT}"
+    chmod 775 "${COMOUT}"
+fi
+
+export COMINgdas=${COMINgdas:-${ROTDIR}}
+export DCOMIN=${DCOMIN:-${DCOMROOT:-"/lfs/h1/ops/prod/dcom"}}
+
+export model=${model:-noah}
+export MODEL=${MODEL:-"${model} |tr 'a-z' 'A-Z'"}
+
+
+###############################################################
+# Run relevant exglobal script
+
+${GLDASSH:-${HOMEgldas}/scripts/exgdas_atmos_gldas.sh}
+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
+

parm/config/config.base.emc.dyn

@@ -162,6 +162,7 @@ export CCPP_SUITE="FV3_GFS_v17_p8"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO"
 export cplwav2atm=".false."
+export FRAC_GRID=".true."
 
 case "${APP}" in
   ATM)