Add GDASapp (first wave of JEDI changes)

.gitignore

@@ -76,6 +76,7 @@ sorc/gfs_post.fd
 sorc/gfs_wafs.fd
 sorc/gldas.fd
 sorc/gsi.fd
+sorc/gdas.cd
 sorc/ufs_utils.fd
 sorc/verif-global.fd
 
@@ -139,6 +140,8 @@ jobs/JGDAS_ENKF_POST
 jobs/JGDAS_ENKF_SELECT_OBS
 jobs/JGDAS_ENKF_SFC
 jobs/JGDAS_ENKF_UPDATE
+jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS
+jobs/JGDAS_GLOBAL_ATMOS_ENSANAL
 jobs/JGFS_ATMOS_VMINMON
 jobs/JGFS_ATMOS_WAFS
 jobs/JGFS_ATMOS_WAFS_BLENDING
@@ -205,6 +208,7 @@ ush/radmon_verf_angle.sh
 ush/radmon_verf_bcoef.sh
 ush/radmon_verf_bcor.sh
 ush/radmon_verf_time.sh
+ush/ufsda
 ush/wafs_blending.sh
 ush/wafs_grib2.regrid.sh
 ush/wafs_intdsk.sh

env/ORION.env

@@ -4,7 +4,8 @@ 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 "anal fcst post vrfy metp"
+    echo "atmanalrun atmensanalrun"
+    echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
     exit 1
@@ -49,6 +50,30 @@ elif [ $step = "waveinit" -o $step = "waveprep" -o $step = "wavepostsbs" -o $ste
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd}
 
+elif [ $step = "atmanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmanalrun))
+
+    export NTHREADS_ATMANAL=${nth_atmanalrun:-$nth_max}
+    [[ $NTHREADS_ATMANAL -gt $nth_max ]] && export NTHREADS_ATMANAL=$nth_max
+    export APRUN_ATMANAL="$launcher -n $npe_atmanalrun"
+
+elif [ $step = "atmensanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmensanalrun))
+
+    export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-$nth_max}
+    [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
+    export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
+
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4
@@ -78,6 +103,14 @@ elif [ $step = "anal" ]; then
 
     export APRUN_GAUSFCANL="$launcher -n $npe_gausfcanl"
 
+elif [ $step = "sfcanl" ]; then
+    nth_max=$(($npe_node_max / $npe_node_sfcanl))
+
+    export NTHREADS_CYCLE=${nth_sfcanl:-14}
+    [[ $NTHREADS_CYCLE -gt $npe_node_max ]] && export NTHREADS_CYCLE=$npe_node_max
+    npe_sfcanl=${ntiles:-6}
+    export APRUN_CYCLE="$launcher -n $npe_sfcanl"
+
 elif [ $step = "gldas" ]; then
 
     nth_max=$(($npe_node_max / $npe_node_gldas))

jobs/JGLOBAL_ATMOS_SFCANL

@@ -0,0 +1,179 @@
+#!/bin/ksh
+set -x
+
+export RUN_ENVIR=${RUN_ENVIR:-"nco"}
+export PS4='$SECONDS + '
+date
+
+
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+configs="base sfcanl"
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env sfcanl
+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 $DATA
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+. ./PDY
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+export COMPONENT=${COMPONENT:-atmos}
+if [ $RUN_ENVIR = "nco" ]; then
+    export ROTDIR=${COMROOT:?}/$NET/$envir
+fi
+export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"} 
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$($NDATE -$assim_freq $CDATE)
+gPDY=$(echo $GDATE | cut -c1-8)
+gcyc=$(echo $GDATE | cut -c9-10)
+GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+export GSUFFIX=${GSUFFIX:-$SUFFIX}
+export ASUFFIX=${ASUFFIX:-$SUFFIX}
+
+
+if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
+    export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+else
+    export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMIN_OBS="$DMPDIR/$CDATE/$CDUMP"
+    export COMIN_GES_OBS="$DMPDIR/$GDATE/$GDUMP"
+fi
+mkdir -m 775 -p $COMOUT
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
+export COMIN_GES_ENS="$ROTDIR/enkfgdas.$gPDY/$gcyc/$COMPONENT"
+
+
+export ATMGES="$COMIN_GES/${GPREFIX}atmf006${GSUFFIX}"
+if [ ! -f $ATMGES ]; then
+    echo "FATAL ERROR: FILE MISSING: ATMGES = $ATMGES"
+    exit 1
+fi
+
+
+# Get LEVS
+if [ ${GSUFFIX} = ".nc" ]; then
+    export LEVS=$($NCLEN $ATMGES pfull) 
+    status=$?
+else
+    export LEVS=$($NEMSIOGET $ATMGES dimz | awk '{print $2}')
+    status=$?
+fi
+[[ $status -ne 0 ]] && exit $status
+
+
+##if [ $DOHYBVAR = "YES" ]; then
+##    export ATMGES_ENSMEAN="$COMIN_GES_ENS/${GPREFIX}atmf006.ensmean$GSUFFIX"
+##    if [ ! -f $ATMGES_ENSMEAN ]; then
+##        echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = $ATMGES_ENSMEAN"
+##        exit 2
+##    fi
+##fi
+
+
+# Link observational data
+export PREPQC="${COMOUT}/${OPREFIX}prepbufr"
+if [ ! -f $PREPQC ]; then
+    echo "WARNING: PREPBUFR FILE $PREPQC MISSING"
+    msg="WARNING : Global PREPBUFR file is missing"
+    postmsg "$jlogfile" "$msg"
+fi
+export PREPQCPF="${COMOUT}/${OPREFIX}prepbufr.acft_profiles"
+export TCVITL="${COMOUT}/${OPREFIX}syndata.tcvitals.tm00"
+[[ $DONST = "YES" ]] && export NSSTBF="${COMOUT}/${OPREFIX}nsstbufr"
+
+
+# Update surface fields with global_cycle
+export DOGCYCLE=${DOGCYCLE:-"YES"}
+
+
+###############################################################
+# Run relevant script
+env
+msg="HAS BEGUN on `hostname`"
+postmsg "$jlogfile" "$msg"
+$LOGSCRIPT
+
+
+${SFCANALSH:-$SCRgfs/exglobal_atmos_sfcanl.sh}
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [ -e "$pgmout" ] ; then
+  cat $pgmout
+fi
+
+
+msg="ENDED NORMALLY."
+postmsg "$jlogfile" "$msg"
+
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd $DATAROOT
+[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+
+date
+exit 0

jobs/rocoto/atmanalpost.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmanal atmanalpost"
+export EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_post.py}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS
+status=$?
+exit $status

jobs/rocoto/atmanalprep.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmanal atmanalprep"
+export EXSCRIPT=${GDASPREPPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_prep.py}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS
+status=$?
+exit $status

jobs/rocoto/atmanalrun.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmanal atmanalrun"
+export EXSCRIPT=${GDASRUNSH:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_run.sh}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS
+status=$?
+exit $status

jobs/rocoto/atmensanalpost.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmensanal atmensanalpost"
+export EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_ensanal_post.py}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL
+status=$?
+exit $status

jobs/rocoto/atmensanalprep.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmensanal atmensanalprep"
+export EXSCRIPT=${GDASPREPPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_prep.py}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL
+status=$?
+exit $status

jobs/rocoto/atmensanalrun.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# set JJOB variables
+export configs="base atmensanal atmensanalrun"
+export EXSCRIPT=${GDASRUNSH:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_ensanal_run.sh}
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL
+status=$?
+exit $status