Updates to GLDAS scripts

- Convert from ksh to bash. - Convert backticks to substitutions. - Add preamble. - Remove announcements and general cleanup. Refs NOAA-EMC#1014
KateFriedman-NOAA · Sep 8, 2022 · 8f45611 · 8f45611
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commit 8f45611
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diff --git a/jobs/JGDAS_ATMOS_GLDAS b/jobs/JGDAS_ATMOS_GLDAS
@@ -1,9 +1,6 @@
-#!/bin/ksh
-set -x
+#! /usr/bin/env bash
 
-#export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-export PS4='$SECONDS + '
-date
+source "$HOMEgfs/ush/preamble.sh"
 
 #############################
 # Source relevant config files
@@ -96,14 +93,11 @@ export COMINgdas=${COMINgdas:-$ROTDIR}
 export DCOMIN=${DCOMIN:-${DCOMROOT:-"/lfs/h1/ops/prod/dcom"}}
 
 export model=${model:-noah}
-export MODEL=${MODEL:-`echo $model |tr '[a-z]' '[A-Z]'`}
+export MODEL=${MODEL:-$(echo $model |tr '[a-z]' '[A-Z]')}
 
 
 ###############################################################
 # Run relevant exglobal script
-env
-msg="HAS BEGUN on `hostname`"
-$LOGSCRIPT
 
 ${GLDASSH:-$HOMEgldas/scripts/exgdas_atmos_gldas.sh}
 status=$?
@@ -120,14 +114,11 @@ if [ -e "$pgmout" ] ; then
   cat $pgmout
 fi
 
-msg="ENDED NORMALLY."
-
 ##########################################
 # Remove the Temporary working directory
 ##########################################
 cd $DATAROOT
 [[ $KEEPDATA = "NO" ]] && rm -rf $DATA
 
-date
 exit 0
 
diff --git a/scripts/exgdas_atmos_gldas.sh b/scripts/exgdas_atmos_gldas.sh
@@ -1,4 +1,5 @@
-#!/bin/ksh
+#! /usr/bin/env bash
+
 ################################################################################
 ####  UNIX Script Documentation Block
 #                      .                                             .
@@ -10,12 +11,7 @@
 #  20191123 Fanglin Yang, restructure for global workflow
 ################################################################################
 
-#  Set environment 
-export VERBOSE=${VERBOSE:-"YES"}
-if [ $VERBOSE = "YES" ]; then
-   echo $(date) EXECUTING $0 $* >&2
-   set -x
-fi
+source "$HOMEgfs/ush/preamble.sh"
 
 #################################
 # Set up UTILITIES
@@ -42,20 +38,20 @@ export COMPONENT=${COMPONENT:-atmos}
 export assim_freq=${assim_freq:-6}
 export gldas_spinup_hours=${gldas_spinup_hours:-72}
 export gldas_cdate=$CDATE
-export gldas_eymd=`echo $gldas_cdate |cut -c 1-8`                 
-export gldas_ecyc=`echo $gldas_cdate |cut -c 9-10`                 
-export gldas_sdate=`$NDATE -$gldas_spinup_hours $CDATE`
-export gldas_symd=`echo $gldas_sdate |cut -c 1-8`                 
-export gldas_scyc=`echo $gldas_sdate |cut -c 9-10`                 
+export gldas_eymd=$(echo $gldas_cdate |cut -c 1-8)                 
+export gldas_ecyc=$(echo $gldas_cdate |cut -c 9-10)                 
+export gldas_sdate=$($NDATE -$gldas_spinup_hours $CDATE)
+export gldas_symd=$(echo $gldas_sdate |cut -c 1-8)                 
+export gldas_scyc=$(echo $gldas_sdate |cut -c 9-10)                 
 
 export iau_cdate=$CDATE
 if [ "$DOIAU" = "YES" ]; then
  IAU_OFFSET=${IAU_OFFSET:-0}
  IAUHALH=$((IAU_OFFSET/2))
- export iau_cdate=`$NDATE -$IAUHALH $CDATE`
+ export iau_cdate=$($NDATE -$IAUHALH $CDATE)
 fi
-export iau_eymd=`echo $iau_cdate |cut -c 1-8`
-export iau_ecyc=`echo $iau_cdate |cut -c 9-10`
+export iau_eymd=$(echo $iau_cdate |cut -c 1-8)
+export iau_ecyc=$(echo $iau_cdate |cut -c 9-10)
 echo "GLDAS runs from $gldas_sdate to $iau_cdate"
 
 export CASE=${CASE:-C768}
@@ -119,15 +115,15 @@ elif [ $JCAP -eq  382 ]; then
 elif [ $JCAP -eq  190 ]; then
   gds='255 4  384  192 89284 0 128 -89284 -938 938  96 0 0 0 0 0 0 0 0 0 255 0 0 0 0 0'
 else
- echo "JCAP=$JCAP no supportted, exit"
+ echo "JCAP=$JCAP not supported, exit"
  export err=4
  $ERRSCRIPT || exit 4
 fi
 
 echo $JCAP
 echo $gds
-ymdpre=`sh $FINDDATE $gldas_symd d-1` 
-ymdend=`sh $FINDDATE $gldas_eymd d-2`
+ymdpre=$(sh $FINDDATE $gldas_symd d-1) 
+ymdend=$(sh $FINDDATE $gldas_eymd d-2)
 ymd=$ymdpre
 
 if [ $USE_CFP = "YES" ] ; then
@@ -154,7 +150,7 @@ while [ $ymd -le $ymdend ]; do
       $COPYGB -i3 -g"$gds" -x $GDAS/cpc.$ymd/precip.gldas.${ymd}18 $RUNDIR/cmap.gdas.${ymd}18
     fi
   fi
-  ymd=`sh $FINDDATE $ymd d+1`
+  ymd=$(sh $FINDDATE $ymd d+1)
 done
 
 if [ $USE_CFP = "YES" ] ; then
@@ -258,7 +254,7 @@ $ERRSCRIPT || exit 8
 
 # 5c) use gldas_post to replace soil moisture and temperature
 
-yyyy=`echo $iau_eymd | cut -c1-4`
+yyyy=$(echo $iau_eymd | cut -c1-4)
 gbin=$RUNDIR/EXP901/NOAH/$yyyy/$iau_eymd/LIS.E901.${iau_eymd}${iau_ecyc}.NOAHgbin
 sfcanl=sfc.gaussian.nemsio
 rm -rf fort.11 fort.12
@@ -320,9 +316,5 @@ fi
 # Clean up before leaving
 if [ $mkdata = "YES" ]; then rm -rf $DATA; fi
 
-set +x
-if [ $VERBOSE = "YES" ] ; then
-  echo $(date) EXITING $0 with return code $err >&2
-fi
 exit $err
 
diff --git a/ush/gldas_archive.sh b/ush/gldas_archive.sh
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#! /usr/bin/env bash
 #
 #########################################################
 # This script collects gldas output to archive directory
@@ -13,44 +13,34 @@
 # RUNDIR - run directory
 # GDAS   - /lfs/h1/ops/prod/com/gfs/prod
 #
-# gldas runs 72 hrs, from day1.00z to day4.00z
-# first 36 hr obs precip forcing
-# second 36 hrs gdas model forcing to bring it to realtime.
-#
-# save all output to day1 directory
-# save noah.rst.day2 to day2 directory for next day restart
-# save gdas.t00z.sfcanl.nemsio.gldas.day4 to day4 directory for gfs restart
-#
-# script history:
-# 20190604 Jesse Meng - first version
-# 20191010 Youlong Xia - modified
 #########################################################
-set -ux
+
+source "$HOMEgfs/ush/preamble.sh"
 
 if [ $# -lt 1 ]; then
-echo "usage: ksh $0 sdate [edate]"
-exit $?
+  echo "usage: $0 sdate [edate]"
+  exit $?
 fi
 
 sdate=$1
-edate=`sh $FINDDATE $1 d+1`
+edate=$(sh $FINDDATE $1 d+1)
 if [ $# -gt 1 ]; then edate=$2 ; fi
 
-yyyy=`echo $sdate | cut -c1-4`
+yyyy=$(echo $sdate | cut -c1-4)
 
 ### save all output to day1 directory
 export COMDIR=${COM_OUT}
 
 mkdir -p $COMDIR/gldas.$sdate
-yyyymmdd=`sh $FINDDATE $sdate d+1`
+yyyymmdd=$(sh $FINDDATE $sdate d+1)
 while [ $yyyymmdd -le $edate ]; do
 
 mkdir -p $COMDIR/gldas.$yyyymmdd
 
-yyyy=`echo $yyyymmdd | cut -c1-4`
+yyyy=$(echo $yyyymmdd | cut -c1-4)
 cp $RUNDIR/EXP901/NOAH/$yyyy/$yyyymmdd/* $COMDIR/gldas.$sdate
 
-yyyymmdd=`sh $FINDDATE $yyyymmdd d+1`
+yyyymmdd=$(sh $FINDDATE $yyyymmdd d+1)
 done
 
 cp $RUNDIR/sfc.gaussian.nemsio.$sdate $COMDIR/gldas.$sdate
@@ -61,16 +51,16 @@ yyyymmdd=$sdate
 while [ $yyyymmdd -lt $edate ]; do
 
 day1=$yyyymmdd
-day2=`sh $FINDDATE $yyyymmdd d+1`
+day2=$(sh $FINDDATE $yyyymmdd d+1)
 mv $COMDIR/gldas.$sdate/LIS.E901.${day2}00.NOAH.grb $COMDIR/gldas.$sdate/LIS.E901.${day1}00.NOAH.grb
 
-yyyymmdd=`sh $FINDDATE $yyyymmdd d+1`
+yyyymmdd=$(sh $FINDDATE $yyyymmdd d+1)
 done
 
 ### save noah.rst.day2 to day2 directory for next day gldas restart 
 
-yyyymmdd=`sh $FINDDATE $sdate d+1`
-yyyy=`echo $yyyymmdd | cut -c1-4`
+yyyymmdd=$(sh $FINDDATE $sdate d+1)
+yyyy=$(echo $yyyymmdd | cut -c1-4)
 mkdir -p $COMDIR/gldas.$edate
 cp $RUNDIR/EXP901/NOAH/$yyyy/$edate/LIS.E901.${edate}00.Noahrst $COMDIR/gldas.$yyyymmdd/noah.rst.$edate
 

diff --git a/ush/gldas_forcing.sh b/ush/gldas_forcing.sh
@@ -1,22 +1,14 @@
-#!/bin/ksh
+#! /usr/bin/env bash
 ###########################################################################
 # this script gets cpc daily precipitation and using gdas hourly precipitation
 # to disaggregate daily value into hourly value
-# 20190509 Jesse Meng - first version
-# 20191008 Youlong Xia - modified
-# 20191123 Fanglin Yang - restructured for global-workflow
 ########################################################################### 
 
+source "$HOMEgfs/ush/preamble.sh"
+
 bdate=$1
 edate=$2
 
-# Set environment
-export VERBOSE=${VERBOSE:-"YES"}
-if [ $VERBOSE = "YES" ]; then
-   echo $(date) EXECUTING $0 $* >&2
-   set -x
-fi
-
 # HOMEgldas - gldas directory
 # EXECgldas - gldas exec directory
 # PARMgldas - gldas param directory
@@ -29,11 +21,11 @@ export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 #-------------------------------
 #--- extract variables of each timestep and create forcing files
 sdate=$bdate
-edate=`sh $FINDDATE $edate d-1`
+edate=$(sh $FINDDATE $edate d-1)
 while [ $sdate -lt $edate ]; do
 #-------------------------------
 
-sdat0=`sh $FINDDATE $sdate d-1`
+sdat0=$(sh $FINDDATE $sdate d-1)
 [[ ! -d $xpath/cpc.${sdate} ]] && mkdir -p $xpath/cpc.${sdate}
 [[ ! -d $xpath/cpc.${sdat0} ]] && mkdir -p $xpath/cpc.${sdat0}
 
@@ -43,7 +35,7 @@ rm -f fort.* grib.*
 COMPONENT=${COMPONENT:-"atmos"}
 pathp1=$CPCGAUGE/gdas.$sdate/00/$COMPONENT
 pathp2=$DCOMIN/$sdate/wgrbbul/cpc_rcdas
-yyyy=`echo $sdate |cut -c 1-4`
+yyyy=$(echo $sdate |cut -c 1-4)
 cpc_precip="PRCP_CU_GAUGE_V1.0GLB_0.125deg.lnx.$sdate.RT"
 if [ $RUN_ENVIR = "emc" ] && [ $sdate -gt $bdate ]; then 
     cpc_precip="PRCP_CU_GAUGE_V1.0GLB_0.125deg.lnx.$sdate.RT_early"
@@ -116,7 +108,7 @@ cp fort.24 $xpath/cpc.$sdate/precip.gldas.${sdate}06
 rm -f fort.* grib.*
 
 #-------------------------------
-sdate=`sh $FINDDATE $sdate d+1`
+sdate=$(sh $FINDDATE $sdate d+1)
 done
 #-------------------------------
 

diff --git a/ush/gldas_get_data.sh b/ush/gldas_get_data.sh
@@ -1,17 +1,10 @@
-#!/bin/ksh
+#! /usr/bin/env bash
 #########################################################
 # This script generate gldas forcing from gdas prod sflux
 # script history:
-# 20190509 Jesse Meng - first version
-# 20191008 Youlong Xia - modified
-# 20191123 Fanglin Yang - restructured for global-workflow
 #########################################################
 
-export VERBOSE=${VERBOSE:-"YES"}
-if [ $VERBOSE = "YES" ]; then
-   echo $(date) EXECUTING $0 $* >&2
-   set -x
-fi
+source "$HOMEgfs/ush/preamble.sh"
 
 bdate=$1
 edate=$2
@@ -32,15 +25,15 @@ cycint=${assim_freq:-6}
 # get gdas flux files to force gldas.
 # CPC precipitation is from 12z to 12z. One more day of gdas data is 
 # needed to disaggregate daily CPC precipitation values to hourly values
-cdate=`$NDATE -12 $bdate`
+cdate=$($NDATE -12 $bdate)
 
 iter=0
 
 #-------------------------------
 while [ $cdate -lt $edate ]; do
 #-------------------------------
-  ymd=`echo $cdate |cut -c 1-8`
-  cyc=`echo $cdate |cut -c 9-10`
+  ymd=$(echo $cdate |cut -c 1-8)
+  cyc=$(echo $cdate |cut -c 9-10)
   [[ ! -d $fpath/gdas.${ymd} ]] && mkdir -p $fpath/gdas.${ymd}
   [[ ! -d $gpath/gdas.${ymd} ]] && mkdir -p $gpath/gdas.${ymd} 
 
@@ -73,7 +66,7 @@ while [ $f -le $cycint ]; do
 done
 
 #-------------------------------
-  cdate=`$NDATE +$cycint $cdate` 
+  cdate=$($NDATE +$cycint $cdate) 
 done
 #-------------------------------
 

diff --git a/ush/gldas_liscrd.sh b/ush/gldas_liscrd.sh
@@ -1,21 +1,24 @@
-#!/bin/sh
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"
+
 if [ $# -lt 3 ]; then
-echo usage $0 yyyymmddhh1 yyyymmddhh2 126/382/574/1534
-exit $?
+  echo usage $0 yyyymmddhh1 yyyymmddhh2 126/382/574/1534
+  exit $?
 fi
 
 date1=$1
 date2=$2
 grid=$3
 
-export yyyy1=`echo $date1 | cut -c 1-4`
-export   mm1=`echo $date1 | cut -c 5-6`
-export   dd1=`echo $date1 | cut -c 7-8`
-export   hh1=`echo $date1 | cut -c 9-10`
-export yyyy2=`echo $date2 | cut -c 1-4`
-export   mm2=`echo $date2 | cut -c 5-6`
-export   dd2=`echo $date2 | cut -c 7-8`
-export   hh2=`echo $date2 | cut -c 9-10`
+export yyyy1=$(echo $date1 | cut -c 1-4)
+export   mm1=$(echo $date1 | cut -c 5-6)
+export   dd1=$(echo $date1 | cut -c 7-8)
+export   hh1=$(echo $date1 | cut -c 9-10)
+export yyyy2=$(echo $date2 | cut -c 1-4)
+export   mm2=$(echo $date2 | cut -c 5-6)
+export   dd2=$(echo $date2 | cut -c 7-8)
+export   hh2=$(echo $date2 | cut -c 9-10)
 export  grid=$grid
 export PARM_LM=${PARMgldas}
 export LISCARD=lis.crd

diff --git a/ush/gldas_post.sh b/ush/gldas_post.sh
@@ -1,9 +1,10 @@
-#/bin/sh
-set -x
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"
 
 if [ $# -lt 2 ]; then
-echo "usage: $0 gldas.gbin gdas.sfcanl"
- err_exit 99
+  echo "usage: $0 gldas.gbin gdas.sfcanl"
+  err_exit 99
 fi
 
 cd $RUNDIR
@@ -18,12 +19,9 @@ rm -f fort.11 fort.12 fort.22
 cp $gbin fort.11
 cp $sfcanl fort.12
 
- echo 'running NOAH model'
-  startmsg
-  ${EXECgldas}/gldas_post >>$pgmout 2>errfile
-  export err=$?; err_chk
+${EXECgldas}/gldas_post >>$pgmout 2>errfile
+export err=$?; err_chk
 
-##cp fort.22 ${sfcanl}.gldas
 cp fort.22 ./gldas.nemsio
 cp  fort.22 ${sfcanl}.gldas
 rm -f fort.11 fort.12 fort.22