From 1313ffd7a907d26ece00aa7ddffd13c55de439e4 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Mon, 1 May 2023 18:19:10 +0000
Subject: [PATCH] update atm var and ens ctests to new GFS COM directory
 structure (#455)

---
 test/atm/global-workflow/config.atmanl       |  11 +-
 test/atm/global-workflow/config.base.emc.dyn | 201 +++++++++----------
 test/atm/global-workflow/jjob_ens_init.sh    |  71 +++++--
 test/atm/global-workflow/jjob_var_init.sh    |  70 ++++++-
 4 files changed, 209 insertions(+), 144 deletions(-)

diff --git a/test/atm/global-workflow/config.atmanl b/test/atm/global-workflow/config.atmanl
index d7039cd8d..d39a2d692 100755
--- a/test/atm/global-workflow/config.atmanl
+++ b/test/atm/global-workflow/config.atmanl
@@ -1,7 +1,7 @@
-#!/bin/bash -x
+#! /usr/bin/env bash
 
 ########## config.atmanl ##########
-# configuration common to all atm analysis tasks
+# configuration common to all atm var analysis tasks
 
 echo "BEGIN: config.atmanl"
 
@@ -10,13 +10,6 @@ export OBS_LIST=@OBS_LIST@
 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
diff --git a/test/atm/global-workflow/config.base.emc.dyn b/test/atm/global-workflow/config.base.emc.dyn
index 1c7239931..0f295e8d6 100755
--- a/test/atm/global-workflow/config.base.emc.dyn
+++ b/test/atm/global-workflow/config.base.emc.dyn
@@ -23,16 +23,16 @@ HPSS_PROJECT=emc-global
 
 # Directories relative to installation areas:
 export HOMEgfs=@HOMEgfs@
-export PARMgfs=$HOMEgfs/parm
-export FIXgfs=$HOMEgfs/fix
-export USHgfs=$HOMEgfs/ush
-export UTILgfs=$HOMEgfs/util
-export EXECgfs=$HOMEgfs/exec
-export SCRgfs=$HOMEgfs/scripts
+export PARMgfs=${HOMEgfs}/parm
+export FIXgfs=${HOMEgfs}/fix
+export USHgfs=${HOMEgfs}/ush
+export UTILgfs=${HOMEgfs}/util
+export EXECgfs=${HOMEgfs}/exec
+export SCRgfs=${HOMEgfs}/scripts
 
-export FIXcice=$HOMEgfs/fix/cice
-export FIXmom=$HOMEgfs/fix/mom6
-export FIXreg2grb2=$HOMEgfs/fix/reg2grb2
+export FIXcice=${HOMEgfs}/fix/cice
+export FIXmom=${HOMEgfs}/fix/mom6
+export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
 
 ########################################################################
 
@@ -40,7 +40,7 @@ export FIXreg2grb2=$HOMEgfs/fix/reg2grb2
 export PACKAGEROOT="@PACKAGEROOT@"    # TODO: set via prod_envir in Ops
 export COMROOT="@COMROOT@"    # TODO: set via prod_envir in Ops
 export COMINsyn="@COMINsyn@"
-export DMPDIR=@DUMPDIR@
+export DMPDIR="@DMPDIR@"
 
 # USER specific paths
 export HOMEDIR="@HOMEDIR@"
@@ -74,10 +74,10 @@ export MODE="@MODE@" # cycled/forecast-only
 # CLEAR
 ####################################################
 # Build paths relative to $HOMEgfs
-export FIXgsi="$HOMEgfs/fix/gsi"
-export HOMEfv3gfs="$HOMEgfs/sorc/fv3gfs.fd"
-export HOMEpost="$HOMEgfs"
-export HOMEobsproc="$BASE_GIT/obsproc/v1.0.2"
+export FIXgsi="${HOMEgfs}/fix/gsi"
+export HOMEfv3gfs="${HOMEgfs}/sorc/fv3gfs.fd"
+export HOMEpost="${HOMEgfs}"
+export HOMEobsproc="${BASE_GIT}/obsproc/v1.1.2"
 
 # CONVENIENT utility scripts and other environment parameters
 export NCP="/bin/cp -p"
@@ -87,54 +87,41 @@ export VERBOSE="YES"
 export KEEPDATA="NO"
 export CHGRP_RSTPROD="@CHGRP_RSTPROD@"
 export CHGRP_CMD="@CHGRP_CMD@"
-export NEMSIOGET="$HOMEgfs/exec/nemsio_get"
 export NCDUMP="@NCDUMP@"
 export NCLEN="$HOMEgfs/ush/getncdimlen"
 
 # Machine environment, jobs, and other utility scripts
-export BASE_ENV="$HOMEgfs/env"
-export BASE_JOB="$HOMEgfs/jobs/rocoto"
+export BASE_ENV="${HOMEgfs}/env"
+export BASE_JOB="${HOMEgfs}/jobs/rocoto"
 
 # EXPERIMENT specific environment parameters
 export SDATE=@SDATE@
-export FDATE=@FDATE@
 export EDATE=@EDATE@
 export EXP_WARM_START="@EXP_WARM_START@"
 export assim_freq=6
 export PSLOT="@PSLOT@"
-export EXPDIR="@EXPDIR@/$PSLOT"
-export ROTDIR="@ROTDIR@/$PSLOT"
+export EXPDIR="@EXPDIR@/${PSLOT}"
+export ROTDIR="@ROTDIR@/${PSLOT}"
 export ROTDIR_DUMP="YES"                #Note: A value of "NO" does not currently work
 export DUMP_SUFFIX=""
-if [[ "$CDATE" -ge "2019092100" && "$CDATE" -le "2019110700" ]]; then
+if [[ "${CDATE}" -ge "2019092100" && "${CDATE}" -le "2019110700" ]]; then
     export DUMP_SUFFIX="p"              # Use dumps from NCO GFS v15.3 parallel
 fi
 export DATAROOT="@DATAPATH@/RUNDIR"  # TODO: set via prod_envir in Ops
 export RUNDIR="${DATAROOT}"  # TODO: Should be removed; use DATAROOT instead
-export ARCDIR="$NOSCRUB/archive/$PSLOT"
-export ICSDIR="@ICSDIR@"
+export ARCDIR="${NOSCRUB}/archive/${PSLOT}"
 export ATARDIR="@ATARDIR@"
 
 # Commonly defined parameters in JJOBS
 export envir=${envir:-"prod"}
-export NET="gfs"
-export RUN=${RUN:-${CDUMP:-"gfs"}}
-CDUMP_OBS="${CDUMP}"
-if [ "${CDUMP_OBS}" = "enkfgdas" ]; then
-    CDUMP_OBS="gdas"
-fi
-export COMIN_OBS=${DMPDIR}/${CDUMP_OBS}.${PDY}/$cyc/atmos
-export COMIN_GES_OBS=${DMPDIR}/${CDUMP_OBS}.${PDY}/$cyc/atmos
-export COMINatmos=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos
-export COMOUTatmos=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos
-export COMINwave=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/wave
-export COMOUTwave=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/wave
-export COMINocean=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean
-export COMOUTocean=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean
-export COMINice=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ice
-export COMOUTice=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ice
-export COMINaero=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem
-export COMOUTaero=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem
+export NET="gfs"  # NET is defined in the job-card (ecf)
+export RUN=${RUN:-${CDUMP:-"gfs"}}  # RUN is defined in the job-card (ecf); CDUMP is used at EMC as a RUN proxy
+# TODO: determine where is RUN actually used in the workflow other than here
+# TODO: is it possible to replace all instances of ${CDUMP} to ${RUN} to be
+#       consistent w/ EE2?
+
+# Get all the COM path templates
+source "${EXPDIR}/config.com"
 
 export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 export LOGSCRIPT=${LOGSCRIPT:-""}
@@ -144,13 +131,14 @@ export REDOUT="1>"
 export REDERR="2>"
 
 export SENDECF=${SENDECF:-"NO"}
-export SENDCOM=${SENDCOM:-"NO"}
+export SENDCOM=${SENDCOM:-"YES"}
 export SENDSDM=${SENDSDM:-"NO"}
 export SENDDBN_NTC=${SENDDBN_NTC:-"NO"}
 export SENDDBN=${SENDDBN:-"NO"}
-export UTILROOT=@UTILROOT@
+export UTILROOT="@UTILROOT@"
 export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
 
+
 # APP settings
 export APP=@APP@
 
@@ -167,6 +155,28 @@ export DOBNDPNT_WAVE="NO"
 export cplwav2atm=".false."
 export FRAC_GRID=".true."
 
+# Set operational resolution
+export OPS_RES="C768" # Do not change
+
+# Resolution specific parameters
+export LEVS=128
+export CASE="@CASECTL@"
+export CASE_ANL="$CASE"
+export CASE_ENKF="@CASEENS@"
+
+# TODO: This should not depend on $CASE or $CASE_ENKF
+# These are the currently available grid-combinations
+case "${CASE}" in
+    "C48") export OCNRES=500;;
+    "C96") export OCNRES=100;;
+    "C192") export OCNRES=050;;
+    "C384") export OCNRES=025;;
+    "C768") export OCNRES=025;;
+    *) export OCNRES=025;;
+esac
+export ICERES=${OCNRES}
+export waveGRD='gnh_10m aoc_9km gsh_15m'
+
 case "${APP}" in
   ATM)
     export confignamevarfornems="atm"
@@ -193,19 +203,19 @@ case "${APP}" in
     export CCPP_SUITE="FV3_GFS_v17_coupled_p8"
     export confignamevarfornems="cpld"
 
-    if [[ "$APP" =~ A$ ]]; then
+    if [[ "${APP}" =~ A$ ]]; then
         export DO_AERO="YES"
         export confignamevarfornems="${confignamevarfornems}_aero"
     fi
 
-    if [[ "$APP" =~ ^S2SW ]]; then
+    if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
         export WAVE_CDUMP="both"
         export cplwav2atm=".true."
-        export confignamevarfornems="${confignamevarfornems}_wave"
+        export confignamevarfornems="${confignamevarfornems}_outerwave"
     fi
 
-    source $EXPDIR/config.defaults.s2sw
+    source ${EXPDIR}/config.defaults.s2sw
 
     ;;
   *)
@@ -214,29 +224,11 @@ case "${APP}" in
     ;;
 esac
 
-# Set operational resolution
-export OPS_RES="C768" # Do not change
-
-# Resolution specific parameters
-export LEVS=128
-export CASE="@CASECTL@"
-export CASE_ANL="$CASE"
-export CASE_ENKF="@CASEENS@"
-case "$CASE" in
-    "C48") export OCNRES=500;;
-    "C96") export OCNRES=100;;
-    "C192") export OCNRES=050;;
-    "C384") export OCNRES=025;;
-    "C768") export OCNRES=025;;
-    *) export OCNRES=025;;
-esac
-export ICERES=$OCNRES
-
 # Surface cycle update frequency
-if [[ "$CDUMP" == "gdas" ]] ; then
+if [[ "${CDUMP}" =~ "gdas" ]] ; then
    export FHCYC=1
    export FTSFS=10
-elif [[ "$CDUMP" == "gfs" ]] ; then
+elif [[ "${CDUMP}" =~ "gfs" ]] ; then
    export FHCYC=24
 fi
 
@@ -254,11 +246,11 @@ export gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4:
 # GFS output and frequency
 export FHMIN_GFS=0
 
-export FHMAX_GFS_00=${FHMAX_GFS_00:-384}
-export FHMAX_GFS_06=${FHMAX_GFS_06:-384}
-export FHMAX_GFS_12=${FHMAX_GFS_12:-384}
-export FHMAX_GFS_18=${FHMAX_GFS_18:-384}
-export FHMAX_GFS=$(eval echo \${FHMAX_GFS_$cyc})
+export FHMAX_GFS_00=${FHMAX_GFS_00:-120}
+export FHMAX_GFS_06=${FHMAX_GFS_06:-120}
+export FHMAX_GFS_12=${FHMAX_GFS_12:-120}
+export FHMAX_GFS_18=${FHMAX_GFS_18:-120}
+export FHMAX_GFS=$(eval echo \${FHMAX_GFS_${cyc}})
 
 export FHOUT_GFS=${FHOUT_GFS:-3}
 export FHMAX_HF_GFS=${FHMAX_HF_GFS:-0}
@@ -273,51 +265,30 @@ export ILPOST=1           # gempak output frequency up to F120
 # GFS restart interval in hours
 export restart_interval_gfs=0
 
-# I/O QUILTING, true--use Write Component; false--use GFDL FMS
-# if quilting=true, choose OUTPUT_GRID as cubed_sphere_grid in netcdf or gaussian_grid
-# if gaussian_grid, set OUTPUT_FILE for nemsio or netcdf
-# WRITE_DOPOST=true, use inline POST
 export QUILTING=".true."
 export OUTPUT_GRID="gaussian_grid"
-export OUTPUT_FILE="netcdf"
-export WRITE_DOPOST=".true."
+export WRITE_DOPOST=".true." # WRITE_DOPOST=true, use inline POST
 export WRITE_NSFLIP=".true."
 
-# suffix options depending on file format
-if [ $OUTPUT_FILE = "netcdf" ]; then
-    export SUFFIX=".nc"
-    export NEMSIO_IN=".false."
-    export NETCDF_IN=".true."
-else
-    export SUFFIX=".nemsio"
-    export NEMSIO_IN=".true."
-    export NETCDF_IN=".false."
-fi
-
 # IAU related parameters
 export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
 export IAUFHRS="3,6,9"
-export IAU_FHROT=$(echo $IAUFHRS | cut -c1)
+export IAU_FHROT=$(echo ${IAUFHRS} | cut -c1)
 export IAU_DELTHRS=6
 export IAU_OFFSET=6
 export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
 export IAUFHRS_ENKF="3,6,9"
 export IAU_DELTHRS_ENKF=6
-# Check if cycle is cold starting, DOIAU off, or free-forecast mode
-if [[ "$MODE" = "cycled" && "$SDATE" = "$CDATE" && $EXP_WARM_START = ".false." ]] || [[ "$DOIAU" = "NO" ]] || [[ "$MODE" = "forecast-only" && $EXP_WARM_START = ".false." ]] ; then
-  export IAU_OFFSET=0
-  export IAU_FHROT=0
-fi
 
 # Use Jacobians in eupd and thereby remove need to run eomg
 export lobsdiag_forenkf=".true."
 
 # run GLDAS to spin up land ICs
-export DO_GLDAS="YES"
+export DO_GLDAS="NO"
 export gldas_cyc=00
 
 # Exception handling that when DO_GLDAS is set, the FHOUT must be 1
-if [ $DO_GLDAS = "YES" ]; then
+if [[ ${DO_GLDAS} = "YES" ]]; then
   export FHOUT=1
 fi
 
@@ -331,12 +302,14 @@ export imp_physics=@IMP_PHYSICS@
 
 # Shared parameters
 # DA engine
-export DO_JEDIVAR=@DO_JEDIVAR@
-export DO_JEDIENS=@DO_JEDIENS@
+export DO_JEDIVAR="@DO_JEDIVAR@"
+export DO_JEDIENS="@DO_JEDIENS@"
 export DO_JEDIOCNVAR="NO"
+export DO_JEDILANDDA="NO"
+export DO_MERGENSST="NO"
 
 # Hybrid related
-export DOHYBVAR="YES"
+export DOHYBVAR="@DOHYBVAR@"
 export NMEM_ENKF=@NMEM_ENKF@
 export NMEM_EFCS=30
 export SMOOTH_ENKF="NO"
@@ -344,10 +317,11 @@ export l4densvar=".true."
 export lwrite4danl=".true."
 
 # EnKF output frequency
-if [ $DOHYBVAR = "YES" ]; then
+if [[ ${DOHYBVAR} = "YES" ]]; then
     export FHMIN_ENKF=3
     export FHMAX_ENKF=9
     export FHMAX_ENKF_GFS=120
+    export FHOUT_ENKF_GFS=3
     if [ $l4densvar = ".true." ]; then
         export FHOUT=1
         export FHOUT_ENKF=1
@@ -356,9 +330,23 @@ if [ $DOHYBVAR = "YES" ]; then
     fi
 fi
 
+# if 3DVAR and IAU
+if [[ ${DOHYBVAR} == "NO" && ${DOIAU} == "YES"  ]]; then
+    export IAUFHRS="6"
+    export IAU_FHROT="3"
+    export IAU_FILTER_INCREMENTS=".true."
+    export IAUFHRS_ENKF="6"
+fi
+
+# Check if cycle is cold starting, DOIAU off, or free-forecast mode
+if [[ "${MODE}" = "cycled" && "${SDATE}" = "${CDATE}" && ${EXP_WARM_START} = ".false." ]] || [[ "${DOIAU}" = "NO" ]] || [[ "${MODE}" = "forecast-only" && ${EXP_WARM_START} = ".false." ]] ; then
+  export IAU_OFFSET=0
+  export IAU_FHROT=0
+fi
+
 # turned on nsst in anal and/or fcst steps, and turn off rtgsst
 export DONST="YES"
-if [ $DONST = "YES" ]; then export FNTSFA="        "; fi
+if [[ ${DONST} = "YES" ]]; then export FNTSFA="        "; fi
 
 # The switch to apply SST elevation correction or not
 export nst_anl=.true.
@@ -372,10 +360,8 @@ export MAKE_ACFTBUFR="@MAKE_ACFTBUFR@"
 # Analysis increments to zero in CALCINCEXEC
 export INCREMENTS_TO_ZERO="'liq_wat_inc','icmr_inc'"
 
-if [ $OUTPUT_FILE = "nemsio" ]; then
-    export DO_CALC_INCREMENT="YES"
-    export DO_CALC_ANALYSIS="NO"
-fi
+# Write analysis files for early cycle EnKF
+export DO_CALC_INCREMENT_ENKF_GFS="YES"
 
 # Stratospheric increments to zero
 export INCVARS_ZERO_STRAT="'sphum_inc','liq_wat_inc','icmr_inc'"
@@ -389,11 +375,12 @@ export binary_diag=".false."
 
 # Verification options
 export DO_METP="YES"         # Run METPLUS jobs - set METPLUS settings in config.metp
+export DO_FIT2OBS="NO"      # Run fit to observations package
 
 # Archiving options
 export HPSSARCH="@HPSSARCH@"        # save data to HPSS archive
 export LOCALARCH="@LOCALARCH@"        # save data to local archive
-if [[ $HPSSARCH = "YES" ]] && [[ $LOCALARCH = "YES" ]]; then
+if [[ ${HPSSARCH} = "YES" ]] && [[ ${LOCALARCH} = "YES" ]]; then
    echo "Both HPSS and local archiving selected.  Please choose one or the other."
    exit 2
 fi
diff --git a/test/atm/global-workflow/jjob_ens_init.sh b/test/atm/global-workflow/jjob_ens_init.sh
index fd27980be..8a1aec8f4 100755
--- a/test/atm/global-workflow/jjob_ens_init.sh
+++ b/test/atm/global-workflow/jjob_ens_init.sh
@@ -3,15 +3,16 @@ set -x
 bindir=$1
 srcdir=$2
 
-# run jjob
+# Set g-w HOMEgfs
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
-echo $HOMEgfs
 
-export EXPDIR=$bindir/test/atm/global-workflow/testrun/experiments/gdas_test
+# Set variables for ctest
+export PSLOT=gdas_test
+export EXPDIR=$bindir/test/atm/global-workflow/testrun/experiments/$PSLOT
 export PDY=20210323
 export cyc=18
 export CDATE=${PDY}${cyc}
-export ROTDIR=$bindir/test/atm/global-workflow/testrun/ROTDIRS
+export ROTDIR=$bindir/test/atm/global-workflow/testrun/ROTDIRS/$PSLOT
 export RUN=enkfgdas
 export CDUMP=enkfgdas
 export DATAROOT=$bindir/test/atm/global-workflow/testrun/RUNDIR
@@ -21,40 +22,76 @@ export jobid=$pid
 export COMROOT=$DATAROOT
 export NMEM_ENKF=3
 export ACCOUNT=da-cpu
+export COM_TOP=$ROTDIR
 
-# setup python path for workflow utilities and tasks
+# Set GFS COM paths
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/parm/config/config.com"
+
+# Set python path for workflow utilities and tasks
 pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
 PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
 export PYTHONPATH
 
-# detemine machine from config.base
+# Detemine machine from config.base
 machine=$(echo `grep 'machine=' $EXPDIR/config.base | cut -d"=" -f2` | tr -d '"')
 
-# prepare background from previous cycle
+# Set date variables for previous cycle
 GDATE=`date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - 6 hours"`
 gPDY=$(echo $GDATE | cut -c1-8)
 gcyc=$(echo $GDATE | cut -c9-10)
+GDUMP="gdas"
+
+# Set file prefixes
+gprefix=$GDUMP.t${gcyc}z
+oprefix=$GDUMP.t${cyc}z
+
+# Generate gdas COM variables from templates
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
+    COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
+
+# Link gdas radiance bias correction files
+dpath=gdas.$gPDY/$gcyc/analysis/atmos
+mkdir -p $COM_ATMOS_ANALYSIS_PREV
+flist="amsua_n19.satbias.nc4 amsua_n19.satbias_cov.nc4 amsua_n19.tlapse.txt"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.$file $COM_ATMOS_ANALYSIS_PREV/
+done
 
-mkdir -p $ROTDIR/gdas_test/gdas.$gPDY/$gcyc/atmos/
-flist="satbias tlapse"
+# Link gdas observations
+dpath=gdas.$PDY/$cyc/obs
+mkdir -p $COM_OBS
+flist="amsua_n19.$CDATE.nc4 sondes.$CDATE.nc4"
 for file in $flist; do
-   cp -r $GDASAPP_TESTDATA/lowres/gdas.$gPDY/$gcyc/atmos/*${file}* $ROTDIR/gdas_test/gdas.$gPDY/$gcyc/atmos/
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.$file $COM_OBS/
 done
 
-# Copy tiled ges and atmf006 files to ROTDIR
-mkdir -p $ROTDIR/gdas_test/enkfgdas.$gPDY/$gcyc/atmos/
+
+# Link tiled ges and atmf006 files to ROTDIR
+dpath=enkfgdas.$gPDY/$gcyc
 for imem in $(seq 1 $NMEM_ENKF); do
     memchar="mem"$(printf %03i $imem)
-    source=$GDASAPP_TESTDATA/lowres/enkfgdas.$gPDY/$gcyc/$memchar/atmos
-    target=$ROTDIR/gdas_test/enkfgdas.$gPDY/$gcyc/$memchar/atmos
+
+    MEMDIR=${memchar} RUN=${RUN} YMD=${gPDY} HH=${gcyc} generate_com -x \
+	COM_ATMOS_HISTORY_PREV_ENS:COM_ATMOS_HISTORY_TMPL \
+	COM_ATMOS_RESTART_PREV_ENS:COM_ATMOS_RESTART_TMPL
+    COM_ATMOS_RESTART_PREV_DIRNAME_ENS=$(dirname $COM_ATMOS_RESTART_PREV_ENS)
+
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos
+    target=$COM_ATMOS_RESTART_PREV_DIRNAME_ENS
     mkdir -p $target
-    rm -rf $target/RESTART
-    ln -fs $source/RESTART $target/
+    rm -rf $target/restart
+    ln -fs $source/restart $target/
 
+    source=$GDASAPP_TESTDATA/lowres/$dpath/$memchar/model_data/atmos/history
+    target=$COM_ATMOS_HISTORY_PREV_ENS
+    mkdir -p $target
+    rm -rf $target/enkfgdas.t${gcyc}z.atmf006.nc
     ln -fs $source/enkfgdas.t${gcyc}z.atmf006.nc $target/
-
 done
 
+# Execute j-job
 if [ $machine != 'HERA' ]; then
     ${HOMEgfs}/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
 else
diff --git a/test/atm/global-workflow/jjob_var_init.sh b/test/atm/global-workflow/jjob_var_init.sh
index c0b875502..ac0011e75 100755
--- a/test/atm/global-workflow/jjob_var_init.sh
+++ b/test/atm/global-workflow/jjob_var_init.sh
@@ -1,17 +1,19 @@
-#!/bin/bash
+#! /usr/bin/env bash
+
 set -x
 bindir=$1
 srcdir=$2
 
-# run jjob
+# Set g-w HOMEgfs
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
-echo $HOMEgfs
 
-export EXPDIR=$bindir/test/atm/global-workflow/testrun/experiments/gdas_test
+# Set variables for ctest
+export PSLOT=gdas_test
+export EXPDIR=$bindir/test/atm/global-workflow/testrun/experiments/$PSLOT
 export PDY=20210323
 export cyc=18
 export CDATE=${PDY}${cyc}
-export ROTDIR=$bindir/test/atm/global-workflow/testrun/ROTDIRS
+export ROTDIR=$bindir/test/atm/global-workflow/testrun/ROTDIRS/$PSLOT
 export RUN=gdas
 export CDUMP=gdas
 export DATAROOT=$bindir/test/atm/global-workflow/testrun/RUNDIR
@@ -20,26 +22,72 @@ export pid=${pid:-$$}
 export jobid=$pid
 export COMROOT=$DATAROOT
 export ACCOUNT=da-cpu
+export COM_TOP=$ROTDIR
+
+# Set GFS COM paths
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/parm/config/config.com"
 
-# setup python path for workflow utilities and tasks
+# Set python path for workflow utilities and tasks
 pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
 PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
 export PYTHONPATH
 
-# detemine machine from config.base
+# Detemine machine from config.base
 machine=$(echo `grep 'machine=' $EXPDIR/config.base | cut -d"=" -f2` | tr -d '"')
 
-# prepare background from previous cycle
+# Set date variables for previous cycle
 GDATE=`date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - 6 hours"`
 gPDY=$(echo $GDATE | cut -c1-8)
 gcyc=$(echo $GDATE | cut -c9-10)
-mkdir -p $ROTDIR/gdas_test/gdas.$gPDY/$gcyc/atmos/
+GDUMP="gdas"
+
+# Set file prefixes
+gprefix=$GDUMP.t${gcyc}z
+oprefix=$CDUMP.t${cyc}z
+
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
+
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
+    COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
+    COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL \
+    COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
+
+# Link radiance bias correction files
+dpath=gdas.$gPDY/$gcyc/analysis/atmos
+mkdir -p $COM_ATMOS_ANALYSIS_PREV
+flist="amsua_n19.satbias.nc4 amsua_n19.satbias_cov.nc4 amsua_n19.tlapse.txt"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.$file $COM_ATMOS_ANALYSIS_PREV/
+done
+
+# Link atmospheric background on gaussian grid
+dpath=gdas.$gPDY/$gcyc/model_data/atmos/history
+mkdir -p $COM_ATMOS_HISTORY_PREV
+flist="atmf006.nc"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${gprefix}.${file} $COM_ATMOS_HISTORY_PREV/
+done
+
+# Link atmospheric bacgkround on tiles
+dpath=gdas.$gPDY/$gcyc/model_data/atmos
+COM_ATMOS_RESTART_PREV_DIRNAME=$(dirname $COM_ATMOS_RESTART_PREV)
+mkdir -p $COM_ATMOS_RESTART_PREV_DIRNAME
+flist="restart"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$file $COM_ATMOS_RESTART_PREV_DIRNAME/
+done
 
-flist="abias atmf006 satbias tlapse RESTART"
+# Link observations
+dpath=gdas.$PDY/$cyc/obs
+mkdir -p $COM_OBS
+flist="amsua_n19.$CDATE.nc4 sondes.$CDATE.nc4"
 for file in $flist; do
-   cp -r $GDASAPP_TESTDATA/lowres/gdas.$gPDY/$gcyc/atmos/*${file}* $ROTDIR/gdas_test/gdas.$gPDY/$gcyc/atmos/
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.$file $COM_OBS/
 done
 
+# Execute j-job
 if [ $machine != 'HERA' ]; then
     ${HOMEgfs}/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
 else