From 964b77bc6de67291973c2c70598a1f8cb72501c5 Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue, 28 Nov 2023 18:45:51 +0000
Subject: [PATCH 1/5] Make proper j-job for MET+ (#2090)

Creates a proper j-job for the metp job, moving much of the material
from the `jobs/rocoto` script there (some of it within `jjob_header`).

Also updates the old `COMIN` variable for the COM refactor (although
it does not appear used in the verify scripts currently).

This is a partial step towards restoring/improving metp functionality
and remains untested.

Refs #1575
---
 jobs/JGFS_ATMOS_VERIFICATION | 43 ++++++++++++++++++
 jobs/rocoto/metp.sh          | 88 ++----------------------------------
 2 files changed, 47 insertions(+), 84 deletions(-)
 create mode 100644 jobs/JGFS_ATMOS_VERIFICATION

diff --git a/jobs/JGFS_ATMOS_VERIFICATION b/jobs/JGFS_ATMOS_VERIFICATION
new file mode 100644
index 0000000000..85f01a53e2
--- /dev/null
+++ b/jobs/JGFS_ATMOS_VERIFICATION
@@ -0,0 +1,43 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "metp" -c "base metp"
+
+###############################################################
+## Abstract:
+## Inline METplus verification and diagnostics driver script
+## HOMEgfs   : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE  : current analysis date (YYYYMMDDHH)
+## CDUMP  : cycle name (gdas / gfs)
+## PDY    : current date (YYYYMMDD)
+## cyc    : current cycle (HH)
+## SDATE_GFS  : first date of GFS cycle (YYYYMMDDHHMM)
+## METPCASE : METplus verification use case (g2g1 | g2o1 | pcp1)
+###############################################################
+
+# TODO: This should not be permitted as DATAROOT is set at the job-card level.
+# TODO: DATAROOT is being used as DATA in metp jobs.  This should be rectified in metp.
+# TODO: The temporary directory is DATA and is created at the top of the J-Job.
+# TODO: remove this line
+export DATAROOT=${DATA}
+
+VDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${VRFYBACK_HRS} hours")
+export VDATE
+
+# Since this is currently a one-element list, shellcheck things we would rather run this as a command
+# shellcheck disable=SC2041
+for grid in '1p00'; do
+  prod_dir="COM_ATMOS_GRIB_${grid}"
+  GRID=${grid} YMD=${PDY} HH=${cyc} generate_com -rx "${prod_dir}:COM_ATMOS_GRIB_GRID_TMPL"
+done
+
+# TODO: If none of these are on, why are we running this job?
+if [[ "${RUN_GRID2GRID_STEP1}" == "YES" || "${RUN_GRID2OBS_STEP1}" == "YES" || "${RUN_PRECIP_STEP1}" == "YES" ]]; then
+    ${VERIF_GLOBALSH}
+    status=$?
+	if (( status != 0 )); then exit "${status}"; fi
+fi
+
+if [[ ${KEEPDATA:-"NO"} = "NO" ]] ; then rm -rf "${DATAROOT}" ; fi  # TODO: This should be $DATA
+
diff --git a/jobs/rocoto/metp.sh b/jobs/rocoto/metp.sh
index 95ff2d0f4d..2bf833c1d6 100755
--- a/jobs/rocoto/metp.sh
+++ b/jobs/rocoto/metp.sh
@@ -3,93 +3,13 @@
 source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
-## Abstract:
-## Inline METplus verification and diagnostics driver script
-## HOMEgfs   : /full/path/to/workflow
-## EXPDIR : /full/path/to/config/files
-## CDATE  : current analysis date (YYYYMMDDHH)
-## CDUMP  : cycle name (gdas / gfs)
-## PDY    : current date (YYYYMMDD)
-## cyc    : current cycle (HH)
-## SDATE_GFS  : first date of GFS cycle (YYYYMMDDHHMM)
-## METPCASE : METplus verification use case (g2g1 | g2o1 | pcp1)
-###############################################################
-
-###############################################################
-echo
-echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
-. ${HOMEgfs}/ush/load_fv3gfs_modules.sh
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
 status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
+if (( status != 0 )); then exit "${status}"; fi
 
 export job="metp${METPCASE}"
 export jobid="${job}.$$"
 
-##############################################
-# make temp directory
-##############################################
-export DATA=${DATA:-${DATAROOT}/${jobid}}
-mkdir -p ${DATA}
-cd ${DATA}
-
-
-##############################################
-# Run setpdy and initialize PDY variables
-##############################################
-export cycle="t${cyc}z"
-setpdy.sh
-. ./PDY
-
-###############################################################
-echo
-echo "=============== START TO SOURCE RELEVANT CONFIGS ==============="
-configs="base metp"
-for config in ${configs}; do
-    . ${EXPDIR}/config.${config}
-    status=$?
-    [[ ${status} -ne 0 ]] && exit ${status}
-done
-
-
-###############################################################
-echo
-echo "=============== START TO SOURCE MACHINE RUNTIME ENVIRONMENT ==============="
-. ${BASE_ENV}/${machine}.env metp
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-###############################################################
-export COMPONENT="atmos"
-export VDATE="$(echo $(${NDATE} -${VRFYBACK_HRS} ${CDATE}) | cut -c1-8)"
-export COMIN="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
-
-# TODO: This should not be permitted as DATAROOT is set at the job-card level.
-# TODO: DATAROOT is being used as DATA in metp jobs.  This should be rectified in metp.
-# TODO: The temporary directory is DATA and is created at the top of the J-Job.
-# TODO: remove this line
-export DATAROOT=${DATA}
-
-###############################################################
-echo
-echo "=============== START TO RUN METPLUS VERIFICATION ==============="
-if [ ${CDUMP} = "gfs" ]; then
-
-    if [ ${RUN_GRID2GRID_STEP1} = "YES" -o ${RUN_GRID2OBS_STEP1} = "YES" -o ${RUN_PRECIP_STEP1} = "YES" ]; then
-
-        ${VERIF_GLOBALSH}
-        status=$?
-        [[ ${status} -ne 0 ]] && exit ${status}
-        [[ ${status} -eq 0 ]] && echo "Succesfully ran ${VERIF_GLOBALSH}"
-    fi
-fi
-
-
-if [ ${CDUMP} = "gdas" ]; then
-    echo "METplus verification currently not supported for CDUMP=${CDUMP}"
-fi
-###############################################################
-# Force Exit out cleanly
-if [ ${KEEPDATA:-"NO"} = "NO" ] ; then rm -rf ${DATAROOT} ; fi  # TODO: This should be $DATA
-
+"${HOMEgfs}/jobs/JGFS_ATMOS_VERIFICATION"
 
-exit 0
+exit $?

From 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e Mon Sep 17 00:00:00 2001
From: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed, 29 Nov 2023 11:26:34 -0500
Subject: [PATCH 2/5] Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION
 (#2095)

Add execute permissions (755)
---
 jobs/JGFS_ATMOS_VERIFICATION | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 jobs/JGFS_ATMOS_VERIFICATION

diff --git a/jobs/JGFS_ATMOS_VERIFICATION b/jobs/JGFS_ATMOS_VERIFICATION
old mode 100644
new mode 100755

From c1c025f91ddac73aea595cc9fa4dd0bea80575fc Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed, 29 Nov 2023 17:15:10 +0000
Subject: [PATCH 3/5] Add wave init to GEFS (#2089)

Adds the wave init job to GEFS. Since the output would be the same for
every member, the job is only run once for the control, then links are
created in each of the member directories pointing to that copy.

New ww3_multi and ww3_shell templates for GEFS are copied from the
GFS versions.

The GEFS restart frequency is changed to not be zero, and the comment
about not setting it to zero is copied from the gfs config.base. The restart
interval for the GEFS perturbed members is changed to equal that of the
control.

Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
and another bug in the GEFS stage_ic dependency.

Resolves #2017
---
 ...C48_S2SA_gefs.yaml => C48_S2SWA_gefs.yaml} |   2 +-
 jobs/JGDAS_ENKF_FCST                          |   3 +
 parm/config/gefs/config.base.emc.dyn          |   5 +-
 parm/config/gefs/config.efcs                  |   2 +-
 parm/config/gefs/config.wave                  | 186 +++++++++++++++++-
 parm/config/gefs/config.waveinit              |   1 +
 ..._multi.gfs.inp.tmpl => ww3_multi.inp.tmpl} |   0
 ...w3_shel.gfs.inp.tmpl => ww3_shel.inp.tmpl} |   0
 scripts/exgfs_wave_init.sh                    |  11 ++
 ush/parsing_namelists_WW3.sh                  |   8 +-
 workflow/applications/gefs.py                 |  10 +-
 workflow/rocoto/gefs_tasks.py                 |  21 +-
 12 files changed, 239 insertions(+), 10 deletions(-)
 rename ci/cases/pr/{C48_S2SA_gefs.yaml => C48_S2SWA_gefs.yaml} (96%)
 mode change 120000 => 100644 parm/config/gefs/config.wave
 create mode 120000 parm/config/gefs/config.waveinit
 rename parm/wave/{ww3_multi.gfs.inp.tmpl => ww3_multi.inp.tmpl} (100%)
 rename parm/wave/{ww3_shel.gfs.inp.tmpl => ww3_shel.inp.tmpl} (100%)

diff --git a/ci/cases/pr/C48_S2SA_gefs.yaml b/ci/cases/pr/C48_S2SWA_gefs.yaml
similarity index 96%
rename from ci/cases/pr/C48_S2SA_gefs.yaml
rename to ci/cases/pr/C48_S2SWA_gefs.yaml
index 2abbf0043e..5eb99d9c1e 100644
--- a/ci/cases/pr/C48_S2SA_gefs.yaml
+++ b/ci/cases/pr/C48_S2SWA_gefs.yaml
@@ -4,7 +4,7 @@ experiment:
 
 arguments:
   pslot: {{ 'pslot' | getenv }}
-  app: S2SA
+  app: S2SWA
   resdet: 48
   resens: 48
   nens: 2
diff --git a/jobs/JGDAS_ENKF_FCST b/jobs/JGDAS_ENKF_FCST
index e8f9393363..53408df8cf 100755
--- a/jobs/JGDAS_ENKF_FCST
+++ b/jobs/JGDAS_ENKF_FCST
@@ -30,6 +30,9 @@ fi
 export ENSEND=$((NMEM_EFCSGRP * 10#${ENSGRP}))
 export ENSBEG=$((ENSEND - NMEM_EFCSGRP + 1))
 
+if [[ ${DO_WAVE} == "YES" ]]; then
+  declare -rx RUNwave="${RUN}wave"
+fi
 
 ###############################################################
 # Run relevant script
diff --git a/parm/config/gefs/config.base.emc.dyn b/parm/config/gefs/config.base.emc.dyn
index fbe0937dc7..16775cfc6c 100644
--- a/parm/config/gefs/config.base.emc.dyn
+++ b/parm/config/gefs/config.base.emc.dyn
@@ -242,7 +242,10 @@ export FHMAX_ENKF=${FHMAX_GFS}
 export FHOUT_ENKF=${FHOUT_GFS}
 
 # GFS restart interval in hours
-export restart_interval_gfs=0
+export restart_interval_gfs=12
+# NOTE: Do not set this to zero.  Instead set it to $FHMAX_GFS
+# TODO: Remove this variable from config.base and reference from config.fcst
+# TODO: rework logic in config.wave and push it to parsing_nameslist_WW3.sh where it is actually used
 
 export QUILTING=".true."
 export OUTPUT_GRID="gaussian_grid"
diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
index a6d093968d..9593408848 100644
--- a/parm/config/gefs/config.efcs
+++ b/parm/config/gefs/config.efcs
@@ -54,6 +54,6 @@ export SPPT_LSCALE=500000.
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
 
-export restart_interval=${restart_interval:-6}
+export restart_interval=${restart_interval_gfs}
 
 echo "END: config.efcs"
diff --git a/parm/config/gefs/config.wave b/parm/config/gefs/config.wave
deleted file mode 120000
index 0b9d14a962..0000000000
--- a/parm/config/gefs/config.wave
+++ /dev/null
@@ -1 +0,0 @@
-../gfs/config.wave
\ No newline at end of file
diff --git a/parm/config/gefs/config.wave b/parm/config/gefs/config.wave
new file mode 100644
index 0000000000..e04331e533
--- /dev/null
+++ b/parm/config/gefs/config.wave
@@ -0,0 +1,185 @@
+#! /usr/bin/env bash
+
+########## config.wave ##########
+# Wave steps specific
+
+echo "BEGIN: config.wave"
+
+# Parameters that are common to all wave model steps
+
+# System and version
+export wave_sys_ver=v1.0.0
+
+export EXECwave="${HOMEgfs}/exec"
+export FIXwave="${HOMEgfs}/fix/wave"
+export PARMwave="${HOMEgfs}/parm/wave"
+export USHwave="${HOMEgfs}/ush"
+
+# This config contains variables/parameters used in the fcst step
+# Some others are also used across the workflow in wave component scripts
+
+# General runtime labels
+export CDUMPwave="${RUN}wave"
+
+# In GFS/GDAS, restart files are generated/read from gdas runs
+export CDUMPRSTwave="gdas"
+
+# Grids for wave model
+export waveGRD=${waveGRD:-'mx025'}
+
+#grid dependent variable defaults
+export waveGRDN='1'                   # grid number for ww3_multi
+export waveGRDG='10'                  # grid group for ww3_multi
+export USE_WAV_RMP='NO'               # YES/NO rmp grid remapping pre-processed coefficients
+export waveMULTIGRID='.false.'        # .true./.false. for multi or shel
+export MESH_WAV="mesh.${waveGRD}.nc"  # Mesh grid for wave model for CMEPS
+export waveesmfGRD=' '                # input grid for multigrid
+
+#Grid dependent variables for various grids
+case "${waveGRD}" in
+  "gnh_10m;aoc_9km;gsh_15m")
+    #GFSv16 settings:
+    export waveGRDN='1 2 3'
+    export waveGRDG='10 20 30'
+    export USE_WAV_RMP='YES'
+    export waveMULTIGRID='.true.'
+    export IOSRV='3'
+    export MESH_WAV=' '
+    export waveesmfGRD='glox_10m'
+    export waveuoutpGRD='points'
+    export waveinterpGRD='glo_15mxt at_10m ep_10m wc_10m glo_30m'
+    export wavepostGRD='gnh_10m aoc_9km gsh_15m'
+    ;;
+  "gwes_30m")
+    #Grid used for P8
+    export waveinterpGRD=''
+    export wavepostGRD='gwes_30m'
+    export waveuoutpGRD=${waveGRD}
+    ;;
+  "mx025")
+    #Grid used for HR1 (tripolar 1/4 deg)
+    export waveinterpGRD='reg025'
+    export wavepostGRD=''
+    export waveuoutpGRD=${waveGRD}
+    ;;
+  "glo_025")
+    #GEFSv13 regular lat/lon 1/4 deg grid
+    export waveinterpGRD=''
+    export wavepostGRD='glo_025'
+    export waveuoutpGRD=${waveGRD}
+    ;;
+  "glo_200")
+    #Global regular lat/lon 2deg deg grid
+    export waveinterpGRD=''
+    export wavepostGRD='glo_200'
+    export waveuoutpGRD=${waveGRD}
+    ;;
+  "glo_500")
+    #Global regular lat/lon 5deg deg grid
+    export waveinterpGRD=''
+    export wavepostGRD='glo_500'
+    export waveuoutpGRD=${waveGRD}
+    ;;
+  *)
+    echo "FATAL ERROR: No grid specific wave config values exist for ${waveGRD}. Aborting."
+    exit 1
+    ;;
+esac
+
+# Grids for input wind fields
+export WAVEWND_DID=
+export WAVEWND_FID=
+
+# The start time reflects the number of hindcast hours prior to the cycle initial time
+export FHMAX_WAV=${FHMAX_GFS}
+export WAVHINDH=0
+export FHMIN_WAV=0
+export FHOUT_WAV=3
+export FHMAX_HF_WAV=120
+export FHOUT_HF_WAV=1
+export FHMAX_WAV_IBP=180
+if (( FHMAX_WAV < FHMAX_WAV_IBP )); then export FHMAX_WAV_IBP=${FHMAX_GFS} ; fi
+
+# gridded and point output rate
+export DTFLD_WAV=$(( FHOUT_HF_WAV * 3600 ))
+export DTPNT_WAV=3600
+export FHINCP_WAV=$(( DTPNT_WAV / 3600 ))
+
+# Selected output parameters (gridded)
+export OUTPARS_WAV="WND CUR ICE HS T01 T02 DIR FP DP PHS PTP PDIR CHA"
+
+# Restart file config
+export WAVHCYC=${assim_freq:-6}
+export FHMAX_WAV_CUR=192 # RTOFS forecasts only out to 8 days
+
+# Restart timing business
+
+export RSTTYPE_WAV='T'          # generate second tier of restart files
+rst_dt_gfs=$(( restart_interval_gfs * 3600 ))  # TODO: This calculation needs to move to parsing_namelists_WW3.sh
+if [[ ${rst_dt_gfs} -gt 0 ]]; then
+  export DT_1_RST_WAV=0 #${rst_dt_gfs:-0}   # time between restart files, set to DTRST=1 for a single restart file
+                                        #temporarily set to zero to avoid a clash in requested restart times 
+                                        #which makes the wave model crash a fix for the model issue will be coming
+  export DT_2_RST_WAV=${rst_dt_gfs:-0}   # restart stride for checkpointing restart
+else
+  rst_dt_fhmax=$(( FHMAX_WAV * 3600 ))
+  export DT_1_RST_WAV=0                    # time between restart files, set to DTRST=1 for a single restart file
+  export DT_2_RST_WAV=${rst_dt_fhmax:-0}   # use checkpoint restart file name for creating restart at end of run
+fi
+export RSTIOFF_WAV=0                   # first restart file offset relative to model start
+#
+# Set runmember to default value if not GEFS cpl run
+#  (for a GFS coupled run, RUNMEN would be unset, this should default to -1)
+export RUNMEM=${RUNMEM:--1}
+# Set wave model member tags if ensemble run
+# -1: no suffix, deterministic; xxxNN: extract two last digits to make ofilename prefix=gwesNN
+if [[ ${RUNMEM} = -1 ]]; then
+# No suffix added to model ID in case of deterministic run
+  export waveMEMB=
+else
+# Extract member number only
+  export waveMEMB="${RUNMEM: -2}"
+fi
+
+# Determine if wave component needs input and/or is coupled
+export WW3ATMINP='CPL'
+if [[ ${DO_ICE} == "YES" ]]; then
+  export WW3ICEINP='CPL'
+  export WAVEICE_FID=
+else
+  export WW3ICEINP='YES'
+  export WAVEICE_FID=glix_10m
+fi
+
+export WAVECUR_DID=rtofs
+if [[ ${DO_OCN} == "YES" ]]; then
+  export WW3CURINP='CPL'
+  export WAVECUR_FID=
+else
+  export WW3CURINP='YES'
+  export WAVECUR_FID=glix_10m
+fi
+
+# Determine if input is from perturbed ensemble (T) or single input file (F) for all members
+export WW3ATMIENS='F'
+export WW3ICEIENS='F'
+export WW3CURIENS='F'
+
+export GOFILETYPE=1     # GOFILETYPE=1 one gridded file per output step
+export POFILETYPE=1     # POFILETYPE=1 one point file per output step
+
+# Parameters for ww3_multi/shel.inp
+# Unified output T or F
+export FUNIPNT='T'
+# Output server type (see ww3_shel/multi.inp in WW3 repo)
+export IOSRV=${IOSRV:-'1'}
+# Flag for dedicated output process for unified points
+export FPNTPROC='T'
+# Flag for grids sharing dedicated output processes
+export FGRDPROC='F'
+# Flag for masking computation in two-way nesting
+export FLAGMASKCOMP="F"
+# Flag for masking at printout time.
+export FLAGMASKOUT="F"
+
+echo "END: config.wave"
diff --git a/parm/config/gefs/config.waveinit b/parm/config/gefs/config.waveinit
new file mode 120000
index 0000000000..769bbcf903
--- /dev/null
+++ b/parm/config/gefs/config.waveinit
@@ -0,0 +1 @@
+../gfs/config.waveinit
\ No newline at end of file
diff --git a/parm/wave/ww3_multi.gfs.inp.tmpl b/parm/wave/ww3_multi.inp.tmpl
similarity index 100%
rename from parm/wave/ww3_multi.gfs.inp.tmpl
rename to parm/wave/ww3_multi.inp.tmpl
diff --git a/parm/wave/ww3_shel.gfs.inp.tmpl b/parm/wave/ww3_shel.inp.tmpl
similarity index 100%
rename from parm/wave/ww3_shel.gfs.inp.tmpl
rename to parm/wave/ww3_shel.inp.tmpl
diff --git a/scripts/exgfs_wave_init.sh b/scripts/exgfs_wave_init.sh
index 2be224d1da..ce903a2284 100755
--- a/scripts/exgfs_wave_init.sh
+++ b/scripts/exgfs_wave_init.sh
@@ -203,6 +203,17 @@ source "${HOMEgfs}/ush/preamble.sh"
     fi
   done
 
+# Copy to other members if needed
+if (( NMEM_ENS > 0 )); then
+  for mem in $(seq -f "%03g" 1 "${NMEM_ENS}"); do
+    MEMDIR="mem${mem}" YMD=${PDY} HH=${cyc} generate_com COM_WAVE_PREP_MEM:COM_WAVE_PREP_TMPL
+    mkdir -p "${COM_WAVE_PREP_MEM}"
+    for grdID in ${grdALL}; do
+      ${NLN} "${COM_WAVE_PREP}/${RUN}wave.mod_def.${grdID}" "${COM_WAVE_PREP_MEM}/"
+    done
+  done
+fi
+
 # --------------------------------------------------------------------------- #
 # 2.  Ending
 
diff --git a/ush/parsing_namelists_WW3.sh b/ush/parsing_namelists_WW3.sh
index c53af9f18f..9b0a94695c 100755
--- a/ush/parsing_namelists_WW3.sh
+++ b/ush/parsing_namelists_WW3.sh
@@ -79,8 +79,8 @@ WW3_namelists(){
 
   if [ $waveMULTIGRID = ".true." ]; then
     # ww3_multi template
-    if [ -f $PARMwave/ww3_multi.${NET}.inp.tmpl ]; then
-      cp $PARMwave/ww3_multi.${NET}.inp.tmpl ww3_multi.inp.tmpl
+    if [ -f $PARMwave/ww3_multi.inp.tmpl ]; then
+      cp $PARMwave/ww3_multi.inp.tmpl ww3_multi.inp.tmpl
     fi
     if [ ! -f ww3_multi.inp.tmpl ]; then
       echo "ABNORMAL EXIT: NO TEMPLATE FOR WW3 MULTI INPUT FILE" 
@@ -88,8 +88,8 @@ WW3_namelists(){
     fi
   else 
     # ww3_multi template
-    if [ -f $PARMwave/ww3_shel.${NET}.inp.tmpl ]; then
-      cp $PARMwave/ww3_shel.${NET}.inp.tmpl ww3_shel.inp.tmpl
+    if [ -f $PARMwave/ww3_shel.inp.tmpl ]; then
+      cp $PARMwave/ww3_shel.inp.tmpl ww3_shel.inp.tmpl
     fi
     if [ ! -f ww3_shel.inp.tmpl ]; then
       echo "ABNORMAL EXIT: NO TEMPLATE FOR WW3 SHEL INPUT FILE" 
diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py
index 8ac4cdc18e..b2369e8dfc 100644
--- a/workflow/applications/gefs.py
+++ b/workflow/applications/gefs.py
@@ -19,6 +19,9 @@ def _get_app_configs(self):
         if self.nens > 0:
             configs += ['efcs']
 
+        if self.do_wave:
+            configs += ['waveinit']
+
         return configs
 
     @staticmethod
@@ -32,7 +35,12 @@ def _update_base(base_in):
 
     def get_task_names(self):
 
-        tasks = ['stage_ic', 'fcst']
+        tasks = ['stage_ic']
+
+        if self.do_wave:
+            tasks += ['waveinit']
+
+        tasks += ['fcst']
 
         if self.nens > 0:
             tasks += ['efcs']
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index c5dae3a13d..680c7d8686 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -50,7 +50,7 @@ def stage_ic(self):
         if self.app_config.do_wave:
             prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_WAVIC']}/@Y@m@d@H/mem000/wave"
             for wave_grid in self._configs['waveinit']['waveGRD'].split():
-                data = f"{prefix}/{wave_grid}/@Y@m@d.@H0000.restart.{wave_grid}"
+                data = f"{prefix}/@Y@m@d.@H0000.restart.{wave_grid}"
                 dep_dict = {'type': 'data', 'data': data}
                 deps.append(rocoto.add_dependency(dep_dict))
 
@@ -61,12 +61,25 @@ def stage_ic(self):
 
         return task
 
+    def waveinit(self):
+
+        resources = self.get_resource('waveinit')
+        task = create_wf_task('waveinit', resources, cdump=self.cdump, envar=self.envars, dependency=None)
+
+        return task
+
     def fcst(self):
         # TODO: Add real dependencies
         dependencies = []
         dep_dict = {'type': 'task', 'name': f'{self.cdump}stage_ic'}
         dependencies.append(rocoto.add_dependency(dep_dict))
 
+        if self.app_config.do_wave:
+            dep_dict = {'type': 'task', 'name': f'{self.cdump}waveinit'}
+            dependencies.append(rocoto.add_dependency(dep_dict))
+
+        dependencies = rocoto.create_dependency(dep_condition='and', dep=dependencies)
+
         resources = self.get_resource('fcst')
         task = create_wf_task('fcst', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
 
@@ -77,6 +90,12 @@ def efcs(self):
         dep_dict = {'type': 'task', 'name': f'{self.cdump}stage_ic'}
         dependencies.append(rocoto.add_dependency(dep_dict))
 
+        if self.app_config.do_wave:
+            dep_dict = {'type': 'task', 'name': f'{self.cdump}waveinit'}
+            dependencies.append(rocoto.add_dependency(dep_dict))
+
+        dependencies = rocoto.create_dependency(dep_condition='and', dep=dependencies)
+
         efcsenvars = self.envars.copy()
         efcsenvars.append(rocoto.create_envar(name='ENSGRP', value='#grp#'))
 

From c2d78a61a224678fb804eed19f39d1f07408ae5f Mon Sep 17 00:00:00 2001
From: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed, 29 Nov 2023 12:39:08 -0500
Subject: [PATCH 4/5] Add missing cut to VDATE setting in
 JGFS_ATMOS_VERIFICATION (#2098)

Refs #2097
---
 jobs/JGFS_ATMOS_VERIFICATION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jobs/JGFS_ATMOS_VERIFICATION b/jobs/JGFS_ATMOS_VERIFICATION
index 85f01a53e2..23a450cd55 100755
--- a/jobs/JGFS_ATMOS_VERIFICATION
+++ b/jobs/JGFS_ATMOS_VERIFICATION
@@ -23,7 +23,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "metp" -c "base metp"
 export DATAROOT=${DATA}
 
 VDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${VRFYBACK_HRS} hours")
-export VDATE
+export VDATE=${VDATE:0:8}
 
 # Since this is currently a one-element list, shellcheck things we would rather run this as a command
 # shellcheck disable=SC2041

From c19810cce252fcdb25fd9960c05b08b5f8d8b1ad Mon Sep 17 00:00:00 2001
From: AndrewEichmann-NOAA
 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed, 29 Nov 2023 15:17:36 -0500
Subject: [PATCH 5/5] Added variables to config.prepoceanobs (#2101)

---
 parm/config/gfs/config.prepoceanobs | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index c5a9ddfd22..068ecff1ad 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -4,7 +4,10 @@
 
 echo "BEGIN: config.prepoceanobs"
 
+export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
+
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
+export OBSPROC_YAML=@OBSPROC_CONFIG@
 export OBS_LIST=@SOCA_OBS_LIST@
 [[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
 export OBS_YAML=${OBS_LIST}