Merge remote-tracking branch 'emc/develop' into feature/spack-stack

ci/cases/pr/C48_S2SA_gefs.yaml → 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

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

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} - ${VRFYBACK_HRS} hours")
+export VDATE=${VDATE:0:8}
+
+# 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
+

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 $?

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"

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"

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"

parm/config/gefs/config.waveinit

@@ -0,0 +1 @@
+../gfs/config.waveinit

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}