Support coupled GEFS forecast, use mem000 for GEFS control

jobs/rocoto/ocnpost.sh

@@ -44,7 +44,7 @@ done
 fhrlst=$(echo ${FHRLST} | sed -e 's/_/ /g; s/f/ /g; s/,/ /g')
 
 export OMP_NUM_THREADS=1
-export ENSMEM=${ENSMEM:-01}
+export ENSMEM=${ENSMEM:-000}
 
 export IDATE=${PDY}${cyc}
 

parm/config/gefs/config.aero

@@ -0,0 +1,43 @@
+#! /usr/bin/env bash
+
+# UFS-Aerosols settings
+
+# Turn off warnings about unused variables
+# shellcheck disable=SC2034
+
+# Directory containing GOCART configuration files. Defaults to parm/chem if unset.
+AERO_CONFIG_DIR=${HOMEgfs}/parm/chem
+
+# Path to the input data tree
+case ${machine} in
+  "HERA")
+    AERO_INPUTS_DIR="/scratch1/NCEPDEV/global/glopara/data/gocart_emissions"
+    ;;
+  "ORION")
+    AERO_INPUTS_DIR="/work2/noaa/global/wkolczyn/noscrub/global-workflow/gocart_emissions"
+    ;;
+  "S4")
+    AERO_INPUTS_DIR="/data/prod/glopara/gocart_emissions"
+    ;;
+  "WCOSS2")
+    AERO_INPUTS_DIR="/lfs/h2/emc/global/noscrub/emc.global/data/gocart_emissions"
+    ;;
+  "JET")
+    AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
+    ;;
+  *)
+    echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
+    exit 2
+    ;;
+esac
+
+# Biomass burning emission dataset. Choose from: GBBEPx, QFED, NONE (default)
+AERO_EMIS_FIRE=QFED
+
+# Aerosol convective scavenging factors (list of string array elements)
+# Element syntax: '<tracer_name>:<factor>'. Use <tracer_name> = * to set default factor for all aerosol tracers
+# Scavenging factors are set to 0 (no scavenging) if unset
+aero_conv_scav_factors="'*:0.3','so2:0.0','msa:0.0','dms:0.0','nh3:0.4','nh4:0.6','bc1:0.6','bc2:0.6','oc1:0.4','oc2:0.4','dust1:0.6','dust2:0.6', 'dust3:0.6','dust4:0.6','dust5:0.6','seas1:0.5','seas2:0.5','seas3:0.5','seas4:0.5','seas5:0.5'"
+#
+# Number of diagnostic aerosol tracers (default: 0)
+aero_diag_tracers=2

parm/config/gefs/config.base.emc.dyn

@@ -276,6 +276,11 @@ export DO_MERGENSST="NO"
 # Hybrid related
 export NMEM_ENS=@NMEM_ENS@
 
+# set default member number memdir for control
+# this will be overwritten for the perturbed members
+export ENSMEM="000"
+export MEMDIR="mem${ENSMEM}"
+
 # Check if cycle is cold starting
 if [[ "${EXP_WARM_START}" = ".false." ]]; then
     export IAU_FHROT=0

parm/config/gefs/config.defaults.s2sw

@@ -0,0 +1,29 @@
+#! /usr/bin/env bash
+
+# Empty variables must include a space otherwise they will be overwritten
+
+# Turn off warnings about unused variables
+# shellcheck disable=SC2034
+
+# config.base
+FHMAX_GFS_00=48
+FHMAX_GFS_06=48
+FHMAX_GFS_12=48
+FHMAX_GFS_18=48
+FHOUT_GFS=6
+FHOUT_HF_GFS=-1
+
+# config.fcst
+min_seaice="1.0e-6"
+use_cice_alb=".true."
+
+# config.wave
+FHOUT_HF_WAV=3
+DTPNT_WAV=10800
+OUTPARS_WAV="WND CUR ICE HS T01 T02 DIR FP DP PHS PTP PDIR CHA"
+DOBNDPNT_WAVE='NO'
+
+# config.arch
+export ARCH_GAUSSIAN="YES"
+export ARCH_GAUSSIAN_FHMAX=${FHMAX_GFS_00}
+export ARCH_GAUSSIAN_FHINC=${FHOUT_GFS}

parm/config/gefs/config.efcs

@@ -5,12 +5,6 @@
 
 echo "BEGIN: config.efcs"
 
-# TODO: the _ENKF counterparts need to be defined in config.base
-export DO_AERO=${DO_AERO_ENKF:-"NO"}
-export DO_OCN=${DO_OCN_ENKF:-"NO"}
-export DO_ICE=${DO_ICE_ENKF:-"NO"}
-export DO_WAVE=${DO_WAVE_ENKF:-"NO"}
-
 # TODO: Possibly need OCNRES_ENKF, ICERES_ENKF, WAVRES_ENKF too
 if [[ ${DO_OCN} == "YES" ]]; then
   case "${CASE_ENS}" in
@@ -66,7 +60,6 @@ export SPPT_LSCALE=500000.
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
 
-# FV3 model namelist parameters to over-ride
 export restart_interval=${restart_interval:-6}
 
 echo "END: config.efcs"

parm/config/gefs/config.ice

@@ -0,0 +1,5 @@
+#! /usr/bin/env bash
+
+echo "BEGIN: config.ice"
+
+echo "END: config.ice"

parm/config/gefs/config.ocn

@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+echo "BEGIN: config.ocn"
+
+# MOM_input template to use
+export MOM_INPUT="MOM_input_template_${OCNRES}"
+
+export DO_OCN_SPPT="NO"  # In MOM_input, this variable is determines OCN_SPPT (OCN_SPPT = True|False)
+export DO_OCN_PERT_EPBL="NO"  # In MOM_input, this variable determines PERT_EPBL (PERT_EPBL = True|False)
+
+# Templated variables in MOM_input_template
+export MOM6_USE_LI2016="True" # set to False for restart reproducibility
+export MOM6_THERMO_SPAN="False"
+export MOM6_ALLOW_LANDMASK_CHANGES="False"
+
+if [[ "${DO_JEDIOCNVAR}" == "YES" ]]; then
+  export ODA_INCUPD="True"
+else
+  export ODA_INCUPD="False"
+fi
+export ODA_INCUPD_NHOURS="3.0"  # In MOM_input, this is time interval for applying increment
+
+echo "END: config.ocn"

parm/config/gefs/config.wave

@@ -0,0 +1,202 @@
+#! /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 ${waveGRD}. Aborting."
+    exit 1
+    ;;
+esac
+
+# Grids for input wind fields
+export WAVEWND_DID=
+export WAVEWND_FID=
+
+# The start time reflects the number of hindcast hours prior to the cycle initial time
+if [[ "${CDUMP}" = "gdas" ]]; then
+  export FHMAX_WAV=${FHMAX:-9}
+else
+  export FHMAX_WAV=${FHMAX_GFS}
+fi
+export WAVHINDH=${WAVHINDH:-0}
+export FHMIN_WAV=${FHMIN_WAV:-0}
+export FHOUT_WAV=${FHOUT_WAV:-3}
+export FHMAX_HF_WAV=${FHMAX_HF_WAV:-120}
+export FHOUT_HF_WAV=${FHOUT_HF_WAV:-1}
+export FHMAX_WAV_IBP=180
+if (( FHMAX_WAV < FHMAX_WAV_IBP )); then export FHMAX_WAV_IBP=${FHMAX_GFS} ; fi
+
+# gridded and point output rate
+export DTFLD_WAV=$(( FHOUT_HF_WAV * 3600 ))
+export DTPNT_WAV=${DTPNT_WAV:-3600}
+export FHINCP_WAV=$(( DTPNT_WAV / 3600 ))
+
+# Selected output parameters (gridded)
+export OUTPARS_WAV=${OUTPARS_WAV:-"WND HS FP DP PHS PTP PDIR"}
+
+# Restart file config
+if [[ "${CDUMP}" = "gdas" ]]; then
+  export WAVNCYC=4
+  export WAVHCYC=${assim_freq:-6}
+  export FHMAX_WAV_CUR=${FHMAX_WAV_CUR:-48} # RTOFS forecasts only out to 8 days
+elif [[ ${gfs_cyc} -ne 0 ]]; then
+  export WAVHCYC=${assim_freq:-6}
+  export FHMAX_WAV_CUR=${FHMAX_WAV_CUR:-192} # RTOFS forecasts only out to 8 days
+else
+  export WAVHCYC=0
+  export FHMAX_WAV_CUR=${FHMAX_WAV_CUR:-192} # RTOFS forecasts only out to 8 days
+fi
+
+# Restart timing business
+
+export RSTTYPE_WAV='T'          # generate second tier of restart files
+if [[ "${CDUMP}" != gfs ]]; then    # Setting is valid for GDAS and GEFS
+  export DT_1_RST_WAV=10800       # time between restart files, set to DTRST=1 for a single restart file
+  export DT_2_RST_WAV=43200       # restart stride for checkpointing restart
+  export RSTIOFF_WAV=0            # first restart file offset relative to model start
+else                              # This is a GFS run
+  rst_dt_gfs=$(( restart_interval_gfs * 3600 ))  # TODO: This calculation needs to move to parsing_namelists_WW3.sh
+  if [[ ${rst_dt_gfs} -gt 0 ]]; then
+    export DT_1_RST_WAV=${rst_dt_gfs:-0}   # time between restart files, set to DTRST=1 for a single restart file
+    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=${rst_dt_fhmax:-0}   # use checkpoint restart file name for creating restart at end of run
+  fi
+  export RSTIOFF_WAV=0                   # first restart file offset relative to model start
+fi
+#
+# Set runmember to default value if not GEFS cpl run
+#  (for a GFS coupled run, RUNMEN would be unset, this should default to -1)
+export RUNMEM=${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/gfs/config.aero

@@ -2,11 +2,14 @@
 
 # UFS-Aerosols settings
 
+# Turn off warnings about unused variables
+# shellcheck disable=SC2034
+
 # Directory containing GOCART configuration files. Defaults to parm/chem if unset.
-AERO_CONFIG_DIR=$HOMEgfs/parm/chem
+AERO_CONFIG_DIR=${HOMEgfs}/parm/chem
 
 # Path to the input data tree
-case $machine in
+case ${machine} in
   "HERA")
     AERO_INPUTS_DIR="/scratch1/NCEPDEV/global/glopara/data/gocart_emissions"
     ;;
@@ -23,7 +26,7 @@ case $machine in
     AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
     ;;
   *)
-    echo "FATAL ERROR: Machine $machine unsupported for aerosols"
+    echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
     exit 2
     ;;
 esac

parm/config/gfs/config.defaults.s2sw

@@ -2,6 +2,9 @@
 
 # Empty variables must include a space otherwise they will be overwritten
 
+# Turn off warnings about unused variables
+# shellcheck disable=SC2034
+
 # config.base
 FHMAX_GFS_00=48
 FHMAX_GFS_06=48

scripts/exgdas_enkf_earc.sh

@@ -234,7 +234,7 @@ if [[ "${ENSGRP}" -eq 0 ]]; then
                         # shellcheck disable=SC2312
                         templates=$(compgen -A variable | grep 'COM_OCEAN_.*_TMPL')
                         for template in ${templates}; do
-                            YMEMDIR="${mem}" MD="${gPDY}" HH="${gcyc}" generate_com "directory:${template}"
+                            MEMDIR="${mem}" YMD="${gPDY}" HH="${gcyc}" generate_com "directory:${template}"
                             remove_files "${directory}" "${exclude_list[@]}"
                         done