Support coupled GEFS forecast, use mem000 for GEFS control (#1755)

Makes the necessary updates to allow the workflow to run (non-wave) coupled
forecasts. Some of the coupled functions in postdet had to be updated because
they only checked for gfs and gdas runs, so necessary code was never executed.

Also updates so that the GEFS control uses `mem000` as the memdir so it
appears at the same level as the perturbed members. Relatedly, the default
member number in coupled files is changed to 000 instead of 01.

Finally, an unrelated error in the earc job is corrected where a character
from the middle of the line was moved to the beginning.

Resolves #1754

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 @@
+../gfs/config.aero

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 @@
+../gfs/config.defaults.s2sw

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 @@
+../gfs/config.ice

parm/config/gefs/config.ocn

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

parm/config/gefs/config.wave

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

scripts/exgdas_enkf_fcst.sh

@@ -112,16 +112,17 @@ for imem in $(seq "${ENSBEG}" "${ENSEND}"); do
 
    cd "${DATATOP}"
 
-   cmem=$(printf %03i "${imem}")
-   memchar="mem${cmem}"
+   ENSMEM=$(printf %03i "${imem}")
+   export ENSMEM
+   memchar="mem${ENSMEM}"
 
-   echo "Processing MEMBER: ${cmem}"
+   echo "Processing MEMBER: ${ENSMEM}"
 
    ra=0
 
    skip_mem="NO"
    if [[ -f ${EFCSGRP}.fail ]]; then
-      memstat=$(grep "MEMBER ${cmem}" "${EFCSGRP}.fail" | grep -c "PASS")
+      memstat=$(grep "MEMBER ${ENSMEM}" "${EFCSGRP}.fail" | grep -c "PASS")
       [[ ${memstat} -eq 1 ]] && skip_mem="YES"
    fi
 
@@ -166,7 +167,7 @@ for imem in $(seq "${ENSBEG}" "${ENSEND}"); do
 
       # Notify a member forecast failed and abort
       if [[ ${ra} -ne 0 ]]; then
-         err_exit "FATAL ERROR:  forecast of member ${cmem} FAILED.  Aborting job"
+         err_exit "FATAL ERROR:  forecast of member ${ENSMEM} FAILED.  Aborting job"
       fi
 
       rc=$((rc+ra))
@@ -192,9 +193,9 @@ for imem in $(seq "${ENSBEG}" "${ENSEND}"); do
    [[ -f log ]] && rm log
    [[ -f log_new ]] && rm log_new
    if [[ ${ra} -ne 0 ]]; then
-      echo "MEMBER ${cmem} : FAIL" > log
+      echo "MEMBER ${ENSMEM} : FAIL" > log
    else
-      echo "MEMBER ${cmem} : PASS" > log
+      echo "MEMBER ${ENSMEM} : PASS" > log
    fi
    if [[ -s log_old ]] ; then
        cat log_old log > log_new

ush/forecast_postdet.sh

@@ -502,8 +502,8 @@ FV3_out() {
       done
       local idate=$(date -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
     done
-  elif [[ ${RUN} =~ "gfs" ]]; then
-    # No need to copy FV3 restart files when RUN=gfs
+  else
+    # No need to copy FV3 restart files when RUN=gfs or gefs
     ${NCP} "${DATA}/input.nml" "${COM_ATMOS_HISTORY}/input.nml"
   fi
   echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
@@ -736,11 +736,10 @@ MOM6_postdet() {
   [[ ! -d ${COM_OCEAN_HISTORY} ]] && mkdir -p "${COM_OCEAN_HISTORY}"
 
   # Link output files
-  if [[ "${RUN}" =~ "gfs" ]]; then
+  if [[ "${RUN}" =~ "gfs" || "${RUN}" =~ "gefs" ]]; then
     # Link output files for RUN = gfs
 
     # TODO: get requirements on what files need to be written out and what these dates here are and what they mean
-    export ENSMEM=${ENSMEM:-01}
 
     if [[ ! -d ${COM_OCEAN_HISTORY} ]]; then mkdir -p "${COM_OCEAN_HISTORY}"; fi
 
@@ -875,7 +874,7 @@ CICE_postdet() {
 
   if [[ "${RUN}" =~ "gdas" ]]; then
     cice_hist_avg=".false."   # DA needs instantaneous
-  elif [[ "${RUN}" =~ "gfs" ]]; then
+  else
     cice_hist_avg=".true."    # P8 wants averaged over histfreq_n
   fi
 
@@ -914,14 +913,12 @@ CICE_postdet() {
   if [[ ! -d "${COM_ICE_HISTORY}" ]]; then mkdir -p "${COM_ICE_HISTORY}"; fi
   mkdir -p "${COM_ICE_RESTART}"
 
-  if [[ "${RUN}" =~ "gfs" ]]; then
+  if [[ "${RUN}" =~ "gfs" || "${RUN}" =~ "gefs" ]]; then
     # Link output files for RUN = gfs
 
     # TODO: make these forecast output files consistent w/ GFS output
     # TODO: Work w/ NB to determine appropriate naming convention for these files
 
-    export ENSMEM=${ENSMEM:-01}
-
     # TODO: consult w/ NB on how to improve on this.  Gather requirements and more information on what these files are and how they are used to properly catalog them
     local vdate seconds vdatestr fhr last_fhr
     for fhr in ${FV3_OUTPUT_FH}; do

ush/forecast_predet.sh

@@ -52,6 +52,7 @@ common_predet(){
   CDUMP=${CDUMP:-gdas}
   CASE=${CASE:-C768}
   CDATE=${CDATE:-2017032500}
+  ENSMEM=${ENSMEM:-000}
 
   FCSTEXECDIR=${FCSTEXECDIR:-${HOMEgfs}/exec}
   FCSTEXEC=${FCSTEXEC:-ufs_model.x}