Merge remote-tracking branch 'origin/develop' into ss160

.gitignore

@@ -36,7 +36,6 @@ fix/gsi
 fix/lut
 fix/mom6
 fix/orog
-fix/reg2grb2
 fix/sfc_climo
 fix/ugwd
 fix/verif
@@ -99,6 +98,9 @@ parm/post/postxconfig-NT-GFS-WAFS.txt
 parm/post/postxconfig-NT-GFS.txt
 parm/post/postxconfig-NT-gefs-aerosol.txt
 parm/post/postxconfig-NT-gefs-chem.txt
+parm/post/ocean.csv
+parm/post/ice.csv
+parm/post/ocnicepost.nml.jinja2
 parm/ufs/noahmptable.tbl
 parm/ufs/model_configure.IN
 parm/ufs/MOM_input_*.IN
@@ -137,7 +139,6 @@ sorc/radmon_bcor.fd
 sorc/radmon_time.fd
 sorc/rdbfmsua.fd
 sorc/recentersigp.fd
-sorc/reg2grb2.fd
 sorc/supvit.fd
 sorc/syndat_getjtbul.fd
 sorc/syndat_maksynrc.fd
@@ -147,6 +148,7 @@ sorc/tocsbufr.fd
 sorc/upp.fd
 sorc/vint.fd
 sorc/webtitle.fd
+sorc/ocnicepost.fd
 
 # Ignore scripts from externals
 #------------------------------

ci/cases/pr/C48mx500_3DVarAOWCDA.yaml

@@ -17,6 +17,7 @@ arguments:
   start: warm
   yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_gfs_defaults_ci.yaml
 
-skip_ci_on_hosts:
+skip_ci_on_host:
   - orion
+  - hera
   - hercules

ci/scripts/run-check_ci.sh

@@ -25,6 +25,7 @@ pslot=${2:-${pslot:-?}}        # Name of the experiment being tested by this scr
 # TODO: Make this configurable (for now all scripts run from gfs for CI at runtime)
 HOMEgfs="${TEST_DIR}/gfs"
 RUNTESTS="${TEST_DIR}/RUNTESTS"
+run_check_logfile="${RUNTESTS}/ci-run_check.log"
 
 # Source modules and setup logging
 echo "Source modules."
@@ -77,15 +78,16 @@ while true; do
     {
       echo "Experiment ${pslot} Terminated with ${num_failed} tasks failed at $(date)" || true
       echo "Experiment ${pslot} Terminated: *FAILED*"
-    } >> "${RUNTESTS}/ci.log"
-
+    } | tee -a "${run_check_logfile}"
     error_logs=$(rocotostat -d "${db}" -w "${xml}" | grep -E 'FAIL|DEAD' | awk '{print "-c", $1, "-t", $2}' | xargs rocotocheck -d "${db}" -w "${xml}" | grep join | awk '{print $2}') || true
     {
      echo "Error logs:"
      echo "${error_logs}"
-    } >> "${RUNTESTS}/ci.log"
-    sed -i "s/\`\`\`//2g" "${RUNTESTS}/ci.log"
-    sacct --format=jobid,jobname%35,WorkDir%100,stat | grep "${pslot}" | grep "${pr}\/RUNTESTS" |  awk '{print $1}' | xargs scancel || true
+    } | tee -a  "${run_check_logfile}"
+    # rm -f "${RUNTESTS}/error.logs"
+    for log in ${error_logs}; do
+      echo "RUNTESTS${log#*RUNTESTS}" >> "${RUNTESTS}/error.logs"
+    done
     rc=1
     break
   fi
@@ -95,8 +97,7 @@ while true; do
       echo "Experiment ${pslot} Completed at $(date)" || true
       echo "with ${num_succeeded} successfully completed jobs" || true
       echo "Experiment ${pslot} Completed: *SUCCESS*"
-    } >> "${RUNTESTS}/ci.log"
-    sed -i "s/\`\`\`//2g" "${RUNTESTS}/ci.log"
+    } | tee -a "${run_check_logfile}"
     rc=0
     break
   fi
@@ -107,3 +108,4 @@ while true; do
 done
 
 exit "${rc}"
+

ci/scripts/utils/ci_utils.sh

@@ -102,6 +102,14 @@ function get_pslot () {
 
 }
 
+function cancel_all_batch_jobs () {
+  local RUNTESTS="${1}"
+  pslot_list=$(get_pslot_list "${RUNTESTS}")
+  for pslot in ${pslot_list}; do
+    cancel_batch_jobs "${pslot}"
+  done
+}
+
 function create_experiment () {
 
   local yaml_config="${1}"

env/HERA.env

@@ -199,6 +199,13 @@ elif [[ "${step}" = "atmos_products" ]]; then
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation on Hera
 
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
 elif [[ "${step}" = "ecen" ]]; then
 
     nth_max=$((npe_node_max / npe_node_ecen))

env/HERCULES.env

@@ -207,10 +207,20 @@ case ${step} in
     [[ ${NTHREADS_UPP} -gt ${nth_max} ]] && export NTHREADS_UPP=${nth_max}
     export APRUN_UPP="${launcher} -n ${npe_upp} --cpus-per-task=${NTHREADS_UPP}"
  ;;
+
  "atmos_products")
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation
  ;;
+
+"oceanice_products")
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+;;
+
  "ecen")
 
     nth_max=$((npe_node_max / npe_node_ecen))

env/JET.env

@@ -190,6 +190,13 @@ elif [[ "${step}" = "atmos_products" ]]; then
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation
 
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
 elif [[ "${step}" = "ecen" ]]; then
 
     nth_max=$((npe_node_max / npe_node_ecen))

env/ORION.env

@@ -209,6 +209,13 @@ elif [[ "${step}" = "atmos_products" ]]; then
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation
 
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
 elif [[ "${step}" = "ecen" ]]; then
 
     nth_max=$((npe_node_max / npe_node_ecen))

env/S4.env

@@ -177,6 +177,13 @@ elif [[ "${step}" = "atmos_products" ]]; then
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation
 
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
 elif [[ "${step}" = "ecen" ]]; then
 
     nth_max=$((npe_node_max / npe_node_ecen))

env/WCOSS2.env

@@ -193,6 +193,13 @@ elif [[ "${step}" = "atmos_products" ]]; then
 
     export USE_CFP="YES"  # Use MPMD for downstream product generation
 
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    nth_max=$((npe_node_max / npe_node_oceanice_products))
+
+    export NTHREADS_OCNICEPOST=${nth_oceanice_products:-1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 -ppn ${npe_node_oceanice_products} --cpu-bind depth --depth ${NTHREADS_OCNICEPOST}"
+
 elif [[ "${step}" = "ecen" ]]; then
 
     nth_max=$((npe_node_max / npe_node_ecen))

jobs/JGLOBAL_ARCHIVE

@@ -14,16 +14,15 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS COM_ATMOS_BUFR COM_ATMO
   COM_ATMOS_TRACK COM_ATMOS_WMO \
   COM_CHEM_HISTORY COM_CHEM_ANALYSIS\
   COM_MED_RESTART \
-  COM_ICE_HISTORY COM_ICE_INPUT COM_ICE_RESTART \
+  COM_ICE_HISTORY COM_ICE_INPUT COM_ICE_RESTART COM_ICE_GRIB \
   COM_OBS COM_TOP \
-  COM_OCEAN_HISTORY COM_OCEAN_INPUT COM_OCEAN_RESTART COM_OCEAN_XSECT COM_OCEAN_2D COM_OCEAN_3D \
+  COM_OCEAN_HISTORY COM_OCEAN_INPUT COM_OCEAN_RESTART COM_OCEAN_GRIB COM_OCEAN_NETCDF \
   COM_OCEAN_ANALYSIS \
   COM_WAVE_GRID COM_WAVE_HISTORY COM_WAVE_STATION \
   COM_ATMOS_OZNMON COM_ATMOS_RADMON COM_ATMOS_MINMON COM_CONF
 
 for grid in "0p25" "0p50" "1p00"; do
   YMD=${PDY} HH=${cyc} GRID=${grid} generate_com -rx "COM_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"
-  YMD=${PDY} HH=${cyc} GRID=${grid} generate_com -rx "COM_OCEAN_GRIB_${grid}:COM_OCEAN_GRIB_GRID_TMPL"
 done
 
 ###############################################################

jobs/JGLOBAL_OCEANICE_PRODUCTS

@@ -0,0 +1,40 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "oceanice_products" -c "base oceanice_products"
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+# Construct COM variables from templates
+YMD="${PDY}" HH="${cyc}" generate_com -rx "COM_${COMPONENT^^}_HISTORY"
+YMD="${PDY}" HH="${cyc}" generate_com -rx "COM_${COMPONENT^^}_GRIB"
+YMD="${PDY}" HH="${cyc}" generate_com -rx "COM_${COMPONENT^^}_NETCDF"
+
+###############################################################
+# Run exglobal script
+"${HOMEgfs}/scripts/exglobal_oceanice_products.py"
+status=$?
+(( status != 0 )) && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]]; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ "${KEEPDATA:-NO}" == "NO" ]] && rm -rf "${DATA}"
+
+
+exit 0

jobs/rocoto/oceanice_products.sh

@@ -0,0 +1,37 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+## ocean ice products driver script
+## FHRLST : forecast hour list to post-process (e.g. f000, f000_f001_f002, ...)
+###############################################################
+
+# Source FV3GFS workflow modules
+. "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+if (( status != 0 )); then exit "${status}"; fi
+
+###############################################################
+# setup python path for workflow utilities and tasks
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
+export PYTHONPATH
+
+export job="oceanice_products"
+export jobid="${job}.$$"
+
+###############################################################
+# shellcheck disable=SC2153,SC2001
+IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's and convert to array
+
+#---------------------------------------------------------------
+# Execute the JJOB
+for fhr in "${fhrs[@]}"; do
+    export FORECAST_HOUR=$(( 10#${fhr} ))
+    "${HOMEgfs}/jobs/JGLOBAL_OCEANICE_PRODUCTS"
+    status=$?
+    if (( status != 0 )); then exit "${status}"; fi
+done
+
+exit 0