Merge remote-tracking branch 'upsteam/develop' into feature/rename_atm

* upsteam/develop:
  Archiving cleanup (NOAA-EMC#2621)
  Switch to Rocky 9 built external packages on Hercules (NOAA-EMC#2608)
  Add the capability to use slurm reservation nodes (NOAA-EMC#2627)
  Update forecast job to use COMIN/COMOUT (NOAA-EMC#2622)
  Update to add 1-deg global wave grid (NOAA-EMC#2619)
  Add C384mx025_3DVarAOWCDA yamls (NOAA-EMC#2625)
  Script to keep Jenkins Agent persistent from cron (NOAA-EMC#2634)

ci/cases/gfsv17/C384mx025_3DVarAOWCDA.yaml

@@ -0,0 +1,18 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: S2S
+  resdetatmos: 384
+  resdetocean: 0.25
+  nens: 0
+  gfs_cyc: 4
+  start: cold
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  idate: 2021063000
+  edate: 2021070306
+  icsdir: /scratch1/NCEPDEV/climate/Jessica.Meixner/cycling/IC_2021063000_V2
+  yaml: {{ HOMEgfs }}/ci/cases/gfsv17/ocnanal.yaml

ci/cases/gfsv17/ocnanal.yaml

@@ -0,0 +1,30 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+
+base:
+  DOIAU: "YES"
+  DO_JEDIATMVAR: "NO"
+  DO_JEDIATMENS: "NO"
+  DO_JEDIOCNVAR: "YES"
+  DO_JEDISNOWDA: "NO"
+  DO_MERGENSST: "NO"
+  DOHYBVAR: "NO"
+  DO_FIT2OBS: "YES"
+  DO_VERFOZN: "YES"
+  DO_VERFRAD: "YES"
+  DO_VRFY_OCEANDA: "NO"
+  FHMAX_GFS: 240
+
+ocnanal:
+  SOCA_INPUT_FIX_DIR: /scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/1440x1080x75/soca
+  CASE_ANL: 'C24'
+  SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
+  SOCA_NINNER: 100
+  SABER_BLOCKS_YAML: ''
+  NICAS_RESOL: 1
+  NICAS_GRID_SIZE: 15000
+
+prepoceanobs:
+  SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml 
+  OBSPREP_YAML: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obsprep/obsprep_config.yaml
+  DMPDIR: /scratch1/NCEPDEV/da/common/

ci/platforms/config.hera

@@ -5,3 +5,6 @@ export ICSDIR_ROOT=/scratch1/NCEPDEV/global/glopara/data/ICSDIR
 export HPC_ACCOUNT=nems
 export max_concurrent_cases=5
 export max_concurrent_pr=4
+
+export JENKINS_AGENT_LANUCH_DIR=/scratch1/NCEPDEV/global/Terry.McGuinness/Jenkins
+export JENKINS_WORK_DIR=/scratch1/NCEPDEV/global/Terry.McGuinness

ci/platforms/config.hercules

@@ -5,3 +5,6 @@ export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
 export HPC_ACCOUNT=nems
 export max_concurrent_cases=5
 export max_concurrent_pr=4
+
+export JENKINS_AGENT_LANUCH_DIR=/home/role-nems/GFS_CI_ROOT_JENKINS/AGENT_mterry
+export JENKINS_WORK_DIR=/home/role-nems/GFS_CI_ROOT_JENKINS

ci/platforms/config.orion

@@ -5,3 +5,6 @@ export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
 export HPC_ACCOUNT=nems
 export max_concurrent_cases=5
 export max_concurrent_pr=4
+
+export JENKINS_AGENT_LANUCH_DIR=/home/role-nems/GFS_CI_ROOT_JENKINS/AGENT_mterry
+export JENKINS_WORK_DIR=/home/role-nems/GFS_CI_ROOT_JENKINS

ci/scripts/utils/launch_java_agent.sh

@@ -0,0 +1,77 @@
+#!/bin/env bash
+set -e
+
+controller_url="https://jenkins.epic.oarcloud.noaa.gov"
+controller_user="terry.mcguinness"
+HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../../.." >/dev/null 2>&1 && pwd )"
+host=$(hostname)
+
+#########################################################################
+#  Set up runtime environment varibles for accounts on supproted machines
+#########################################################################
+
+source "${HOMEgfs}/ush/detect_machine.sh"
+case ${MACHINE_ID} in
+  hera | orion | hercules | wcoss2)
+    echo "Launch Jenkins Java Controler on ${MACHINE_ID}"
+    ;;
+  *)
+    echo "Unsupported platform. Exiting with error."
+    exit 1
+    ;;
+esac
+
+LOG=lanuched_agent-$(date +%Y%m%d%M).log
+rm -f "${LOG}"
+
+source "${HOMEgfs}/ush/module-setup.sh"
+module use "${HOMEgfs}/modulefiles"
+module load "module_gwsetup.${MACHINE_ID}"
+source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+
+JAVA_HOME="${JENKINS_AGENT_LANUCH_DIR}/JAVA/jdk-17.0.10"
+if [[ ! -d "${JAVA_HOME}" ]]; then
+  JAVA_HOME=/usr/lib/jvm/jre-17
+  if [[ ! -d "${JAVA_HOME}" ]]; then
+    echo "ERROR: JAVA_HOME not found. Exiting with error."
+    exit 1
+  fi
+fi
+
+JAVA="${JAVA_HOME}/bin/java"
+echo "JAVA VERSION: "
+${JAVA} -version
+
+export GH="${HOME}/bin/gh"
+command -v "${GH}"
+${GH} --version
+
+if [[ -d "${JENKINS_AGENT_LANUCH_DIR}" ]]; then
+  echo "Jenkins Agent Lanuch Directory: ${JENKINS_AGENT_LANUCH_DIR}"
+else
+  echo "ERROR: Jenkins Agent Lanuch Directory not found. Exiting with error."
+  exit 1
+fi
+cd "${JENKINS_AGENT_LANUCH_DIR}"
+
+if ! [[ -f agent.jar ]]; then
+  curl -sO "${controller_url}/jnlpJars/agent.jar"
+fi
+
+JENKINS_TOKEN=$(cat jenkins_token)
+
+# 
+offline=$(curl --silent -u "${controller_user}:${JENKINS_TOKEN}" "${controller_url}/computer/${MACHINE_ID^}-EMC/api/json?pretty=true" | grep '\"offline\"' | awk '{gsub(/,/,"");print $3}') || true
+echo "Jenkins Agent offline setting: ${offline}"
+
+if [[ "${offline}" == "true" ]]; then
+  echo "Jenkins Agent is offline. Lanuching Jenkins Agent on ${host}"
+  command="nohup ${JAVA} -jar agent.jar -jnlpUrl ${controller_url}/computer/${MACHINE_ID^}-EMC/jenkins-agent.jnlp  -secret @jenkins-secret-file -workDir ${JENKINS_WORK_DIR}"
+  echo -e "Lanuching Jenkins Agent on ${host} with the command:\n${command}" >& "${LOG}"
+  ${command} >> "${LOG}" 2>&1 &
+  nohup_PID=$!
+  echo "Java agent running on PID: ${nohup_PID}" >> "${LOG}" 2>&1
+  echo "Java agent running on PID: ${nohup_PID}"
+else
+  echo "Jenkins Agent is online (nothing done)"
+fi

jobs/JGFS_ATMOS_CYCLONE_GENESIS

@@ -3,6 +3,10 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis" -c "base genesis"
 
+# Hack to temporary skip this as the tracker has not been build
+#   on Hercules Rocky 9 yet
+# TODO: Remove this after tracker has been built for Rocky 9 #2639
+if [[ "${machine}" == 'HERCULES' ]]; then exit 0; fi
 
 ##############################################
 # Set variables used in the exglobal script

jobs/JGFS_ATMOS_CYCLONE_TRACKER

@@ -3,6 +3,10 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "tracker" -c "base tracker"
 
+# Hack to temporary skip this as the tracker has not been build
+#   on Hercules Rocky 9 yet
+# TODO: Remove this after tracker has been built for Rocky 9 #2639
+if [[ "${machine}" == 'HERCULES' ]]; then exit 0; fi
 
 export COMPONENT="atmos"
 

jobs/JGFS_ATMOS_FSU_GENESIS

@@ -3,6 +3,11 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis_fsu" -c "base genesis_fsu"
 
+# Hack to temporary skip this as the tracker has not been build
+#   on Hercules Rocky 9 yet
+# TODO: Remove this after tracker has been built for Rocky 9 #2639
+if [[ "${machine}" == 'HERCULES' ]]; then exit 0; fi
+
 export COMPONENT="atmos"
 
 

jobs/JGLOBAL_FORECAST

@@ -35,34 +35,51 @@ declare -rx gPDY="${GDATE:0:8}"
 declare -rx gcyc="${GDATE:8:2}"
 
 # Construct COM variables from templates (see config.com)
-YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \
-  COM_ICE_ANALYSIS COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_TOP COM_CONF
+YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+  COMIN_ATMOS_INPUT:COM_ATMOS_INPUT_TMPL \
+  COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+  COMOUT_CONF:COM_CONF_TMPL \
+  COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL \
+  COMOUT_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL \
+  COMOUT_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL
 
 RUN="${rCDUMP}" YMD="${gPDY}" HH="${gcyc}" declare_from_tmpl -rx \
-  COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
+  COMIN_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
 
 if [[ "${DO_WAVE}" == "YES" ]]; then
-  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_WAVE_RESTART COM_WAVE_PREP COM_WAVE_HISTORY
+  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+    COMIN_WAVE_PREP:COM_WAVE_PREP_TMPL \
+    COMOUT_WAVE_RESTART:COM_WAVE_RESTART_TMPL \
+    COMOUT_WAVE_HISTORY:COM_WAVE_HISTORY_TMPL
   RUN="${rCDUMP}" YMD="${gPDY}" HH="${gcyc}" declare_from_tmpl -rx \
-    COM_WAVE_RESTART_PREV:COM_WAVE_RESTART_TMPL
+    COMIN_WAVE_RESTART_PREV:COM_WAVE_RESTART_TMPL
 fi
 
 if [[ "${DO_OCN}" == "YES" ]]; then
-  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_MED_RESTART COM_OCEAN_RESTART COM_OCEAN_INPUT \
-    COM_OCEAN_HISTORY COM_OCEAN_ANALYSIS
+  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+    COMIN_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
+    COMIN_OCEAN_INPUT:COM_OCEAN_INPUT_TMPL \
+    COMOUT_MED_RESTART:COM_MED_RESTART_TMPL \
+    COMOUT_OCEAN_RESTART:COM_OCEAN_RESTART_TMPL \
+    COMOUT_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL
   RUN="${rCDUMP}" YMD="${gPDY}" HH="${gcyc}" declare_from_tmpl -rx \
-    COM_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL \
-    COM_MED_RESTART_PREV:COM_MED_RESTART_TMPL
+    COMIN_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL \
+    COMIN_MED_RESTART_PREV:COM_MED_RESTART_TMPL
 fi
 
 if [[ "${DO_ICE}" == "YES" ]]; then
-  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_ICE_HISTORY COM_ICE_INPUT COM_ICE_RESTART
+  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+    COMIN_ICE_INPUT:COM_ICE_INPUT_TMPL \
+    COMIN_ICE_ANALYSIS:COM_ICE_ANALYSIS_TMPL \
+    COMOUT_ICE_RESTART:COM_ICE_RESTART_TMPL \
+    COMOUT_ICE_HISTORY:COM_ICE_HISTORY_TMPL
   RUN="${rCDUMP}" YMD="${gPDY}" HH="${gcyc}" declare_from_tmpl -rx \
-    COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
+    COMIN_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 fi
 
 if [[ "${DO_AERO}" == "YES" ]]; then
-  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx COM_CHEM_HISTORY
+  YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+    COMOUT_CHEM_HISTORY:COM_CHEM_HISTORY_TMPL
 fi
 
 
@@ -79,7 +96,7 @@ if [[ "${RUN}" =~ "enkf" ]] && [[ "${SENDDBN:-}" == YES ]]; then
   for (( fhr = FHOUT; fhr <= FHMAX; fhr + FHOUT )); do
     if (( fhr % 3 == 0 )); then
       fhr3=$(printf %03i "${fhr}")
-      "${DBNROOT}/bin/dbn_alert" MODEL GFS_ENKF "${job}" "${COM_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${fhr3}.nc"
+      "${DBNROOT}/bin/dbn_alert" MODEL GFS_ENKF "${job}" "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${fhr3}.nc"
     fi
   done
 fi