Merge remote-tracking branch 'origin/develop' into feature/remove_fin…

…ddate

* origin/develop:
  Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307)
  Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286)

.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
 #------------------------------

Jenkinsfile

@@ -9,7 +9,7 @@ pipeline {
 
     options {
         skipDefaultCheckout()
-        buildDiscarder(logRotator(numToKeepStr: '2'))
+        parallelsAlwaysFailFast()
     }
 
     stages { // This initial stage is used to get the Machine name from the GitHub labels on the PR
@@ -45,14 +45,14 @@ pipeline {
                     properties([parameters([[$class: 'NodeParameterDefinition', allowedSlaves: ['built-in', 'Hera-EMC', 'Orion-EMC'], defaultSlaves: ['built-in'], name: '', nodeEligibility: [$class: 'AllNodeEligibility'], triggerIfResult: 'allCases']])])
                     HOME = "${WORKSPACE}/TESTDIR"
                     commonworkspace = "${WORKSPACE}"
-                    sh(script: "mkdir -p ${HOME}/RUNTESTS", returnStatus: true)
+                    sh(script: "mkdir -p ${HOME}/RUNTESTS")
                     pullRequest.addLabel("CI-${Machine}-Building")
                     if (pullRequest.labels.any { value -> value.matches("CI-${Machine}-Ready") }) {
                         pullRequest.removeLabel("CI-${Machine}-Ready")
+                    }
                 }
             }
         }
-    }
 
         stage('Build System') {
             matrix {
@@ -71,35 +71,41 @@ pipeline {
                         steps {
                             script {
                                 def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to build the system on per system basis under the common workspace HOME
-                                sh(script: "mkdir -p ${HOMEgfs}", returnStatus: true)
+                                sh(script: "mkdir -p ${HOMEgfs}")
                                 ws(HOMEgfs) {
                                     env.MACHINE_ID = machine // MACHINE_ID is used in the build scripts to determine the machine and is added to the shell environment
                                     if (fileExists("${HOMEgfs}/sorc/BUILT_semaphor")) { // if the system is already built, skip the build in the case of re-runs
                                         sh(script: "cat ${HOMEgfs}/sorc/BUILT_semaphor", returnStdout: true).trim() // TODO: and user configurable control to manage build semphore
-                                        ws(commonworkspace) { pullRequest.comment("Cloned PR already built (or build skipped) on ${machine} in directory ${HOMEgfs}") }
+                                        pullRequest.comment("Cloned PR already built (or build skipped) on ${machine} in directory ${HOMEgfs}<br>Still doing a checkout to get the latest changes")
+                                        sh(script: 'source workflow/gw_setup.sh; git pull --recurse-submodules')
+                                        dir('sorc') {
+                                            sh(script: './link_workflow.sh')
+                                        }
                                     } else {
                                         checkout scm
-                                        sh(script: 'source workflow/gw_setup.sh;which git;git --version;git submodule update --init --recursive', returnStatus: true)
+                                        sh(script: 'source workflow/gw_setup.sh;which git;git --version;git submodule update --init --recursive')
                                         def builds_file = readYaml file: 'ci/cases/yamls/build.yaml'
                                         def build_args_list = builds_file['builds']
                                         def build_args = build_args_list[system].join(' ').trim().replaceAll('null', '')
                                         dir("${HOMEgfs}/sorc") {
-                                            sh(script: "${build_args}", returnStatus: true)
-                                            sh(script: './link_workflow.sh', returnStatus: true)
-                                            sh(script: "echo ${HOMEgfs} > BUILT_semaphor", returnStatus: true)
+                                            sh(script: "${build_args}")
+                                            sh(script: './link_workflow.sh')
+                                            sh(script: "echo ${HOMEgfs} > BUILT_semaphor")
                                         }
                                     }
-                                    if (pullRequest.labels.any { value -> value.matches("CI-${Machine}-Building") }) {
-                                        pullRequest.removeLabel("CI-${Machine}-Building")
-                                }
-                                    pullRequest.addLabel("CI-${Machine}-Running")
-                            }
+                                    if (env.CHANGE_ID && system == 'gfs') {
+                                       if (pullRequest.labels.any { value -> value.matches("CI-${Machine}-Building") }) {
+                                           pullRequest.removeLabel("CI-${Machine}-Building")
+                                       }
+                                       pullRequest.addLabel("CI-${Machine}-Running")
+                                    }
+                               }
+                           }
                         }
                     }
                 }
             }
         }
-}
 
         stage('Run Tests') {
             matrix {
@@ -108,19 +114,19 @@ pipeline {
                     axis {
                         name 'Case'
                         // TODO add dynamic list of cases from env vars (needs addtional plugins)
-                        values 'C48_ATM', 'C48_S2SWA_gefs', 'C48_S2SW', 'C96_atm3DVar', 'C48mx500_3DVarAOWCDA', 'C96C48_hybatmDA', 'C96_atmsnowDA'
+                        values 'C48_ATM', 'C48_S2SWA_gefs', 'C48_S2SW', 'C96_atm3DVar', 'C96C48_hybatmDA', 'C96_atmsnowDA'  // 'C48mx500_3DVarAOWCDA'
                     }
                 }
                 stages {
                     stage('Create Experiment') {
                         steps {
                                 script {
-                                    sh(script: "sed -n '/{.*}/!p' ${HOME}/gfs/ci/cases/pr/${Case}.yaml > ${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp", returnStatus: true)
+                                    sh(script: "sed -n '/{.*}/!p' ${HOME}/gfs/ci/cases/pr/${Case}.yaml > ${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp")
                                     def yaml_case = readYaml file: "${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp"
                                     system = yaml_case.experiment.system
                                     def HOMEgfs = "${HOME}/${system}"   // local HOMEgfs is used to populate the XML on per system basis
                                     env.RUNTESTS = "${HOME}/RUNTESTS"
-                                    sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh create_experiment ${HOMEgfs}/ci/cases/pr/${Case}.yaml", returnStatus: true)
+                                    sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh create_experiment ${HOMEgfs}/ci/cases/pr/${Case}.yaml")
                                 }
                         }
                     }
@@ -130,16 +136,27 @@ pipeline {
                                 HOMEgfs = "${HOME}/gfs"  // common HOMEgfs is used to launch the scripts that run the experiments
                                 ws(HOMEgfs) {
                                     pslot = sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh get_pslot ${HOME}/RUNTESTS ${Case}", returnStdout: true).trim()
-                                    pullRequest.comment("**Running** experiment: ${Case} on ${Machine}<br>With the experiment in directory:<br>`${HOME}/RUNTESTS/${pslot}`")
-                                    try {
-                                        sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${HOME} ${pslot}", returnStatus: true)
-                                    } catch (Exception e) {
+                                    // pullRequest.comment("**Running** experiment: ${Case} on ${Machine}<br>With the experiment in directory:<br>`${HOME}/RUNTESTS/${pslot}`")
+                                    err =  sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${HOME} ${pslot}")
+                                    if (err != 0) {
                                         pullRequest.comment("**FAILURE** running experiment: ${Case} on ${Machine}")
+                                        sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cancel_all_batch_jobs ${HOME}/RUNTESTS")
+                                        ws(HOME) {
+                                            if (fileExists('RUNTESTS/error.logs')) {
+                                                def fileContent = readFile 'RUNTESTS/error.logs'
+                                                def lines = fileContent.readLines()
+                                                for (line in lines) {
+                                                    echo "archiving: ${line}"
+                                                    archiveArtifacts artifacts: "${line}", fingerprint: true
+                                                }   
+                                            }
+                                        }
                                         error("Failed to run experiments ${Case} on ${Machine}")
                                     }
-                                    pullRequest.comment("**SUCCESS** running experiment: ${Case} on ${Machine}")
+                                   // pullRequest.comment("**SUCCESS** running experiment: ${Case} on ${Machine}")
                                 }
                             }
+
                         }
                     }
                 }
@@ -175,14 +192,6 @@ pipeline {
                     def timestamp = new Date().format('MM dd HH:mm:ss', TimeZone.getTimeZone('America/New_York'))
                     pullRequest.comment("**CI FAILED** ${Machine} at ${timestamp}<br>Built and ran in directory `${HOME}`")
                 }
-                if (fileExists('${HOME}/RUNTESTS/ci.log')) {
-                    def fileContent = readFile '${HOME}/RUNTESTS/ci.log'
-                    fileContent.eachLine { line ->
-                        if (line.contains('.log')) {
-                            archiveArtifacts artifacts: "${line}", fingerprint: true
-                        }
-                    }
-                }
             }
         }
     }

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
 
 ###############################################################