Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_1219

.gitignore

@@ -30,7 +30,6 @@ fix/chem
 fix/cice
 fix/cpl
 fix/datm
-fix/gdas
 fix/gldas
 fix/gsi
 fix/lut
@@ -47,7 +46,7 @@ fix/wafs
 #--------------------------
 parm/config/config.base
 parm/gldas
-parm/mon
+parm/monitor
 parm/post/AEROSOL_LUTS.dat
 parm/post/nam_micro_lookup.dat
 parm/post/optics_luts_DUST.dat

ci/platforms/config.orion

@@ -2,7 +2,7 @@
 
 export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT
 export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
-export STMP="/work/noaa/stmp/${USER}"
+export STMP="/work2/noaa/stmp/${USER}"
 export SLURM_ACCOUNT=nems
 export max_concurrent_cases=5
 export max_concurrent_pr=4

ci/scripts/check_ci.sh

@@ -33,6 +33,7 @@ case ${MACHINE_ID} in
 esac
 set +x
 source "${ROOT_DIR}/ush/module-setup.sh"
+source "${ROOT_DIR}/ci/scripts/utils/ci_utils.sh"
 module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
 module list
@@ -86,7 +87,7 @@ for pr in ${pr_list}; do
   if [[ -z $(ls -A "${pr_dir}/RUNTESTS/EXPDIR") ]] ; then
     "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Running" --add-label "CI-${MACHINE_ID^}-Passed"
     sed -i "1 i\`\`\`" "${output_ci}"
-    sed -i "1 i\All CI Test Cases Passed:" "${output_ci}"
+    sed -i "1 i\All CI Test Cases Passed on ${MACHINE_ID^}:" "${output_ci}"
     "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${output_ci}"
     "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
     # Check to see if this PR that was opened by the weekly tests and if so close it if it passed on all platforms
@@ -131,8 +132,8 @@ for pr in ${pr_list}; do
       "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Running" --add-label "CI-${MACHINE_ID^}-Failed"
       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 "Experiment ${pslot} Terminated: *** FAILED ***"
-       echo "Experiment ${pslot} Terminated with ${num_failed} tasks failed at $(date)" || true
+       echo "Experiment ${pslot}  *** FAILED *** on ${MACHINE_ID^}"
+       echo "Experiment ${pslot}  with ${num_failed} tasks failed at $(date +'%D %r')" || true
        echo "Error logs:"
        echo "${error_logs}"
       } >> "${output_ci}"
@@ -141,7 +142,7 @@ for pr in ${pr_list}; do
       "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
       for kill_cases in "${pr_dir}/RUNTESTS/"*; do
          pslot=$(basename "${kill_cases}")
-         sacct --format=jobid,jobname%35,WorkDir%100,stat | grep "${pslot}" | grep "PR\/${pr}\/RUNTESTS" |  awk '{print $1}' | xargs scancel || true
+         cancel_slurm_jobs "${pslot}"
       done
       break
     fi
@@ -151,9 +152,9 @@ for pr in ${pr_list}; do
       rm -Rf "${pr_dir}/RUNTESTS/COMROT/${pslot}"
       rm -f "${output_ci_single}"
       # echo "\`\`\`" > "${output_ci_single}"
-      DATE=$(date)
-      echo "Experiment ${pslot} **SUCCESS** ${DATE}" >> "${output_ci_single}"
-      echo "Experiment ${pslot} **SUCCESS** at ${DATE}" >> "${output_ci}"
+      DATE=$(date +'%D %r')
+      echo "Experiment ${pslot} **SUCCESS** on ${MACHINE_ID^} at ${DATE}" >> "${output_ci_single}"
+      echo "Experiment ${pslot} *** SUCCESS *** at ${DATE}" >> "${output_ci}"
       "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${output_ci_single}"
 
     fi

ci/scripts/clone-build_ci.sh

@@ -72,16 +72,17 @@ cd sorc || exit 1
 set +e
 ./checkout.sh -c -g -u >> log.checkout 2>&1
 checkout_status=$?
+DATE=$(date +'%D %r')
 if [[ ${checkout_status} != 0 ]]; then
   {
     echo "Checkout: *** FAILED ***"
-    echo "Checkout: Failed at $(date)" || true
+    echo "Checkout: Failed at ${DATE}"
     echo "Checkout: see output at ${PWD}/log.checkout"
   } >> "${outfile}"
   exit "${checkout_status}"
 else
   {
-    echo "Checkout: Completed at $(date)" || true
+    echo "Checkout: Completed at ${DATE}"
   } >> "${outfile}"
 fi
 
@@ -92,25 +93,30 @@ rm -rf log.build
 ./build_all.sh  >> log.build 2>&1
 build_status=$?
 
+DATE=$(date +'%D %r')
 if [[ ${build_status} != 0 ]]; then
   {
     echo "Build: *** FAILED ***"
-    echo "Build: Failed at $(date)" || true
-    echo "Build: see output at ${PWD}/log.build"
+    echo "Build: Failed at ${DATE}"
+    cat "${PWD}/log.build"
   } >> "${outfile}"
   exit "${build_status}"
 else
   {
-    echo "Build: Completed at $(date)" || true
+    echo "Build: Completed at ${DATE}"
   } >> "${outfile}"
 fi
 
-./link_workflow.sh
+LINK_LOGFILE_PATH=link_workflow.log
+rm -f "${LINK_LOGFILE_PATH}"
+./link_workflow.sh >> "${LINK_LOGFILE_PATH}" 2>&1
 link_status=$?
 if [[ ${link_status} != 0 ]]; then
+  DATE=$(date +'%D %r')
   {
     echo "Link: *** FAILED ***"
-    echo "Link: Failed at $(date)" || true
+    echo "Link: Failed at ${DATE}"
+    cat "${LINK_LOGFILE_PATH}"
   } >> "${outfile}"
   exit "${link_status}"
 fi

ci/scripts/driver.sh

@@ -25,7 +25,7 @@ export REPO_URL=${REPO_URL:-"https://github.com/NOAA-EMC/global-workflow.git"}
 ################################################################
 ROOT_DIR="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
 scriptname=$(basename "${BASH_SOURCE[0]}")
-echo "Begin ${scriptname} at $(date -u)" || true
+echo "Begin ${scriptname} at $(date  +'%D %r')" || true
 export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
 
 #########################################################################
@@ -48,6 +48,7 @@ esac
 # setup runtime env for correct python install and git
 ######################################################
 set +x
+source "${ROOT_DIR}/ci/scripts/utils/ci_utils.sh"
 source "${ROOT_DIR}/ush/module-setup.sh"
 module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
@@ -68,24 +69,57 @@ pr_list=$(${GH} pr list --repo "${REPO_URL}" --label "CI-${MACHINE_ID^}-Ready" -
 for pr in ${pr_list}; do
   pr_dir="${GFS_CI_ROOT}/PR/${pr}"
   db_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --add_pr "${pr}" --dbfile "${pr_list_dbfile}")
-  pr_id=0
+  output_ci_single="${GFS_CI_ROOT}/PR/${pr}/output_single.log"
   #############################################################
   # Check if a Ready labeled PR has changed back from once set
-  # and in that case remove all previous jobs in scheduler and
-  # and remove PR from filesystem to start clean
+  # and in that case completely kill the previose driver.sh cron
+  # job and all its decedands as well as  removing all previous
+  # jobs in scheduler and associated files in the PR
   #############################################################
   if [[ "${db_list}" == *"already is in list"* ]]; then
-    pr_id=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display "${pr}" | awk '{print $4}') || true
-    pr_id=$((pr_id+1))
-    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Ready "${pr_id}"
-    for cases in "${pr_dir}/RUNTESTS/"*; do
-      if [[ -z "${cases+x}" ]]; then
-         break
+    # Get the the PID and HOST of the driver.sh cron job
+    # that is stored int he CI database for this PR
+    driver_ID=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display "${pr}" | awk '{print $4}') || true
+    driver_PID=$(echo "${driver_ID}" | cut -d":" -f1) || true
+    driver_HOST=$(echo "${driver_ID}" | cut -d":" -f2) || true
+    host_name=$(hostname -s)
+    rm -f "${output_ci_single}"
+    {
+      echo "CI Update on ${MACHINE_ID^} at $(date +'%D %r')" || true
+      echo "================================================="
+      echo "PR:${pr} Reset to ${MACHINE_ID^}-Ready by user and is now restarting CI tests" || true
+    } >> "${output_ci_single}"
+    if [[ "${driver_PID}" -ne 0 ]]; then
+      echo "Driver PID: ${driver_PID} no longer running this build having it killed"
+      if [[ "${driver_HOST}" == "${host_name}"  ]]; then
+        # shellcheck disable=SC2312
+        pstree -A -p "${driver_PID}" | grep -Pow "(?<=\()[0-9]+(?=\))" | xargs kill
+      else
+        # shellcheck disable=SC2312
+        ssh "${driver_HOST}" 'pstree -A -p "${driver_PID}" | grep -Eow "[0-9]+" | xargs kill'
       fi
-      pslot=$(basename "${cases}")
-      sacct --format=jobid,jobname%35,WorkDir%100,stat | grep "${pslot}" | grep "PR\/${pr}\/RUNTESTS" |  awk '{print $1}' | xargs scancel || true
-    done
-    rm -Rf "${pr_dir}"
+      {
+        echo "Driver PID: Requested termination of ${driver_PID} and children on ${driver_HOST}"
+        echo "Driver PID: has restarted as $$ on ${host_name}"
+      } >> "${output_ci_single}"
+    fi
+
+    experiments=$(find "${pr_dir}/RUNTESTS/EXPDIR" -mindepth 1 -maxdepth 1 -type d) || true
+    if [[ -z "${experiments}" ]]; then
+       echo "No current experiments to cancel in PR: ${pr} on ${MACHINE_ID^}" >> "${output_ci_single}"
+    else
+      for case in ${experiments}; do
+        case_name=$(basename "${case}")
+        cancel_slurm_jobs "${case_name}"
+        {
+          echo "Canceled all jobs for experiment ${case_name} in PR:${pr} on ${MACHINE_ID^}"
+        } >> "${output_ci_single}"
+      done
+    fi
+    sed -i "1 i\`\`\`" "${output_ci_single}"
+    "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${output_ci_single}"
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --add_pr "${pr}" --dbfile "${pr_list_dbfile}"
   fi
 done
 
@@ -110,34 +144,44 @@ for pr in ${pr_list}; do
   if [[ -z "${pr_building+x}" ]]; then
       continue
   fi
-  "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Ready" --add-label "CI-${MACHINE_ID^}-Building"
-  "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Building
-  echo "Processing Pull Request #${pr}"
+  id=$("${GH}" pr view "${pr}" --repo "${REPO_URL}" --json id --jq '.id')
   pr_dir="${GFS_CI_ROOT}/PR/${pr}"
+  output_ci="${pr_dir}/output_ci_${id}"
+  output_ci_single="${GFS_CI_ROOT}/PR/${pr}/output_single.log"
+  driver_build_PID=$$
+  driver_build_HOST=$(hostname -s)
+  "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Ready" --add-label "CI-${MACHINE_ID^}-Building"
+  "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Building "${driver_build_PID}:${driver_build_HOST}"
   rm -Rf "${pr_dir}"
   mkdir -p "${pr_dir}"
-  # call clone-build_ci to clone and build PR
-  id=$("${GH}" pr view "${pr}" --repo "${REPO_URL}" --json id --jq '.id')
+  {
+    echo "CI Update on ${MACHINE_ID^} at $(date +'%D %r')" || true
+    echo "============================================"
+    echo "Cloning and Building global-workflow PR: ${pr}"
+    echo "with PID: ${driver_build_PID} on host: ${driver_build_HOST}"
+    echo ""
+  } >> "${output_ci_single}"
+  sed -i "1 i\`\`\`" "${output_ci_single}"
+  "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${output_ci_single}"
   set +e
-  output_ci="${pr_dir}/output_build_${id}"
-  rm -f "${output_ci}"
   "${ROOT_DIR}/ci/scripts/clone-build_ci.sh" -p "${pr}" -d "${pr_dir}" -o "${output_ci}"
-  #echo "SKIPPING: ${ROOT_DIR}/ci/scripts/clone-build_ci.sh"
   ci_status=$?
   ##################################################################
   # Checking for special case when Ready label was updated
-  # that cause a running driver exit fail because was currently
-  # building so we force and exit 0 instead to does not get relabled
+  # but a race condtion caused the clone-build_ci.sh to start
+  # and this instance fails before it was killed.  In th case we
+  # we need to exit this instance of the driver script
   #################################################################
   if [[ ${ci_status} -ne 0 ]]; then
-     pr_id_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}') || true
-     if [[ "${pr_id}" -ne "${pr_id_check}" ]]; then
+     build_PID_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}' | cut -d":" -f1) || true
+     if [[ "${build_PID_check}" -ne "$$" ]]; then
+        echo "Driver build PID: ${build_PID_check} no longer running this build ... exiting"
         exit 0
      fi
   fi
   set -e
   if [[ ${ci_status} -eq 0 ]]; then
-    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Built
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Built "0:0"
     #setup space to put an experiment
     # export RUNTESTS for yaml case files to pickup
     export RUNTESTS="${pr_dir}/RUNTESTS"
@@ -159,7 +203,7 @@ for pr in ${pr_list}; do
       set +e
       export LOGFILE_PATH="${HOMEgfs}/ci/scripts/create_experiment.log"
       rm -f "${LOGFILE_PATH}"
-      "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml" 2>&1 "${LOGFILE_PATH}"
+      "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml"  > "${LOGFILE_PATH}" 2>&1
       ci_status=$?
       set -e
       if [[ ${ci_status} -eq 0 ]]; then
@@ -174,7 +218,7 @@ for pr in ${pr_list}; do
         } >> "${output_ci}"
       else
         {
-          echo "*** Failed *** to create experiment: ${pslot}"
+          echo "*** Failed *** to create experiment: ${pslot} on ${MACHINE_ID^}"
           echo ""
           cat "${LOGFILE_PATH}"
         } >> "${output_ci}"
@@ -186,7 +230,7 @@ for pr in ${pr_list}; do
     done
 
     "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Building" --add-label "CI-${MACHINE_ID^}-Running"
-    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Running
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Running "0:0"
     "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${output_ci}"
 
   else

ci/scripts/utils/ci_utils.sh

@@ -0,0 +1,24 @@
+#!/bin/env bash
+
+function cancel_slurm_jobs() {
+
+  # Usage: cancel_slurm_jobs <substring>
+  # Example: cancel_slurm_jobs "C48_ATM_3c4e7f74"
+  #
+  # Cancel all Slurm jobs that have the given substring in their name
+  # So like in the example all jobs with "C48_ATM_3c4e7f74"
+  # in their name will be canceled
+
+  local substring=$1
+  local job_ids
+  job_ids=$(squeue -u "${USER}" -h -o "%i")
+
+  for job_id in ${job_ids}; do
+    job_name=$(sacct -j "${job_id}" --format=JobName%100 | head -3 | tail -1 | sed -r 's/\s+//g') || true
+    if [[ "${job_name}" =~ ${substring} ]]; then
+      echo "Canceling Slurm Job ${job_name} with: scancel ${job_id}"
+      scancel "${job_id}"
+      continue
+    fi
+  done
+}