Merge branch 'develop' into feature/com_reorg

WalterKolczynski-NOAA · Apr 23, 2023 · 5c70fba · 5c70fba
2 parents df77536 + f159d39
commit 5c70fba
Show file tree

Hide file tree

Showing 64 changed files with 1,314 additions and 852 deletions.
diff --git a/.github/ISSUE_TEMPLATE/fix_file.md b/.github/ISSUE_TEMPLATE/fix_file.md
@@ -0,0 +1,24 @@
+---
+name: Fix File Update
+about: Use this template for adding, updating, or removing fix files from global dataset
+title:
+labels: Fix Files
+assignees:
+  - KateFriedman-NOAA
+  - WalterKolczynski-NOAA
+
+---
+
+**Description**
+<!-- Provide a consise description of the fix file update being requested. -->
+<!-- State if this is adding, updating, and/or removing fix files from dataset. -->
+<!-- Include related issues in component repositories. -->
+<!-- Are there related workflow or component changes to use the affected fix files? -->
+<!-- Provide pickup locations for new/altered fix files or list files to be removed. -->
+
+**Tasks**
+<!-- Update task list as needed for request. -->
+- [ ] Discuss needs with global-workflow developer assigned to request.
+- [ ] Add/update/remove fix file(s) in fix sets on supported platforms (global-workflow assignee task).
+- [ ] Update "Fix File Management" spreadsheet (https://docs.google.com/spreadsheets/d/1BeIvcz6TO3If4YCqkUK-oz_kGS9q2wTjwLS-BBemSEY/edit?usp=sharing).
+- [ ] Make related workflow/component updates.
diff --git a/ci/cases/C96C48_hybatmDA.yaml b/ci/cases/C96C48_hybatmDA.yaml
@@ -0,0 +1,15 @@
+experiment:
+  mode: cycled
+
+arguments:
+  app: ATM
+  resdet: 96
+  resens: 48
+  comrot: ${RUNTESTS}/${pslot}/COMROT
+  expdir: ${RUNTESTS}/${pslot}/EXPDIR
+  icsdir: ${ICSDIR_ROOT}/C96C48
+  idate: 2021122018
+  edate: 2021122200
+  nens: 2
+  gfs_cyc: 1
+  start: cold
diff --git a/ci/cases/C96_atm3DVar.yaml b/ci/cases/C96_atm3DVar.yaml
@@ -0,0 +1,14 @@
+experiment:
+  mode: cycled
+
+arguments:
+  app: ATM
+  resdet: 96
+  comrot: ${RUNTESTS}/${pslot}/COMROT
+  expdir: ${RUNTESTS}/${pslot}/EXPDIR
+  icsdir: ${ICSDIR_ROOT}/C96C48
+  idate: 2021122018
+  edate: 2021122100
+  nens: 0
+  gfs_cyc: 1
+  start: cold
diff --git a/ci/experiments/C96C48_hybatmDA.yaml b/ci/experiments/C96C48_hybatmDA.yaml
diff --git a/ci/experiments/C96C48_hybatmDA_also.yaml b/ci/experiments/C96C48_hybatmDA_also.yaml
diff --git a/ci/environments/hera.sh → ci/platforms/hera.sh b/ci/environments/hera.sh → ci/platforms/hera.sh
@@ -1,10 +1,7 @@
 #!/usr/bin/bash
 export GFS_CI_ROOT=/scratch1/NCEPDEV/global/Terry.McGuinness/GFS_CI_ROOT
-export GFS_MODULE_USE="${GFS_CI_ROOT}/global-workflow/modulefiles"
 export SLURM_ACCOUNT=fv3-cpu
 export SALLOC_ACCOUNT="${SLURM_ACCOUNT}"
 export SBATCH_ACCOUNT="${SLURM_ACCOUNT}"
 export SLURM_QOS=debug
-export repo_url="https://github.com/NOAA-EMC/global-workflow.git"
-#export repo_url="https://github.com/TerrenceMcGuinness-NOAA/global-workflow.git"
 export ICSDIR_ROOT="/scratch1/NCEPDEV/global/glopara/data/ICSDIR"
diff --git a/ci/environments/orion.sh → ci/platforms/orion.sh b/ci/environments/orion.sh → ci/platforms/orion.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export GFS_CI_ROOT="TDB" #TODO
-export GFS_MODULE_USE="${GFS_CI_ROOT}/global-workflow/modulefiles"
+export GFS_CI_ROOT=/work2/noaa/global/mterry/GFS_CI_ROOT
+export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
 export SLURM_ACCOUNT=fv3-cpu
 export SALLOC_ACCOUNT=${SLURM_ACCOUNT}
 export SBATCH_ACCOUNT=${SLURM_ACCOUNT}

diff --git a/ci/scripts/check_ci.sh b/ci/scripts/check_ci.sh
@@ -0,0 +1,115 @@
+#!/bin/bash
+set -eux
+#####################################################################################
+#
+# Script description: BASH script for checking for cases in a given PR and 
+#                     running rocotostat on each to determine if the experiment has
+#                     succeeded or faild.  This script is intended
+#                     to run from within a cron job in the CI Managers account
+# Abstract TODO
+#####################################################################################
+
+HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
+scriptname=$(basename "${BASH_SOURCE[0]}")
+echo "Begin ${scriptname} at $(date -u)" || true
+export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
+
+GH=${HOME}/bin/gh
+REPO_URL=${REPO_URL:-"https://github.com/NOAA-EMC/global-workflow.git"}
+
+#########################################################################
+#  Set up runtime environment varibles for accounts on supproted machines
+#########################################################################
+
+source "${HOMEgfs}/ush/detect_machine.sh"
+case ${MACHINE_ID} in
+  hera | orion)
+   echo "Running Automated Testing on ${MACHINE_ID}"
+   source "${HOMEgfs}/ci/platforms/${MACHINE_ID}.sh"
+   ;;
+ *)
+   echo "Unsupported platform. Exiting with error."
+   exit 1
+   ;;
+esac
+set +x
+source "${HOMEgfs}/ush/module-setup.sh"
+module use "${HOMEgfs}/modulefiles"
+module load "module_gwsetup.${MACHINE_ID}"
+module list
+set -x
+rocotostat=$(which rocotostat)
+if [[ -z ${rocotostat+x} ]]; then
+  echo "rocotostat not found on system"
+  exit 1
+else
+  echo "rocotostat being used from ${rocotostat}"
+fi
+
+pr_list_file="open_pr_list"
+
+if [[ -s "${GFS_CI_ROOT}/${pr_list_file}" ]]; then
+  pr_list=$(cat "${GFS_CI_ROOT}/${pr_list_file}")
+else
+  echo "no PRs to process .. exit"
+  exit 0
+fi
+
+#############################################################
+# Loop throu all PRs in PR List and look for expirments in
+# the RUNTESTS dir and for each one run runcotorun on them
+#############################################################
+
+for pr in ${pr_list}; do
+  id=$("${GH}" pr view "${pr}" --repo "${REPO_URL}" --json id --jq '.id')
+  echo "Processing Pull Request #${pr} and looking for cases"
+  pr_dir="${GFS_CI_ROOT}/PR/${pr}"
+
+  # If there is no RUNTESTS dir for this PR then cases have not been made yet
+  if [[ ! -d "${pr_dir}/RUNTESTS" ]]; then
+     continue
+  fi
+  num_cases=$(find "${pr_dir}/RUNTESTS" -mindepth 1 -maxdepth 1 -type d | wc -l) || true
+
+  #Check for PR success  when ${pr_dir}/RUNTESTS is void of subfolders
+  # since all successfull ones where previously removed
+  if [[ "${num_cases}" -eq 0 ]] && [[ -d "${pr_dir}/RUNTESTS" ]]; then
+    "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Running" --add-label "CI-${MACHINE_ID^}-Passed"
+    "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
+    sed -i "/${pr}/d" "${GFS_CI_ROOT}/${pr_list_file}"
+    # Completely remove the PR and its cloned repo on sucess of all cases
+    rm -Rf "${pr_dir}" 
+    continue 
+  fi
+
+  for cases in "${pr_dir}/RUNTESTS/"*; do
+    pslot=$(basename "${cases}")
+    xml="${pr_dir}/RUNTESTS/${pslot}/EXPDIR/${pslot}/${pslot}.xml"
+    db="${pr_dir}/RUNTESTS/${pslot}/EXPDIR/${pslot}/${pslot}.db"
+    rocoto_stat_output=$("${rocotostat}" -w "${xml}" -d "${db}" -s | grep -v CYCLE) || true
+    num_cycles=$(echo "${rocoto_stat_output}" | wc -l) || true
+    num_done=$(echo "${rocoto_stat_output}" | grep -c Done) || true
+    num_succeeded=$("${rocotostat}" -w "${xml}" -d "${db}" -a | grep -c SUCCEEDED) || true
+    echo "${pslot} Total Cycles: ${num_cycles} number done: ${num_done}" || true
+    num_failed=$("${rocotostat}" -w "${xml}" -d "${db}" -a | grep -c -E 'FAIL|DEAD') || true
+    if [[ ${num_failed} -ne 0 ]]; then
+      {
+        echo "Experiment ${pslot} Terminated: *FAILED*"
+        echo "Experiment ${pslot} Terminated with ${num_failed} tasks failed at $(date)" || true
+      } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
+      "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Running" --add-label "CI-${MACHINE_ID^}-Failed"
+      "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
+      sed -i "/${pr}/d" "${GFS_CI_ROOT}/${pr_list_file}"
+    fi
+    if [[ "${num_done}" -eq  "${num_cycles}" ]]; then
+      {
+        echo "Experiment ${pslot} completed: *SUCCESS*"
+        echo "Experiment ${pslot} Completed at $(date)" || true
+        echo -n "with ${num_succeeded} successfully completed jobs" || true
+      } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
+      "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
+      #Remove Experment cases that completed successfully
+      rm -Rf "${pr_dir}/RUNTESTS/${pslot}"
+    fi
+  done
+done
diff --git a/ci/scripts/clone-build_ci.sh b/ci/scripts/clone-build_ci.sh
@@ -1,11 +1,6 @@
 #!/bin/bash
 set -eux
 
-#################################################################
-# TODO using static build for GitHub CLI until fixed in HPC-Stack
-#################################################################
-GH=/home/Terry.McGuinness/bin/gh
-repo_url=${repo_url:-"https://github.com/global-workflow.git"}
 #####################################################################
 #  Usage and arguments for specfifying cloned directgory
 #####################################################################
@@ -45,25 +40,14 @@ while getopts "p:d:o:h" opt; do
   esac
 done
 
-####################################################################
-# start output file
-{
- echo "Automated global-workflow Testing Results:"
- echo "Machine: ${CI_HOST}"
- echo '```'
- echo "Start: $(date) on $(hostname)" || true
- echo "---------------------------------------------------"
-}  >> "${outfile}"
-######################################################################
-
-cd "${repodir}"
+cd "${repodir}" || exit 1
 # clone copy of repo
 if [[ -d global-workflow ]]; then
   rm -Rf global-workflow
 fi
 
-git clone "${repo_url}"
-cd global-workflow
+git clone "${REPO_URL}"
+cd global-workflow || exit 1
 
 pr_state=$(gh pr view "${PR}" --json state --jq '.state')
 if [[ "${pr_state}" != "OPEN" ]]; then
@@ -73,34 +57,63 @@ if [[ "${pr_state}" != "OPEN" ]]; then
 fi  
 
 # checkout pull request
-"${GH}" pr checkout "${PR}" --repo "${repo_url}"
+"${GH}" pr checkout "${PR}" --repo "${REPO_URL}"
+HOMEgfs="${PWD}"
+source "${HOMEgfs}/ush/detect_machine.sh"
+
+####################################################################
+# start output file
+{
+ echo "Automated global-workflow Testing Results:"
+ echo '```'
+ echo "Machine: ${MACHINE_ID^}"
+ echo "Start: $(date) on $(hostname)" || true
+ echo "---------------------------------------------------"
+}  >> "${outfile}"
+######################################################################
 
 # get commit hash
 commit=$(git log --pretty=format:'%h' -n 1)
 echo "${commit}" > "../commit"
 
-# run build script
-cd sorc
+# run checkout script
+cd sorc || exit 1
+set +e
+./checkout.sh -c -g -u &>> log.checkout
+checkout_status=$?
+if [[ ${checkout_status} != 0 ]]; then
+  {
+    echo "Checkout:                      *FAILED*"
+    echo "Checkout: Failed at $(date)" || true
+    echo "Checkout: see output at ${PWD}/log.checkout"
+  } >> "${outfile}"
+  exit "${checkout_status}"
+else
+  {
+    echo "Checkout:                      *SUCCESS*"
+    echo "Checkout: Completed at $(date)" || true
+  } >> "${outfile}"
+fi
+
+# build full cycle
+source "${HOMEgfs}/ush/module-setup.sh"
 export BUILD_JOBS=8
 rm -rf log.build
-./checkout.sh -g -c
-# build full cycle
-./build_all.sh -g &>> log.build
-
-# Validations
+./build_all.sh  &>> log.build
 build_status=$?
-if [[ ${build_status} -eq 0 ]]; then
-{
-  echo "Build:                                 *SUCCESS*"
-  echo "Build: Completed at $(date)" || true
-}  >> "${outfile}"
+
+if [[ ${build_status} != 0 ]]; then
+  {
+    echo "Build:                         *FAILED*"
+    echo "Build: Failed at $(date)" || true
+    echo "Build: see output at ${PWD}/log.build"
+  } >> "${outfile}"
+  exit "${build_status}"
 else
-{
-  echo "Build:                                  *FAILED*"
-  echo "Build: Failed at $(date)" || true
-  echo "Build: see output at ${PWD}/log.build"
-}
-  echo '```' >> "${outfile}"
+  {
+    echo "Build:                         *SUCCESS*"
+    echo "Build: Completed at $(date)" || true
+  } >> "${outfile}"
 fi
 
 ./link_workflow.sh