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Merge branch 'NOAA-EMC:develop' into develop
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jderrico-noaa authored Feb 20, 2024
2 parents 3e6b1e2 + a23b7f2 commit e2d88dd
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6 changes: 4 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ fix/gsi
fix/lut
fix/mom6
fix/orog
fix/reg2grb2
fix/sfc_climo
fix/ugwd
fix/verif
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -147,6 +148,7 @@ sorc/tocsbufr.fd
sorc/upp.fd
sorc/vint.fd
sorc/webtitle.fd
sorc/ocnicepost.fd

# Ignore scripts from externals
#------------------------------
Expand Down
198 changes: 198 additions & 0 deletions Jenkinsfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,198 @@
def Machine = 'none'
def machine = 'none'
def HOME = 'none'
def localworkspace = 'none'
def commonworkspace = 'none'

pipeline {
agent { label 'built-in' }

options {
skipDefaultCheckout()
parallelsAlwaysFailFast()
}

stages { // This initial stage is used to get the Machine name from the GitHub labels on the PR
// which is used to designate the Nodes in the Jenkins Controler by the agent label
// Each Jenknis Node is connected to said machine via an JAVA agent via an ssh tunnel

stage('Get Machine') {
agent { label 'built-in' }
steps {
script {
localworkspace = env.WORKSPACE
machine = 'none'
for (label in pullRequest.labels) {
echo "Label: ${label}"
if ((label.matches('CI-Hera-Ready'))) {
machine = 'hera'
} else if ((label.matches('CI-Orion-Ready'))) {
machine = 'orion'
} else if ((label.matches('CI-Hercules-Ready'))) {
machine = 'hercules'
}
} // createing a second machine varible with first letter capital
// because the first letter of the machine name is captitalized in the GitHub labels
Machine = machine[0].toUpperCase() + machine.substring(1)
}
}
}

stage('Get Common Workspace') {
agent { label "${machine}-emc" }
steps {
script {
properties([parameters([[$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 ${HOME}/RUNTESTS")
pullRequest.addLabel("CI-${Machine}-Building")
if (pullRequest.labels.any { value -> value.matches("CI-${Machine}-Ready") }) {
pullRequest.removeLabel("CI-${Machine}-Ready")
}
}
}
}

stage('Build System') {
matrix {
agent { label "${machine}-emc" }
//options {
// throttle(['global_matrix_build'])
//}
axes {
axis {
name 'system'
values 'gfs', 'gefs'
}
}
stages {
stage('build system') {
steps {
script {
def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to build the system on per system basis under the common workspace HOME
sh(script: "mkdir -p ${HOMEgfs}")
ws(HOMEgfs) {
env.MACHINE_ID = machine // MACHINE_ID is used in the build scripts to determine the machine and is added to the shell environment
if (fileExists("${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
pullRequest.comment("Cloned PR already built (or build skipped) on ${machine} in directory ${HOMEgfs}<br>Still doing a checkout to get the latest changes")
sh(script: 'source workflow/gw_setup.sh; git pull --recurse-submodules')
dir('sorc') {
sh(script: './link_workflow.sh')
}
} else {
checkout scm
sh(script: 'source workflow/gw_setup.sh;which git;git --version;git submodule update --init --recursive')
def builds_file = readYaml file: 'ci/cases/yamls/build.yaml'
def build_args_list = builds_file['builds']
def build_args = build_args_list[system].join(' ').trim().replaceAll('null', '')
dir("${HOMEgfs}/sorc") {
sh(script: "${build_args}")
sh(script: './link_workflow.sh')
sh(script: "echo ${HOMEgfs} > BUILT_semaphor")
}
}
if (env.CHANGE_ID && system == 'gfs') {
if (pullRequest.labels.any { value -> value.matches("CI-${Machine}-Building") }) {
pullRequest.removeLabel("CI-${Machine}-Building")
}
pullRequest.addLabel("CI-${Machine}-Running")
}
}
}
}
}
}
}
}

stage('Run Tests') {
matrix {
agent { label "${machine}-emc" }
axes {
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', '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")
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")
}
}
}
stage('Run Experiments') {
steps {
script {
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/${pslot}`")
err = sh(script: "${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}")
}
}

}
}
}
}
}
}

post {
always {
script {
if(env.CHANGE_ID) {
for (label in pullRequest.labels) {
if (label.contains("${Machine}")) {
pullRequest.removeLabel(label)
}
}
}
}
}
success {
script {
if(env.CHANGE_ID) {
pullRequest.addLabel("CI-${Machine}-Passed")
def timestamp = new Date().format('MM dd HH:mm:ss', TimeZone.getTimeZone('America/New_York'))
pullRequest.comment("**CI SUCCESS** ${Machine} at ${timestamp}\n\nBuilt and ran in directory `${HOME}`")
}
}
}
failure {
script {
if(env.CHANGE_ID) {
pullRequest.addLabel("CI-${Machine}-Failed")
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}`")
}
}
}
}
}
22 changes: 22 additions & 0 deletions ci/cases/pr/C48C48_ufs_hybatmDA.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
experiment:
system: gfs
mode: cycled

arguments:
pslot: {{ 'pslot' | getenv }}
app: ATM
resdetatmos: 48
resensatmos: 48
comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
idate: 2021032312
edate: 2021032400
nens: 2
gfs_cyc: 1
start: warm
yaml: {{ HOMEgfs }}/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml

skip_ci_on_hosts:
- hera
- orion
- hercules
5 changes: 5 additions & 0 deletions ci/cases/pr/C48_S2SWA_gefs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,8 @@ arguments:
idate: 2021032312
edate: 2021032312
yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml

skip_ci_on_hosts:
- hera
- orion
- hercules
23 changes: 23 additions & 0 deletions ci/cases/pr/C48mx500_3DVarAOWCDA.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
experiment:
system: gfs
mode: cycled

arguments:
pslot: {{ 'pslot' | getenv }}
app: S2S
resdetatmos: 48
resdetocean: 5.0
comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500
idate: 2021032412
edate: 2021032418
nens: 0
gfs_cyc: 0
start: warm
yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_gfs_defaults_ci.yaml

skip_ci_on_hosts:
- orion
- hera
- hercules
3 changes: 3 additions & 0 deletions ci/cases/yamls/build.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
builds:
- gefs: './build_all.sh'
- gfs: './build_all.sh -wgu'
5 changes: 5 additions & 0 deletions ci/cases/yamls/soca_gfs_defaults_ci.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
defaults:
!INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
base:
ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
DO_JEDIOCNVAR: "YES"
14 changes: 14 additions & 0 deletions ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
defaults:
!INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
base:
DOIAU: "NO"
DO_JEDIATMVAR: "YES"
DO_JEDIATMENS: "YES"
ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
esfc:
DONST: "NO"
nsst:
NST_MODEL: "1"
sfcanl:
DONST: "NO"

23 changes: 12 additions & 11 deletions ci/scripts/check_ci.sh
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ set -eux
# to run from within a cron job in the CI Managers account
#####################################################################################

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
HOMEgfs="$(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}]'
Expand All @@ -20,21 +20,22 @@ REPO_URL="https://github.com/NOAA-EMC/global-workflow.git"
# Set up runtime environment varibles for accounts on supproted machines
#########################################################################

source "${ROOT_DIR}/ush/detect_machine.sh"
source "${HOMEgfs}/ush/detect_machine.sh"
case ${MACHINE_ID} in
hera | orion | hercules)
echo "Running Automated Testing on ${MACHINE_ID}"
source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
;;
*)
echo "Unsupported platform. Exiting with error."
exit 1
;;
esac
set +x
source "${ROOT_DIR}/ush/module-setup.sh"
source "${ROOT_DIR}/ci/scripts/utils/ci_utils.sh"
module use "${ROOT_DIR}/modulefiles"
export HOMEgfs
source "${HOMEgfs}/ush/module-setup.sh"
source "${HOMEgfs}/ci/scripts/utils/ci_utils.sh"
module use "${HOMEgfs}/modulefiles"
module load "module_gwsetup.${MACHINE_ID}"
module list
set -x
Expand All @@ -57,7 +58,7 @@ pr_list_dbfile="${GFS_CI_ROOT}/open_pr_list.db"

pr_list=""
if [[ -f "${pr_list_dbfile}" ]]; then
pr_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display | grep -v Failed | grep Running | awk '{print $1}') || true
pr_list=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display | grep -v Failed | grep Running | awk '{print $1}') || true
fi
if [[ -z "${pr_list+x}" ]]; then
echo "no PRs open and ready to run cases on .. exiting"
Expand Down Expand Up @@ -89,13 +90,13 @@ for pr in ${pr_list}; do
sed -i "1 i\`\`\`" "${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 "${pr_list_dbfile}"
"${HOMEgfs}/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
weekly_labels=$(${GH} pr view "${pr}" --repo "${REPO_URL}" --json headRefName,labels,author --jq 'select(.author.login | contains("emcbot")) | select(.headRefName | contains("weekly_ci")) | .labels[].name ') || true
if [[ -n "${weekly_labels}" ]]; then
num_platforms=$(find "${ROOT_DIR}/ci/platforms" -type f -name "config.*" | wc -l)
num_platforms=$(find "${HOMEgfs}/ci/platforms" -type f -name "config.*" | wc -l)
passed=0
for platforms in "${ROOT_DIR}"/ci/platforms/config.*; do
for platforms in "${HOMEgfs}"/ci/platforms/config.*; do
machine=$(basename "${platforms}" | cut -d. -f2)
if [[ "${weekly_labels}" == *"CI-${machine^}-Passed"* ]]; then
((passed=passed+1))
Expand Down Expand Up @@ -139,7 +140,7 @@ for pr in ${pr_list}; do
} >> "${output_ci}"
sed -i "1 i\`\`\`" "${output_ci}"
"${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}"
"${HOMEgfs}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
for kill_cases in "${pr_dir}/RUNTESTS/"*; do
pslot=$(basename "${kill_cases}")
cancel_slurm_jobs "${pslot}"
Expand Down
2 changes: 1 addition & 1 deletion ci/scripts/clone-build_ci.sh
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ set +e
source "${HOMEgfs}/ush/module-setup.sh"
export BUILD_JOBS=8
rm -rf log.build
./build_all.sh -gu >> log.build 2>&1
./build_all.sh -guw >> log.build 2>&1
build_status=$?

DATE=$(date +'%D %r')
Expand Down
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