Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (#2246)

Adding top level Jenkins file for CI tests running on Jenkins Controller:

- Declarative Multi-branch Pipeline (has enhanced restart capabilities
on a per section bases)
- Starts Pipeline from Label PR same as BASH system (for now)
- Progress and restarts can me managed with CAC Login at [EPIC OAR
Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
- Has logic for multi **gfs/gefs** system builds (arguments based on a
configuration file `ci/casts/yamls/build.yaml`)
  - Any number of **systems** may be added by manual adding an ele-
ment to the matrix in the Jenkinsfile
  - _It may be possible to dynamic add matrix values with a specialty
plug-in_
- Currently only runs on **Orion** and **Hera** using `mterry` account

Resolves #2119
Resolves #2118

Jenkinsfile

@@ -0,0 +1,188 @@
+def Machine = 'none'
+def machine = 'none'
+def HOME = 'none'
+def localworkspace = 'none'
+def commonworkspace = 'none'
+
+pipeline {
+    agent { label 'built-in' }
+
+    options {
+        skipDefaultCheckout()
+        buildDiscarder(logRotator(numToKeepStr: '2'))
+    }
+
+    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 ${HOME}/RUNTESTS", returnStatus: true)
+                    pullRequest.addLabel("CI-${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 ${HOMEgfs}", returnStatus: true)
+                                ws(HOMEgfs) {
+                                    env.MACHINE_ID = machine // MACHINE_ID is used in the build scripts to determine the machine and is added to the shell environment
+                                    if (fileExists("${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 ${HOMEgfs}") }
+                                    } else {
+                                        checkout scm
+                                        sh( script: "source workflow/gw_setup.sh;which git;git --version;git submodule update --init --recursive", returnStatus: true)
+                                        def builds_file = readYaml file: "ci/cases/yamls/build.yaml"
+                                        def build_args_list = builds_file['builds']
+                                        def build_args = build_args_list[system].join(" ").trim().replaceAll("null", "")
+                                        dir("${HOMEgfs}/sorc") {
+                                            sh( script: "${build_args}", returnStatus: true)
+                                            sh( script: "./link_workflow.sh", returnStatus: true)
+                                            sh( script: "echo ${HOMEgfs} > BUILT_semaphor", returnStatus: true)
+                                        }
+                                    }
+                                    if ( pullRequest.labels.any{ value -> value.matches("CI-${Machine}-Building") } ) {
+                                         pullRequest.removeLabel("CI-${Machine}-Building")
+                                    }
+                                    pullRequest.addLabel("CI-${Machine}-Running")
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+
+        stage('Run Tests') {
+            matrix {
+                agent { label "${machine}-emc" }
+                axes {
+                    axis {
+                        name "Case"
+                        values "C48_ATM", "C48_S2SWA_gefs", "C48_S2SW", "C96_atm3DVar" // TODO add dynamic list of cases from env vars (needs addtional plugins)
+                    }
+                }
+                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)
+                                    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)
+                                } 
+                        }
+                    }
+                    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 experiments: ${Case} on ${Machine}**<br>Built against system **${system}** in directory:<br>`${HOMEgfs}`<br>With the experiment in directory:<br>`${HOME}/RUNTESTS/${pslot}`")
+                                   try {
+                                      sh( script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${HOME} ${pslot}", returnStatus: true)
+                                    } catch (Exception e) {
+                                       pullRequest.comment("**FAILURE** running experiments: ${Case} on ${Machine}")
+                                       error("Failed to run experiments ${Case} on ${Machine}")
+                                    }
+                                    pullRequest.comment("**SUCCESS** running experiments: ${Case} on ${Machine}")
+                                }
+                            } 
+                        }
+                        post {
+                            always {
+                                script {
+                                    ws (HOMEgfs) {
+                                        for (label in pullRequest.labels) {
+                                           if (label.contains("${Machine}")) {
+                                               pullRequest.removeLabel(label)
+                                            }
+                                        }
+                                    }
+                               }
+                            }
+                            success {
+                                script {
+                                    ws (HOMEgfs) {
+                                       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 {
+                                    ws (HOMEgfs) {
+                                    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}`")
+                                    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/yamls/build.yaml

@@ -0,0 +1,3 @@
+builds:
+ - gefs: './build_all.sh'
+ - gfs: './build_all.sh -gu'

ci/scripts/run-check_ci.sh

@@ -21,7 +21,9 @@ pslot=${2:-${pslot:-?}}        # Name of the experiment being tested by this scr
 #     │   └── ${pslot}
 #     └── EXPDIR
 #         └── ${pslot}
-HOMEgfs="${TEST_DIR}/HOMEgfs"
+# Two system build directories created at build time gfs, and gdas
+# TODO: Make this configurable (for now all scripts run from gfs for CI at runtime)
+HOMEgfs="${TEST_DIR}/gfs"
 RUNTESTS="${TEST_DIR}/RUNTESTS"
 
 # Source modules and setup logging

ci/scripts/utils/ci_utils.sh

@@ -1,24 +1,120 @@
 #!/bin/env bash
 
-function cancel_slurm_jobs() {
+function determine_scheduler() {
+  if command -v sbatch &> /dev/null; then
+    echo "slurm";
+  elif command -v qsub &> /dev/null; then
+    echo "torque";
+  else
+    echo "unknown"
+  fi
+}
 
-  # Usage: cancel_slurm_jobs <substring>
-  # Example: cancel_slurm_jobs "C48_ATM_3c4e7f74"
+function cancel_batch_jobs() {
+  # Usage: cancel_batch_jobs <substring>
+  # Example: cancel_batch_jobs "C48_ATM_3c4e7f74"
   #
-  # Cancel all Slurm jobs that have the given substring in their name
+  # Cancel all batch 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
+
+  scheduler=$(determine_scheduler)
+
+  if [[ "${schduler}" == "torque" ]]; then
+    job_ids=$(qstat -u "${USER}" | awk '{print $1}') || true
+
+    for job_id in ${job_ids}; do
+      job_name=$(qstat -f "${job_id}" | grep Job_Name | awk '{print $3}') || true
+      if [[ "${job_name}" =~ ${substring} ]]; then
+        echo "Canceling PBS Job ${job_name} with: qdel ${job_id}"
+        qdel "${job_id}"
+        continue
+      fi
+    done
+
+  elif [[ "${scheduler}" == "slurm" ]]; then
+
+    job_ids=$(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
+
+  else
+      echo "FATAL: Unknown/unsupported job scheduler"
+      exit 1
+  fi
+}
+
+
+function get_pr_case_list () {
+
+    #############################################################
+    # loop over every yaml file in the PR's ci/cases
+    # and create an run directory for each one for this PR loop
+    #############################################################
+    for yaml_config in "${HOMEgfs}/ci/cases/pr/"*.yaml; do
+      case=$(basename "${yaml_config}" .yaml) || true
+      echo "${case}"
+    done
+}
+
+function get_pslot_list () {
+
+    local RUNTESTS="${1}"
+
+    #############################################################
+    # loop over expdir directories in RUNTESTS
+    # and create list of the directory names (pslot) with the hash tag
+    #############################################################
+    for pslot_dir in "${RUNTESTS}/EXPDIR/"*; do
+      pslot=$(basename "${pslot_dir}") || true
+      echo "${pslot}"
+    done
+
+}
+
+function get_pslot () {
+
+    local RUNTESTS="${1}"
+    local case="${2}"
+
+    #############################################################
+    # loop over expdir directories in RUNTESTS
+    # and return the name of the pslot with its tag that matches the case
+    #############################################################
+    for pslot_dir in "${RUNTESTS}/EXPDIR/"*; do
+      pslot=$(basename "${pslot_dir}")
+      check_case=$(echo "${pslot}" | rev | cut -d"_" -f2- | rev) || true
+      if [[ "${check_case}" == "${case}" ]]; then
+        echo "${pslot}"
+        break
+      fi
+    done
+
+}
+
+function create_experiment () {
+
+  local yaml_config="${1}"
+  cd "${HOMEgfs}" || exit 1
+  pr_sha=$(git rev-parse --short HEAD)
+  case=$(basename "${yaml_config}" .yaml) || true
+  export pslot=${case}_${pr_sha}
+
+  source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+  source "${HOMEgfs}/workflow/gw_setup.sh"
+
+  # system=$(grep "system:" "${yaml_config}" | cut -d":" -f2 | tr -d " ") || true
+
+  "${HOMEgfs}/${system}/workflow/create_experiment.py" --overwrite --yaml "${yaml_config}"
+
 }

ci/scripts/utils/ci_utils_wrapper.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../../.." >/dev/null 2>&1 && pwd )"
+source "${HOMEgfs}/ush/detect_machine.sh"
+
+utitilty_function="${1}"
+
+source "${HOMEgfs}/ci/scripts/utils/ci_utils.sh"
+${utitilty_function} "${@:2}"

modulefiles/module_gwsetup.hera.lua

@@ -14,5 +14,7 @@ load(pathJoin("python", python_ver))
 load("py-jinja2")
 load("py-pyyaml")
 load("py-numpy")
+local git_ver=os.getenv("git_ver") or "2.40.0"
+load(pathJoin("git", git_ver))
 
 whatis("Description: GFS run setup environment")