update

.cicd/Jenkinsfile

@@ -0,0 +1,217 @@
+pipeline {
+    agent none
+
+    options {
+        disableConcurrentBuilds()
+        overrideIndexTriggers(false)
+        skipDefaultCheckout(true)
+    }
+
+    parameters {
+        // Allow job runner to filter based on platform
+        // Use the line below to enable all PW clusters
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', 'hera', 'jet', 'orion', 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'], description: 'Specify the platform(s) to use')
+        // Use the line below to enable the PW AWS cluster
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', 'hera', 'jet', 'orion', 'pclusternoaav2use1'], description: 'Specify the platform(s) to use')
+        choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', 'hera', 'jet', 'orion'], description: 'Specify the platform(s) to use')
+        // Allow job runner to filter based on compiler
+        choice(name: 'SRW_COMPILER_FILTER', choices: ['all', 'gnu', 'intel'], description: 'Specify the compiler(s) to use to build')
+        booleanParam name: 'SRW_WE2E_COMPREHENSIVE_TESTS', defaultValue: false, description: 'Whether to execute the comprehensive end-to-end tests'
+    }
+
+    stages {
+        // Uncomment the following block to re-enable PW clusters
+        /*
+        // Start the NOAA Parallel Works clusters, if necessary
+        stage('Start Parallel Works Clusters') {
+            matrix {
+                // Start all clusters by default or only the specified cluster given by SRW_PLATFORM_FILTER
+                when {
+                    anyOf {
+                        expression { params.SRW_PLATFORM_FILTER == 'all' }
+                        expression { params.SRW_PLATFORM_FILTER == env.SRW_PLATFORM }
+                    }
+                }
+
+                axes {
+                    axis {
+                        name 'SRW_PLATFORM'
+                        values 'pclusternoaav2use1' //, 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                    }
+                }
+
+                stages {
+                    // Call the parallel-works-jenkins-client/start-cluster job using SRW_PLATFORM for the
+                    // PW_CLUSTER_NAME parameter
+                    stage('Start Cluster') {
+                        steps {
+                            build job: 'parallel-works-jenkins-client/start-cluster', parameters: [string(name: 'PW_CLUSTER_NAME', value: env.SRW_PLATFORM), string(name: 'PW_CLUSTER_SSH_KEY', value: '~/.ssh/id_rsa'), string(name: 'JAVA_VERSION', value: '11')]
+                        }
+                    }
+                }
+            }
+        }
+        */
+
+        // Build and test the SRW application on all supported platforms using the supported compilers for each platform
+        stage('Build and Test') {
+            matrix {
+                // Run on all platform/compiler combinations by default or build and test only on the platform(s) and
+                // compiler(s) specified by SRW_PLATFORM_FILTER and SRW_COMPILER_FILTER
+                when {
+                    allOf {
+                        anyOf {
+                            expression { params.SRW_PLATFORM_FILTER == 'all' }
+                            expression { params.SRW_PLATFORM_FILTER == env.SRW_PLATFORM }
+                        }
+
+                        anyOf {
+                            expression { params.SRW_COMPILER_FILTER == 'all' }
+                            expression { params.SRW_COMPILER_FILTER == env.SRW_COMPILER }
+                        }
+                    }
+                }
+
+                axes {
+                    axis {
+                        name 'SRW_PLATFORM'
+                        values 'cheyenne', 'gaea', 'hera', 'jet', 'orion' //, 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                    }
+
+                    axis {
+                        name 'SRW_COMPILER'
+                        values 'gnu', 'intel'
+                    }
+                }
+
+                excludes {
+                    // Exclude GNU from platforms that don't support it
+                    exclude {
+                            axis {
+                            name 'SRW_PLATFORM'
+                            values 'gaea', 'hera', 'jet', 'orion' //, 'pclusternoaav2use1' , 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                        }
+
+                        axis {
+                            name 'SRW_COMPILER'
+                            values 'gnu'
+                        }
+                    }
+                }
+
+                environment {
+                    BRANCH_NAME_ESCAPED = env.BRANCH_NAME.replace('/', '_')
+                    BUILD_VERSION = "${env.SRW_PLATFORM}-${env.SRW_COMPILER}-${env.BRANCH_NAME_ESCAPED}-${env.BUILD_NUMBER}"
+                    BUILD_NAME = "ufs-srweather-app_${env.BUILD_VERSION}"
+                    INSTALL_NAME = "install_${env.SRW_COMPILER}"
+                }
+
+                stages {
+                    // Clean the workspace, checkout the repository, and run checkout_externals
+                    stage('Initialize') {
+                        agent {
+                            label env.SRW_PLATFORM
+                        }
+
+                        steps {
+                            echo "Initializing SRW (${env.SRW_COMPILER}) build environment on ${env.SRW_PLATFORM}"
+                            cleanWs()
+                            checkout scm
+                            sh '"${WORKSPACE}/manage_externals/checkout_externals"'
+                        }
+                    }
+
+                    // Run the unified build script; if successful create a tarball of the build and upload to S3
+                    stage('Build') {
+                        agent {
+                            label env.SRW_PLATFORM
+                        }
+
+                        steps {
+                            echo "Building SRW (${env.SRW_COMPILER}) on ${env.SRW_PLATFORM}"
+                            sh 'bash --login "${WORKSPACE}/.cicd/scripts/srw_build.sh"'
+                        }
+
+                        post {
+                            success {
+                                sh 'cd "${WORKSPACE}/${INSTALL_NAME}" && tar --create --gzip --verbose --file "${WORKSPACE}/${BUILD_NAME}.tgz" *'
+                                s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: true, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.BUILD_NAME}.tgz", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false], [bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: true, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "build_${env.SRW_COMPILER}/srw_build-${env.SRW_PLATFORM}-${env.SRW_COMPILER}.log", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
+                            }
+                        }
+                    }
+
+                    // Run the unified test script
+                    stage('Test') {
+                        agent {
+                            label env.SRW_PLATFORM
+                        }
+
+                        environment {
+                            SRW_WE2E_EXPERIMENT_BASE_DIR = "${env.WORKSPACE}/expt_dirs"
+                        }
+
+                        steps {
+                            echo "Testing SRW (${env.SRW_COMPILER}) on ${env.SRW_PLATFORM}"
+
+                            // If executing for a Pull Request, check for the run_we2e_comprehensive_tests. If set,
+                            // override the value of the SRW_WE2E_COMPREHENSIVE_TESTS parameter
+                            script {
+                                def run_we2e_comprehensive_tests = params.SRW_WE2E_COMPREHENSIVE_TESTS
+                                def run_we2e_comprehensive_tests_label = 'run_we2e_comprehensive_tests'
+
+                                if (env.CHANGE_ID) {
+                                    pullRequest.labels.each {
+                                        if (it == run_we2e_comprehensive_tests_label) {
+                                            run_we2e_comprehensive_tests = true
+                                        }
+                                    }
+                                }
+
+                                sh "SRW_WE2E_COMPREHENSIVE_TESTS=${run_we2e_comprehensive_tests}" + ' bash --login "${WORKSPACE}/.cicd/scripts/srw_test.sh"'
+                            }
+                        }
+
+                        post {
+                            always {
+                                // Archive the test log files
+                                sh 'cd "${SRW_WE2E_EXPERIMENT_BASE_DIR}" && tar --create --gzip --verbose --file "${WORKSPACE}/we2e_test_logs-${SRW_PLATFORM}-${SRW_COMPILER}.tgz" */log.generate_FV3LAM_wflow */log.launch_FV3LAM_wflow */log/*'
+                                // Remove the data sets from the experiments directory to conserve disk space
+                                sh 'find "${SRW_WE2E_EXPERIMENT_BASE_DIR}" -regextype posix-extended -regex "^.*(orog|[0-9]{10})$" -type d | xargs rm -rf'
+                                s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: 'we2e_test_results-*-*.txt', storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false], [bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: 'we2e_test_logs-*-*.tgz', storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    // Uncomment the following block to re-enable PW clusters
+    /*
+    post {
+        always {
+            // Stop any Parallel Works clusters that were started during the pipeline execution
+            script {
+                // def pw_clusters = ['pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1']
+                def pw_clusters = ['pclusternoaav2use1']
+                def clusters = []
+
+                // Determine which clusters need to be stopped, if any
+                if (params.SRW_PLATFORM_FILTER == 'all') {
+                    clusters = pw_clusters
+                } else if (params.SRW_PLATFORM_FILTER in pw_clusters) {
+                    clusters = [params.SRW_PLATFORM_FILTER]
+                } else {
+                    echo 'No Parallel Works clusters were used in build'
+                }
+
+                for (int i = 0; i < clusters.size(); ++i) {
+                    // Call the parallel-works-jenkins-client/stop-cluster job using clusters[i] for the
+                    // PW_CLUSTER_NAME parameter
+                    build job: 'parallel-works-jenkins-client/stop-cluster', parameters: [string(name: 'PW_CLUSTER_NAME', value: clusters[i])]
+                }
+            }
+        }
+    }
+    */
+}

.cicd/scripts/srw_build.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+#
+# A unified build script for the SRW application. This script is expected to
+# build the SRW application for all supported platforms.
+#
+set -e -u -x
+
+script_dir="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" > /dev/null 2>&1 && pwd)"
+
+# Get repository root from Jenkins WORKSPACE variable if set, otherwise, set
+# relative to script directory.
+declare workspace
+if [[ -n "${WORKSPACE}" ]]; then
+    workspace="${WORKSPACE}"
+else
+    workspace="$(cd -- "${script_dir}/../.." && pwd)"
+fi
+
+# Normalize Parallel Works cluster platform value.
+declare platform
+if [[ "${SRW_PLATFORM}" =~ ^(az|g|p)clusternoaa ]]; then
+    platform='noaacloud'
+else
+    platform="${SRW_PLATFORM}"
+fi
+
+# Build and install
+cd ${workspace}/test
+./build.sh ${platform} ${SRW_COMPILER}
+cd -
+
+# Create combined log file for upload to s3
+build_dir="${workspace}/build_${SRW_COMPILER}"
+cat ${build_dir}/log.cmake ${build_dir}/log.make \
+    >${build_dir}/srw_build-${platform}-${SRW_COMPILER}.log
+

.cicd/scripts/srw_test.sh

@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+#
+# A unified test script for the SRW application. This script is expected to
+# test the SRW application for all supported platforms. NOTE: At this time,
+# this script is a placeholder for a more robust test framework.
+#
+set -e -u -x
+
+script_dir="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" > /dev/null 2>&1 && pwd)"
+
+# Get repository root from Jenkins WORKSPACE variable if set, otherwise, set
+# relative to script directory.
+declare workspace
+if [[ -n "${WORKSPACE}" ]]; then
+    workspace="${WORKSPACE}"
+else
+    workspace="$(cd -- "${script_dir}/../.." && pwd)"
+fi
+
+# Normalize Parallel Works cluster platform value.
+declare platform
+if [[ "${SRW_PLATFORM}" =~ ^(az|g|p)clusternoaa ]]; then
+    platform='noaacloud'
+else
+    platform="${SRW_PLATFORM}"
+fi
+
+# Test directories
+we2e_experiment_base_dir="${workspace}/expt_dirs"
+we2e_test_dir="${workspace}/tests/WE2E"
+
+# Run the end-to-end tests.
+if "${SRW_WE2E_COMPREHENSIVE_TESTS}"; then
+    test_type="comprehensive"
+else
+    test_type="fundamental"
+fi
+
+cd ${we2e_test_dir}
+./setup_WE2E_tests.sh ${platform} ${SRW_PROJECT} ${SRW_COMPILER} ${test_type} ${we2e_experiment_base_dir}
+
+# Allow the tests to start before checking for status.
+# TODO: Create a parameter that sets the initial start delay.
+sleep 300
+
+# Progress file
+progress_file="${workspace}/we2e_test_results-${platform}-${SRW_COMPILER}.txt"
+
+# Wait for all tests to complete.
+while true; do
+
+    # Check status of all experiments
+    ./get_expts_status.sh expts_basedir="${we2e_experiment_base_dir}" \
+         verbose="FALSE" | tee ${progress_file}
+
+    # Exit loop only if there are not tests in progress
+    set +e
+    grep -q "Workflow status:  IN PROGRESS" ${progress_file}
+    exit_code=$?
+    set -e
+
+    if [[ $exit_code -ne 0 ]]; then
+       break
+    fi
+
+    # TODO: Create a paremeter that sets the poll frequency.
+    sleep 60
+done
+
+# Allow we2e cron jobs time to complete and clean up themselves
+# TODO: Create parameter that sets the interval for the we2e cron jobs; this
+# value should be some factor of that interval to ensure the cron jobs execute
+# before the workspace is cleaned up.
+sleep 600
+
+# Set exit code to number of failures
+set +e
+failures=$(grep "Workflow status:  FAILURE" ${progress_file} | wc -l)
+set -e
+exit ${failures}

.github/CODEOWNERS

@@ -3,7 +3,7 @@
 
 # These owners will be the default owners for everything in the repo.
 #*       @defunkt
-*       @JulieSchramm @mkavulich @gsketefian @JeffBeck-NOAA @RatkoVasic-NOAA @BenjaminBlake-NOAA
+*       @mkavulich @gsketefian @JeffBeck-NOAA @RatkoVasic-NOAA @BenjaminBlake-NOAA @ywangwof @chan-hoo @panll @christinaholtNOAA @christopherwharrop-noaa @danielabdi-noaa @mark-a-potts @jkbk2004 @willmayfield @dmwright526 @gspetro-NOAA @natalie-perlin @EdwardSnyder-NOAA @MichaelLueken
 
 # Order is important. The last matching pattern has the most precedence.
 # So if a pull request only touches javascript files, only these owners

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,26 +7,38 @@ assignees: ''
 
 ---
 
-# Description
+<!-- Please remove unwanted/unrelated/irrelevant information such as comments.
+Please copy any output files into a public Github gist (see https://gist.github.com/) and link to the gist, rather than relying on paths that might change. -->
 
-Provide a clear and concise description of the bug and what behavior you are expecting.
+Your bug may already be reported!
+Please search on the [Issue tracker](https://github.com/ufs-community/ufs-srweather-app/issues) before creating a new issue. 
+If an issue already exists, please use that issue to add any additional information.
 
-## Steps to Reproduce
+## Expected behavior
+<!-- Tell us what should happen. -->
 
-Please provide detailed steps for reproducing the issue.
+## Current behavior
+<!-- Tell us what happens instead of the expected behavior. -->
 
-1. step 1
-2. step 2
-3. see the bug...
+## Machines affected
+<!--- Please provide any relevant information about your setup, including machine/compiler combination. -->
+<!-- Reference other issues or PRs in other repositories that this issue is related to, and how they are related. -->
 
-## Additional Context
+## Steps To Reproduce
+<!--- Provide a link to a live example, a code snippet, and/or an explicit set of steps to reproduce this bug.
+1. Step 1
+2. Step 2
+3. See the bug... -->
 
-Please provide any relevant information about your setup. This is important in case the issue is not reproducible except for under certain conditions.
+## Detailed Description of Fix (optional)
+<!--- Provide a detailed description of the change or addition you are proposing. -->
 
-* Machine
-* Compiler
-* Reference other issues or PRs in other repositories that this is related to, and how they are related.
+## Additional Information (optional)
+<!-- Any other relevant information that we should know to correctly understand and reproduce the issue. 
+Please describe in as much detail as possible. -->
 
-## Output
+## Possible Implementation (optional)
+<!--- Suggest an idea for implementing addition or change. -->
 
-Please include any relevant log files, screenshots or other output here.
+## Output (optional)
+<!-- Please include any relevant log files, screenshots or other output here. -->