rrfs_ci: Update to top of authoritative develop

.cicd/Jenkinsfile

@@ -0,0 +1,169 @@
+pipeline {
+    agent none
+
+    options {
+        skipDefaultCheckout(true)
+    }
+
+    parameters {
+        // Allow job runner to filter based on platform
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', 'orion', 'pcluster_noaa_v2_use1', 'azcluster_noaa', 'gcluster_noaa_v2_usc1'], description: 'Specify the platform(s) to use')
+        choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', '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')
+    }
+
+    stages {
+        /*
+        // 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 'pcluster_noaa_v2_use1', 'azcluster_noaa', 'gcluster_noaa_v2_usc1'
+                    }
+                }
+
+                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', 'orion', 'pcluster_noaa_v2_use1', 'azcluster_noaa', 'gcluster_noaa_v2_usc1'
+                        values 'cheyenne', 'gaea', 'orion'
+                    }
+
+                    axis {
+                        name 'SRW_COMPILER'
+                        values 'gnu', 'intel'
+                    }
+                }
+
+                excludes {
+                    // Exclude GNU from platforms that don't support it
+                    exclude {
+                            axis {
+                            name 'SRW_PLATFORM'
+                            values 'gaea', 'orion'
+                        }
+
+                        axis {
+                            name 'SRW_COMPILER'
+                            values 'gnu'
+                        }
+                    }
+                }
+
+                agent {
+                    label env.SRW_PLATFORM
+                }
+
+                environment {
+                    BUILD_VERSION = "${env.SRW_PLATFORM}-${env.SRW_COMPILER}-${env.BRANCH_NAME}-${env.BUILD_NUMBER}"
+                    BUILD_NAME = "ufs-srweather-app_${env.BUILD_VERSION}"
+                }
+
+                stages {
+                    // Clean the workspace, checkout the repository, and run checkout_externals
+                    stage('Initialize') {
+                        steps {
+                            echo "Initializing SRW (${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') {
+                        steps {
+                            echo "Building SRW (${env.SRW_COMPILER}) on ${env.SRW_PLATFORM}"
+                            sh 'bash --login "${WORKSPACE}/.cicd/scripts/srw_build.sh"'
+                        }
+
+                        post {
+                            success {
+                                sh 'tar --create --gzip --verbose --file "${WORKSPACE}/${BUILD_NAME}.tgz" bin include lib share'
+                                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: "${env.BUILD_NAME}.tgz", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
+                            }
+                        }
+                    }
+
+                    // Run the unified test script
+                    stage('Test') {
+                        steps {
+                            echo "Testing SRW (${env.SRW_COMPILER}) on ${env.SRW_PLATFORM}"
+                            sh 'bash --login "${WORKSPACE}/.cicd/scripts/srw_test.sh"'
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    /*
+    post {
+        always {
+            // Stop any Parallel Works clusters that were started during the pipeline execution
+            script {
+                def pw_clusters = ['pcluster_noaa_v2_use1', 'azcluster_noaa', 'gcluster_noaa_v2_usc1']
+                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 +1,31 @@
+#!/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 -- "${script_dir}/../.." && pwd)"
+fi
+
+build_dir="${workspace}/build"
+
+# Set build related environment variables and load required modules.
+source "${workspace}/etc/lmod-setup.sh" "${SRW_PLATFORM}"
+module use "${workspace}/modulefiles"
+module load "build_${SRW_PLATFORM}_${SRW_COMPILER}"
+
+# Compile SRW application and install to repository root.
+mkdir "${build_dir}"
+pushd "${build_dir}"
+    cmake -DCMAKE_INSTALL_PREFIX="${workspace}" "${workspace}"
+    make -j "${MAKE_JOBS}"
+popd

.cicd/scripts/srw_test.sh

@@ -0,0 +1,21 @@
+#!/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 -- "${script_dir}/../.." && pwd)"
+fi
+
+# Verify that there is a non-zero sized weather model executable.
+[[ -s "${workspace}/bin/ufs_model" ]] || [[ -s "${workspace}/bin/NEMS.exe" ]]

.github/CODEOWNERS

@@ -4,7 +4,6 @@
 # These owners will be the default owners for everything in the repo.
 #*       @defunkt
 *       @robgonzalezpita @venitahagerty @christopherwharrop-NOAA @christinaholtNOAA
-
 # Order is important. The last matching pattern has the most precedence.
 # So if a pull request only touches javascript files, only these owners
 # will be requested to review.

.github/ISSUE_TEMPLATE/textonly_request.md

@@ -0,0 +1,20 @@
+---
+name: Text-only request
+about: Suggest an idea for this project
+title: ''
+labels: textonly
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of the problem to be solved.
+
+## Solution
+Add a clear and concise description of the proposed solution.
+
+## Alternatives (optional)
+If applicable, add a description of any alternative solutions or features you've considered.
+
+## Related to (optional)
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related.

.github/workflows/build.yml

@@ -0,0 +1,21 @@
+name: Build SRW
+on: [push]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: [self-hosted, ncar]
+    steps:
+      - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
+      - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - run: |
+             cd ufs-srweather-app
+             ./manage_externals/checkout_externals
+             module use modulefiles
+             module load build_cheyenne_intel
+             mdkir build
+             cd build
+             cmake -DCMAKE_INSTALL_PREFIX=.. ..
+             make -j 4
+      - run: echo "🍏 This job's status is ${{ job.status }}."

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "hpc-stack-mod"]
+	path = hpc-stack-mod
+	url = https://github.com/NOAA-EMC/hpc-stack.git

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/UsersGuide/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/UsersGuide/requirements.txt
+
+submodules:
+   include:
+   - hpc-stack-mod
+   recursive: true
+

Externals.cfg

@@ -11,7 +11,7 @@ protocol = git
 repo_url = https://github.com/ufs-community/UFS_UTILS
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = f30740e
+hash = 31271f7
 local_path = src/UFS_UTILS
 required = True
 
@@ -20,7 +20,7 @@ protocol = git
 repo_url = https://github.com/ufs-community/ufs-weather-model
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = e593349
+hash = 96dffa1
 local_path = src/ufs-weather-model
 required = True
 
@@ -29,7 +29,7 @@ protocol = git
 repo_url = https://github.com/NOAA-EMC/UPP
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 4a16052
+hash = 394917e
 local_path = src/UPP
 required = True
 

README.md

@@ -2,12 +2,11 @@
 
 The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth modeling system. It is designed to be the source system for NOAA’s operational numerical weather prediction applications while enabling research, development, and contribution opportunities for the broader weather enterprise. For more information about the UFS, visit the UFS Portal at https://ufscommunity.org/.
 
-The UFS can be configured for multiple applications (see a complete list at https://ufscommunity.org/#/science/aboutapps). The configuration described here is the UFS Short-Range Weather (SRW) Application, which targets predictions of atmospheric behavior on a limited spatial domain and on time scales from less than an hour out to several days. The development branch of the application is continually evolving as the system undergoes open development. The SRW App v1.0.0 represents a snapshot of this continuously evolving system. The SRW App includes a prognostic atmospheric model, pre- and post-processing, and a community workflow for running the system end-to-end. 
+The UFS includes multiple applications (see a complete list at https://ufscommunity.org/science/aboutapps/) that support different forecast durations and spatial domains. This documentation describes the UFS Short-Range Weather (SRW) Application, which targets predictions of atmospheric behavior on a limited spatial domain and on time scales from minutes to several days. The development branch of the application is continually evolving as the system undergoes open development. The SRW App release branches represent a snapshot of this continuously evolving system. The SRW Application includes a prognostic atmospheric model, pre- and post-processing, and a community workflow for running the system end-to-end. These components are documented within the User's Guide and supported through a community forum (https://forums.ufscommunity.org/). 
 
-The UFS SRW App User's Guide associated with the development branch is at: https://ufs-srweather-app.readthedocs.io/en/latest/, while that specific to the SRW App v1.0.0 release can be found at: https://ufs-srweather-app.readthedocs.io/en/ufs-v1.0.0/. The repository is at: https://github.com/ufs-community/ufs-srweather-app.
+The UFS SRW App User's Guide associated with the development branch can be found at: https://ufs-srweather-app.readthedocs.io/en/develop/, while the guide specific to the SRW App v1.0.1 release can be found at: https://ufs-srweather-app.readthedocs.io/en/ufs-v1.0.1/. The GitHub repository link is: https://github.com/ufs-community/ufs-srweather-app.
 
 For instructions on how to clone the repository, build the code, and run the workflow, see:
 https://github.com/ufs-community/ufs-srweather-app/wiki/Getting-Started
 
-UFS Development Team. (2021, March 4). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.4534994
-
+UFS Development Team. (2021, March 4). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.4534994