Merge branch 'ufs-community:develop' into develop

gspetro-NOAA · Feb 16, 2024 · 6851ed6 · 6851ed6
2 parents a0d1e67 + 869761c
commit 6851ed6
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diff --git a/.cicd/Jenkinsfile b/.cicd/Jenkinsfile
@@ -10,15 +10,14 @@ pipeline {
     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', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules', 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'], description: 'Specify the platform(s) to use')
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaeac5', 'hera', 'jet', 'orion', 'hercules', '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', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules', 'pclusternoaav2use1'], description: 'Specify the platform(s) to use')
-        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaea', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules'], description: 'Specify the platform(s) to use')
-        choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'gaea', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules'], description: 'Specify the platform(s) to use')
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'cheyenne', 'gaeac5', 'hera', 'jet', 'orion', 'hercules', 'pclusternoaav2use1'], description: 'Specify the platform(s) to use')
+        // choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'derecho', 'gaeac5', 'hera', 'jet', 'orion', 'hercules'], description: 'Specify the platform(s) to use')
+        choice(name: 'SRW_PLATFORM_FILTER', choices: ['all', 'derecho', 'hera', 'jet', 'orion', 'hercules'], 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')
-        // Uncomment the following line to re-enable comprehensive tests
-        // booleanParam name: 'SRW_WE2E_COMPREHENSIVE_TESTS', defaultValue: false, description: 'Whether to execute the comprehensive end-to-end tests'
+        booleanParam name: 'SRW_WE2E_COMPREHENSIVE_TESTS', defaultValue: false, description: 'Whether to execute the comprehensive end-to-end tests'
     }
 
     stages {
@@ -88,8 +87,8 @@ pipeline {
                 axes {
                     axis {
                         name 'SRW_PLATFORM'
-                        // values 'cheyenne', 'gaea', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'
-                        values 'gaea', 'gaea-c5', 'hera', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                        // values 'derecho', 'gaeac5', 'hera', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                        values 'derecho', 'hera', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1', 'azclusternoaav2eus1', 'gclusternoaav2usc1'
                     }
 
                     axis {
@@ -103,7 +102,8 @@ pipeline {
                     exclude {
                             axis {
                             name 'SRW_PLATFORM'
-                            values 'gaea', 'gaea-c5', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1' , 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                            // values 'derecho', 'gaeac5', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1' , 'azclusternoaav2eus1', 'gclusternoaav2usc1'
+                            values 'derecho', 'jet', 'orion', 'hercules' //, 'pclusternoaav2use1' , 'azclusternoaav2eus1', 'gclusternoaav2usc1'
                         }
 
                         axis {
@@ -184,11 +184,6 @@ pipeline {
                             dir ("${env.SRW_PLATFORM}") {
                             echo "Testing SRW (${env.SRW_COMPILER}) on ${env.SRW_PLATFORM} (using ${env.WORKSPACE}/${env.SRW_PLATFORM})"
 
-                            // Remove the following line to re-enable comprehensive tests
-                            sh 'SRW_WE2E_COMPREHENSIVE_TESTS=false bash --login "${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/srw_test.sh"'
-
-                            // Uncomment the following block to re-enable comprehensive tests
-                            /*
                             // 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 {
@@ -205,7 +200,6 @@ pipeline {
 
                                 sh "SRW_WE2E_COMPREHENSIVE_TESTS=${run_we2e_comprehensive_tests}" + ' bash --login "${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/srw_test.sh"'
                             }
-                            */
                             }
                         }
 

diff --git a/.cicd/scripts/srw_ftest.sh b/.cicd/scripts/srw_ftest.sh
@@ -85,7 +85,12 @@ module load build_${platform,,}_${SRW_COMPILER}
 module load wflow_${platform,,}
 
 [[ ${FORGIVE_CONDA} == true ]] && set +e +u    # Some platforms have incomplete python3 or conda support, but wouldn't necessarily block workflow tests
-conda activate srw_app
+# Gaea-C5 special case missing jinja2
+if [ "${platform}" == "gaea-c5" ]; then
+  conda activate workflow_tools
+else
+  conda activate srw_app
+fi
 set -e -u
 
 # Adjust for strict limitation of stack size 

diff --git a/.cicd/scripts/wrapper_srw_ftest.sh b/.cicd/scripts/wrapper_srw_ftest.sh
@@ -23,11 +23,6 @@ else
 fi
 
 # Customize wrapper scripts
-if [[ "${SRW_PLATFORM}" == gaea ]]; then
-    sed -i '15i #SBATCH --clusters=c4' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
-    sed -i 's|qos=batch|qos=windfall|g' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
-fi
-
 if [[ "${SRW_PLATFORM}" == gaea-c5 ]]; then
     sed -i '15i #SBATCH --clusters=c5' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
     sed -i 's|qos=batch|qos=normal|g' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh

diff --git a/devbuild.sh b/devbuild.sh
@@ -212,6 +212,11 @@ printf "PLATFORM(MACHINE)=${PLATFORM}\n" >&2
 if [ "${PLATFORM}" = "wcoss2" ]; then
     BUILD_CONDA="off"
 fi
+# Conda is not used on Gaea-c5 F2 filesystem 
+# it needs to be reevaluated when moved to F2 filesystem
+if [ "${PLATFORM}" = "gaea-c5" ]; then
+    BUILD_CONDA="off"
+fi
 
 # build conda and conda environments, if requested.
 if [ "${BUILD_CONDA}" = "on" ] ; then
@@ -244,8 +249,10 @@ if [ "${BUILD_CONDA}" = "on" ] ; then
   fi
 
 else
-  source ${CONDA_BUILD_DIR}/etc/profile.d/conda.sh
-  conda activate
+  if [ -d "${CONDA_BUILD_DIR}" ] ; then
+    source ${CONDA_BUILD_DIR}/etc/profile.d/conda.sh
+    conda activate
+  fi
 fi
 
 # Conda environment should have linux utilities to perform these tasks on macos.
@@ -281,7 +288,7 @@ set -eu
 # automatically determine compiler
 if [ -z "${COMPILER}" ] ; then
   case ${PLATFORM} in
-    jet|hera|gaea|gaea-c5) COMPILER=intel ;;
+    jet|hera|gaea-c5) COMPILER=intel ;;
     orion) COMPILER=intel ;;
     wcoss2) COMPILER=intel ;;
     cheyenne) COMPILER=intel ;;

diff --git a/devclean.sh b/devclean.sh
@@ -135,12 +135,13 @@ elif [ "${CLEAN}" = true ]; then
     "${INSTALL_DIR}/include" \
     "${INSTALL_DIR}/lib" \
     "${INSTALL_DIR}/lib64" \
-    "${SRW_DIR}/manage_externals/manic" \
   )
-  for directory in $directories; do
-    [[ -d $directory ]] && rm -rfv $directory
-  done
+  if [ ${#directories[@]} -ge 1 ]; then
+    for dir in ${directories[@]}; do 
+     [[ -d "${dir}" ]] &&  rm -rfv ${dir} 
+    done
   echo " "
+  fi
 fi
 # Clean all the submodules if requested. Note: Need to check out them again before attempting subsequent builds, by sourcing ${SRW_DIR}/manage_externals/checkout_externals
 if [ ${INCLUDE_SUB_MODULES} == true ]; then

diff --git a/docs/UsersGuide/Makefile b/docs/UsersGuide/Makefile
@@ -1,19 +1,26 @@
-# Minimal makefile for Sphinx documentation
-#
+# Makefile for Sphinx documentation
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -a -n #-W
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
+LINKCHECKDIR  = $(BUILDDIR)/linkcheck
+
+.PHONY: help Makefile linkcheck
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)
+
+docs:
+	$(MAKE) linkcheck
+	$(MAKE) html
 
-.PHONY: help Makefile
+linkcheck:
+	make clean && $(SPHINXBUILD) -b linkcheck $(SPHINXOPTS) $(SOURCEDIR) $(LINKCHECKDIR)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) -w $(BUILDDIR)/warnings.log
diff --git a/docs/UsersGuide/source/BackgroundInfo/Components.rst b/docs/UsersGuide/source/BackgroundInfo/Components.rst
@@ -102,7 +102,7 @@ The SRW Application allows users to configure various elements of the workflow.
 
 An optional Python plotting task can also be included in the workflow to create basic visualizations of the model output. The task outputs graphics in PNG format for several standard meteorological variables on the pre-defined :term:`CONUS` domain. A difference plotting option is also included to visually compare two runs for the same domain and resolution. These plots may be used to perform a visual check to verify that the application is producing reasonable results. Configuration instructions are provided in :numref:`Section %s <PlotOutput>`.
 
-The SRW Application has been tested on a variety of platforms widely used by researchers, including NOAA High-Performance Computing (HPC) systems (e.g., Hera, Jet); the National Center for Atmospheric Research (:term:`NCAR`) Derecho system; cloud environments; and generic Linux and MacOS systems using Intel and GNU compilers. Four `levels of support <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__ have been defined for the SRW Application, including pre-configured (Level 1), configurable (Level 2), limited-test (Level 3), and build-only (Level 4) platforms. 
+The SRW Application has been tested on a variety of platforms widely used by researchers, including NOAA High-Performance Computing (HPC) systems (e.g., Hera, Jet); the National Center for Atmospheric Research (:term:`NCAR`) Derecho system; cloud environments; and generic Linux and MacOS systems using Intel and GNU compilers. Four :srw-wiki:`levels of support <Supported-Platforms-and-Compilers>` have been defined for the SRW Application, including pre-configured (Level 1), configurable (Level 2), limited-test (Level 3), and build-only (Level 4) platforms. 
 
 Preconfigured (Level 1) systems already have the required external libraries available in a central location (via :term:`spack-stack` or :term:`HPC-Stack`). The SRW Application is expected to build and run out-of-the-box on these systems, and users can :ref:`download the SRW App code <DownloadSRWApp>` without first installing prerequisites.
 
@@ -112,5 +112,5 @@ Limited-Test (Level 3) and Build-Only (Level 4) computational platforms are thos
 
 On all platforms, the SRW App can be :ref:`run within a container <QuickstartC>` that includes the prerequisite software.
 
-A complete description of the levels of support, along with a list of preconfigured and configurable platforms can be found in the `SRW Application Wiki <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__.
+A complete description of the levels of support, along with a list of preconfigured and configurable platforms can be found in the :srw-wiki:`SRW Application Wiki <Supported-Platforms-and-Compilers>`.
 
diff --git a/docs/UsersGuide/source/BackgroundInfo/Introduction.rst b/docs/UsersGuide/source/BackgroundInfo/Introduction.rst
@@ -14,7 +14,7 @@ Since the last release, developers have added a variety of features:
    * Addition of the supported ``FV3_RAP`` physics suite (`PR #811 <https://github.com/ufs-community/ufs-srweather-app/pull/811>`__) and support for the ``RRFS_NA_13km`` predefined grid
    * Addition of ``FV3_GFS_v17_p8`` physics suite (`PR #574 <https://github.com/ufs-community/ufs-srweather-app/pull/574>`__)
    * Updates to :term:`CCPP` that target the top of the ``main`` branch (which is ahead of CCPP v6.0.0). See :ref:`this page <CCPPUpdates>` for a detailed summary of updates that came in ahead of the v2.2.0 release.
-   * Expansion of `Level 1 platforms <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__ to include Derecho, Hercules, and Gaea C5 (PRs `#894 <https://github.com/ufs-community/ufs-srweather-app/pull/894>`__, `#898 <https://github.com/ufs-community/ufs-srweather-app/pull/898>`__, `#911 <https://github.com/ufs-community/ufs-srweather-app/pull/911>`__)
+   * Expansion of :srw-wiki:`Level 1 platforms <Supported-Platforms-and-Compilers>` to include Derecho, Hercules, and Gaea C5 (PRs `#894 <https://github.com/ufs-community/ufs-srweather-app/pull/894>`__, `#898 <https://github.com/ufs-community/ufs-srweather-app/pull/898>`__, `#911 <https://github.com/ufs-community/ufs-srweather-app/pull/911>`__)
    * Transition to spack-stack modulefiles for most supported platforms to align with the UFS WM shift to spack-stack (PRs `#913 <https://github.com/ufs-community/ufs-srweather-app/pull/913>`__ and `#941 <https://github.com/ufs-community/ufs-srweather-app/pull/941>`__)
    * Overhaul of the WE2E testing suite (see, e.g., PRs `#686 <https://github.com/ufs-community/ufs-srweather-app/pull/686>`__, `#732 <https://github.com/ufs-community/ufs-srweather-app/pull/732>`__,  `#864 <https://github.com/ufs-community/ufs-srweather-app/pull/864>`__, `#871 <https://github.com/ufs-community/ufs-srweather-app/pull/871>`__)
    * Improvements to the CI/CD automated testing pipeline (see, e.g., PRs `#707 <https://github.com/ufs-community/ufs-srweather-app/pull/707>`__ and `#847 <https://github.com/ufs-community/ufs-srweather-app/pull/847>`__)
@@ -48,7 +48,7 @@ Background Information
 Building, Running, and Testing the SRW App
 --------------------------------------------
 
-   * :numref:`Section %s: Quick Start Guide <NCQuickstart>` is an overview of the workflow and gives instructions for its use on `Level 1 platforms <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__.
+   * :numref:`Section %s: Quick Start Guide <NCQuickstart>` is an overview of the workflow and gives instructions for its use on :srw-wiki:`Level 1 platforms <Supported-Platforms-and-Compilers>`.
    * :numref:`Section %s: Container-Based Quick Start Guide <QuickstartC>` explains how to run the SRW Application in a container. Containers may be run on a broad range of systems and come with SRW App prerequisites already installed. 
    * :numref:`Section %s: Building the SRW App <BuildSRW>` provides a *detailed* explanation of how to build the SRW App. 
    * :numref:`Section %s: Running the SRW App <RunSRW>` provides a *detailed* explanation of how to run the SRW App after it has been built/compiled. It includes information on standard workflow tasks, additional optional tasks (e.g., METplus verification, plotting), and different techniques for running the workflow. 
@@ -60,7 +60,7 @@ Building, Running, and Testing the SRW App
 .. hint:: 
    * To get started with the SRW App, it is recommended that users try one of the following options: 
 
-      #. View :numref:`Section %s: Quick Start Guide <NCQuickstart>` for a quick overview of the workflow steps. Especially helpful for users with access to a `Level 1 platform <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__.
+      #. View :numref:`Section %s: Quick Start Guide <NCQuickstart>` for a quick overview of the workflow steps. Especially helpful for users with access to a :srw-wiki:`Level 1 platform <Supported-Platforms-and-Compilers>`.
       #. To build the application in a container, which provides a more uniform work environment, users can refer to :numref:`Section %s: Container-Based Quick Start Guide <QuickstartC>`. 
       #. For detailed instructions on building and running the SRW App, users can refer to :numref:`Section %s: Building the SRW App <BuildSRW>` and :numref:`Section %s: Running the SRW App <RunSRW>`. 
 
@@ -136,7 +136,7 @@ A list of available component documentation is shown in :numref:`Table %s <list_
    * - Unified Post Processor Scientific Documentation
      - https://noaa-emc.github.io/UPP/
    * - Unified Workflow User's Guide
-     - https://uwtools.readthedocs.io/en/develop/
+     - https://uwtools.readthedocs.io/en/main/
    * - METplus User's Guide
      - https://metplus.readthedocs.io/en/latest/Users_Guide/index.html
    * - HEMCO User's Guide (a component of the NEXUS AQM system)
@@ -175,7 +175,7 @@ Community Contributions
 
 The UFS community is encouraged to contribute to the development efforts of all related
 utilities, model code, and infrastructure. As described above, users can post issues in the SRW App to report bugs or to announce upcoming contributions to the code base. 
-Contributions to the `ufs-srweather-app <https://github.com/ufs-community/ufs-srweather-app>`__ repository should follow the guidelines contained in the `SRW App Contributor's Guide <https://github.com/ufs-community/ufs-srweather-app/wiki/Contributor's-Guide>`__. 
+Contributions to the `ufs-srweather-app <https://github.com/ufs-community/ufs-srweather-app>`__ repository should follow the guidelines contained in the :srw-wiki:`SRW App Contributor's Guide <Contributor's-Guide>`. 
 Additionally, users can file issues in component repositories for contributions that directly concern those repositories. For code to be accepted into a component repository, users must follow the code management rules of that component's authoritative repository. These rules are usually outlined in the component's User's Guide (see :numref:`Table %s <list_of_documentation>`) or GitHub wiki for each respective repository (see :numref:`Table %s <top_level_repos>`).
 
 Future Direction