Merge branch 'ufs-community:develop' into develop

.cicd/Jenkinsfile

@@ -235,19 +235,19 @@ pipeline {
 
                                 sh "SRW_WE2E_COMPREHENSIVE_TESTS=${run_we2e_comprehensive_tests} SRW_WE2E_SINGLE_TEST=${single_test}" + ' bash --login "${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/srw_test.sh"'
 
-                                // Archive the test log files
-                                sh "[[ -d ${SRW_WE2E_EXPERIMENT_BASE_DIR} ]] && cd ${SRW_WE2E_EXPERIMENT_BASE_DIR} && tar --create --gzip --verbose --dereference --file ${WORKSPACE}/${SRW_PLATFORM}/we2e_test_logs-${SRW_PLATFORM}-${SRW_COMPILER}.tgz */log.generate_FV3LAM_wflow */log/* ${WORKSPACE}/${SRW_PLATFORM}/tests/WE2E/WE2E_tests_*yaml WE2E_summary*txt ${WORKSPACE}/${SRW_PLATFORM}/tests/WE2E/log.* || cat /dev/null > ${WORKSPACE}/${SRW_PLATFORM}/we2e_test_logs-${SRW_PLATFORM}-${SRW_COMPILER}.tgz"
                                 }
                                 sh "STAGE_NAME=${env.STAGE_NAME} " + 'bash --login "${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/disk_usage.sh"'
                             }
                         }
 
                         post {
                             success {
-                                s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}/*_test_results-*-*.txt", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false], [bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}/we2e_test_logs-${env.SRW_PLATFORM}-${env.SRW_COMPILER}.tgz", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
                                 s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}/*-skill-score.txt", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
                             }
                             always {
+                                // Archive the test log files
+                                sh "[[ -d ${SRW_WE2E_EXPERIMENT_BASE_DIR} ]] && cd ${SRW_WE2E_EXPERIMENT_BASE_DIR} && tar --create --gzip --verbose --dereference --file ${env.WORKSPACE}/${env.SRW_PLATFORM}/we2e_test_logs-${env.SRW_PLATFORM}-${env.SRW_COMPILER}.tgz */log.generate_FV3LAM_wflow */log/* ${env.WORKSPACE}/${env.SRW_PLATFORM}/tests/WE2E/WE2E_tests_*yaml WE2E_summary*txt ${env.WORKSPACE}/${env.SRW_PLATFORM}/tests/WE2E/log.* || cat /dev/null > ${env.WORKSPACE}/${env.SRW_PLATFORM}/we2e_test_logs-${env.SRW_PLATFORM}-${env.SRW_COMPILER}.tgz"
+                                s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}/*_test_results-*-*.txt", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false], [bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}/we2e_test_logs-${env.SRW_PLATFORM}-${env.SRW_COMPILER}.tgz", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
                                 s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}-*-time-srw_test.json", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
                                 s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'noaa-epic-prod-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: "${env.SRW_PLATFORM}-*-disk-usage${env.STAGE_NAME}.csv", storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []
                                 // Remove the data sets from the experiments directory to conserve disk space

.cicd/scripts/qsub_srw_ftest.sh

@@ -9,7 +9,5 @@
 #PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
 #PBS -l walltime=00:30:00
 #PBS -V
-#PBS -o log_wrap.%j.log
-#PBS -e err_wrap.%j.err 
 
 bash ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/srw_ftest.sh

.cicd/scripts/srw_ftest.sh

@@ -66,6 +66,9 @@ sed "s|^workflow:|workflow:\n  EXEC_SUBDIR: ${workspace}/install_${SRW_COMPILER}
 # Decrease forecast length since we are running all the steps
 sed "s|^  FCST_LEN_HRS: 12|  FCST_LEN_HRS: 6|g" -i ush/config.yaml
 
+# Update compiler 
+sed "s|^  COMPILER: intel|  COMPILER: ${SRW_COMPILER}|g" -i ush/config.yaml
+
 # DATA_LOCATION differs on each platform ... find it.
 export DATA_LOCATION=$(grep TEST_EXTRN_MDL_SOURCE_BASEDIR ${workspace}/ush/machine/${platform,,}.yaml | awk '{printf "%s", $2}')
 echo "DATA_LOCATION=${DATA_LOCATION}"
@@ -85,6 +88,8 @@ source etc/lmod-setup.sh ${platform,,}
 module use modulefiles
 module load build_${platform,,}_${SRW_COMPILER}
 module load wflow_${platform,,}
+# Deactivate conflicting conda env on GCP
+[[ "${SRW_PLATFORM}" =~ "gclusternoaa" ]] && conda deactivate
 
 [[ ${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

.cicd/scripts/srw_metric.sh

@@ -78,6 +78,8 @@ cd ${workspace}
 
 # Activate workflow environment
 module load wflow_${platform,,}
+# Deactivate conflicting conda env on GCP
+[[ "${SRW_PLATFORM}" =~ "gclusternoaa" ]] && conda deactivate
 
 [[ ${FORGIVE_CONDA} == true ]] && set +e +u    # Some platforms have incomplete python3 or conda support, but would not necessarily block workflow tests
 conda activate srw_app
@@ -98,17 +100,17 @@ if [[ ${RUN_STAT_ANLY_OPT} == true ]]; then
     # Clear out data
     rm -rf ${workspace}/Indy-Severe-Weather/
     # Check if metprd data exists locally otherwise get it from S3
-    TEST_EXTRN_MDL_SOURCE_BASEDIR=$(grep TEST_EXTRN_MDL_SOURCE_BASEDIR ${workspace}/ush/machine/${SRW_PLATFORM}.yaml | awk '{print $NF}')
+    TEST_EXTRN_MDL_SOURCE_BASEDIR=$(grep TEST_EXTRN_MDL_SOURCE_BASEDIR ${workspace}/ush/machine/${platform}.yaml | awk '{print $NF}')
     if [[ -d $(dirname ${TEST_EXTRN_MDL_SOURCE_BASEDIR})/metprd/point_stat ]] ; then
         mkdir -p Indy-Severe-Weather/metprd/point_stat
         cp -rp $(dirname ${TEST_EXTRN_MDL_SOURCE_BASEDIR})/metprd/point_stat Indy-Severe-Weather/metprd
     elif [[ -f Indy-Severe-Weather.tgz ]]; then
         tar xvfz Indy-Severe-Weather.tgz 
     else
-        wget https://noaa-ufs-srw-pds.s3.amazonaws.com/sample_cases/release-public-v2.1.0/Indy-Severe-Weather.tgz
+        wget https://noaa-ufs-srw-pds.s3.amazonaws.com/experiment-user-cases/release-public-v2.1.0/METplus-vx-sample/Indy-Severe-Weather.tgz
         tar xvfz Indy-Severe-Weather.tgz
     fi
-    [[ -f ${platform,,}-${srw_compiler}-skill-score.txt ]] && rm ${platform,,}-${srw_compiler}-skill-score.txt
+    [[ -f ${SRW_PLATFORM,,}-${srw_compiler}-skill-score.txt ]] && rm ${SRW_PLATFORM,,}-${srw_compiler}-skill-score.txt
     # Skill score index is computed over several terms that are defined in parm/metplus/STATAnalysisConfig_skill_score. 
     # It is computed by aggregating the output from earlier runs of the Point-Stat and/or Grid-Stat tools over one or more cases.
     # In this example, skill score index is a weighted average of 4 skill scores of RMSE statistics for wind speed, dew point temperature, 
@@ -126,15 +128,15 @@ if [[ ${RUN_STAT_ANLY_OPT} == true ]]; then
        sed -i 's|--load("conda")|load("conda")|g' ${workspace}/modulefiles/tasks/${platform,,}/run_vx.local.lua
     fi
     # Run stat_analysis
-    stat_analysis -config parm/metplus/STATAnalysisConfig_skill_score -lookin ${workspace}/Indy-Severe-Weather/metprd/point_stat -v 2 -out ${platform,,}-${srw_compiler}-skill-score.txt
+    stat_analysis -config parm/metplus/STATAnalysisConfig_skill_score -lookin ${workspace}/Indy-Severe-Weather/metprd/point_stat -v 2 -out ${SRW_PLATFORM,,}-${srw_compiler}-skill-score.txt
 
     # check skill-score.txt
-    cat ${platform,,}-${srw_compiler}-skill-score.txt
+    cat ${SRW_PLATFORM,,}-${srw_compiler}-skill-score.txt
 
     # get skill-score (SS_INDEX) and check if it is significantly smaller than 1.0
     # A value greater than 1.0 indicates that the forecast model outperforms the reference, 
     # while a value less than 1.0 indicates that the reference outperforms the forecast.
-    tmp_string=$( tail -2 ${platform,,}-${srw_compiler}-skill-score.txt | head -1 )
+    tmp_string=$( tail -2 ${SRW_PLATFORM,,}-${srw_compiler}-skill-score.txt | head -1 )
     SS_INDEX=$(echo $tmp_string | awk -F " " '{print $NF}')
     echo "Skill Score: ${SS_INDEX}"
     if [[ ${SS_INDEX} < "0.700" ]]; then

.cicd/scripts/wrapper_srw_ftest.sh

@@ -24,7 +24,8 @@ fi
 if [[ "${SRW_PLATFORM}" == gaea ]]; 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/${workflow_cmd}_srw_ftest.sh
-    sed -i 's|${JOBSdir}/JREGIONAL_RUN_POST|$USHdir/load_modules_run_task.sh "run_post" ${JOBSdir}/JREGIONAL_RUN_POST|g' ${WORKSPACE}/${SRW_PLATFORM}/ush/wrappers/run_post.sh
+    sed -i 's|00:30:00|00:45:00|g' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
+    sed -i 's|${JOBSdir}/JREGIONAL_RUN_POST|$USHdir/load_modules_run_task.sh "gaea" "run_post" ${JOBSdir}/JREGIONAL_RUN_POST|g' ${WORKSPACE}/${SRW_PLATFORM}/ush/wrappers/run_post.sh
 fi
 
 if [[ "${SRW_PLATFORM}" == hera ]]; then
@@ -66,7 +67,7 @@ do
         # Return exit code and check for results file first
         results_file="${WORKSPACE}/${SRW_PLATFORM}/functional_test_results_${SRW_PLATFORM}_${SRW_COMPILER}.txt"
         if [ ! -f "$results_file" ]; then
-            echo "Missing results file! \nexit 1"
+            echo -e "Missing results file! \nexit 1"
             exit 1
         fi
 

README.md

@@ -1,13 +1,13 @@
 # UFS Short-Range Weather Application
 
-The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth modeling system. NOAA's operational model suite for numerical weather prediction (NWP) is quickly transitioning to the UFS from a number of legacy modeling systems. The UFS enables research, development, and contribution opportunities within the broader Weather Enterprise (including government, industry, and academia). For more information about the UFS, visit the UFS Portal at https://ufscommunity.org/.
+The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth modeling system. NOAA's operational model suite for numerical weather prediction (NWP) is quickly transitioning to the UFS from a number of legacy modeling systems. The UFS enables research, development, and contribution opportunities within the broader Weather Enterprise (including government, industry, and academia). For more information about the UFS, visit the UFS Portal at https://ufs.epic.noaa.gov/.
 
-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 development branch of 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 latest SRW App release (v2.2.0) represents a snapshot of this continuously evolving system. 
+The UFS includes multiple applications (see a complete list at https://ufs.epic.noaa.gov/applications/) that support different forecast durations and spatial domains. This documentation describes the development branch of 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 latest SRW App release (v2.2.0) represents a snapshot of this continuously evolving system. 
 
 The UFS SRW App User's Guide associated with the development branch is at: https://ufs-srweather-app.readthedocs.io/en/develop/, while the guide specific to the SRW App v2.2.0 release can be found at: https://ufs-srweather-app.readthedocs.io/en/release-public-v2.2.0/. The repository is at: 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://ufs-srweather-app.readthedocs.io/en/develop/BuildingRunningTesting/Quickstart.html
+- https://ufs-srweather-app.readthedocs.io/en/develop/UsersGuide/BuildingRunningTesting/Quickstart.html
 
 For a debugging guide for users and developers in the field of Earth System Modeling, please see:
 https://epic.noaa.gov/wp-content/uploads/2022/12/Debugging-Guide.pdf

aqm_environment.yml

@@ -9,5 +9,5 @@ dependencies:
   - pylint=2.17*
   - pytest=7.2*
   - scipy=1.10.*
-  - uwtools=2.1*
+  - uwtools=2.3*
   - xarray=2022.11.*

doc/README

@@ -20,10 +20,11 @@ Steps to build and use the Sphinx documentation tool:
 
 To build html:
 
-$ cd ufs-srweather-app/docs/UsersGuide
-$ make clean && sphinx-build -b html source build
+$ cd ufs-srweather-app/doc
+$ make clean && sphinx-build -b html . build
 
 The "make html" command can often be used in place of the previous command.
+"make doc" will both build the html and run the linkchecker. 
 
 Sphinx uses Latex to export the documentation as a PDF file.  To build pdf:
 

doc/UsersGuide/BuildingRunningTesting/AQM.rst

@@ -123,7 +123,7 @@ The community AQM configuration assumes that users have :term:`HPSS` access and
       USE_USER_STAGED_EXTRN_FILES: true
       EXTRN_MDL_SOURCE_BASEDIR_LBCS: /path/to/data
 
-On Level 1 systems, users can find :term:`ICs/LBCs` in the usual :ref:`input data locations <Data>` under ``FV3GFS/netcdf/2023021700`` and ``FV3GFS/netcdf/2023021706``. Users can also download the data required for the community experiment from the `UFS SRW App Data Bucket <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#input_model_data/FV3GFS/netcdf/>`__. 
+On Level 1 systems, users can find :term:`ICs/LBCs` in the usual :ref:`input data locations <Data>` under ``FV3GFS/netcdf/2023021700`` and ``FV3GFS/netcdf/2023021706``. Users can also download the data required for the community experiment from the `UFS SRW App Data Bucket <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#develop-20240618/input_model_data/FV3GFS/netcdf/>`__. 
 
 Users may also wish to change :term:`cron`-related parameters in ``config.yaml``. In the ``config.aqm.community.yaml`` file, which was copied into ``config.yaml``, cron is used for automatic submission and resubmission of the workflow:
 

doc/UsersGuide/BuildingRunningTesting/ContainerQuickstart.rst

@@ -188,8 +188,8 @@ The SRW App requires input files to run. These include static datasets, initial
 
 .. code-block:: console
 
-   wget https://noaa-ufs-srw-pds.s3.amazonaws.com/current_srw_release_data/fix_data.tgz
-   wget https://noaa-ufs-srw-pds.s3.amazonaws.com/current_srw_release_data/gst_data.tgz
+   wget https://noaa-ufs-srw-pds.s3.amazonaws.com/experiment-user-cases/release-public-v2.2.0/out-of-the-box/fix_data.tgz
+   wget https://noaa-ufs-srw-pds.s3.amazonaws.com/experiment-user-cases/release-public-v2.2.0/out-of-the-box/gst_data.tgz
    tar -xzf fix_data.tgz
    tar -xzf gst_data.tgz
 
@@ -439,4 +439,4 @@ If users have the PBS resource manager installed on their system, the allocation
 
 For more information on the ``qsub`` command options, see the `PBS Manual §2.59.3 <https://2021.help.altair.com/2021.1/PBSProfessional/PBS2021.1.pdf>`__, (p. 1416).
 
-These commands should output a hostname. Users can then run ``ssh <hostname>``. After "ssh-ing" to the compute node, they can run the container from that node. To run larger experiments, it may be necessary to allocate multiple compute nodes. 
+These commands should output a hostname. Users can then run ``ssh <hostname>``. After "ssh-ing" to the compute node, they can run the container from that node. To run larger experiments, it may be necessary to allocate multiple compute nodes. 

doc/UsersGuide/BuildingRunningTesting/RunSRW.rst

@@ -584,7 +584,7 @@ the same cycle starting date/time and forecast hours. Other parameters may diffe
 Cartopy Shapefiles
 `````````````````````
 
-The Python plotting tasks require a path to the directory where the Cartopy Natural Earth shapefiles are located. The medium scale (1:50m) cultural and physical shapefiles are used to create coastlines and other geopolitical borders on the map. On :srw-wiki:`Level 1 <Supported-Platforms-and-Compilers>` systems, this path is already set in the system's machine file using the variable ``FIXshp``. Users on other systems will need to download the shapefiles and update the path of ``$FIXshp`` in the machine file they are using (e.g., ``$SRW/ush/machine/macos.yaml`` for a generic MacOS system, where ``$SRW`` is the path to the ``ufs-srweather-app`` directory). The subset of shapefiles required for the plotting task can be obtained from the `SRW Data Bucket <https://noaa-ufs-srw-pds.s3.amazonaws.com/NaturalEarth/NaturalEarth.tgz>`__. The full set of medium-scale (1:50m) Cartopy shapefiles can be downloaded `here <https://www.naturalearthdata.com/downloads/>`__. 
+The Python plotting tasks require a path to the directory where the Cartopy Natural Earth shapefiles are located. The medium scale (1:50m) cultural and physical shapefiles are used to create coastlines and other geopolitical borders on the map. On :srw-wiki:`Level 1 <Supported-Platforms-and-Compilers>` systems, this path is already set in the system's machine file using the variable ``FIXshp``. Users on other systems will need to download the shapefiles and update the path of ``$FIXshp`` in the machine file they are using (e.g., ``$SRW/ush/machine/macos.yaml`` for a generic MacOS system, where ``$SRW`` is the path to the ``ufs-srweather-app`` directory). The subset of shapefiles required for the plotting task can be obtained from the `SRW Data Bucket <https://noaa-ufs-srw-pds.s3.amazonaws.com/develop-20240618/NaturalEarth/NaturalEarth.tgz>`__. The full set of medium-scale (1:50m) Cartopy shapefiles can be downloaded `here <https://www.naturalearthdata.com/downloads/>`__. 
 
 Task Configuration
 `````````````````````