[develop] Update ufs-weather-model hash to July 9 version (#1383)

* doc/conf.py - Add https://www.nssl.noaa.gov/ to the ignore check listing due to certificate errors
* doc/ContribGuide/contributing.rst - Update URLs for docs.github.com to address warnings
* Externals.cfg - Update ufs-weather-model hash to 5040b33 (July 9)
* parm/wflow/aqm_prep.yaml - Add exclusive flag for task_nexus_emission
* parm/wflow/coldstart.yaml - Add exclusive falgs for task_make_ics and task_make_lbcs
* ush/aqm-use-cases/config.aqm.FallOzone.yaml - Increase walltime from 1 hour and 20 minutes to 2 hours to allow the use case to run on Orion
* ush/aqm-use-cases/config.aqm.AEROMMA.yaml - Increase walltime from 1 hour and 20 minutes to 2 hours to allow the use case to run on Orion
* ush/config_defaults.yaml - Add exclusive to task_nexus_emission, task_make_ics, and task_make_lbcs

Author: MichaelLueken

Externals.cfg

@@ -12,7 +12,7 @@ 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 = 04a67f0
+hash = 5040b33
 local_path = sorc/ufs-weather-model
 required = True
 

doc/ContribGuide/contributing.rst

@@ -9,7 +9,7 @@ Fork and PR Overview
 
    Thank you to the Unified Workflow (UW) team for allowing us to adapt their Fork and PR Model overview for use in the SRW App. The original can be viewed in the `uwtools` :uw:`documentation <sections/contributor_guide/fork_pr_model.html>`.
 
-Contributions to the ``ufs-srweather-app`` project are made via a :github-docs:`Fork<pull-requests/collaborating-with-pull-requests/working-with-forks/about-forks>` and :github-docs:`Pull Request (PR)<pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests>` model. GitHub provides a thorough description of this contribution model in their `Contributing to a project` :github-docs:`Quickstart<get-started/exploring-projects-on-github/contributing-to-a-project>`, but the steps, with respect to ``ufs-srweather-app`` contributions, can be summarized as:
+Contributions to the ``ufs-srweather-app`` project are made via a :github-docs:`Fork<pull-requests/reference/forks>` and :github-docs:`Pull Request (PR)<pull-requests/reference/pull-requests>` model. GitHub provides a thorough description of this contribution model in their `Contributing to a project` :github-docs:`Quickstart<get-started/exploring-projects-on-github/contributing-to-a-project>`, but the steps, with respect to ``ufs-srweather-app`` contributions, can be summarized as:
 
 #. :github-docs:`Create an issue <issues/tracking-your-work-with-issues/using-issues/creating-an-issue>` to document proposed changes.
 #. :github-docs:`Fork<get-started/exploring-projects-on-github/contributing-to-a-project#creating-your-own-copy-of-a-project>` the :srw-repo:`ufs-srweather-app repository<>` into your personal GitHub account.
@@ -18,7 +18,7 @@ Contributions to the ``ufs-srweather-app`` project are made via a :github-docs:`
 #. :github-docs:`Make, commit, and push changes<get-started/exploring-projects-on-github/contributing-to-a-project#making-and-pushing-changes>` in your clone / to your fork. 
 #. When your work is complete, :github-docs:`create a pull request (PR)<get-started/exploring-projects-on-github/contributing-to-a-project#making-a-pull-request>` to merge your changes. 
 
-For future contributions, you may delete and then recreate your fork or configure the official ``ufs-srweather-app`` repository as a :github-docs:`remote repository<pull-requests/collaborating-with-pull-requests/working-with-forks/configuring-a-remote-repository-for-a-fork>` on your clone and :github-docs:`sync upstream changes<pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork>` to stay up-to-date with the official repository.
+For future contributions, you may delete and then recreate your fork or configure the official ``ufs-srweather-app`` repository as a :github-docs:`remote repository<pull-requests/how-tos/work-with-forks/configuring-a-remote-repository-for-a-fork>` on your clone and :github-docs:`sync upstream changes<pull-requests/how-tos/work-with-forks/syncing-a-fork>` to stay up-to-date with the official repository.
 
 
 Development and Testing Process
@@ -179,7 +179,7 @@ All changes to the SRW App ``develop`` branch should be handled via GitHub’s "
 
 * Ensure that your PR is targeting the base repository ``ufs-community/ufs-srweather-app`` and an appropriate base branch (usually ``develop``).
 * **Complete PR template.** Your PR will appear pre-populated with a :ref:`template <pr-template>` that you should complete. Provide an informative synopsis of your contribution, then mark appropriate checklist items by placing an "X" between their square brackets. You may tidy up the description by removing boilerplate text and non-selected checklist items. View :ref:`useful PR template guidance <pr-template-guidance>` and information on :ref:`best practices <tips-best-practices>` for completing each section below.  
-* **Create draft PR.** Use the pull-down arrow on the green button below the description to initially create a :github-docs:`draft pull request<pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests#draft-pull-requests>`. 
+* **Create draft PR.** Use the pull-down arrow on the green button below the description to initially create a :github-docs:`draft pull request<pull-requests/reference/pull-requests>`. 
 
    * Once your draft PR is open, visit its *Files changed* tab and add comments to any lines of code where you think reviewers will benefit from more explanation. Try to save time by proactively answering questions you suspect reviewers will ask.
 

doc/conf.py

@@ -131,6 +131,7 @@
                     r'https://gsl.noaa.gov/',
                     r'https://gsl.noaa.gov/research/predictions',
                     r'https://fvcom.smast.umassd.edu',
+                    r'https://www.nssl.noaa.gov/',
                    ]
 
 # Ignore anchor tags for SRW App data bucket. Shows Not Found even when they exist.

parm/wflow/aqm_prep.yaml

@@ -73,6 +73,7 @@ metatask_nexus_emission:
         value:  '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     nodes: '{{ task_nexus_emission.execution.batchargs.nodes }}:ppn={{ task_nexus_emission.execution.batchargs.tasks_per_node }}'
     walltime: '{{ task_nexus_emission.execution.batchargs.walltime }}'
+    exclusive: '{{ task_nexus_emission.execution.batchargs.exclusive }}'
     envars:
       <<: *default_vars
       nspt: "#nspt#"

parm/wflow/coldstart.yaml

@@ -115,6 +115,7 @@ metatask_run_ensemble:
         value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     nodes: '{{ task_make_ics.chgres_cube.execution.batchargs.nodes // 1 }}:ppn={{ task_make_ics.chgres_cube.execution.batchargs.tasks_per_node }}'
     walltime: '{{ task_make_ics.chgres_cube.execution.batchargs.walltime }}'
+    exclusive: '{{ task_make_ics.chgres_cube.execution.batchargs.exclusive }}'
     dependency:
       and: &make_ics_deps
         taskdep_get_extrn:
@@ -162,6 +163,7 @@ metatask_run_ensemble:
         value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     nodes: '{{ task_make_lbcs.chgres_cube.execution.batchargs.nodes // 1 }}:ppn={{ task_make_lbcs.chgres_cube.execution.batchargs.tasks_per_node }}'
     walltime: '{{ task_make_lbcs.chgres_cube.execution.batchargs.walltime }}'
+    exclusive: '{{ task_make_lbcs.chgres_cube.execution.batchargs.exclusive }}'
     dependency:
       and:
         <<: *make_ics_deps

ush/aqm-use-cases/config.aqm.AEROMMA.yaml

@@ -44,7 +44,7 @@ task_run_fcst:
   fv3:
     execution:
       batchargs:
-        walltime: 01:20:00
+        walltime: 02:00:00
   envvars:
     DT_ATMOS: 180
     OMP_NUM_THREADS_RUN_FCST: 1
@@ -113,4 +113,4 @@ melodies_monet_parm:
         observation_template: <path to AQM data>/Observations/AirNow/AirNow_20230601_20230701.nc
       ish:
         active: true
-        observation_template: <path to AQM data>/Observations/ISH/ISH-Lite_20230601_20230701.nc
+        observation_template: <path to AQM data>/Observations/ISH/ISH-Lite_20230601_20230701.nc

ush/aqm-use-cases/config.aqm.FallOzone.yaml

@@ -43,7 +43,7 @@ task_run_fcst:
   fv3:
     execution:
       batchargs:
-        walltime: 01:20:00
+        walltime: 02:00:00
   envvars:
     DT_ATMOS: 180
     OMP_NUM_THREADS_RUN_FCST: 1

ush/config_defaults.yaml

@@ -1478,6 +1478,7 @@ task_make_ics:
         nodes: 4
         tasks_per_node: 12
         walltime: 00:30:00
+        exclusive: True
       threads: !int '{{ task_make_ics.envvars.OMP_NUM_THREADS_MAKE_ICS }}'
   #-----------------------------------------------------------------------
   # KMP_AFFINITY_MAKE_ICS: 
@@ -1550,6 +1551,7 @@ task_make_lbcs:
         nodes: 4
         tasks_per_node: 12
         walltime: 01:00:00
+        exclusive: True
       threads: !int '{{ task_make_lbcs.envvars.OMP_NUM_THREADS_MAKE_ICS }}'
   #------------------------------------------------------------------------
   #
@@ -2099,6 +2101,7 @@ task_nexus_emission:
       nodes: 4
       tasks_per_node: !int '{{ platform.NCORES_PER_NODE // task_nexus_emission.envvars.OMP_NUM_THREADS_NEXUS_EMISSION }}'
       walltime: 01:00:00
+      exclusive: True
     threads: !int '{{ task_nexus_emission.envvars.OMP_NUM_THREADS_NEXUS_EMISSION }}'
   envvars:
     KMP_AFFINITY_NEXUS_EMISSION: "scatter"