Address some compiler warnings in UFSATM and stochastic physics: round 1 // Broad WM Documentation Update (#2928)

[NickSzapiro-NOAA]

Commit Queue Requirements:

• This PR addresses a relevant WM issue (if not, create an issue).
• All subcomponent pull requests (if any) have been reviewed by their code managers.
• Run the full Intel+GNU RT suite (compared to current baselines), preferably on Ursa (Derecho or Hercules are acceptable alternatives). Exceptions: documentation-only PRs, CI-only PRs, etc.
  • Commit log file w/full results from RT suite run (if applicable).
  • Verify that test_changes.list indicates which tests, if any, are changed by this PR. Commit test_changes.list, even if it is empty.
• Fill out all sections of this template.

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Description:

#2935

One round of straight-forward fixes for some of the compiler warnings raised in compiling cpld_debug_gfsv17 to improve code quality and prepare for operational implementation

#2928

This PR updates several parts of the UFS WM documentation to include the following. All instances of "Hera" were updated to "Ursa". Common modules in the build/run chapter were updated. Instances of "FV3atm" were updated to "UFSatm". File paths pertaining to the UFSatm and Ursa were updated/added. Default variables were updated in the building/running chapter. FHZ was added to the operational requirement table. HSD run directory path was updated. Directory structure was updated to reflect UFSatm change. Added valid -DAPP configuration options, aswell as updated list of supported physics suites. Added additional cmake build options that were not previously documented, Added three new terms to the glossary. Updated MOM6, CICE6, and HYCOM input files.

Commit Message:

* UFSWM - Address some compiler warnings for cpld_debug_gfsv17 & update documentation
  * UFSATM - Address some compiler warnings for cpld_debug_gfsv17
    * ccpp-physics - Address some compiler warnings for cpld_debug_gfsv17
    * atmos_cubed_sphere - Address some compiler warnings for cpld_debug_gfsv17
  * stochastic_physics - Address some compiler warnings for cpld_debug_gfsv17

Priority:

• Critical Bugfix: Reason
• High: For GFS.v17
• Normal

Git Tracking

UFSWM:

• Part of Compile warnings in UFS and subcomponents #2703
• Closes Update "Hera" to "Ursa" in the documentation #2875

Sub component Pull Requests:

• UFSATM: Address some compiler warnings in UFSATM NOAA-EMC/ufsatm#1025
  • ccpp-physics: Reduce "Explicit interface or EXTERNAL declaration is required" compiler warnings in sfcsub ccpp-physics#312
  • atmos_cubed_sphere: Fix intel debug warnings (implicit i,j,k; explicit mpi interface) NOAA-GFDL/GFDL_atmos_cubed_sphere#396
• stochastic_physics: Address some compiler warnings in stochastic_physics NOAA-PSL/stochastic_physics#93

UFSWM Blocking Dependencies:

• None

Documentation:

• Documentation update required.
  • Relevant updates are included with this PR. This PR includes a documentation update PR
  • A WM issue has been opened to track the need for a documentation update; a person responsible for submitting the update has been assigned to the issue (link issue).
• [] Documentation update NOT required.
  • Explanation:

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Changes

Regression Test Changes (Please commit test_changes.list):

• No Baseline Changes.

Input data Changes:

• None.

Library Changes/Upgrades:

• No Updates

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Testing Log:

• RDHPCS
  • Hera
  • Orion
  • Hercules
  • GaeaC6
  • Derecho
  • Ursa
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
• opnReqTest (complete task if unnecessary)

[gspetro-NOAA]

Tests have passed on all systems, so we can begin the merging process! I'll leave a note on sub-PRs.

[jkbk2004]

@NickSzapiro-NOAA new stochi hash is NOAA-PSL/stochastic_physics@42429ca

[gspetro-NOAA]

@NickSzapiro-NOAA You can go ahead an update .gitmodules and the hashes for UFSATM and stochastic_physics.
NOAA-EMC/ufsatm#1025 @ 6277c9e and NOAA-PSL/stochastic_physics#93 @ 42429ca

[NickSzapiro-NOAA]

Thanks! Please let me know if ok