Add support for optional arguments in ccpp physics and framework AND add end of run restart functionality to MOM6 (was #2286)

[climbfuji]

Commit Queue Requirements:

• Fill out all sections of this template.
• All sub component pull requests have been reviewed by their code managers.
• Run the full Intel+GNU RT suite (compared to current baselines) on either Hera/Derecho/Hercules
• Commit 'test_changes.list' from previous step
  • I couldn't - test_changes.list was empty from previous PR, and since my PRs don't change results I can't commit an unmodified file (see 5588f99)

---

Description:

This set of PRs adds support for optional arguments in CCPP physics schemes to the metadata and framework, with related changes in fv3atm, gfdl_atmos_cubed_sphere, and stochastic_physics.

From 2286:
This PR allows the user to create restart files at the end of a run in MOM using the write_restart_at_endofrun configuration option in CMEPS.

Commit Message:

* UFSWM - Add support for optional arguments in ccpp physics and framework 
  * FV3 - [Add support for optional arguments in ccpp physics and framework](https://github.com/NOAA-EMC/fv3atm/pull/807#top)
    * ccpp-physics - Introduce optional arguments in ccpp schemes and metadata
    * ccpp-framework - Add support (and tests) for optional arguments in ccpp_prebuild
    * atmos_cubed_sphere - Set cdata%thrd_cnt in driver/fvGFS/atmosphere.F90
  * MOM6 - Add end of run restart functionality to MOM6
  * stochastic_physics - Add optional attribute for variables where necessary

Priority:

• High: Timeline - my transition to NRL (selfish, I know, sorry) and another large set of PRs (conversion to contiguous arrays) waiting for these changes

Git Tracking

UFSWM Issues:

• Closes add writing end of run restart file in MOM6  #2285

Sub component Pull Requests:

This is part of a large set of PRs:

• Add support for optional arguments in ccpp physics and framework NOAA-EMC/fv3atm#807
• Set cdata%thrd_cnt in driver/fvGFS/atmosphere.F90 NOAA-GFDL/GFDL_atmos_cubed_sphere#338
• Add support (and tests) for optional arguments in ccpp_prebuild NCAR/ccpp-framework#552
• Add missing MPI target in src/CMakeLists.txt NCAR/ccpp-framework#556 (can be scheduled and merged anytime beforehand)
• Introduce optional arguments in ccpp schemes and metadata ccpp-physics#189
• Add optional attribute for variables where necessary NOAA-PSL/stochastic_physics#79
• MOM6: PR Add end of run restart functionality to MOM6 NOAA-EMC/MOM6#133 (PR#2286)

UFSWM Blocking Dependencies:

• None.

---

Changes

Regression Test Changes (Please commit test_changes.list):

• No Baseline Changes - everything is bit-for-bit identical!

Input data Changes:

• None.

Library Changes/Upgrades:

• No Updates

---

Testing Log:

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

[BrianCurtis-NOAA]

@FernandoAndrade-NOAA can you bring in the PR information from the combined PR into this one?

[FernandoAndrade-NOAA]

Ok, we should be all set to continue the merge process, I'll leave a note on the component PRs.

[jiandewang]

Ok, we should be all set to continue the merge process, I'll leave a note on the component PRs.

time ot merge MOM6 ?

[FernandoAndrade-NOAA]

Ok, we should be all set to continue the merge process, I'll leave a note on the component PRs.

time ot merge MOM6 ?

Yes please go ahead and merge in MOM6, we should be all set there.

[jiandewang]

just merged MOM6. Hash # b32aea7bf3

[climbfuji]

fv3atm should be ready to merge, please check

[FernandoAndrade-NOAA]

fv3atm should be ready to merge, please check

All component PRs merged in, please go ahead and revert gitmodules / update hashes, thanks!

[climbfuji]

Thanks for shepherding this PR set through - should be good to go