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Merge feature/no_physics_dependencies_based_on_dev_emc into release-stable (aka "overwrite release-stable with climbfuji's branch") #6

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Description

This PR merges feature/no_physics_dependencies_based_on_dev_emc into release-stable and applies additional changes so that release-stable is identical to feature/no_physics_dependencies_based_on_dev_emc.

Issue(s) addressed

This PR is required for updating JEDI to a later version of the FV3 dycore (branch dev/emc of https://github.com/noaa-gfdl/atmos_cubed_sphere with additional changes on top of it, added by @climbfuji to be able to build the branch without the CCPP framework and physics dependencies).

Dependencies

Associated PRs:

Impact

See required changes in fv3-jedi-linearmodel, fv3-jedi, jedi-bundle

Checklist

  • I have performed a self-review of my own code
  • I have made corresponding changes to the documentation
  • I have run the unit tests before creating the PR

XiaqiongZhou-NOAA and others added 30 commits June 11, 2020 12:57
Modify the halo extents of u and vt in the regional_boundary_update call
Merge dev/emc branch from upstream (NOAA-GFDL/GFDL_atmos_cubed_sphere)
…all that caused a reproducibility issue. (NOAA-GFDL#55)

Co-authored-by: Chan-hoo.Jeon <chan-hoo.jeon@noaa.gov>
…public-v2

Revert "merge ufs-release/public-v2 -> dev/emc"
Merge 'regional_boundary_update' from upstream
* updating doxygen documentation as requested from EMC for UFS MRW release of version 1.1

* updated documentation for ufs v1.1 specifically: updated d2_bg_k2 description per Jeff Whitaker, and removed sections A.2, A.8, and A.9 from the documentation Parameters List.

* Further updates to ufs documentation

* removing version number form Doxyfile

Co-authored-by: bensonr <6594772+bensonr@users.noreply.github.com>
Add a positive-definite advection option
JiliDong-NOAA and others added 16 commits April 18, 2023 23:23
* Bringing over internal updates to nh_core and nh_utils which includes a revision to the semi-implicit solver to linearize vertical sound wave propagation about the hydrostatic state.

* resolve inconsistent use of single and double precision in rayleigh damping.  Address spacing change.

* rename tau_w

* Modify the rff calculation to be fully double precision.  Fixed a mistake in the previous cherry-pick commit

* fully implement the name change of tau_w to fast_tau_w_sec
… intrinsic functions instead of a loop nest in range_check_3d()
dev/emc: Release FV3 Solver Updates (cherry-pick)
…s_quilting_restart

Write BCs restart files from fv_dyn_restart_output
Update to latest in order to merge hafs-rangeCheck3d into mainline.
…tmos_cubed_sphere into feature/no_physics_dependencies_based_on_dev_emc_20230717
…ttps://github.com/jcsda/gfdl_atmos_cubed_sphere into HEAD

2. Resolve conflicts and make release-stable identical to feature/no_physics_dependencies_based_on_dev_emc
@climbfuji climbfuji requested a review from shlyaeva May 14, 2024 20:38
@climbfuji climbfuji added INFRA JEDI Infrastructure ALGO JEDI Algorithms labels May 14, 2024
@climbfuji climbfuji self-assigned this May 14, 2024
@svahl991
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Coordinated merge for this is planned for Monday, July 1. Are there other qualified reviewers we could add? Anna is on PTO until Monday.

@aerorahul
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Despite looking like a big change of 96 files, the actual changes between dev/emc and this branch results in 24 changed files.

gfdl/CMakeLists.txt jcsda/CMakeLists.txt
gfdl/cmake/compiler_flags_Intel_Fortran.cmake jcsda/cmake/compiler_flags_Intel_Fortran.cmake
gfdl/driver/fvGFS/atmosphere.F90 jcsda/driver/fvGFS/atmosphere.F90
gfdl/driver/fvGFS/fv_nggps_diag.F90 jcsda/driver/fvGFS/fv_nggps_diag.F90
gfdl/driver/fvGFS/fv_ufs_restart_io.F90 jcsda/driver/fvGFS/fv_ufs_restart_io.F90
gfdl/model/fv_arrays.F90 jcsda/model/fv_arrays.F90
gfdl/model/fv_control.F90 jcsda/model/fv_control.F90
gfdl/model/fv_dynamics.F90 jcsda/model/fv_dynamics.F90
gfdl/model/fv_fill.F90 jcsda/model/fv_fill.F90
gfdl/model/fv_mapz.F90 jcsda/model/fv_mapz.F90
gfdl/model/fv_nesting.F90 jcsda/model/fv_nesting.F90
gfdl/model/fv_regional_bc.F90 jcsda/model/fv_regional_bc.F90
gfdl/model/fv_sg.F90 jcsda/model/fv_sg.F90
gfdl/model/molecular_diffusion.F90 jcsda/model/molecular_diffusion.F90
gfdl/model/multi_gases.F90 jcsda/model/multi_gases.F90
gfdl/tools/external_ic.F90 jcsda/tools/external_ic.F90
gfdl/tools/fv_diagnostics.F90 jcsda/tools/fv_diagnostics.F90
gfdl/tools/fv_grid_tools.F90 jcsda/tools/fv_grid_tools.F90
gfdl/tools/fv_iau_mod.F90 jcsda/tools/fv_iau_mod.F90
gfdl/tools/fv_io.F90 jcsda/tools/fv_io.F90
gfdl/tools/fv_nudge.F90 jcsda/tools/fv_nudge.F90
gfdl/tools/fv_restart.F90 jcsda/tools/fv_restart.F90
gfdl/tools/module_diag_hailcast.F90 jcsda/tools/module_diag_hailcast.F90
gfdl/tools/test_cases.F90 jcsda/tools/test_cases.F90

I inspected and diff-ed these files individually, and note the following:

  • ecbuild is removed from the build in this PR
  • NO_PHYS option is added
  • HYDRO option is removed. This option set MOIST_CAPPA and USE_COND which would conflict w/ NO_PHYS (I assume)
  • lots of little code updates to .F90, which will be resolved if this PR branch is rebased on dev/emc sooner rather than later.

I did not compile and run any tests. The changes look right to me.

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See detailed review comment here
Changes look good.

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