Merge pull request #110 from climbfuji/update_gsl_develop_from_develo…

…p_20211116

Update gsl/develop from develop 2021/11/17

.github/pull_request_template.md

@@ -7,7 +7,9 @@
 - [ ] An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR 
 are specified below.
 
-- [ ] If new or updated input data is required by this PR, it is clearly stated in the text of the PR.
+- [ ] Results for one or more of the regression tests change and the reasons for the changes are understood and explained below.
+
+- [ ] New or updated input data is required by this PR. If checked, please work with the code managers to update input data sets on all platforms.
 
 ## Instructions: All subsequent sections of text should be filled in as appropriate.
 
@@ -37,6 +39,7 @@ How were these changes tested? What compilers / HPCs was it tested with? Are the
 - [ ] jet.intel
 - [ ] wcoss_cray
 - [ ] wcoss_dell_p3
+- [ ] opnReqTest for newly added/changed feature
 - [ ] CI
 
 ## Dependencies

MOM6-interface/mom6_files.cmake

@@ -189,6 +189,7 @@ list(APPEND mom6_src_files
   MOM6/src/tracer/MOM_generic_tracer.F90
   MOM6/src/tracer/MOM_lateral_boundary_diffusion.F90
   MOM6/src/tracer/MOM_neutral_diffusion.F90
+  MOM6/src/tracer/nw2_tracers.F90
   MOM6/src/tracer/MOM_offline_aux.F90
   MOM6/src/tracer/MOM_offline_main.F90
   MOM6/src/tracer/MOM_tracer_Z_init.F90

cmake/Intel.cmake

@@ -52,3 +52,9 @@ set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_BITFORBIT       "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_BITFORBIT     "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_BITFORBIT "-O2 -fPIC" CACHE STRING "" FORCE)
+
+if(APPLE)
+  # The linker on macOS does not include `common symbols` by default
+  # Passing the -c flag includes them and fixes an error with undefined symbols
+  set(CMAKE_Fortran_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+endif()

doc/UsersGuide/source/BuildingAndRunning.rst

@@ -152,6 +152,24 @@ For the ufs-weather-model S2SW app (atm/ice/ocean/wave):
 
     export CMAKE_FLAGS="-DAPP=S2SW -DCCPP_SUITES=FV3_GFS_2017_coupled,FV3_GFS_v15p2_coupled,FV3_GFS_v16_coupled,FV3_GFS_v16_coupled_noahmp"
 
+For the ufs-weather-model HAFS app (atm/ocean) in 32 bit:
+
+.. code-block:: console
+
+    export CMAKE_FLAGS="-DAPP=HAFS -D32BIT=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf_nonsst,FV3_HAFS_v0_gfdlmp_tedmf,FV3_HAFS_v0_hwrf_thompson,FV3_HAFS_v0_hwrf"
+
+For the ufs-weather-model HAFSW app (atm/ocean/wave) in 32 bit:
+
+.. code-block:: console
+
+    export CMAKE_FLAGS="-DAPP=HAFSW -D32BIT=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf_nonsst,FV3_HAFS_v0_gfdlmp_tedmf,FV3_HAFS_v0_hwrf_thompson,FV3_HAFS_v0_hwrf"
+
+For the ufs-weather-model HAFS-ALL app (data/atm/ocean/wave) in 32 bit:
+
+.. code-block:: console
+
+    export CMAKE_FLAGS="-DAPP=HAFS-ALL -D32BIT=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf_nonsst,FV3_HAFS_v0_gfdlmp_tedmf,FV3_HAFS_v0_hwrf_thompson,FV3_HAFS_v0_hwrf"
+
 ------------------
 Building the model
 ------------------

doc/UsersGuide/source/CodeOverview.rst

@@ -34,6 +34,8 @@ The ufs-weather-model repository supports the short- and medium-range UFS applic
     - https://github.com/noaa-psd/stochastic_physics
   * - Modular Ocean Model (MOM6)
     - https://github.com/NOAA-EMC/MOM6
+  * - HYbrid Coordinate Ocean Model (HYCOM)
+    - https://github.com/NOAA-EMC/HYCOM-src
   * - Los Alamos sea ice model (CICE6)
     - https://github.com/NOAA-EMC/CICE
   * - NOAA/NCEP WAVEWATCH III Model (WW3)
@@ -61,6 +63,8 @@ The umbrella repository for the UFS Weather Model is named ufs-weather-model.  U
    ├── stochastic_physics                      https://github.com/noaa-psd/stochastic_physics
    ├── MOM6-interface
    │    └── MOM6                               https://github.com/NOAA-EMC/MOM6
+   ├── HYCOM-interface
+   │    └── HYCOM                              https://github.com/NOAA-EMC/HYCOM-src
    ├── CICE-interface
    │    └── CICE                               https://github.com/NOAA-EMC/CICE
    ├── WW3                                     https://github.com/NOAA-EMC/WW3
@@ -103,6 +107,10 @@ When the ufs-weather-model is cloned, the basic directory structure will be simi
    │    └── MOM6
    │        ├── src                              --------- MOM6 ocean model
    │        └── config_source/drivers/nuopc_cap  --------- NUOPC MOM6 cap
+   ├── HYCOM-interface
+   │    └── HYCOM                                --------- HYCOM ocean model
+   │        └── NUOPC                            --------- NUOPC HYCOM cap
+   ├── CICE-interface
    ├── CICE-interface
    │    └── CICE                                 --------- CICE6 sea ice model
    │        ├── icepack                          --------- Sea ice column physics
@@ -112,8 +120,8 @@ When the ufs-weather-model is cloned, the basic directory structure will be simi
    │        └── esmf                             --------- NUOPC WW3 cap
    ├── CDEPS-interface
    │     └── CDEPS
-   │         └── datm                            --------- CDEPS DATM
-   │
+   │         ├── datm                            --------- CDEPS DATM
+   │         └── docn                            --------- CDEPS DOCN
    ├── modulefiles          -------- system module files for supported HPC systems
    ├── tests                -------- regression test infrastructure
    │   └── parm