…ity#209)

* Use top-level build.sh to compile executables in for regression tests
* Do not copy the executable from build to the top-level directory

- All `#ifdef OPENMP` are replaced with `#ifdef _OPENMP` to follow standard compiler macro for OpenMP.
- CCPP code generation is moved inside of `FV3/`.  This will be redundant when the Data Atmosphere component comes in. Updates to the python script was performed to remove the hard-wired `FV3/` path name in the file.
- `cmake/GNU.cmake` and `cmake/Intel.cmake` hard-wire global compiler definitions with `add_definitions`.  These are now applied with `target_compile_definitions`. 
- CMakeLists.txt is passed through cmake-norm checker.
- `INSTALL_INTERFACE` is added, so that this component can be installed and linked in downstream applications e.g. JEDI. 
This may be incomplete, so will need more work.

…ep 1) to develop (ufs-community#216)

Preparation for transitioning to the next-generation code generator of the ccpp-framework (cap_gen.py).

)

Change horizontal advection options by replacing hord=-6 or -8 with hord=6 or 8 in all ~tests/parm/ *.nml.IN files

* Option to build coupled model
* fix in build.sh
* update modulefiles for orion, hera and wcoss to load pio.  Make PIO optional in CMakeLists.txt if not building S2S
* FMS needs to be linked in MOM6 objects. Add 32BIT and S2S check
* add S2S option to MAKE_OPT
* Add standard s2s tests
* add CICE_IO option (default: NetCDF). Add MOM6 solo executable option (default: OFF) MOM6 library and NUOPC cap are 2 separate entities.
* add debug flags for MOM6 and CICE from @MinsukJi-NOAA
* add debug modulefiles for hera, orion and wcoss_dell_p3
* enable VERBOSE on build only when requested.  Remove -warn flags from CMEPS and MOM6 as they drown out any error messages.  The warnings should be resolved at the upstream repos.  When building with -DDEBUG=ON, set CMAKE_BUILD_TYPE=Debug.

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

…fs-community#219)

add RT_suffix for warm start dependencies
add nsout as a variable in model_configure
white space

Fixes CA test for coupled model
Uses RESTART_N for the coupled model
Removes CNTLMED from tests since weather RT does not use it
links parm/fd_nems.yaml from CMEPS/mediator

* add DATM submodule
* point to aerorahul fork of DATM
* update CMakeList.txt to build data atmosphere.  Add compile test only since there are currently no regression tests for data atmosphere
* update README.md
* missed rsync from develop
* Update README.md
* update DATM submodule pointer and point to NOAA-EMC/NEMSdatm
* create MOM6 solo executable for use in SOCA science
* add compilation tests for s2s and datm for hera.gnu
* commit wcoss_cray RT log, hera.intel RT log
* rsync S2S baselines for intel only on hera and orion
* add orion.intel RT log
* add hera.gnu RT log
* add wcoss_dell_p3 RT log

skip-ci

Replaces current coupled tests, default vars and other files to implement low resolution tests from ufs-s2s-model in the unified repository.

See ufs-s2s-model PR # 204 (ufs-community/ufs-s2s-model#204) and PR # 194 (ufs-community/ufs-s2s-model#194) for more detail.

* Added the following files for datm-mom6-cice6 tests:
fv3_conf/cpld_datm_cfsr.IN
fv3_conf/cpld_datm_gefs.IN
parm/datm_configure.IN
parm/datm_data_table.IN
parm/input.mom6.nml.IN
parm/nems.configure.datm.IN
tests/datm_ocn_ice_mx025_cfsr
tests/datm_ocn_ice_mx025_gefs
tests/datm_ocn_ice_mx100_cfsr
tests/datm_ocn_ice_mx100_gefs
Revised default_vars.sh and run_test.sh.
* Removed blank space in some coupled test files.
* Revised scripts.
* Revised test description.
* Revised scripts and added log file from Hera.
* Added log file from Orion.

* update FV3 and NEMS with regional parellel netcdf and output restart/forecast time at non-integer forecast time
* add fv3_ccpp_regional_quilt_netcdf_parallel test
* comment out fv3_ccpp_regional_quilt_netcdf_parallel as it needs nccmp (in PR#261)
* update to nems develop branch
* update orion log files
* update cray and hera RT log files; skip-ci
* update dell log files
* point fv3 and nems back to develop branch
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

This PR adds missing HWRF physics parameterizations and updates the Ferrier-Aligo microphysics:
- WRFv4 Noah LSM
- GFDL surface layer
- Unified HEDMF PBL
- icloud=4 option in RRTMG

In addition, this PR:
- cleans up old/unused/unnecessary HWRF regression tests
- adds the missing `effr_in=.true.` for all Thompson MP based runs (there is now a guard in fv3atm's `GFS_typedefs.F90` to prevent running Thompson MP with `effr_in=.false.`
- shortens the runtime for the `fv3_ccpp_rrfs_v1beta` run from 48h to 24h
- in ccpp-physics: update `tsfc` correctly when there is ice on open water grid points (fixes NCAR/ccpp-physics#515)
- set `OMP_STACKSIZE` in orion and wcoss_dell_p3 job submission scripts to avoid errors with threaded tests

Co-authored-by: Bin Liu <bin.liu@noaa.gov>
Co-authored-by: Jili Dong <Jili.Dong@noaa.gov>
Co-authored-by: Zhan Zhang <zhan.zhang@noaa.gov>
Co-authored-by: Grant Firl <grantf@ucar.edu>
Co-authored-by: Man.Zhang <Man.Zhang@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>

…led model (ufs-community#254)

* Implements a bugfix for the mapping of ifrac for both nems_orig and nems_frac in CMEPS: issue (ufs-community#17)[NOAA-EMC/CMEPS#17]
* Adds field-packing for performance improvements in CMEPS: issue (ufs-community#23)[NOAA-EMC/CMEPS#23]
* Uses module file fv3_debug when DEBUG=Y is specified and fv3_debug is available
* Shortens the nems.configure file name used with the coupled model

…GP. (ufs-community#262)

* Changes to regression test files for recent changes to RRTMG and RRTMGP.
* Removed redundant importing of kind_phys in physics
* add units to index_for_diagnostic_printout metadata
* Replace iovr_{lw,sw} with iovr for HWRF regression tests
* Bugfix in GP sampling routines.
* Increase number of nodes for test fv3_ccpp_gocart_clm on Cheyenne

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* bring GFS.v16 code changes back to develop branch
* update upp lib in hera module
* use test hpc stack lib
* update upp lib in fv3 for cmake
* update post control files
* update upp lib in hpcstack on hera, orion and dell and in nceplibs on cray
* add change in fv3 dycore ufs-community#35
* remove duplicate read_data in fms_mod in external_ic.F90
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

…r-model into gsd/develop

* If ufs.cpld.cpl.r.* files do not reproduce, try nccmp
* Modify/add to run cpld 35d bmark tests
* Fix nccmp implementation. Fix a bug for 35d tests
* Use env var NCCMP
* Add hera.intel to rt_35 and rt_wave_35d
* Use which to find nccmp path. Apply nccmp to all files that fail cmp. Fix a bug in fv3_ccpp_wrtGauss_netcdf_parallel
* Change compare method from nccmp to compare_ncfile.py
* Netcdf compare changes on Hera; skip-ci
* Netcdf compare changes on WCOSS Dell P3; skip-ci
* Modify comopare_ncfile.py
* Netcdf compare changes on wcoss cray
* Implement Dusan's ecflow fix ufs-community#273
* Move miniconda3 to emc.nemspara on Hera and Orion. Minor change in default_vars.sh

…r-model into update_gsd_develop_from_develop_20201118