…hanges from IPD, bugfixes for both IPD and CCPP GFSv16, #refs 66372, CCPP changes for HAFS physics, 65796, re-enable NEMSfv3gfs on Gaea and Jet, and in addition: add a stub inline post module for systems that do not have EMC post installed, move ccpp directory from top level directory to underneath FV3 (this includes out-of-source build capabilities for ccpp), update submodule pointer to point to head of GFS-FMS branch of FMS, update ESMF to 8.0.0

…anges_from_gmtb_develop_as_of_20191016

Update ufs-weather-model/develop with changes from gmtb/develop as of 2019/10/16

* Squashed commit from JessicaMeixner-NOAA/ww3update branch
* remove fv3_regional_c768 test on cray
* remove jobs with exclusive nodes on hera and jet
* add ww3 files in rt.sh
* add README.md and reset tasks for rt.sh test fv3_gfdlmprad
* comment out rt.sh fv3_wrtGauss_nemsio_c768 as it takes too long to run
* remove weightfiles for comparison in fv3-ww3 tests
* update regression test log files from dell and cray
* update regression log files on hera
* update fv3atm repo to NOAA-EMC

* Enable outputting a grid (regional_latlon, rotated_latlon, or lambert_conformal) larger than the native computation grid for the regional or nested domain/tile.

* Enable writing out the output on the native computation grid directly without any interpolation for the regional or nested domain/tile.

* Also the missing value in physics bundle is changed from real(kind_phys) to real in io/FV3GFS_io.F90 as the file could be compiled in 32bit real or 64bit real.

fv3atm github issue #13:  change ifmin to zero at fh00 for inline post

* add fh00 post control file, add restart output at specified forecast hours, ugwd bug fixes
* update module files to use g2tmpl v1.6.0 and post v8.0.1
* add fh00 post control file in fv3.input for inline post
* update in runduration in atmos
* update RT baseline directory on hera and wcoss
* comment out fv3_wrtGauss_nemsio_c768 on dell
* update grib2 table for g2tmpl 1.6.0
* update post
* comment out print line in FV3

* update FMS to point to tag 2019.01 of NOAA-GFDL
* update stochastic_physics to point to hash 1745422af76d830757cd6035b6ea101e92b4cac1 @pjpegion
* update of path to CCPP physics library for CCPP regression tests
* add -Wall to compiler flags for GNU compilers
* remove warnings for non-existent include directories for GNU compiler
* update of regression testing scripts to detect errors in tests/run_test.sh
* new regression tests fv3_ccpp_gfs_v15p2, fv3_ccpp_gfs_v15p2_debug, fv3_ccpp_gfs_v16beta, fv3_ccpp_gfs_v16beta_debug
* update of rt.conf: remove Cheyenne.intel entries (so that rt.conf is an EMC-maintained regression test configuration; move Cheyenne Intel tests into a separate file that resides in the NCAR dtc/develop branch)
* make compile_cmake.sh work with Cheyenne Intel/GNU, and bugfixes for compile_cmake.sh
* allow environment variable NEMS_MACHINE to overwrite (or set) MACHINE_ID (see #20 for the corresponding PR for the ufs_public_release branch)
* new regression test fv3_ccpp_gsd_sar_25km_debug (but not exercised in default rt.conf)
* updates for jet and gaea (note: only supporting rt.sh, not NEMSCompsetRun)

* Updated fv3atm (see fv3atm PR #48 NOAA-EMC/fv3atm#48)
* Updated WW3

* update parallel netcdf module files on dell

* update fv3 to netcdf_parallel branch

* update module files for hera, dell and conf file for cray

* update post lib in cray module file

* fix netlib on hera

* Update FV3 submodule

* Update baselines to develop-20200202

* Regtest logs on wcoss_dell_p3

* Regtest logs on wcoss_cray

* Regtest logs on hera

* update FV3 to point to NOAA-EMC develop branch

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>

* update with new iau_drymassfixer option
* fix syntax error in fv3
* update fv3_iau test case
* revert iau-drymassfixer change in fv3_gfdlmprad_32bit_post
* update ww3 with bug fix for OpenMp b4b
* update fv3 with coupled model dump field changes
* update nemscompset run c768 fv3-ww3 to use threads
* update NEMS to the latest version
* update post lib to 8.0.5

* add 2 way atm-wav test

* update FV3 with gcycle change reverted

* update RTPWD and change the coupling frequency

* update RT baseline directory

* Regression test log files on WCOSS Dell

* Regression test log files on WCOSS Cray

* Regression test log files on Hera

* Update FV3 submodule

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* Update FV3 submodule

* Regression test log files on Hera

* Regression test log files on WCOSS Cray

* Regression test log files on WCOSS Dell

* Update FV3 submodule

* hera.gnu build target with regression test config rt_gnu.conf (same as used on Cheyenne); this initial version uses the UFS public release v1.0.0 NCEPLIBS
* re-enable IPD REPRO, CCPP REPRO, CCPP PROD regression tests; IPD REPRO and CCPP REPRO are bit-for-bit identical
* bugfixes for some CCPP regression tests (IAU dry mass fixer)
* addition of two-way coupled CCPP regression tests, removal of old IPD Thompson test, addition of several debug tests (Thompson non-aero and GSD suite) to cover more physics options in DEBUG mode
* change logic in rt.sh that COMPILE or APPBUILD lines without a machine name are executed on all machines (similar to what is done for the RUN lines)

…physics (#91)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing

* Regression test logs for hera.intel using rt.sh

* Regression test logs for wcoss_dell_p3 using NEMSCompsetRun

* Update submodule pointer for FV3 after renaming S2S suite suite_FV3_GFS_2017_coupled_satmedmf.xml to suite_FV3_GFS_2017_satmedmf_coupled.xml

* Regression test logs for wcoss_dell_p3 using rt.sh; regression test logs for wcoss_cray using rt.sh and NEMSCompsetRun

* Regression test logs for hera.intel using NEMSCompsetRun

* Revert change to .gitmodules and update submodule pointer for fv3atm

Add two options for IN/CCN activation and have total three options now:
* iccn=0 for temperature dependence, iccn=1 for climatological IN/CCN, and iccn=2 for MERRA2aersol
* add the option to enable RRTMg aerosol attenuation to be determined from prescribed MERRA2 climatology
* add aerosol optical depth outputs for total, dust, black carbon, organic carbon, sulfate, and sea salt

Add 4 regression tests:
 1) SAS+GFDL with enabled RRTMg aerosol attenuation from prescribed MERRA2 climatology (fv3_gocart_clm in rt.conf_csaw),
 2) CSAW+MG3 with with enabledRRTMg aerosol attenuation from prescribed MERRA2 climatology (fv3_gfsv16_csawmg  in rt.conf_csaw),
 3) CSAW+MG3 with enabled RRTMg aerosol attenuation from OPAC (fv3_gfsv16_csawmgt in rt.conf_csaw), and
 4) CSAW+MG3 with climatological IN/CCN with enabled RRTMg aerosol attenuation from prescribed MERRA2climatology (fv3_csawmg)

* add s4 rules

* update submodule pointers

* update the branch in gitmodules to point to NEMS::feature/s4

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Merge NCAR:dtc/develop into ufs-community:develop

- for macOS with LLVM clang, turn off OpenMP (from UFS public release)
- switch to Intel 18 on wcoss_cray
- new regression tests with RRTMGP using current control as basis

Co-authored-by: Rahul Mahajan <rmahajan@s4-submit.ssec.wisc.edu>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>

* Remove CCPP dynamic build from ufs-weather-model
* Remove LD_LIBRARY_PATH entries in regression test setup scripts

* update post lib to 8.0.6
* Add chsp to gfsphysics and ccpp-physics
add global_latlon grid on write grid comp for netcdf output
add landsfcmdl attribute to fv3 sfc history file
update post to post/8.0.6
* Bugfix for Intel 18 on wcoss_cray, remove Intel 16 options for gaea
* add global latlon grid test
* Add regression tests for lheatstrg to IPD REPRO, CCPP REPRO, CCPP PROD; add regression tests for satmedmfvidfq for IPD PROD, IPD REPRO, CCPP REPRO, CCPP PROD; add ecflow config for cheyenne
* add cmeps integration changes

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Jongil Han <Jongil.Han@noaa.gov>
Co-authored-by: Jeffrey Whitaker <Jeffrey.S.Whitaker@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: Denise Worthen <Denise.Worthen@noaa.gov>
Co-authored-by: Jun Wang <junwang@Orion-login-3.HPC.MsState.Edu>

Updates to cellular automata stochastic physics. Added new regression test. Added possibility to run global and sub-grid CA, updates to coupling to convection.

* Remove unused and unsupported code (See #21)
* Remove APPBUILD step from rt.conf

…c-v4 back to master (#120)

* Bugfixes for CCPP: check for and correct syntax of \htmlinclude lines
* Fix formatting (tabs, whitespaces) in tests/rt.conf

…te regional tests, ... (#126)

* Move ccpp_prebuild from build scripts to CMakeLists.txt
* Add find_package(Python) to CMakeLists.txt
* Update to compile scripts and top-level CMakeLists.txt for not specifying suites for CCPP
* Update of regional tests to reflect changes in suite definition files
* Use cmake 3.16.1 on hera
* Require cmake 3.15 or later in top-level CMakeLists.txt
* Bugfix in tests/fv3_conf/ccpp_regional_run.IN
* Python 3 compatibility for tests/abort_dep_tasks.py

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

* update orion slurm job card

* udpate orion log files

* update hera log files

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

…gi, check for GNU compiler version (#139)

* update stampede config, remove cheyenne.pgi config, bugfixes for Python3 on stampede (from @climbfuji)
* check version of GNU compiler #134 (from @edwardhartnett)
* submit compile jobs with ecflow to batch system instead of running them on frontend nodes (from @DusanJovic-NOAA)

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

…with GNU compiler (segmentation fault) (#140)

* tests/rt_gnu.conf: turn off IPD tests, no longer working on Cheyenne with GNU compiler (segmentation fault)
* update of jet modulefile and correction of cmake name from jet to jet.intel (to match gnumake)

Changes in this PR:

* add a new regression test that uses the HWRF versions of saSAS deep and shallow convection
* update how the sutils module is loaded on hera and jet
* contains @MinsukJi-NOAA's unit testing branch
* contains @DusanJovic-NOAA's butterfly effect branch (changes in GFDL_atmos_cubed_sphere only)

Note: The changes in the ccpp-physics PR NCAR/ccpp-physics#423 lead to different results for two existing regression tests in PROD mode: fv3_ccpp_regional_c768 and fv3_ccpp_stretched_nest. In a separate comment below, I will describe in detail my investigation that allowed me to conclude that this change is acceptable.

Co-authored-by: MinsukJi-NOAA <Minsuk.Ji@noaa.gov>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* Update FMS to the 2020.02 version
* Add -DENABLE_QUAD_PRECISION in the compiling flag when QUAD_PRECISION=Y (DEFAULT). Starting with FMS 2019.01.01, quad-precision arithmetic is enabled it the ENABLE_QUAD_PRECISION macro. This is used to determine whether certain grid metric terms code within FMS/FV3-dycore use quad-precision arithmetic.
* Revise CMakeList to work with FMS 2020.02
* Use write component instead of FMS2 IO for ccpp_regional_c768

* GFS.v16.0.4 physics udpate
* remove whitespaces in sfc_diff.f
* keep z0 unchanged in coupled mode in sfc_diff.f
* fix IPD run

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Update modulefile for hera.gnu
* build.sh: bring in update from public release branch
* cmake/configure_jet.intel.cmake: bugfix for Jet to compile CCPP with multiple SIMD instructions

…155)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing

* Regression test logs for hera.intel and hera.gnu

* Regression test logs for orion.intel

* Regression test logs for wcoss_cray and wcoss_dell_p3

* Revert change to .gitmodules and update submodule pointer for fv3atm

- updates to GSL regression tests, add three tests to `rt.conf`, remove unnecessary regression test configuration files for GSL physics
- turn on AVX2 flags for wcoss_dell_p3

* Add the option to run regression test with MULTI_GASES=Y
* Add multi_gases CCPP regression test

* add Toms dycore regional DA fix
* update hera intel RT log files
* update fv3 with levp change
* upate baseline to develop-20200713
* copy regional control RESTART

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Allow multiple regtest ecflow suites to run on the same server
* implement running a single rt test
* Update 'usage' function in rt.sh (added -n option)

Co-authored-by: MinsukJi-NOAA <Minsuk.Ji@noaa.gov>

* add PR templates for feature and bugfix
Change-Id: Iad15dd1a584f4bd2fbaadf88359a55efd7b1925c
* add codeowners for automatic review requests
Change-Id: If6050e6411519223f514435801e09a63ed696a02
* Update CODEOWNERS

* This is EMC flake model
* Updated .gitmodules file under ufs-weather-model and tests/rt.conf
* Updated .gitmodules file under usf-weather-model
* Point to fv3 flake branch
* Updated ccpp_gfs_v16_flake_run.IN to use the new oro data for flake test
* Updated the following files and directories
* update to  the latest ccpp/physics branch
* Updated compile and regression test log files
* Updated ccpp-physics
* point to NOAA-EMC fv3 repo

…0/07/21) (#173)

- new regression test configurations for `fv3_ccpp_rrfs_v1beta` and `fv3_ccpp_rrfs_v1beta_debug` (required for SRW App release)
- added `fv3_ccpp_rrfs_v1beta` test to various `rt*.conf` files; note: not adding `fv3_ccpp_rrfs_v1beta_debug` because this test crashes on hera with both Intel and GNU (it runs on Cheyenne with Intel but not with GNU) - see issue #174
- moved the flake regression test in `rt_gnu.conf` from the DEBUG to the PROD section (this was a mistake not caught in the previous PR when flake was merged)
- remove all `tests/Compile*.log` log files

Top level CMakeLists.txt and CMakeLists.txt file in FV3 have been changed (and cleaned up) to use imported targets (mostly for NCEPLIBS).
Remove *.appBuilder compsets and log.
Remove outdated doc directory

…on Tier-2 platforms (#177)

- updates the modulefiles and cmake configurations for Tier-2 platforms in order to work with the new NCEP libraries (imported targets)
- cleans up cmake configurations (AVX2 flags, DEBUG and REPRO mode) and declares SIMDMULTIARCH flags as a real alternative to the AVX2 flags
- removes old build targets cheyenne.intel-mpi and supermuc-phase2.intel
- clean up of build.sh

Downgrade FMS to 2019.01.03.
Small changes in cmake build system due to FMS version change.
Improve error handling in rt.sh when ecflow is used. Scripts cleanup and refactoring.

* Update CMakeLists.txt to build stochastic_physics
* Update gnumake build to include stochastic_physics wrapper
* Update gnumake build config for macosx.gnu to work with new NCEPLIBS and downgraded FMS
* Update submodule pointer for fv3atm
* Regression test logs for orion.intel, hera.intel, hera.gnu
* Rename rt_stampede_cheyenne.conf to rt_stampede.conf, add rt_cheyenne.conf for cheyenne.intel from NCAR dtc/develop branch
* Regression test logs for wcoss_cray and wcoss_dell_p3
* Revert stochastic_physics change in .gitmodules and update submodule pointer for stochastic_physics
* Revert change to .gitmodules and update submodule pointer for fv3atm
* Revert unintential addition of tests/rt_stochy_ca.conf

Add functionality to use the GFS suite definition files (SDFs) with the RRTMGP radiation scheme. v15p2 and v16beta.

#183)

Diagnostic cldfra array outputs 3D instantaneous cloud fractions. Works with WSM6, Thompson and GFDL mp schemes.
Provided a bug fix to GFS_restart.F90 with an if condition added in the ifdef CCPP block to test for reflectivity flag.  
No results changed.

* udpate to netcdf 4.7.4 release and esmf810bs21
* update netcdf4.7.4.release and esmf810bs21 on hera
* update module files on dell and cray
* update gcc module and conf file on cray
* update fv3 merged with latest develop branch
* change mom6 src directory in nems
* add a parallel netcdf test
* merge rt_orion.conf into rt.conf
* update nems for ww3 build
* update log files from hera
* remove rt_orion.conf and update orion log files
* update log files from cray and dell
* Updates of hera.gnu build config
* fix esmf810bs21 module and update hera intel and gnu log files
* point fv3 and nems back to NOAA-EMC repo

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Chnage default tasks per node on Orion. Cleanup tests configuration files.
* Delete old Theia job card templates
* Remove NAM physics switches from conf/configure.fv3.*, remove endeavor.intel build config, remove tests/rt_cheyenne.conf
* modulefiles/orion.intel/fv3: bugfix, remove old post-intel-sandybridge/8.0.5 module
* Update tests/rt.conf: add cheyenne, remove unnecessary COMPILE lines, rearrange tests
* conf/configure.fv3.orion.intel: remove legacy CCPP-STATIC switches

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

* update to pre-existing land perts scheme, ready for addition of the new scheme
* updates to land perts scheme, so that namelist input and control_type variables are in generic (i.e., variable agnostic) arrays
* Phil's ccpp changes
* minor bug fix
* Comitting stochastic physics updates
* Comitting FV3 submodules updates
* Updates for minimal set of regression tests.
* lndp sub-module clean-up
* Updates to tests to include new input parameters for revised land pert scheme (lndp).

* Update modulefiles for cheyenne.{gnu,intel}, gaea.intel, jet.intel; change  modulefile for hera.gnu so that it matches the other modulefiles
* Correct typo EMSF -> ESMF in modulefiles

Add the capability to specify dependencies for CCPP modules/DDTs/schemes in the scheme metadata. This allows us to remove the DDT/scheme dependency information from the CCPP prebuild config in fv3atm and only compile the dependencies and schemes that are used by the selected suite definition files. Until now, all schemes and scheme dependencies are compiled, regardless whether they are in use in any of the selected suites.

Add compiler flags for gfortran-10

Don't run csawmg tests on Cheyenne, both crash with a "bus error"

* add ci-related files. update utest
* modify to auto-run different cases based on ci.test
* Improve CI workflow
* Separate builds and tests into different jobs
* Separate input data from build image; instead, use it as a volume before running tests
* Make ci subdirectory to contain ci-related files
* add clean-up after utest run
* add workflow manage files
* move parsing in main.yml to a separate script file

…h, fix RRTMGP regression tests (#201)

* Enable inline post for gnumake builds on hera.gnu, cheyenne.intel, cheyenne.gnu; skip-ci
* Update pull request template, use correct Python interpreter when calling ccpp_prebuild.py in CMakeLists.txt; skip-ci
* tests/rt_utils.sh: remove machine-dependent configuration; skip-ci
* Update ESMF from 8.1.0bs21 to 8.1.0bs27 on almost all machines; skip-ci
* Update .gitmodules and submodule pointer for fv3atm for code review and testing; skip-ci
* Fix RRTMGP regression test setups, temporarily disable RRTMGP tests in tests/rt.conf and tests/rt_gnu.conf
* Updates for docker/ci
* Add note about unit test availability to pull request template
* Update rt.sh configuration for jet, remove tests/rt_rrtmgp.conf, add tests/fv3_conf/compile_slurm.IN_jet

* add link_mpi=dbg for debug test
* add dbg_mt in debug option when OPENMP is on
* update log files for hera, orion, wcoss cray and dell; skip-ci
* update hera.gnu log file
* Set DEBUG_LINKMPI=OFF for cheyenne.intel and gaea.intel; fix post library dependencies for cheyenne.{intel,gnu} gnumake config
* Regression test log for cheyenne.intel

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* update to latest WW3, 
* update to latest NEMS and stochastic physics branches
* point to new baseline in rt.sh
* wcoss_dell_p3 log, wcoss_cray log, hera.intel log,* orion.intel log

…193)

- updates `.gitmodules` and the submodule pointer for fv3atm for code review and testing of the following changes in fv3atm and ccpp-physics:
    - add two new cloud overlap methods for RRTMG to ccpp-physics - see detailed description in NCAR/ccpp-physics#477.
    - add necessary variables to `GFS_typedefs.{F90,meta} and fix a few metadata entries - see NOAA-EMC/fv3atm#157
- contains changes from @DusanJovic-NOAA from branch https://github.com/DusanJovic-NOAA/ufs-weather-model/commits/update_compile_script that removes the old gnumake `compile.sh` script and replaces it with the new cmake `compile_cmake.sh` script (which is renamed to `compile.sh`)
- contains follow-up work in the regression test scripts to use `NEMS_COMPILER` throughout instead of a mixture of `NEMS_COMPILER` and `COMPILER` (note: `NEMS_COMPILER` should be renamed to something like `UFS_COMPILER` or `RT_COMPILER` in the future, along with corresponding changes for `NEMS_MACHINE` etc.)
- fixes the `readlink` command in the top-level `build.sh` and in `tests/compile.sh` for macOS (similar to what was done for branch release/public-v1
- remove lines `cp ${PATHRT}/../FV3/ccpp/suites/suite_${CCPP_SUITE}.xml suite_${CCPP_SUITE}.xml` from `tests/fv3_conf/ccpp*.IN`, i.e. no longer copy suite definition files to regression test run directories
- replace GSL drag suite with CIRES UGWP/GFS GWD in `tests/tests/fv3_ccpp_rrfs_v1beta` and `tests/tests/fv3_ccpp_rrfs_v1beta_debug` (cherry-picked from PR #205 for branch release/public-v2)

…ry update in dycore (#208)

- updates the submodule pointers for fv3atm, GFDL_atmos_cubed_sphere and ccpp-physics for the following changes:
    - bugfixes for CCPP tendencies output (from @grantfirl)
    - global restart reproducibility (from @SMoorthi-emc)
    - bugfix for halo boundary layer update in FV3 dycore (from @chan-hoo)
- moves directory `parm` into directory `tests`
- updates regression test run scripts for HAFS and SAR to copy input data (`diag_table`, `field_table`, initial conditions) from the regression baseline instead of a temporary directory on hera
- note: the following existing diag_table files in the regression test baseline directory `FV3_input_data_gsd` have been updated to match the requirements for running cycled experiments with the GSL physics (@jkhender @joeolson42 FYI)
    - diag_table_gf_thompson
    - diag_table_gsd_noah
    - diag_table_gsd_ruc
    - diag_table_gsd_ruc_diag3d

* 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 (#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>

)

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 (#254)

* Implements a bugfix for the mapping of ifrac for both nems_orig and nems_frac in CMEPS: issue (#17)[NOAA-EMC/CMEPS#17]
* Adds field-packing for performance improvements in CMEPS: issue (#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. (#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 #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>