ufs-community#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 <[email protected]>
Co-authored-by: Dom Heinzeller <[email protected]>

* 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 <[email protected]>

* 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).

…nity#191)

* 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"

…r-model into gsd/develop

…nd testing

* 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 (ufs-community#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 <[email protected]>
Co-authored-by: Dom Heinzeller <[email protected]>

* 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

…fs-community#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 ufs-community#205 for branch release/public-v2)

…ry update in dycore (ufs-community#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

…r-model into update_gsd_develop_from_develop_20200903