…3-jun-27 (ufs-community#1811)

* WW3: updates

* Add new BL_DATE

Update inline post with:

*Clean up legacy code in inline post interface

*Relocate computation of diagnostic variables

*Sync changes from offline post interface

*Update upp revision

* Update empty_output_bundle

* Update pull_request_template.md from 1813

Co-authored-by: Brian Curtis <Brian.Curtis@noaa.gov>
Co-authored-by: Dusan Jovic <Dusan.Jovic@noaa.gov>

* Update control_CubedSphereGrid_parallel test

* The control_CubedSphereGrid_parallel test has been updated to run post
and create native grid history files

* reverting the bug fix for ktherm=2 allows all cpld tests to pass
and the single datm test using ktherm=2 (datm_cdeps_gfs) to also pass
all other datm tests which use ktherm=1 fail

* update CICE

* change freq in for ice_diag.d global values

* remove unused history* settings

* update DISKNM with epic and rt log

* Update bl.py for new Hera blstore

* add gridtype to gocart CAP.rc

* move to GOCART 20230227 version with threading capability

* udpate to netcdf/4.9.2 and add threading capability for gocart

* update esmf library

* update GOCART to allow no-Nitrates run

…r CMEPS (ufs-community#1807)

* commit changes for sensible heat flux

* add sensible heat changes

* update submodules and fd for evap fields

* backup to pre-evap changes to test

…s-community#1864)

* modify mom6_files.cmake to reflect files being removed/added

* update FV3 submodule pointer after GT combined his physics PRs

…ng PR#1863) (ufs-community#1844)

* Changes to logging and initialization of the CLM Lake Model.
* merge ccpp-physics NCAR#91 (UFS-SRW v3.0.0 SciDoc updates)

1. Use ice thickness hice(i) to find the level in the lake where ice is
   zero.
2. Do not allow lake temperature to be below freezing point if there is
   no ice.
3. If there is no snow or ice, do not allow surface lake temperature to
   be below freezing point.
   These changes fixed the problem with large errors in the energy budget
   at the beginning of the cold-start run with lakes.
4. Added flag to turn on debug print statements in the CLM lake model.

* explicitly turn of frac_ice for flake

* t_grnd(i) should be t_grnd(c)
-------------------------------------------------------------------
Co-authored-by: Samuel Trahan <samuel.trahan@noaa.gov>
Co-authored-by: Grant Firl <grant.firl@noaa.gov>

…ity#1707)

*Modulefiles to be updated through this PR include: Acorn, Gaea, Hera, Jet, Linux, MacOSX, Orion, NOAA Cloud (Parallelworks), and S4 to spack-stack 1.4.1.

*Update Cheyenne's fv3_conf files to address switch from mpt to impi, 

* Update hdf5 version in ufs_common; 

* Update ufs_common, ufs_orion.intel; cherry-pick GOCART parm file and hash updates from Jun's newmapl branch.

* update CMEPS w/ fix for error condition

update cmeps build to implement check4nans feature using module stored in cdeps repo

* make pio rearranger=box the default for all tests

* update configurations for ocnalb changes

* set the ocean albedo limit in config and use it to set logical
flag
* albdir and albdif can be set as non-std values in nems.configure
will default to 0.07 and 0.06 if not set

* ocean albedo changes were merged at ESCOMP

* fix variable name in 2 nems.configure files

* update CMEPs with fioi_swpen fix

* remove albedo limiter for DATM cases

… & FV3_HRRR_gf (ufs-community#1880)

* replacement 13km conus regtests

* delete old conus13km tests

* temporary file with list of new tests

* fix errors in new compile lines

* simplify test specifications for hrrr and conus13km

* bug fix to quilt servers & use clm lake in hrrr c3 & gf

* correct errors in rt.conf for new tests

* revert bug fix to avoid a GFDL_atmos_cubed_sphere PR

* missing a "+ hera cheyenne" for one new test

…bining PRs ufs-community#1853 & 1834) (ufs-community#1467)

* Update fms to 2022.04. Update acorn modulefiles

* Remove fms_io_nml and mpp_io_nml namelists from input.nml templates

* Update FMS to 2023.01

* Use netcdf4 fms2_io option

* replace tabs with spaces

* Update rt.sh to allow creating new baselines only for a subset of tests

* Update rt.sh to run compile tasks only if needed during baseline creation (-b option)

* Revert MAX_BUILDS back to 10

* Fix hrrr qutlting restart tests.

* update module file

* update rt.conf with pdlib tests on wcoss2

…1870)

* 2D advection of cellular automata

* add Configuration.rst change from 1804

* add Glossary.rst change from 1804

* Delete doc/UsersGuide/build/.gitignore

…fs-community#1823)

* add fv3atm/mom6/cice6 run time info

* update fv3 and cice

* fix mom6 output

* use Denises cice6 branch and fix atm log file

* using stdout for mom6 timing info

* update mom6 runtime

* update CICE and mom6 output log file

* remove icepack_zsalinity.F90

* add stochastic parameterization perturbations to support to Grell-Freitas deep convection

* fix reproducibility issue in G-F deep convection

* WW3: CI fix

* MYNN SFC OpenACC directives

* Update rt.sh

* Create RegressionTests_noaacloud.log

* Create Jenkinsfile.noaacloud

* Update rt.conf

* Update bl.py

* Update several RT files to add Hercules support. Add hercules intel lua file.

* Update rt.sh

* Use dusan's formatting in ufs_common. Change hdf5 version.

* Update rt_utils.sh

* Remove git diff syntax from rt_utils.sh

* Add regnerated cdeps_share files; add DCPRGNU and DCPRINTEL flags to CMEPS and CDEPS CMakeliststo allow for GNU builds; remove the Intel compiler directive in the current cdeps_share files.

* turn off control_wam_debug for intel as well

move CPRGNU CPP flag to apply to all gnu versions (fixes hera failures)

* Add Hercules as a machine in pull_request_template.md

* update CICE

* remove comment lines from genf90.pl preprocessing

* Update bl_date.conf

…a variables (ufs-community#1903)

* Update fv3atm io routines to use same type kind for both axes and data variables

*add pbl_tapering for SPPT

*Add possibility to run the CA on a single tile, ensure decomposition of domain is proportional between the atmosphere domain and the higher resolution CA domain

…sics, and string length mismatch in dycore (plus PR ufs-community#1913, ufs-community#1917, and ufs-community#1926) (ufs-community#1893)

* GFDL_atmos_cubed_sphere: consistent string lengths in array

* stop FV3_HRRR_c3 from crashing with gnu debug

* 1hr forecast limit for conus13km_debug_qr

* fv3atm: bug fix from Dusan to recover_fields crash

* disable conus13km_debug_qr_gnu due to 25% failure rate on Hera

* FV3 dycore: initialize srf_wnd_var2 and tracers_var3 arrays

* enable conus13km_debug_qr_gnu

* Fix race condition in GFS_phys_time_vary.fv3.F90 error detection

* More bug fixes to GFS_phys_time_vary.fv3.F90:
1. detect empty errmsg from subroutines
2. Initialize err variables in set_soilveg.f, which is called from GFS_phys_time_vary.fv3.F90

* ccpp-physics: initialize errmsg & errflg in noahmp_tables.f90

* ccpp-physics: only read h2odata, ozdata and noahmp table when they are needed

* "point to the dimension fix of smc for dust emission"

* FV3: more dycore bug fixes from GFDL_atmos_cubed_sphere PR 285

* merge ufs-community#1926

* merge GFDL_atmos_cubed_sphere ufs-community#276

* bugfix: 12hr hrrr tests

* add GAEA rocoto support

* fv3: merge GF radar fixes

* check that baseline directory exists and is non-empty

---------

Co-authored-by: Haiqin.Li <Haiqin.Li@noaa.gov>

* update CMEPS

* update CMEPS w/ fix for error condition

* turning off regional_atmaq_debug: time-out issue on cheyenne.intel

*update cmeps build to implement check4nans feature using module stored in cdeps repo

* initial sw fix branch

* make pio rearranger=box the default for all tests

* update configurations for ocnalb changes

…ommunity#1906)

* update CMEPS w/ fix for error condition

* turning off regional_atmaq_debug: time-out issue on cheyenne.intel

*update cmeps build to implement check4nans feature using module stored in cdeps repo

* make pio rearranger=box the default for all tests

* update configurations for ocnalb changes

* set the ocean albedo limit in config and use it to set logical
flag

* albdir and albdif can be set as non-std values in nems.configure
will default to 0.07 and 0.06 if not set

* swap signs for latent heat flux used by HYCOM

* test latent flux change for hycom

remove mean prefix for fields imported to FV3atm from CICE or CMEPS
rename fv3atm export fields for snow and rain as inst

* add cpld_bmark_p8_iau test

* set up cpld_gfsv17 c96 iau test

* add tests/cpld_control_gfsv17_iau

* remove cpld_bmark_p8_iau

* sync MOM input template with global-workflow

* add a diag_table that works with fms fix

…community#1915)

* establish mrfd

* bug fixed for mraerosol

* updated upp

* sync up CICE/CMEPS/MOM6/Stoch

…e-opening ufs-community#1943) (ufs-community#1947)

* Allow instantaneous SW and LW fluxes to be used when cpllnd=.true. (re-opening ufs-community#1943) (ufs-community#1947)

…#1923)

* Updated fv3atm and ccpp-physics submodules as part of fixing ccpp UGWP OGWD stability issues in the upper atmosphere

* Change RF damping parameters and n_split for HR3

* Corrected new 'ugwpv1' SDF's in fv3atm

* Added UGWPv1 tests: control_p8_ugwpv1 and cpld_control_gfsv17_ugwpv1

* Changed n_split from 4 to 5 in tests/parm/cpld_control.nml.IN and cpld_control_ugwpv1.nml.IN

…PR111