generalization of number of soil layers #31

…(branch Maie) (ufs-community#1815) * establish maie * optimized the code and decrease the stratosphere warm bias for mraerosol=T * Update detect_machine.sh * Update compile.sh --------- Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Anning Cheng <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Wen Meng <[email protected]>

…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 <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>

* 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 ufs-community#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 <[email protected]> Co-authored-by: Grant Firl <[email protected]>

…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 <[email protected]>

* 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

…ufs-community#1922) * update to gocart hash f7b34e - important updates for FENGSHA * Add additional inputs in GOCART control file for FENGSHA

… compile, also re-enable 3 hafs tests for WCOSS2. (ufs-community#1907) * Adjust timestep to 120 second to avoid saturation vapor pressure table issue * Update rt.conf to re-enable regional_atmaq_faster for wcoss2 and acorn * re-enable 3 hafs tests for WCOSS2 to fix issue ufs-community#1896

…nity#1920) * Update modulefiles/ufs_common.lua modulefiles/ufs_hera.gnu.lua modulefiles/ufs_hera.intel.lua for testing ESMF 8.5.0 and MAPL 2.40.3 * Replace [email protected] with [email protected] in ufs_common.lau * Remove miniconda from tests/rt.sh for spack-stack systems * Switch to mvapich2 on Hercules with GNU * Add gfortran-10 argument mismatch compatibility flags in CICE-interface/CMakeLists.txt, needed for mvapich2 * Add export MV2_SHMEM_COLL_NUM_COMM=128 to hercules gnu job card

… "ufs", allow file clobbering for GOCART history files (was ufs-community#1948) (ufs-community#1932) * Enable zstd compression in several tests * update FD and some nems configs * all except lnd sbs run * update aero_history to allow file clobber

* FV3 changes for refactored ozone physics scheme * SDF cleanup. physics updates * Some polishing. Merge 2006 ozone into module_ozphys

* Add -mcmodel=medium for builds targeting multiple cores (prevents link failure on jet) * Updated FV3/ccpp/physics (NSSL MP)

* update FD and some nems configs * all except lnd sbs run * update FD and nems.configure * remove temporary test settings * remove history_n settings from one more test

…active (ufs-community#1953) Added new condition turning off samfdeepcnv, when the MYNN shallow convection is active.

…tart (ufs-community#1946) * Convert most global (uncoupled) and regional tests to use quilting restart * use MOM6 test branch, modify mom6_files.cmake * update MOM6 to include 20231106 NOAA-GFDL/rtd_fix * Update cpld_control_p8 remove hera_gnu wall clock stipulation --------- Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]>

@lisa-bengtsson

* update FD and nems.configure * add new suite_FV3_global_nest_v1 to FV3 * new tests for global_nest_v1 suite * update tests to match new gwd scheme * Namelist changes from Mike Toy & adapt to changes from develop in FV3 * Merge FV3 NOAA-EMC/fv3atm#715 from @lisa-bengtsson * remove unused tests/rap_clm_lake * Update bl_date.conf * note that gnv1_nested might work on s4 * Update cpld_control_p8 remove hera_gnu wall clock stipulation

ufs-community#1945) .* MYNN-EDMF, MYNN surface layer, and Thompson AA updates (combines 1940) (ufs-community#1945) --------- Co-authored-by: tanyasmirnova <[email protected]> Co-authored-by: Grant Firl <[email protected]>

*fixed grv function used by NST *point to FV3 with grv fix

* enable pdlib tests on more platforms * fix bug and use scotch 7.0.4

* Convert tests to use netcdf quantize options

* point to nst kind fix branch

* Convective reflectivity added for NSSL,Thompson mp,SAS,GF shal/deep * Bug fix: htop intent set to in, modified if condition for convective refl. * if do_deep is false, set deep and shal parameters to -1. This will prevent conv refl from being computed. * Revert imfhsalcnv and imfdeepcnv changes * Bug fix for conv refl,remove conv refl computation from the cu_gf driver * change imfshallow and imfdeep to -1 since no convection is used, otherwise it will try to compute convective reflectivity * Replace 273.16 with already defined physical constant, con_t0c

…s added to support RRFS multiphysics ensemble and add tob in ocean output)(Includes PR ufs-community#1997) (ufs-community#1784) * Reinstate all the c5 changes that I botched with my git ignorance. * Update ufs_common. Upate c5 modulefile. * TPN adjustments for C5 regional_atmaq tests. * Remove set -eu from module-setup.sh * Update rt.sh adding new DISKNM for Gaea_C5 * updates for gaea-c5 modulefiles, scripts * Update rt.conf fix gaea machine name

…chunk sizes in restart files (ufs-community#2021) * Acorn RT Log, failure due to Acorn queue limits, not system or code issue * revert change in cpld_debug_p8 and increase wlclk for cpld_debug_pdlib_p8/jet

…fs-community#1979) * Update MOM templates to be in sync with recent additions to g-w and update 5 deg template to be in line with g-w and OM4 settings * Revert manual copying of file now that new file is in input directory

… for application, cleanup tests (ufs-community#2010) * additional template variables for CICE namelist * rename templates, add component level defaults * clean up unnecessary quotes in tests * add cmeps restart directory variable * add MOM6 variables to some standalone tests * add missing mom6 variables for two restart tests

…ommunity#2009) * Add cpld_s2sa_p8 regression test * Reduce output in cpld_s2sa_p8

UFS: - Remove Cheyenne (retiring UCAR HPC) support. - Add UCAR's new Derecho HPC system to supported Tier 1 Platforms.

… AND ufs-community#2040 and ufs-community#2043 (ufs-community#2041) General clean-up, and CCPP concurrency bug fixes 1. Remove nfhout, nfhmax_hf, nfhout_hf and nsout from fv3atm and the regression tests. ( Remove nfhout, nfhmax_hf, nfhout_hf etc configuration parameters NOAA-EMC/fv3atm#731 ) 2. Add comments to smc pert and fix bug in stc pert ( Fix bugs in soil temperature perturbation ufs-community#2042 ) 3. Disable concurrency in NetCDF calls within CCPP GFS_phys_time_vary_init subroutine to avoid crashes

…nodi + ufs-community#2047, ufs-community#2053, and ufs-community#2056 (ufs-community#2044) FV3 diagnostic fixes, CCPP fixes for model crashes, new PR template - UFS: - commit message in PR template (ufs-community#2053) - fix hercules crashes (ufs-community#2015) - CMEPS & FV3: Bad data from in CCPP CLM Lake physics scheme caused model crashes - Communicate changes to lake ice (Closes ufs-community#2055, NOAA-EMC/CMEPS#105, NOAA-EMC/fv3atm#741) - unit mismatch (NOAA-EMC/fv3atm#736) - FV3: correct errors in diagnostic calculations - snodi had weasdi data in it (NOAA-EMC/fv3atm#736) - revisions to RUC LSM snowfall melting and accumulation (NOAA-EMC/fv3atm#739)

* "update smoke/dust for RRFS code freeze" * "point to the chem3d dimension update in GF for hercules/gnu"

* Metafile cleanup * Move rte-rrtmgp submodule * Re-organization of physical parameterizations into process and scheme subdirectories * Modifications to CCPP metadata files to accommodate source file location changes * File location update referenced in CMEPS

…build system to allow CMAKE_<COMPILER>_FLAGS to be specified for submodules ufs-community#2052 (ufs-community#2013) * bmark time increase * spack-stack-151 & common updates * switch to fms/2023.02.01 * remove gaea c4 * switch to fv3/use_fms_mpp Reverts gaea TPN statement, this includes gaea c5 in its configuration. * WCOSS2 LUA changes to match updates in spack-stack 1.5.1 * Fixing CMAKE_Fortran_FLAGS to be passed from top level to submodules * fixed c flags for cice * turn off some gnu cases: hercules/gnu issue * Bring in lua changes on Acorn --------- Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Mark A Potts <[email protected]> Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: zach1221 <[email protected]>

…2069) (ufs-community#2027) * update CICE * update CICE source file list * updates to ice_in.IN for use in global applications --------- Co-authored-by: Rahul Mahajan <[email protected]>

…dd stochastic physics pattern update frequency options within SPP and LNDP ('sppint' and 'lndpint') ufs-community#2077 + Updates to ufs.configure for use in global applications ufs-community#2074 + Doc Updates ufs-community#2030 (ufs-community#2080) * Update MOM6 to its main repository 20231218 updating (disable FPEs) * Updates ufs.configure templates for use in global-applications. * Adds the stochastic pattern interval (sppint) option to SPP and (lndpint) to the land perturbations (LNDP) * Doc update for LND & CDEPS Input files required for land configurations --------- Co-authored-by: “gspetro-NOAA” <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Jeff <[email protected]> Co-authored-by: Jong Kim <[email protected]> Co-authored-by: FernandoAndrade-NOAA <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: zach1221 <[email protected]>

) * fix array out of bounds issue in physics aerinterpol.F90 (ufs-community/ccpp-physics#152)

@adams-selin

…FS on WCOSS2 (ufs-community#2064) * Eliminate an out-of-bounds write in FV3 dynamical core hail diagnostic code. * FV3 component GFDL_atmos_cubed_sphere submodule: * The module_diag_hailcast.F90 has a KBAS index which can have the value of 1. When it has that value, a later line writes to address 0 of a 1-based array. This caused the RRFS ensemble to crash on WCOSS2. * fix out-of-bounds write in module_diag_hailcast * remove unused variable DO_MYJPBL from default_vars.sh (it has a typo in its value) * only correct RWA_new where RWA_adiabat(k).ge.1.E-12 * module_diag_hailcast.F90: update comments; changes from @adams-selin

…ommunity#2086); Allow MOM6 to write non-interval restarts (was ufs-community#2099) (ufs-community#2085) fix potential divide by zero in WW3 appendtail routine add timers to WW3 mesh cap add non-interval restart capability to MOM6

…rent (ufs-community#2059) use single MPI_Bcast (via mpp_broadcast()) instead of multiple point-to-point messages (via mpp_send/mpp_recv) address issue maxing out the SlingShot-10 link on the first node resulting in a .15s hit every fifth time step

…ufs-community#2090) Update diag_able for global coupled iau test cpld_control_gfsv17_iau for mom6 history output

…nity#1845) Enable fully could atmosphere-land configuration Supplementary physics updates (MYNN, GF, RUC_LSM, smoke and dust) for RRFS code freeze

CCPP physics code update for HR4 related to surface roughness, background diffusivity and shallow convection + CI fix

…es (ufs-community#2098) fix NSSL MP init issue when initialized from other microphysics schemes

@binli2337

…osphere-ocean coupling (ufs-community#2104) Enable the capability of considering sea surface current's impact on air-sea flux calculation for atmosphere-ocean coupling. A namelist option is added to control whether or not to use this feature (default is off). Fixes ufs-community#1975 Co-authored by: @binli2337, @BinLiu-NOAA, @WeiguoWang-NOAA, @BijuThomas-NOAA, @hyunsookkim-NOAA, @XuLi-NOAA, @MariaAristizabal-NOAA, @JohnSteffen-NOAA

Developed and enabled using CMEPS with inline CDEPS capability for UFS regional coupling. Two HAFS regional moving nest atm_ocn_wav coupling regression tests were added to test this capability. Note: This is a collaborative effort among the ESMF team, EMC/EIB, and EMC hurricane project team.

- Add three new regression tests for version 2 of the surface coldstart file. (Closes ufs-community#1977)

UPP will be brought to the commit to fix the missing reflectivity bug for NSSL MP cases.

…lock_atmos_copy routines in fv3atm ufs-community#2124 (ufs-community#2115) - Gaea C5 modulefile & DISKNM update: closes issues Gaea F2 to F5 file system migration ufs-community#2101 - Bring in the global-workflow detect_machine.sh to keep consistent between projects. (Closes Bring in detect_machine.sh from global workflow for consistency across the community. ufs-community#2096 ) - Fix out of bound errors in block_atmos_copy routines in fv3atm

…ty#2118) Add ice temperature in CICE output

…file (ufs-community#2062) Add option to write 3d soilt, soilw and soill variables to a history file

…f support, simplify RT logs. (ufs-community#2061) * UFSWM * Re-work test verification in rt.sh for developers to use in PR process. (Closes ufs-community#2058) * fail_<test_number> file name upgraded to use compile/test name instead of number. * Regression test logs do not clearly indicate when a test fails to run. (Closes ufs-community#1821) * New test_changes.list file: * Verification of what tests change for each PR. * Used with './rt.sh -c -b test_changes.list` to help create new baselines for each PR.

…run compile jobs of regression test suite only & -mcmodel=medium gnu.cmake option (also includes ufs-community#2142) (ufs-community#2066) * UFSWM - Add option to `rt.sh` to run compile-only tests * FV3 - Update submodule pointer (NOAA-EMC/fv3atm#747) * ccpp-physics - Update submodule pointer (ufs-community/ccpp-physics#150) * ccpp-framework - Update submodule pointer (NCAR/ccpp-framework#519) * Update WM license and documentation logo * Update GNU.cmake: -mcmodel=medium

Changes to physics code such that the ice model is used to determine the ice temperature over both sea ice and lake ice

* MOM6 - update MOM6 to its main repo. 20240228 updating (which is the original GFDL 20231113 candidate PR)

…ll on macOS arm64 (also contains ufs-community#2017) (ufs-community#2164) * UFSWM - "Add conflict for MOVING_NEST option with GNU Fortran, use mcmodel=small on macOS arm64" * FV3 - "Bug fix for unallocated array sfcprop%wetness in GFS_diagnostics.F90" * ccpp-physics - * ccpp-framework - "Bug fix required to use chunked arrays and retain backward compatibility with blocked data structures in ccpp_prebuild.py" * Creation of UFS-WM jenkinsfile for pipeline integration * Jet Rocky8 updates * spack-stack module path * eflow location and version

…g templates for global apps and append _esmf for templates using ESMF-managed threading (was ufs-community#2179) (ufs-community#2172) * CICE and CMEPS - Remove compiler warnings. * UFSWM - Allow flexibility to use traditional or ESMF-managed threading for global apps.

…ommunity#2180) * UFSWM - Update the CS convection scheme * FV3 - Update the CS convection scheme * ccpp-physics - Update the CS convection scheme

…ure/capgen into main/20240308) Combined PR ufs-community#2190 (ufs-community#2181) * FV3 - Update submodule pointers for ccpp-framework and ccpp-physics. Change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes. * ccpp-physics - In physics/Interstitials/UFS_SCM_NEPTUNE/maximum_hourly_diagnostics.meta: change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes. * ccpp-framework - Update main from feature/capgen as of 2024-03-08 (includes optional argument updates in feature/capgen). Only commit on top of the merge is NCAR/ccpp-framework@6cdd38a which is required to parse the metadata in the Unified Forecast System / ccpp-physics (underscores in units, e.g. degree_north).

…allow-argument-mismatch' flag (ufs-community#1147) * UFSWM - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag. * FV3 - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag. * ccpp-physics - Resolve various subroutine argument mismatches. * ccpp-framework - Add support to use mpi_f08 MPI module . * stochastic_physics - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.

- update module paths in Hera intel/gnu lua files for Rocky8 OS spack-stack libraries.

…ity#2197), add xr_cnvcld flag to FV3 (ufs-community#2185) (ufs-community#2202) * UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh. * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite * ccpp - physics-level changes to implement new namelist variable * MOM6 - update MOM6 code to eliminate all compiler warnings

* WW3 - Langmuir turbulence parameterization

…#2193) * UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs

…ommunity#2175) * CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files * CMEPS - fix mapping mask for lnd->atm * FV3 - add export of cpl_scalars * NOAHMP - add export of cpl_scalars

…fs-community#2223) cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)

Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE

…m wrong for nests (ufs-community#2201) * UFSWM - None. * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP. * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.

*doc/UserGuide *requirements.txt - updates inda version from 3.6 to 3.7

* UFSWM * doc/Userguide * source * conf.py * Configurations.rst * FAQ.rst * InputsOutputs.rst * Introduction.rst

…Adds -v Verbose option. (ufs-community#2218) Remove nowarn Intel compiler flag (ufs-community#2225) * UFSWM - Add bash linting to CI: - uses superlinter to check for consistent bash code writing - Cleans up .sh scripts to comply with superlinter - Cleans up .sh scripts to be more consistent, easier to read. - Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's. - Addresses smaller bugs - quota/timeout search logic adjusted. - check for dirs existing (DISKNM, STMP, PTMP) before starting. - adjustments/cleanup to ecflow/rocoto sections - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh. - fix for issue where run_dir will not delete properly. * FV3: Address compiler warnings * atmos_cubed_sphere: Address compiler warnings.

* UFSWM - Update inline post * FV3 - Update upp submodule for inline post

* UFSWM - global_control.nml_IN has been added as the new regression test namelist template for all global regression tests. The namelist now uses pointers (i.e. @[abc]) for variables and default values have been added to the default_vars.sh script. A new section in default_vars.sh has been added (export_tiled) to account for tiled RTs that pulls the correct parameter files using the ATMRES variable. Regression tests have been modified to account for these changes. Tests that were not compatible with the GFSv17_p8 core have been disabled for now. They will be turned on as they are updated from GFSv16 to GFSv17.

* UFSWM - * MOM6 - update MOM6 to its main repo. 20240401 commit (NCAR-candidate-20240319)

* UFSWM - fix fully coupled land component configuration * NOAHMP - get fixed information from surface file

@DusanJovic-NOAA

…community#2221) * NWFA Induced evaporation is turn off , but evaporation not related to aerosol is turned on to prevent excessive evaporation when Inner loop and mraerosol=T * ccpp/framework hash update * Cleanup unused code and variables, fix wcoss2 issue starting ecflow * Bring in @DusanJovic-NOAA trap changes * Merge some machine ecflow starts together and move to case statements

…fs-community#2235) * UFSWM - update input data directory to fix CICE grid files for incorrect Bu angle, update C48 coupled warmstart files and remove 4-deg ocean files

…ion to specify fv3atm history and inline post files output directory ufs-community#2254 + Bump jinja2 from 3.1.3 to 3.1.4 in /doc/UsersGuide ufs-community#2270 (ufs-community#2215) * UFSWM - Add several aliases in `fd_ufs.yaml` needed for JEDI-UFS. Add new model_configure option (fv3atm_output_dir) to specify directory in which all fv3atm history and inline post files will be saved. * FV3 - Add new model_configure option (fv3atm_output_dir) to specify directory in which all history and inline post files will be saved. --------- Co-authored-by: Fabio L R Diniz <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>

…epo. 20240508 commit ufs-community#2275 (ufs-community#2259) * UFSWM - Update CICE to CICE-Consortium (2024-05-01) and mom6 to its main repo (2024-05-08) * CICE - Update CICE to CICE-Consortium (2024-05-01) * MOM6 - Update mom6 to its main repo. 20240508 commit

* UFSWM - Add a RT for SFS with hydrostatic options * FV3 - Remove -DUSE_COND and -DMOIST_CAPPA compiling flags for hydrostatic runs; Fix the issue to write out geopotential height for inline post in hydrostatic runs; Use omega from the model if defined in diag_table instead calculated in post * atmos_cubed_sphere - Remove -DUSE_COND and -DMOIST_CAPPA compiling flags for hydrostatic runs

…gfixes, sfcsub.F landmask bugfix, and canopy resistance output (ufs-community#2264) * UFSWM, CMEPS, FV3/ccpp_physics - CCPP Physics bugfixes for metadata intents and sfcsub.f landmask and output changes for ozone diagnostics and canopy resistance

…add end of run restart functionality to MOM6 (was ufs-community#2286) (ufs-community#2205) * UFSWM - Add support for optional arguments in ccpp physics and framework * FV3 - [Add support for optional arguments in ccpp physics and framework](NOAA-EMC/fv3atm#807 (comment)) * ccpp-physics - Introduce optional arguments in ccpp schemes and metadata * ccpp-framework - Add support (and tests) for optional arguments in ccpp_prebuild * atmos_cubed_sphere - Set cdata%thrd_cnt in driver/fvGFS/atmosphere.F90 * MOM6 - Add end of run restart functionality to MOM6 * stochastic_physics - Add optional attribute for variables where necessary

…fs-community#2273) * MERRA2 climatology upgraded to 2014 to 2024 mean

…+ develop]: Minor documentation bug fixes ufs-community#2296 (ufs-community#2281) * UFSWM - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * FV3 - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * UFSWM - Update requirements.txt; fix EMC broken link in Glossary; fix sample rt.sh run command for single RT run (add compiler)

@BrianCurtis-NOAA

…ity#2301) (ufs-community#2302) * UFSWM - A few miscellaneous minor fixes to regression test scripts - Bring in changes for WCOSS2 to match the spack-stack 1.6.0 setup - Bring in updated pnetcdf/pio for CICE - Print 'ECFLOW Tasks Remaining' message only when the number of tasks changes - Remove explicit 'set -e'. Use -v command line option for verbose mode - Remove 'Computing PET bounds and tasks' message - Fix bugs with log generation script (from @BrianCurtis-NOAA) - Uncomment new_compile=true in rocoto_create_compile_task - Removed unneeded colonifnco

*UFSWM: *Updates modulefiles to spack-stack version 1.6.0 *Updates Hera GNU version to 13.3

…or perturbation/increments for cold starts ufs-community#2271 (ufs-community#2269) UFSWM - Update modulefiles/ufs_gaea.intel.lua to compile ufs_weather_model on Gaea-C5 FV3 - - atmos_cubed_sphere - move the call to read_da_inc outside the if external_ic/restart logic

…nts (ATM_DS2S and ATM_DS2S-PCICE) and regression tests (atm_ds2s_docn_dice and atm_ds2s_docn_pcice) (ufs-community#2186) * UFSWM - Add ATM_DS2S and ATM_DS2S-PCICE applications by adding CDEPS dice and enabling prescribed ice CICE. Add corresponding atm_ds2s_docn_dice and atm_ds2s_docn_dice-pcice regression tests. New gnv1_nested regression test with Water in the West domain at C96 resolution using templates compatible with global-workflow * CDEPS - Add dice cplhist datamode * CICE - Enable ice prescribed CICE mode

*UFSWM - update WAM RT compatible with v17 *UFSWM - fix derecho modulefile path for Spack Stackv1.6

…s_cubed_sphere to fix a typo when printing out the nest grid corner locations ufs-community#2323+Bump urllib3 from 2.2.1 to 2.2.2 in /doc/UsersGuide ufs-community#2329 + Orion changes for switch to new OS - Rocky-9 ufs-community#2336 (ufs-community#2324) * CICE - Adds restart write capability at the end of a run for CICE * FV3 - * atmos_cubed_sphere - Update submodule FV3/atmos_cubed_sphere to fix a typo when printing out the nest grid corner locations * doc/UsersGuide/requirements.txt: Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.1 to 2.2.2. * Orion Spack stack modulefile update: Rocky-9 * update detect_machine.sh: hercules

… similar to hydrostatic method (ufs-community#2327) * atmos_cubed_sphere - A new parameter, pass_full_omega_to_physics_in_non_hydrostatic_mode, has been added in dycore. When set to true, the omega calculation will match that of hydrostatic runs, using the formula omega = dp/dt. The default value is false, where the calculation remains omega = w * dp/dz as before.

* HR4 GWD update for FV3 * point to PR#549 of ccpp-framework * Update default_vars.sh: GWD parameters * Update global_control.nml.IN * update cpld case GWD parameters: gfsv17 * Update Jenkinsfile.combined fix multi-label removal * Update Jenkinsfile for ORT Pipeline * update input oro files for control_run.IN: gsfv17 --------- Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Jong Kim <[email protected]> Co-authored-by: Dustin Swales <[email protected]> Co-authored-by: zach1221 <[email protected]>

* UFSWM - * FV3 - * atmos_cubed_sphere - bug fix to address debug mode crashes caused by floating-point exception in subroutine a2b_ord2 in model/a2b_edge.F90

…nd PR#2265) (ufs-community#2335) * UFSWM - restore error checking to regression test system and add a self-test suite - Detect_machine.sh identifies Frontera --------- Co-authored-by: Sam Trahan <[email protected]> Co-authored-by: Benjamin Cash <[email protected]>

… in the GFS physics suite (ufs-community#2340) * ccpp-physics - update convection and PBL schemes to improve cloud/convection interaction * Output updraft value of convective cloud condensate in FV3 and CCPP * update xkinv1 to 0.15 * add check if progsigma is true

* HR4 land surface upgrades to address surface cold biases * update noahmp table

* CMEPS - Sync CMEPS with ESCOMP/main.

…ity#2355) * UFSWM - Fix dumpfields=true option in FV3 by using ESMF_FieldBundleWrite * FV3 - Fix dumpfields=true option by using ESMF_FieldBundleWrite * Update rt_utils.sh. Set ECF_HOST on wcoss2 explicitly

…y#2373) * UFSWM - Adds pass_full_omega_to_physics_in_non_hydrostatic_model parameter in the global_control.nml.IN namelist and sets it to true for non-hydrostatic runs. An additional field (omga) has been added to the diag_tables.

Commits on Nov 7, 2023

update submodules

HelinWei-NOAA committed Nov 7, 2023

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generalization of number of soil layers #31

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generalization of number of soil layers #31

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