Merge with ufs-community #ee3d52d (2025Feb05) #174
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* 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.
…omponents (ufs-community#2370) * UFSWM - * CICE - initialize scalar field when created * MOM6 - initialize scalar field when created * WW3 - initialize scalar field when created
…s arrays (ufs-community#2183) * UFSWM - In fv3atm and submodules, convert internal GFS DDTs from blocked data structures to contiguous arrays. This excludes the (external) `GFS_extdiag` and `GFS_restart` DDTs. * AQM - * CDEPS - * CICE - * CMEPS - * CMakeModules - * FV3 - Convert GFS DDTs from blocked data structures to contiguous arrays (not including GFS_restart and GFS_extdiag DDTs) * ccpp-physics - Convert GFS DDTs from blocked data structures to contiguous arrays (affects `GFS_debug.{F90,meta} only`) * atmos_cubed_sphere - Convert GFS DDTs from blocked data structures to contiguous arrays and remove IPD_Data super DDT * GOCART - * HYCOM - * MOM6 - * NOAHMP - * WW3 - * stochastic_physics -
… FV3 diag table documentation ufs-community#2277 + SKEB fix with d_con = zero ufs-community#2374 (ufs-community#2278) * UFSWM - python scripts for yaml and rocoto-xml conversion, experiment setup, and test log output * Add python superlint option * Documentation update: doc/UsersGuide/source/tables/fv3_diag_table.rst * FV3 - * atmos_cubed_sphere - bugfix: allocates heat_source when skeb is True and d_con is zero
…mmunity#2381) * using MOM6 test branch add MOM_dynamics_split_RK2b.F90 and MOM_EOS_base_type.F90 in cmake list add extra 8PE for cpld_debug_pdlib job set DEFAULT_ANSWER_DATE=20231231 in 5x5 case add USE_HUYNH_STENCIL_BUG = True in MOM_input using MOM6 restart file as BL for sfs and hafs_mom jobs * remove USE_HUYNH_STENCIL_BUG = True in MOM_input switch FIX_USTAR_GUSTLESS_BUG=F to USTAR_GUSTLESS_BUG=T * switch FIX_USTAR_GUSTLESS_BUG to USTAR_GUSTLESS_BUG for MOM_input_hafs * set USE_HUYNH_STENCIL_BUG = True
…s-community#2375) * UFSWM - Update the MOM_input templates and RT scripts to allow use of downscaled MOM6 and CICE6 warmstarts. * update script variables and sfs test
* UFSWM - update g2tmpl library, g2 library, UPP hash. Sync parm files with new UPP version. * FV3 - update inline post for UPP, point UPP submodule to head of develop, revise spack.yaml
…ng in rt.sh (2388) + Add ability to read increment files on native cubed sphere grid (2304) (ufs-community#2389) * UFSWM - Unify CDEPS gfs, cfsr, and gefs datm datamodes. Add ability to read increment files on native cubed sphere grid. Update rt scripts to fix checking the job exit status from Slurm and PBS schedulers. * FV3 - Add namelist parameter for cubed sphere increment read and update atmos_cubed_sphere hash for GFDL Atmospheric Cubed Sphere PR #[342](NOAA-GFDL/GFDL_atmos_cubed_sphere#342) * atmos_cubed_sphere - Add ability to read increments from files on native cubed sphere grid * CDEPS - Unify CDEPS gfs, cfsr, and gefs datm datamodes. Rename CDEPS-related FILENAME_BASE to FILEBASE_DATM in tests. Sunset gfs_hafs datamode.
…(H2O scheme refactor and C3/SAS/MYNN fix) (ufs-community#2408) * UFSWM - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme * FV3 - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme * ccpp-physics - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme
…Switch to using Aux history files in atm_ds2s_docn_dice test; Remove IFI tests (was ufs-community#2417) (ufs-community#2395) * UFSWM - * CMEPS - fix aux history functionality; sync with ESCOMP * UFSWM - use auxiliary history files as input for atm_ds2s_docn_dice; remove the IFI tests
*MOM6 - update MOM6 to its main repo. 20240824 updating (GFDL's FMA PR)
* UFSWM - Update default parameter values for damping based off of work done for GW
…#2220) * UFSWM - The fire_behavior component has been added and a new application created 'ATMF'. This work also includes a new regression test 'cpld_regional_atm_fbh' for testing two-way coupling of the atm component (fv3atm) and fbh component (fire_behavior) * CMEPS - CMEPS required modifications to be aligned with the changes to the ccpp physics package * FV3 - the fv3 cap has been modified to export atmosphere forcing data to the fire component when 'cpl_fire' is set to true. It will also import new fields for physics. * ccpp-physics - the ccpp physics package has been modified to add heat fluxes, upward specific humidity flux, and a smoke tracer from the fire component.
…ufs-community#2430) * UFSWM - Use EMC/CICE:develop branch from CICE-Consortium:main * CICE - Use EMC/CICE:develop branch from CICE-Consortium:main
…to fms/2024.01 (ufs-community#2431) * UFSWM - Bump libraries on WCOSS2 to ip/4.0.0 w3emc/2.12.0 and fms/2024.01 * Adjust FMS location and bump ufs_common.lua * Acorn lua update for fms bump, remove ifi library load
* UFSWM - Add support for Intel LLVM compiler
* CICE - Add support for Intel LLVM compiler
* FV3 - Add support for Intel LLVM compiler
* ccpp-physics - Add support for Intel LLVM compiler
* atmos_cubed_sphere - Add support for Intel LLVM compiler
* upp - Add support for Intel LLVM compiler
* WW3 - Add support for Intel LLVM compiler
* UFSWM - Adds GFDL Land Model version 4 (LM4) as a component model, functional in Data Atmosphere mode * CMEPS - Small modifications for coupling of LM4 * LM4-NUOPC driver - new model component hosted at github.com/NOAA-GFDL/LM4-NUOPC-driver. NUOPC Cap for LM4 * LM4.0 - submodule of LM4 NUOPC driver, hosted at https://github.com/NOAA-GFDL/LM4/
* UFSWM - physics updates for RRFS.v1 code freeze
* FV3 - physics updates for RRFS.v1 code freeze
* ccpp-physics - physics updates for RRFS.v1 code freeze
* apply gaea job card fix for MPI issue: FI_VERBS_PREFER_XRC
…ccpp-framework) for ccpp-framework PR 600 (bug fix for unit conversion error in ccpp_prebuild.py ) ufs-community#2464 + Update chunksizes for cubed sphere grid ufs-community#2465 (ufs-community#2463) * UFSWM - Update LND I/O docs Add fd_ufs.yaml docs Add tests-dev docs * UFSWM - Change the default chunking for the cubed sphere history files to use only the horizontal grid size of each of the tiles. * FV3 - Change the default chunking for the cubed sphere history files to use only the horizontal grid size of each of the tiles. * FV3 - Submodule pointer update for ccpp-framework PR 600 (bug fix for unit conversion error in ccpp_prebuild.py) --------- Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> Co-authored-by: Dom Heinzeller <dom.heinzeller@ucar.edu>
* UFSWM - Modify global_control.nml to add compatibility with Global Workflow
…fs-community#2475) * UFSWM - Updates cpld_control_sfs to use the most up-to-date configuration specs * UFSWM - Update units attributes in netCDF output to be machine-readable * FV3 - Update units attributes in netCDF output to be machine-readable * atmos_cubed_sphere - Update units attributes in netCDF output to be machine-readable
…n PR from production/RRFS.v1 ufs-community#2481 (ufs-community#2458) * UFSWM - Enable some of the intel llvm tests in rt conf * UFSWM - Second reconciliation PR from production/RRFS.v1 related to FV3 unused and optional variables * FV3 - Second reconciliation PR from production/RRFS.v1 related to FV3 unused and optional variables * ccpp-physics - Second reconciliation PR from production/RRFS.v1 related to FV3 unused and optional variables --------- Co-authored-by: Grant Firl <grant.firl@noaa.gov>
… CAPE cases + ufs-community#2459 (ufs-community#2461) * UFSWM - Add tests-dev ATM-only idealized dry baroclinic wave test and a 2020 July CAPE case * UFSWM - Update modulefile to support Rocky 8 on CSPs, with ParallelWorks --------- Co-authored-by: Wei Huang <wei.huang@noaa.gov> Co-authored-by: Jong Kim <jong.kim@noaa.gov>
* UFSWM - add PIO settings to WAV attributes in ufs.configure templates * UFSWM - update ww3_shel.nml to allow for the ice field to be written to the restart file when required (i.e, waves in the slow loop) * UFSWM - add WW3 restart files to comparison lists * WW3 - Add netCDF PIO capability for restarts and run-time history
* UFSWM
* FV3
* ccpp-physics - Add Incremental Analysis Update (IAU) capability to update soil temperature and moisture for CCPP's NoahMP land model
…-community#2498 (ufs-community#2489) * UFSWM - Documentation for HSD cases * FV3 - * upp - update upp hash to ce258fca with update inline post interface. --------- Co-authored-by: gspetro-NOAA <gillian.petro@noaa.gov> Co-authored-by: cameronbook <cameron.book@noaa.gov>
…WW3 to avoid build errors ufs-community#2512 (ufs-community#2483) * UFSWM - MYNN PBL, Smoke and subgrid cloud fraction. * FV3 - MYNN PBL, Smoke and subgrid cloud fraction. * ccpp-physics - MYNN PBL, Smoke and subgrid cloud fraction. * atmos_cubed_sphere - hail diagnostics, and average of smoke/dust. * WW3 - Updated to add PIO switch to avoid build error
…-community#2419) * UFSWM - Flexible restart write times (restart_fh) for med, ocn, ice, wav * CICE - Flexible restart write times (restart_fh) * CMEPS - Flexible restart write times (restart_fh) * MOM6 - Flexible restart write times (restart_fh) * WW3 - Flexible restart write times (restart_fh)
… on GW specs (ufs-community#2528) + Sync with ESCOMP/CMEPS (ufs-community#2469) * UFSWM - Sync with ESCOMP/CDEPS (2024-12). Sync with ESCOMP/CMEPS (2024-12). Make additional changes to global_control.nml.IN based on GW needs. * CDEPS - Sync with ESCOMP/main (2024-12) * CMEPS - Sync with ESCOMP/main (2024-12)
* UFSWM - Gaea C6 Support --------- Co-authored-by: JONG KIM <jong.kim@noaa.gov> Co-authored-by: Ratko Vasic <ratko.vasic@noaa.gov>
…eading (ufs-community#2533) (ufs-community#2538) * UFSWM - This PR adds support for traditional (non esmf managed) threading. ESMF managed threading is still default. * UFSWM - Sync with ESCOMP/CDEPS (2024-12-16) * CDEPS - Sync with ESCOMP/CDEPS (2024-12-16) --------- Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
* UFSWM - Fix improperly assigned fire emissions for ebb_dcycle==1 for retrospectives (NOT operational!)
* FV3 - Fix improperly assigned fire emissions for ebb_dcycle==1 for retrospectives (NOT operational!)
* ccpp-physics - Fix improperly assigned fire emissions for ebb_dcycle==1 for retrospectives (NOT operational!)
* UFSWM - to compile the model with new fms/2024.01; Update the RUC LSM deep soil temperature from climatology to real forecast
* FV3 - to compile the model with new fms/2024.01; Update the RUC LSM deep soil temperature from climatology to real forecast
* ccpp-physics - Update the RUC LSM deep soil temperature from climatology to real forecast
* UFSWM - minor bugfixes for smoke/dust for RRFS.v1
* FV3 - minor bugfixes for smoke/dust for RRFS.v1
* ccpp-physics - minor bugfixes for smoke/dust for RRFS.v1
…s from the jedi model convention (ufs-community#2543) * UFSWM - Fix sedi_semi logic issue in export_ugwpv1() and change affected RTs for more stable and quicker runtimes. * UFSWM - Alias update JEDI-related variables inside the fd_ufs.yaml file.
…ble to track initialization of GFS_phys_time_vary (ufs-community#2544) + develop of WW3 up to 2024-01-11 to dev/ufs-weather-model ufs-community#1342 (ufs-community#2549) (ufs-community#2532) * UFSWM - fix REFS ensemble member and add GF convection cold start parameter; Add CCPP host variable to track initialization of GFS_phys_time_vary; Update WW3 with develop up to 2024-01-11 * FV3 - fix REFS ensemble member and add GF convection cold start parameter; Add CCPP host variable to track initialization of GFS_phys_time_vary, fix bug for MP Thompson init flag * ccpp-physics - fix REFS ensemble member and add GF convection cold start parameter; In GFS_phys_time_vary.fv3: make is_initialized a host model variable to support multiple instances of CCPP physics in a model run * WW3 - Update one commit hash --------- Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com> Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov> Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov>
…0113 commit (original 20241127-PR) (was ufs-community#2556) (ufs-community#2396) * UFSWM - adds additional compile switch and namelist changes required for WW3 in Coastal App * WW3 - add export fields required for coupling with SCHISM * MOM6 - update to main repo. 20250113 commit (origianlly 20241127-PR) --------- Co-authored-by: jiandewang <jiande.wang@noaa.gov>
* add CICD support to collect performace metrics during Build and Test stages Signed-off-by: Bruce Kropp <bruce.kropp@raytheon.com> * [AutoRT] Hera Job Completed. on-behalf-of @ufs-community <ecc.platform@noaa.gov> * [AutoRT] Hercules Job Completed. on-behalf-of @ufs-community <ecc.platform@noaa.gov> * [AutoRT] Derecho Job Completed. on-behalf-of @ufs-community <ecc.platform@noaa.gov> * set logic to remove PR labels on success or failure Signed-off-by: Bruce Kropp <bruce.kropp@raytheon.com> * [AutoRT] Hera Job Completed. on-behalf-of @ufs-community <ecc.platform@noaa.gov> * make sure Jet uses NAGAPE Signed-off-by: Bruce Kropp <bruce.kropp@raytheon.com> --------- Signed-off-by: Bruce Kropp <bruce.kropp@raytheon.com> Co-authored-by: epic-cicd-jenkins <ecc.platform@noaa.gov>
* UFSWM - new RT tests based on S2S configurations: cpld_control_p8_lnd and control_restart_p8_atmlnd.
* CMEPS - flexible way to use same grid in atm-lnd coupling
* FV3 -
* ccpp-physics - new flux calculation method is implemented in CCPP/Physics sfc_land scheme to overcome initialization issues.
* NOAHMP - add new decomposition algorithm to NoahMP component model NUOPC cap to distribute land and ocean points evenly to all the processor.
…temperature and radiative flux biases + Allow model_configure to provide a path for FV3ATM output ufs-community#2581 + Update CICD to move label deletion to Jenkinsfile ufs-community#2568 (ufs-community#2548) * UFSWM - Updates to radiation, cloud, and land processes for improved surface temperature and radiative flux biases + Allow users to provide custom paths for fv3atm output. Default `./` is retained for the regression testing of the ufs-weather-model + Move CI label deletion to Jenkinsfile * FV3 - Updates to radiation, cloud, and land processes for improved surface temperature and radiative flux biases * ccpp-physics - Updates to radiation, cloud, and land processes for improved surface temperature and radiative flux biases
…ations // ufs-community#2585 Update for WW3 initialization (ufs-community#2587) * UFSWM - Add Land IAU variables to default_vars and allow control_c48_lnd_iau to run using the global_control.nml.IN template. * WW3 - Updated hash for WW3 initialization (ufs-community#2585) --------- Co-authored-by: Jessica Meixner <jessica.meixner@noaa.gov>
- Update FV3 to GSL version
CDEPS #2eccb9f CMEPS #cdbed6c CICE #4411a15 MOM6 #6fff095 NOAHMP #1a2d2f
…e> from #40e014f3: Combination for CCPP-physics NOAA-EMC#213 and NOAA-EMC#218 (H2O scheme refactor and C3/SAS/MYNN fix) (NOAA-EMC#865).
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