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Merge gsl/develop to RRFS_dev (NCAR#126)
* Merge ufs-community develop into gsl/develop (NCAR#119) * Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (ufs-community#931) * Add UFS driver, a copy of two fortran files from the NEMS repository. Remove NEMS submodule. * Update CMEPS for current escomp/master. Implement the ability to write mediator history files for ATM on tiles rather than mesh * Update CDEPS component. The updated CDEPS includes code updates for GFS v16 data mode. * Operation requirement test (ORT) for: - cpld_control_p7 thread and decomposition tests - cpld_bmark_p7 thread and decomposition tests - Due to the wave component in these tests, restart and debug do not work Co-authored-by: Minsuk Ji <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: BinLi-NOAA <[email protected]> * fv3atm cap cleanup (ufs-community#954) FV3 nuopc cap code cleanup. Remove used code/variables. Fix minor inconsistencies. * CCPP cloud cover change for Thompson MP associated with Xu Randall, several bug fixes for regression testing scripts (ufs-community#962) This PR contains code changes 1) to remove old comments in GFS_typedefs.F90, increase cloud cover for Thompson MP by passing convective cloud water mixing ratio to progcld6. 2) Updates for auto fixes Co-authored-by: Dusan Jovic <[email protected]> * ccpp-physics ufs-community#806, #807, ufs-community#813, and ort modifications (ufs-community#970) - CCPP Physics changes: see Wrapper for ccpp-physics ufs-community#806, #807, ufs-community#813, NOAA-EMC/fv3atm#447. - UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion ufs-community#965 * Wrapper for ccpp-physics ufs-community#808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (ufs-community#971) * update submodule pointer for regression testing for ccpp-physics ufs-community#808,816: roughness length over ice and NoahMP tsurf bugfix * Reduce time step from 600s to 450s for tests control_csawmg and control_csawmg_debug Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: climbfuji <[email protected]> * Use 'model set run clock' routine in FV3 NUOPC cap. (ufs-community#967) * Update FV3 cap by adding 'model set run clock' specialization routine. Because FV3 cap does not modify 'Earth clock' anymore in case of a restarted run, that adjustment is now done in the UFS driver. * Fix model_configure file for two tests to define `fhrot` parameter. * Revert iovr=4 (exponential cloud overlap method) in RRTMG (ufs-community#963) Revert/cleanup iovr=4 in RRTMG per developer's request. The current exponential cloud overlapping method used in RRTMG represents the method used in the pre-2018 operational HWRF model. * Add fhzero ort test (ufs-community#977) * Fhzero ORT applies to the two tests `control` and `control_p7` * Test can be run by invoking, for example, `./opnReqTest -n control -c fhz` * Add a new CDEPS test to use GSFv16 data mode in CDEPS ,update rt_weekly.conf and update MOM6 to main branch (20211220) (ufs-community#976) * add a new cdeps test using GFS data mode * update rt_weekly.conf to include cpld_bmark_p7_35d tests * update MOM6 Co-authored-by: jiandewang <[email protected]> * Bug fixes for WAM physics and regression tests, remove duplicate modules from ccpp-physics CMakeLists.txt (ufs-community#947) *adds a new regression test control_wam_debug and fixes problems with the existing control_wam test (e.g. IAER was not set as intended). * Update global inline post for outputting foundation temperature (ufs-community#968) Update upp submodule in fv3atm with latest UPP version for outputting foundation temperature and fixing land-sea mask issue in global inline post. * Regression test bug fixes for running on Jet or with Rocoto (ufs-community#981) * Bug fixes for running on jet or with rocoto 1. Correctly detect Jet when deciding build job runtimes 2. Do not delete out and err files in compile & test jobs 3. Correct dependencies for WW3 in Rocoto 4. Do not hard-code ACCNR to h-nems This PR also contains fv3/ccpp physics (CCPP PR#812) updates that implements a vertically-integrated formula to properly compute tracer column mass and ensure mass conservation for all tracers except TKE. See issue NCAR/ccpp-physics#811 for details * MYNN sfclay (RAP suite) restart reproducibility (ufs-community#984) *This PR turns on the rap_restart tests. Bit-for-bit reproducibility is achieved with the bug fixes for MYNN sfclay in the associated fv3atm and ccpp-physics PRs. * fixes on initializing snow over fractional ice and GFS_surface_composite and z0ice value change (ufs-community#996) * Radar-derived microphysics temperature tendencies similar to operational HRRR (ufs-community#986) This PR implements a feature of the operational HRRR, radar-derived microphysics temperature tendencies applied in the first N minutes of the forecast to improve clouds in the first few hours. Two regression tests are added. * Turn on CICE albedo use by ATM for coupled model; update Prototype test suite to initial P8 configuration; (ufs-community#944) * add updates for suites, tests for initial P8 configuration * add IOPT_SFC=3 as default; set IOPT_SFC=1 in p7 tests * change min_seaice to 1e-6; set to 1e-11 in p7 tests * set dddmp=0.1 in both P7 and P8. This matches the final P7 configuration. It will change P7 baselines. * set cdmbwd in both P7 and P8 to the final P7 configuration. (1.0,2.2,1.0,1.0) for all resolutions. It will change P7 baselines. * add dusan's ecflow fix for wcoss2 * update FV3 with Moorthis' snod fix * update rt_weekly to use p8 tests * change integration length to 5 days * Thompson MP cloud tuning (ufs-community#1005) * improves cloud fraction when using Thompson MP. See NCAR/ccpp-physics#809 for more details. * Add a new HAFS regression test with Thompson MP and GFDL surface layer schemes and Corrected S4 template regression testing job card (ufs-community#995) * Added a new regression test for HAFS. * Fixed the S4 RT template job card. Co-authored-by: David Huber <[email protected]> Co-authored-by: Bin Liu <[email protected]> * CCPP: Update consistency checks and effective radii calculation for Thompson MP (ufs-community#1000) This PR contains changes in ccpp-physics (Update consistency checks and effective radii calculation for Thompson MP) and adds two new regression tests for both Intel and GNU that use the new prognostic cloud scheme progcld_thompson with GFS v16 and with RAP. The new cloud scheme is activated by setting icloud == 3 in input.nml. * Rremove nems_datm related code, update CDEPS, and remove run directories that are no longer needed by other tests (ufs-community#1008) * Add fhzero ort to coupled tests (ufs-community#1009) * Add fhz ort to cpld tests * Set ACCNR in rt.sh, not detect_machine.sh. Add some comments explaining where the variable should not be set or used. Co-authored-by: Samuel Trahan <[email protected]> * Unified write_netcdf, add single file 'cubed_sphere_grid' output (ufs-community#1011) * Unify write_netcdf and write_netcdf_parallel modules. * Add support for writing 'cubed_sphere_grid' history files in a single netcdf file. * Change standard name and unit of CCPP error flag variable in CCPP framework and physics (ufs-community#1013) * updates the submodule pointers for fv3atm, ccpp-framework and ccpp-physics for: Change standard name and unit of CCPP error flag variable in CCPP framework and physics. * ESMF managed threading (ufs-community#1018) Add code updates to enable the ESMF managed threading in UFS. Co-authored-by: Gerhard Theurich <[email protected] > * sync-ww3 (ufs-community#1026) * sync with ww3 develop branch * Revisions to repair iovr=5 cloud overlap option (ufs-community#1025) * This PR addresses part 2 of issue ufs-community#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG. RT tests were added for iovr=4 and iovr=5 options * change iovr to use the environment variable in control.nml.IN; modify all tests that use control.nml.IN to set env. var. iovr=3 (except for new tests); remove restart files from new tests * 2D decomposition on write grid, bug fix in FV3GFS_IO.F90, and quad precision in stochastic physics (ufs-community#1028) - The 2D decomposition is enabled on write grid component. - FV3atm PR NOAA-EMC/fv3atm#468 from @MicroTed - stochastic physics PR NOAA-PSL/stochastic_physics#53 from Dom. Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Update CMEPS for wave coupling (ufs-community#1034) * add run phases to allow waves to run in the slow loop * re-order hafs wave test * update aliases in fd_nems.yaml * update CMEPS to prevent advertise conflicts when s2sw is still using connectors * add correct masking variables to hafs nems.configure files * 4DIAU bug fix when iau_filter_increments=T (ufs-community#990) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (ufs-community#1037) Co-authored-by: @SMoorthi-emc * Update esmf 821b04 (ufs-community#1041) * Update the version of ESMF library to 8.2.1b04 * Add the write group lon info for upp 2d decomposition test. * Multiple output (nested) grids from fv3atm (ufs-community#1044) Update fv3atm to support writing multiple history files for parent and nested domains. Nested HAFS regression tests were updated to write out history files from all nested domains. Co-authored-by: Bin Liu <[email protected]> * GPU-enabled version of Grell-Freitas convection in ccpp-physics (ufs-community#1043) * Enable Thompson microphysics with UFS-Aerosols and update GOCART (ufs-community#1049) This update allows the Thompson microphysics scheme to be used with prognostic aerosols (UFS-Aerosols) and updates GOCART to version 2.0.2. * Add support for Stochastically Perturbed Parameterizations (SPP) in FV3 (ufs-community#982) * Update CICE; add support for restart test when running single RT (was PR 1058); update MOM6 (was PR 1060) (ufs-community#1045) * update cice * (1) pointing MOM6 to testing branch (MOM6 main repo PR: mom-ocean/MOM6#1556 (comment)) (2) add three new files in mom_cmake file core/MOM_porous_barriers.F90 external/drifters/MOM_particles.F90 external/drifters/MOM_particles_types.F90 (3) explicitly set in MOM_input for all resolutions to reflect the default value changes in code to retain answer EPBL_MLD_BISECTION = True (default changed from T to F in this MOM6 PR) INTERNAL_WAVE_SPEED_BETTER_EST = False (default changed from F to T in this MOM6 PR) note BBL_USE_EOS now set to use the value of USE_EOS in this MOM6 PR, but we set BBL_USE_EOS explicit so it has no impact * remove duplicated CHL input setting in MOM_input_template_050 * add support for restart tests while running single RT * lateral boundary fix for regional runs (ufs-community#1050) This PR fixes a transient increase in noise caused by incorrect processing of winds along the lateral boundary on the final acoustic time step before fresh boundary information is ingested into the model. * Update pointer to FV3 * Point to Christina's branches. * Update RT log for Hera Intel. * Adding RT log for Hera GNU tests. * Updating RT log for Jet Intel tests. * Latest regression tests on Jet. * Adding regression logs. * Updating regression test date stamp. * Point to GSL repositories for FV3 and FV3/ccpp/physics Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Minsuk Ji <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: BinLi-NOAA <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: mzhangw <[email protected]> Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: Samuel Trahan (NOAA contractor) <[email protected]> Co-authored-by: SMoorthi-emc <[email protected]> Co-authored-by: ChunxiZhang-NOAA <[email protected]> Co-authored-by: David Huber <[email protected]> Co-authored-by: Bin Liu <[email protected]> Co-authored-by: Samuel Trahan <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Gerhard Theurich <[email protected] > Co-authored-by: Ali.Abdolali <[email protected]> Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Jeff Whitaker <[email protected]> Co-authored-by: DomHeinzeller <[email protected]> Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: MatthewPyle-NOAA <[email protected]> * Remove GF Consistency Check & Add SDFs - V2 (NCAR#120) * - Removes consistency check in GF, allows GF to run with different or no shallow scheme - Add additional RAP based SDF * - Add regression test logs * jet intel test * point to gsl/develop for FV3 Co-authored-by: Samuel Trahan <[email protected]> * Update to top of FV3 to get latest ccpp-physics codeowners (NCAR#123) * FV3 submodule: merge gsl/develop into RRFS_dev * Hera gnu tests passed. * Hera intel tests passed. * jet tests passed * Put a comment back in the FV3/ccpp/physics submodule. * point to head of FV3 RRFS_dev branch Co-authored-by: Christina Holt <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Minsuk Ji <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: BinLi-NOAA <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: mzhangw <[email protected]> Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: SMoorthi-emc <[email protected]> Co-authored-by: ChunxiZhang-NOAA <[email protected]> Co-authored-by: David Huber <[email protected]> Co-authored-by: Bin Liu <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Gerhard Theurich <[email protected] > Co-authored-by: Ali.Abdolali <[email protected]> Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Jeff Whitaker <[email protected]> Co-authored-by: DomHeinzeller <[email protected]> Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: MatthewPyle-NOAA <[email protected]> Co-authored-by: Hannah C Barnes <[email protected]>
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