Bugfixes from public release #119

DusanJovic-NOAA · 2020-05-07T18:36:32Z

Cherry pick some bug fixes and cleanup commits from release/public-v1 branch.

…ic_release

(1) Introducing a separate array "tiice" to store internal ice temperature. "tiice" will be added to phyf*nc output only when frac_grid=T. (2) When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable. (3) Adding frac_grid to namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.

New capability to use git submodule info to checkout externals By default, an external with no specified sub-externals configuration file will have its submodules checked out according to the information in that repository's .gitmodules file. This process is recursive. To prevent submodules from being checked out, the external description for that repository should be listed as "externals = none". To use submodule URL, local path, and reference hash information for a sub-external, replace the 'local_path', 'repo_url', and 'branch' 'hash' or 'tag' keywords with "from_submodule = True". User interface changes?: Yes externals keyword can be "none" to prevent loading submodules. from_submodule keyword can be used to replace external configuration information with information from a repository's submodule configuration. Fixes: NOAA-GSL#96 Testing: test removed: none unit tests: all pass system tests: all pass, added TestSubrepoCheckout to test new functionality manual testing: Tests with ESCOMP/MOM_interface (see below) Just run checkout_externals: no change Remove "externals = ../Externals_MOM.cfg" from Externals.cfg: All four submodules of MOM6 checked out Set "externals = none" in Externals.cfg: No submodules checked out (empty directories) Modify da_hooks external in Externals_MOM.cfg (see below): da_hooks is checked out with MOM6 .gitmodules configuration. [pkg/MOM6_DA_hooks] protocol = git from_submodule = True required = True

@MicroTed

* 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]>

@MicroTed

* 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]>

* Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (#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 (#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 (#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 #806, #807, #813, and ort modifications (#970) - CCPP Physics changes: see Wrapper for ccpp-physics #806, #807, #813, NOAA-EMC/fv3atm#447. - UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion #965 * Wrapper for ccpp-physics #808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (#971) * update submodule pointer for regression testing for ccpp-physics #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. (#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 (#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 (#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) (#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 (#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 (#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 (#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 (#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 (#996) * Radar-derived microphysics temperature tendencies similar to operational HRRR (#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; (#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 (#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 (#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 (#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 (#1008) * Add fhzero ort to coupled tests (#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 (#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 (#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 (#1018) Add code updates to enable the ESMF managed threading in UFS. Co-authored-by: Gerhard Theurich <[email protected] > * sync-ww3 (#1026) * sync with ww3 develop branch * Revisions to repair iovr=5 cloud overlap option (#1025) * This PR addresses part 2 of issue #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 (#1028) - The 2D decomposition is enabled on write grid component. - FV3atm PR NOAA-EMC/fv3atm#468 from @MicroTed - stochastic physics PR noaa-psd/stochastic_physics#53 from Dom. Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Update CMEPS for wave coupling (#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 (#990) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (#1037) Co-authored-by: @SMoorthi-emc * Update esmf 821b04 (#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 (#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 (#1043) * Enable Thompson microphysics with UFS-Aerosols and update GOCART (#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 (#982) * Update CICE; add support for restart test when running single RT (was PR 1058); update MOM6 (was PR 1060) (#1045) * update cice * (1) pointing MOM6 to testing branch (MOM6 main repo PR: https://github.com/mom-ocean/MOM6/pull/1556#issuecomment-1043374317) (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 (#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. * Feature: NSSL Microphysics support (#1032) * add new RT that uses NSSL MP; add new NSSL vars to default_vars.sh and rap.nml.IN; add new field table for using NSSL MP with hail on * Merge ufs-community develop into gsl/develop (#119) * Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (#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 (#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 (#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 #806, #807, #813, and ort modifications (#970) - CCPP Physics changes: see Wrapper for ccpp-physics #806, #807, #813, NOAA-EMC/fv3atm#447. - UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion #965 * Wrapper for ccpp-physics #808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (#971) * update submodule pointer for regression testing for ccpp-physics #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. (#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 (#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 (#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) (#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 (#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 (#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 (#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 (#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 (#996) * Radar-derived microphysics temperature tendencies similar to operational HRRR (#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; (#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 (#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 (#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 (#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 (#1008) * Add fhzero ort to coupled tests (#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 (#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 (#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 (#1018) Add code updates to enable the ESMF managed threading in UFS. Co-authored-by: Gerhard Theurich <[email protected] > * sync-ww3 (#1026) * sync with ww3 develop branch * Revisions to repair iovr=5 cloud overlap option (#1025) * This PR addresses part 2 of issue #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 (#1028) - The 2D decomposition is enabled on write grid component. - FV3atm PR NOAA-EMC/fv3atm#468 from @MicroTed - stochastic physics PR noaa-psd/stochastic_physics#53 from Dom. Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Update CMEPS for wave coupling (#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 (#990) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (#1037) Co-authored-by: @SMoorthi-emc * Update esmf 821b04 (#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 (#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 (#1043) * Enable Thompson microphysics with UFS-Aerosols and update GOCART (#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 (#982) * Update CICE; add support for restart test when running single RT (was PR 1058); update MOM6 (was PR 1060) (#1045) * update cice * (1) pointing MOM6 to testing branch (MOM6 main repo PR: https://github.com/mom-ocean/MOM6/pull/1556#issuecomment-1043374317) (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 (#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 (#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]> * p8b (with aerosols) (#1071) updates all p8 tests to the p8b settings, which includes GOCART Co-authored-by: Raffaele Montuoro <[email protected]> * Update to top of FV3 to get latest ccpp-physics codeowners (#123) * Split CCPP finalize into physics_finalize and (framework) finalize, fix CCPP's metadata2html.py (#1061) * add a cdeps test using GFSv16 input data (#1070) * CMAKE for WW3 (#1089) * Use WW3 CMake build Co-authored-by: kgerheiser <[email protected]> * Add 'valid time' variable using ISO string format (#1073) * Require cmake version 3.19 * Update FV3: - Add 'valid time' variable using ISO string format to netcdf history files. - Use double precision variable to set value of 'time' attribute in wrt comp import state - Update ccpp/physics (setting surface-related interstitial variables for SCM prescribed-surface-flux mode) - Update inline_post_stub.F90 subroutine interfaces to match inline_post.F90 * Add hi-res regional test on small domain (#1084) * Add hi-res regional test on small domain * Fix Lambert Conformal Conic mapping in the write component on the southern hemisphere (#1087) * Subroutine `lambert` in the FV3 write component has been fixed to do the mapping on the southern hemisphere correctly. * CI fix - Docker container library updated. CI input data updated. Add chm_petlist_bounds. - Change gocart output file name for debug test - Changes for opnReqTest to also scan rt_gnu.conf - Change CI tests to noaero Co-authored-by: Minsuk Ji <[email protected]> * Rectify total number of Thompson MP species and add UFS-Aerosols to S2S and S2SW (#1118) * Rectify total number of Thompson MP species * Implement S2SWA/S2SA build app as the only one enabling prognostic aerosols in fully coupled model. * Update output_fh documentation. * Add a cdeps test and update mom6, fv3, and weekly tests (#1136) Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: DusanJovic-NOAA <[email protected]> * Updates to the MYNN-EDMF (#129) * update submodule pointer for fv3atm * Fault tolerance in rt.sh usage of rocoto. * Update baseline date. * Bug fixes to rocoto changes. * Hera gnu tests passed. * Sleep 60 seconds betwen calls to rocotorun to avoid seeing submitted jobs in an inconsistent state when the batch scheduler is overwhelmed. * Hera intel tests passed. * Jet intel tests passed. * Corrections to Rocoto reliability changes * Point to gsl/develop for FV3 Co-authored-by: samuel.trahan <[email protected]> * GWD, LSM and MYNN physics updates from RRFS_dev branch (#130) * GWD, LSM and MYNN physics updates from RRFS_dev branch * Temporary push to fork for transfer to Jet. * Added regression test logs required for PR * Reverting back to original rt.sh * hera.gnu tests passed * Jet intel tests passed. * Hera intel tests passed * Point to gsl/develop for FV3 Co-authored-by: samuel.trahan <[email protected]> * update submodule pointer for fv3atm * Update fms to 2021.04 (#1135) * Update fms to 2021.04 * Add RT for ocean IAU * Update documentation Co-authored-by: Phil Pegion <[email protected]> Co-authored-by: Jun Wang <[email protected]> * Point to top of gsl/develop for ccpp-physics * land surface upgrades for p8 (#1095) * reset the Noah-MP default options for those well tested * P8c: Added capability for cdmbgwd(1) to scale GSL blocking drag (#1110) * Update ESMF to version 8.3.0bs09 (#1146) * Update ESMF to version 8.3.0b09 * Increase wall clock limit for tests/regional_3km to 15 min * Update AutoRT to use tfe01 ecflow node on Jet * Updated Cheyenne baseline epicufsrt path * Updated Cheyenne epicufsrt hpc-stack build Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> * Update rrfs conus regression tests to compute fluxes. * Remove nst_anl and a comment from the rrfs_conus13km_hrrr.nml.IN namelist template * release/p8c: updated the TKE-EDMF PBL and saSAS cumulus scheme plus bug fix for the Thompson scheme (issue #881) (#1120) * release/p8c: it is related to ccpp-physics PBL and cumulus updates plus a bug fix to the Thompson scheme * Bring AQM model into UFS & Update MOM6 mixed FMS (#1137) * Add AQM submodule to integrate NOAA's Air Quality Model embedding the U.S. EPA Community Multiscale Air Quality Model (CMAQ). * MOM6: An alternate fix to class(*) issues with FMS 2022-01 Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: jiandewang <[email protected]> * Radiation changes for prototype 8 (#1090) * New feature in RRTMGP enabled ccpp-physics. * Updated physics. New FV3 interstitials. * Cleanup of RRTMGP regression tests. * Replaced cld_mynn_ naming convention with cld_pbl_ * Some more cleanup of cloud-fraction... * Pulled in Qingfu's changes to ccpp-physics * New RT's for RRTMGP p8. Revert change in ccpp-physics * Changed arguments to implied shape. in ccpp-physics * Updated RRTMGP regression tests * Changes to FV3/ccpp-physics. * RRTMGP RT cleanup, again. Bug-fix in FV3/ccpp-physics * Revert changes to names in FV3/ccpp-physics * Cleanup p8 tests. * More RT cleanup for p8. * Add GP setting to non-coupled p8 tests. * Added bounding to temperature at layer-interface used by RRTMGP. * Reorder loop * Combined gp sw and lw aerosol routines. Modest speedup (~4%). Add GP setting to test setup. * Add GP settings to cpld_control_c96_noaero_p8 test. * update test resources default_vars.sh * HAFS moving-nesting related developments (#1104) * Add the storm-following or specified moving-nesting capability for both the regional and global configuration. * Expand the UFS/HAFS FV3ATM-HYCOM ocean coupling to support the static and moving nesting configuration. * Expand the write grid component to support outputting the moving nest domain properly. * Five HAFS related moving-nesting regression tests are added to test these newly added features. The regional_hafs RT was removed. Co-authored-by: Daniel Rosen <[email protected]> Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: uturuncoglu <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: A-Kyle <[email protected]> * fv3atm: Split GFS_typedefs.F90, rename CCPP_interstitial, import ccpp_t from ccpp_types; contains bug fix for WW3 debug (#1130) Co-authored-by: Jessica Meixner <[email protected]> * Close MOM6 1deg at j=1; Update input-data for P8c (#909) * update all tests using 1deg MOM6/CICE6 * pre-pend ufs to existing topo edits filename when creating the new file * update input-data directory * Fix uninitialized min_rand variable in Thompson MP when using SPP (#1152) * Updates to stochastic_physics and fv3 and CI * Add RRFS-Smoke and regression tests. * "update .gitmodules to point to the gsl/develop-smoke" * "push tests/tests/rrfs_smoke_conus13km_hrrr_warm" * Point to gsl/develop-smoke for ccpp-physics * "update .gitmodules" * "point to gsl/develop-smoke branch" * "point to gsl/develop-smoke with active flag updates" * "upload the hera.intel and hera.gnu regression test log files" * Add the rrfs_smoke_conus13km_hrrr_warm regression test. * Remove an extra read that went out of bounds * hera.gnu tests passed * hera.intel tests passed * jet.intel tests passed * Point to gsl/develop for FV3 * Point .gitmodules to NOAA-GSL Co-authored-by: samuel.trahan <[email protected]> * A bug fix for wet scavenging of aerosols and a minor modification for moisture property calculation (#1176) * point to one_scheme_to_one_file PR branch (#1175) * merge ufs-community develop * Point to gsl/merge-develop for FV3 * Changes missing from prior commit * use community version of hafs_regional_atm * merge rt.sh changes * Point to gsl/merge-develop-to-community branch for FV3 * Revert gsl-specific changes to rt.sh * Corrections to prior merge * corrections to FV3_HRRR tests * Add rrfs_smoke_conus13km_hrrr_warm test * Add FV3_HRRR_smoke to rt builds * Correct nst and domains_stack_size in rrfs_conus13km_hrrr.nml.IN * Set SFCLAY_COMPUTE_FLUX=.true. for rrfs_smoke tests * hera.gnu tests passed * Hera BUILD_WALLTIME of 1 hour due to occasional extreme contention for intel licenses * hera intel tests passed * Jet tests passed * Revert gsl-specific change to rt.sh * Point FV3/.gitmodules to Sam's fork * Correct issues found by reviewers in ccpp-physics and fv3atm * Rename mynnpbl to mynnedmf in fv3atm and ccpp-physics * FV3: Remove some empty _init and _finalize routines and update a comment in sgscloud_radpre * Feature/lndp noahmp2 : add land perturbation scheme for Noah-MP fractional veg (#1143) Updates to allow land perturbation scheme to be applied for Noah-MP. Currently, for Noah-MP model parameters can perturb only vegetation fraction. Main code changes: -added lsm_noahmp model option to lndp_type==2 land perturbation scheme (fv3-atm, stochastic_physics) -updated comments -cleaned up the namelists to make the different options clearer. Removed misleading lndp_each_step variable from gfs_physics_nml, and replaced it with "lndp_model_type" in the nam_sfcperts namelist for the different forecast types (cycling DA, short forecasts, perturbing only initial conditions) (fv3-atm, stochastic_physics, ufs-weather-model) NOTE: see note below, re: specification of smc perturbation for RAP/HRRR/etc (lndp_model_type==2) -revised code in stochastic_physics_wrapper to only allocate arrays that will be used when passed into lndp_apply_perts (fv3-atm) -deleted unused albedo arrays in stochastic_physics_wrapper and lndp_apply_perts (fv3-atm, stochastic_physics) -fixed bug causing precision errors when calculating the soil moisture ice content (often ~0.0; stochastic_physics) -fixed bug in which lndp_apply_perts wasn't called for nscyc = 0. (fv3-atm) -increased max_nvar_lndp at Jeff Ator's request (fv3-atm) -added a new test for the Noah-MP and lndp==2 combination (ufs-weather-model) * Add \file to smoke files * Update CDEPS component, add hailcast code in FV3/atmos_cubed_sphere and reduce wall clock time used for the cpld_control_c192_p8 test on Jet (#1156) Co-authored-by: Yunheng Wang * Update CMEPS; Add gocart userguide (was #1182) (#1189) * Update CMEPS submodule * Add GOCART documentation Co-authored-by: Li Pan <[email protected]> * Combine PROD and REPRO build options into 'Release' build type (#1171) Combined PROD and REPRO build modes into 'Release' build type. Now only 'Debug' and 'Release' build type are supported. Both build types must produce bit-for-bit reproducible outputs using different number of threads, mpi tasks, different domain decomposition, have reproducible restarts etc. * Unify inline post interfaces (#1181) * replace pwatclm to pwat in the all diag tables under tests/parm/diag_table. * adding bug fix from jili dong and removing U* averaging * adding bug fix from jili dong and removing U* averaging * Hera tests passed. * Remove some commented-out code from cu_gf_driver in ccpp-physics. * In FV3, turn rrtmg smoke band 10 into a model namelist variable * Switch ccpp-physics smoke arguments to implied shape * Remove some stops and gotos from ccpp-physics rrfs-smoke * In FV3, remove some hard-coded constants and rename some meta entries * In FV3, rename some standard_names, change a unit, and remove a "use physcons" * Updated settings for NoahMP, Thompson and RRTMGP in RTs (#1196) * add NoahMP opt_trs to namelist * Updated namelist settings related to NoahMP scheme, Thompson scheme and RRTMGP (issue #1173 and #1185) * Updated some namelist settings and add/remove some RTs related to RRTMGP * Compute petlist bounds for each subcomponent from number of tasks. Update CICE (#1200) * Instead of specifying petlist bounds (lower and upper bound), compute them using the number of tasks for each component. The function that computes petlist bounds assumes that the mediator always runs on the same tasks as ATM component, and that the Chemistry component also always runs on the same tasks as ATM. * Update CICE submodule (@DeniseWorthen) Co-authored-by: Minsuk Ji <[email protected]> * NSSL ccpp-physics bugfixes and new ccpp-framework debugging feature (#1202) * Merge develop * hera.gnu tests passed * hera.intel tests passed * jet intel tests passed * hera.gnu tests passed. * fv3atm: Only add cnv_3d_ud_mf to the restart files when needed * More warnings not to change the conus13km tests * adjust BL_DATE in rt.sh to 20220516 * WCOSS Cray tests passed * fv3atm: pass some chemistry varibles to mynn_bl_driver correctly * [AutoRT] hera.gnu Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] hera.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] cheyenne.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * WCOSS Dell P3 tests passed * Correct argument passing within mynn edmf * [AutoRT] gaea.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] cheyenne.gnu Job Completed. on-behalf-of @ufs-community <[email protected]> * Orion RT Passed * [AutoRT] jet.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * Point to NOAA-EMC develop for FV3 * merge gsl institutional fork (#1195) Merge in GSL institutional fork. * update FV3 to top of gsl/merge-community-to-develop * FV3: point to sam's repo * Point to GSL baseline areas * FV3/ccpp/physics: Change to GSL CODEOWNERS * hera.gnu tests passed * hera.intel passed * jet.intel tests passed * Set regression test path to GSL areas on Hera * FV3: Returned the comments on soil resistance back. * point to gsl/develop for fv3atm * Merge May 16 ufs-community develop to gsl/develop (#138) * Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (#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 (#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 (#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 #806, #807, #813, and ort modifications (#970) - CCPP Physics changes: see Wrapper for ccpp-physics #806, #807, #813, NOAA-EMC/fv3atm#447. - UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion #965 * Wrapper for ccpp-physics #808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (#971) * update submodule pointer for regression testing for ccpp-physics #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. (#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 (#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 (#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) (#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 (#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 (#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 (#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 (#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 (#996) * Radar-derived microphysics temperature tendencies similar to operational HRRR (#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; (#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 (#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 (#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 (#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 (#1008) * Add fhzero ort to coupled tests (#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 (#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 (#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 (#1018) Add code updates to enable the ESMF managed threading in UFS. Co-authored-by: Gerhard Theurich <[email protected] > * sync-ww3 (#1026) * sync with ww3 develop branch * Revisions to repair iovr=5 cloud overlap option (#1025) * This PR addresses part 2 of issue #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 (#1028) - The 2D decomposition is enabled on write grid component. - FV3atm PR NOAA-EMC/fv3atm#468 from @MicroTed - stochastic physics PR noaa-psd/stochastic_physics#53 from Dom. Co-authored-by: Ted Mansell <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Update CMEPS for wave coupling (#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 (#990) * Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (#1037) Co-authored-by: @SMoorthi-emc * Update esmf 821b04 (#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 (#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 (#1043) * Enable Thompson microphysics with UFS-Aerosols and update GOCART (#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 (#982) * Update CICE; add support for restart test when running single RT (was PR 1058); update MOM6 (was PR 1060) (#1045) * update cice * (1) pointing MOM6 to testing branch (MOM6 main repo PR: https://github.com/mom-ocean/MOM6/pull/1556#issuecomment-1043374317) (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 (#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. * Feature: NSSL Microphysics support (#1032) * add new RT that uses NSSL MP; add new NSSL vars to default_vars.sh and rap.nml.IN; add new field table for using NSSL MP with hail on * p8b (with aerosols) (#1071) updates all p8 tests to the p8b settings, which includes GOCART Co-authored-by: Raffaele Montuoro <[email protected]> * Split CCPP finalize into physics_finalize and (framework) finalize, fix CCPP's metadata2html.py (#1061) * add a cdeps test using GFSv16 input data (#1070) * CMAKE for WW3 (#1089) * Use WW3 CMake build Co-authored-by: kgerheiser <[email protected]> * Add 'valid time' variable using ISO string format (#1073) * Require cmake version 3.19 * Update FV3: - Add 'valid time' variable using ISO string format to netcdf history files. - Use double precision variable to set value of 'time' attribute in wrt comp import state - Update ccpp/physics (setting surface-related interstitial variables for SCM prescribed-surface-flux mode) - Update inline_post_stub.F90 subroutine interfaces to match inline_post.F90 * Add hi-res regional test on small domain (#1084) * Add hi-res regional test on small domain * Fix Lambert Conformal Conic mapping in the write component on the southern hemisphere (#1087) * Subroutine `lambert` in the FV3 write component has been fixed to do the mapping on the southern hemisphere correctly. * CI fix - Docker container library updated. CI input data updated. Add chm_petlist_bounds. - Change gocart output file name for debug test - Changes for opnReqTest to also scan rt_gnu.conf - Change CI tests to noaero Co-authored-by: Minsuk Ji <[email protected]> * Rectify total number of Thompson MP species and add UFS-Aerosols to S2S and S2SW (#1118) * Rectify total number of Thompson MP species * Implement S2SWA/S2SA build app as the only one enabling prognostic aerosols in fully coupled model. * Update output_fh documentation. * Add a cdeps test and update mom6, fv3, and weekly tests (#1136) Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]> Co-authored-by: DusanJovic-NOAA <[email protected]> * update submodule pointer for fv3atm * Update fms to 2021.04 (#1135) * Update fms to 2021.04 * Add RT for ocean IAU * Update documentation Co-authored-by: Phil Pegion <[email protected]> Co-authored-by: Jun Wang <[email protected]> * land surface upgrades for p8 (#1095) * reset the Noah-MP default options for those well tested * P8c: Added capability for cdmbgwd(1) to scale GSL blocking drag (#1110) * Update ESMF to version 8.3.0bs09 (#1146) * Update ESMF to version 8.3.0b09 * Increase wall clock limit for tests/regional_3km to 15 min * Update AutoRT to use tfe01 ecflow node on Jet * Updated Cheyenne baseline epicufsrt path * Updated Cheyenne epicufsrt hpc-stack build Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> * Update rrfs conus regression tests to compute fluxes. * Remove nst_anl and a comment from the rrfs_conus13km_hrrr.nml.IN namelist template * release/p8c: updated the TKE-EDMF PBL and saSAS cumulus scheme plus bug fix for the Thompson scheme (issue #881) (#1120) * release/p8c: it is related to ccpp-physics PBL and cumulus updates plus a bug fix to the Thompson scheme * Bring AQM model into UFS & Update MOM6 mixed FMS (#1137) * Add AQM submodule to integrate NOAA's Air Quality Model embedding the U.S. EPA Community Multiscale Air Quality Model (CMAQ). * MOM6: An alternate fix to class(*) issues with FMS 2022-01 Co-authored-by: Raffaele Montuoro <[email protected]> Co-authored-by: jiandewang <[email protected]> * Radiation changes for prototype 8 (#1090) * New feature in RRTMGP enabled ccpp-physics. * Updated physics. New FV3 interstitials. * Cleanup of RRTMGP regression tests. * Replaced cld_mynn_ naming convention with cld_pbl_ * Some more cleanup of cloud-fraction... * Pulled in Qingfu's changes to ccpp-physics * New RT's for RRTMGP p8. Revert change in ccpp-physics * Changed arguments to implied shape. in ccpp-physics * Updated RRTMGP regression tests * Changes to FV3/ccpp-physics. * RRTMGP RT cleanup, again. Bug-fix in FV3/ccpp-physics * Revert changes to names in FV3/ccpp-physics * Cleanup p8 tests. * More RT cleanup for p8. * Add GP setting to non-coupled p8 tests. * Added bounding to temperature at layer-interface used by RRTMGP. * Reorder loop * Combined gp sw and lw aerosol routines. Modest speedup (~4%). Add GP setting to test setup. * Add GP settings to cpld_control_c96_noaero_p8 test. * update test resources default_vars.sh * HAFS moving-nesting related developments (#1104) * Add the storm-following or specified moving-nesting capability for both the regional and global configuration. * Expand the UFS/HAFS FV3ATM-HYCOM ocean coupling to support the static and moving nesting configuration. * Expand the write grid component to support outputting the moving nest domain properly. * Five HAFS related moving-nesting regression tests are added to test these newly added features. The regional_hafs RT was removed. Co-authored-by: Daniel Rosen <[email protected]> Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: uturuncoglu <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: A-Kyle <[email protected]> * fv3atm: Split GFS_typedefs.F90, rename CCPP_interstitial, import ccpp_t from ccpp_types; contains bug fix for WW3 debug (#1130) Co-authored-by: Jessica Meixner <[email protected]> * Close MOM6 1deg at j=1; Update input-data for P8c (#909) * update all tests using 1deg MOM6/CICE6 * pre-pend ufs to existing topo edits filename when creating the new file * update input-data directory * Fix uninitialized min_rand variable in Thompson MP when using SPP (#1152) * Updates to stochastic_physics and fv3 and CI * A bug fix for wet scavenging of aerosols and a minor modification for moisture property calculation (#1176) * point to one_scheme_to_one_file PR branch (#1175) * merge ufs-community develop * Point to gsl/merge-develop for FV3 * Changes missing from prior commit * use community version of hafs_regional_atm * merge rt.sh changes * Point to gsl/merge-develop-to-community branch for FV3 * Revert gsl-specific changes to rt.sh * Corrections to prior merge * corrections to FV3_HRRR tests * Add rrfs_smoke_conus13km_hrrr_warm test * Add FV3_HRRR_smoke to rt builds * Correct nst and domains_stack_size in rrfs_conus13km_hrrr.nml.IN * Set SFCLAY_COMPUTE_FLUX=.true. for rrfs_smoke tests * hera.gnu tests passed * Hera BUILD_WALLTIME of 1 hour due to occasional extreme contention for intel licenses * hera intel tests passed * Jet tests passed * Revert gsl-specific change to rt.sh * Point FV3/.gitmodules to Sam's fork * Correct issues found by reviewers in ccpp-physics and fv3atm * Rename mynnpbl to mynnedmf in fv3atm and ccpp-physics * FV3: Remove some empty _init and _finalize routines and update a comment in sgscloud_radpre * Feature/lndp noahmp2 : add land perturbation scheme for Noah-MP fractional veg (#1143) Updates to allow land perturbation scheme to be applied for Noah-MP. Currently, for Noah-MP model parameters can perturb only vegetation fraction. Main code changes: -added lsm_noahmp model option to lndp_type==2 land perturbation scheme (fv3-atm, stochastic_physics) -updated comments -cleaned up the namelists to make the different options clearer. Removed misleading lndp_each_step variable from gfs_physics_nml, and replaced it with "lndp_model_type" in the nam_sfcperts namelist for the different forecast types (cycling DA, short forecasts, perturbing only initial conditions) (fv3-atm, stochastic_physics, ufs-weather-model) NOTE: see note below, re: specification of smc perturbation for RAP/HRRR/etc (lndp_model_type==2) -revised code in stochastic_physics_wrapper to only allocate arrays that will be used when passed into lndp_apply_perts (fv3-atm) -deleted unused albedo arrays in stochastic_physics_wrapper and lndp_apply_perts (fv3-atm, stochastic_physics) -fixed bug causing precision errors when calculating the soil moisture ice content (often ~0.0; stochastic_physics) -fixed bug in which lndp_apply_perts wasn't called for nscyc = 0. (fv3-atm) -increased max_nvar_lndp at Jeff Ator's request (fv3-atm) -added a new test for the Noah-MP and lndp==2 combination (ufs-weather-model) * Add \file to smoke files * Update CDEPS component, add hailcast code in FV3/atmos_cubed_sphere and reduce wall clock time used for the cpld_control_c192_p8 test on Jet (#1156) Co-authored-by: Yunheng Wang * Update CMEPS; Add gocart userguide (was #1182) (#1189) * Update CMEPS submodule * Add GOCART documentation Co-authored-by: Li Pan <[email protected]> * Combine PROD and REPRO build options into 'Release' build type (#1171) Combined PROD and REPRO build modes into 'Release' build type. Now only 'Debug' and 'Release' build type are supported. Both build types must produce bit-for-bit reproducible outputs using different number of threads, mpi tasks, different domain decomposition, have reproducible restarts etc. * Unify inline post interfaces (#1181) * replace pwatclm to pwat in the all diag tables under tests/parm/diag_table. * adding bug fix from jili dong and removing U* averaging * adding bug fix from jili dong and removing U* averaging * Hera tests passed. * Remove some commented-out code from cu_gf_driver in ccpp-physics. * In FV3, turn rrtmg smoke band 10 into a model namelist variable * Switch ccpp-physics smoke arguments to implied shape * Remove some stops and gotos from ccpp-physics rrfs-smoke * In FV3, remove some hard-coded constants and rename some meta entries * In FV3, rename some standard_names, change a unit, and remove a "use physcons" * Updated settings for NoahMP, Thompson and RRTMGP in RTs (#1196) * add NoahMP opt_trs to namelist * Updated namelist settings related to NoahMP scheme, Thompson scheme and RRTMGP (issue #1173 and #1185) * Updated some namelist settings and add/remove some RTs related to RRTMGP * Compute petlist bounds for each subcomponent from number of tasks. Update CICE (#1200) * Instead of specifying petlist bounds (lower and upper bound), compute them using the number of tasks for each component. The function that computes petlist bounds assumes that the mediator always runs on the same tasks as ATM component, and that the Chemistry component also always runs on the same tasks as ATM. * Update CICE submodule (@DeniseWorthen) Co-authored-by: Minsuk Ji <[email protected]> * NSSL ccpp-physics bugfixes and new ccpp-framework debugging feature (#1202) * Merge develop * hera.gnu tests passed * hera.intel tests passed * jet intel tests passed * hera.gnu tests passed. * fv3atm: Only add cnv_3d_ud_mf to the restart files when needed * More warnings not to change the conus13km tests * adjust BL_DATE in rt.sh to 20220516 * WCOSS Cray tests passed * fv3atm: pass some chemistry varibles to mynn_bl_driver correctly * [AutoRT] hera.gnu Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] hera.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] cheyenne.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * WCOSS Dell P3 tests passed * Correct argument passing within mynn edmf * [AutoRT] gaea.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * [AutoRT] cheyenne.gnu Job Completed. on-behalf-of @ufs-community <[email protected]> * Orion RT Passed * [AutoRT] jet.intel Job Completed. on-behalf-of @ufs-community <[email protected]> * Point to NOAA-EMC develop for FV3 * merge gsl institutional fork (#1195) Merge in GSL institutional fork. * update FV3 to top of gsl/merge-community-to-develop * FV3: point to sam's repo * Point to GSL baseline areas * FV3/ccpp/physics: Change to GSL CODEOWNERS * hera.gnu tests passed * hera.intel passed * jet.intel tests passed * Set regression test path to GSL areas on Hera * FV3: Returned the comments on soil resistance back. 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: Jessica Meixner <[email protected]> Co-authored-by: kgerheiser <[email protected]> Co-authored-by: RatkoVasic-NOAA <[email protected]> Co-authored-by: joeolson42 <[email protected]> Co-authored-by: Phil Pegion <[email protected]> Co-authored-by: HelinWei-NOAA <[email protected]> Co-authored-by: mdtoyNOAA <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: dustinswales <[email protected]> Co-authored-by: Daniel Rosen <[email protected]> Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: uturuncoglu <[email protected]> Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: A-Kyle <[email protected]> Co-authored-by: ClaraDraper-NOAA <[email protected]> Co-authored-by: Li Pan <[email protected]> * Correct .gitmodules * Gsl/may16 followup pr (#139) * new tests * point to gsl/may16-followup-pr branch of fv3 * Change suite_FV3_GFS_v15_thompson_mynn to not use mynn surface layer scheme (from T…

Community develop

DusanJovic-NOAA added 13 commits May 5, 2020 12:23

Update FV3 submodule

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Update FV3 submodule

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Update NEMS submodule url and branch

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Update FV3

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Merge remote-tracking branch 'origin/develop' into bugfixes_from_publ…

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…ic_release

Remove unused and unsupported code (See #21)

7d5ec09

Update FV3 submodule

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Update FV3

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Regression test logs on WCOSS Cray.

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Regression test logs on Orion.

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Regression test logs on Hera.

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Regression test logs on WCOSS Dell.

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Remove APPBUILD step from rt.conf

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DusanJovic-NOAA mentioned this pull request May 7, 2020

Bugfixes from public release NOAA-EMC/fv3atm#112

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DusanJovic-NOAA requested review from junwang-noaa and climbfuji May 7, 2020 18:38

junwang-noaa approved these changes May 7, 2020

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climbfuji approved these changes May 7, 2020

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Update FV3 submodule

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DusanJovic-NOAA merged commit 95fcb7c into ufs-community:develop May 8, 2020

DusanJovic-NOAA deleted the bugfixes_from_public_release branch May 8, 2020 14:10

epic-cicd-jenkins pushed a commit that referenced this pull request Apr 17, 2023

Merge pull request #119 from gsketefian/community_develop

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zach1221 mentioned this pull request Aug 16, 2023

update MOM6 to its main repository 20230703 and 20230811 updating #1864

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Bugfixes from public release #119

Bugfixes from public release #119

DusanJovic-NOAA commented May 7, 2020 •

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Bugfixes from public release #119

Bugfixes from public release #119

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