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Implementation of RUC LSM ice model in CCPP * Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop * Add kice=9 to tests/tests/fv3_ccpp_rap and tests/tests/fv3_ccpp_hrrr * Change NEW_BASELINE directory for gsl/develop to avoid conflicts with development work on the authoritative branches * Add KICE=9 to tests/tests/fv3_ccpp_gsd_unified_ugwp and tests/tests/fv3_ccpp_gsd_drag_suite_unified_ugwp * Revert change to .gitmodules and update submodule pointer for fv3atm Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
* Updates to stochastic_physics_wrapper (ufs-community#280) Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> * Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T (ufs-community#304) Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms). The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc). * Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290) * point MOM6 to new branch which corresponding to GFDL 20201022 commit * modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM6 code as this version of MOM6 contains some file deletion, new files being added and renaming of files * manually set MOM6 parameters in order to retain origonal results for 0.25x0.25 resolution * update MOM6 to include Bugfix for mom6solo to be built * modify compile.sh to allow mom6solo compiling * modify MOM_input_template for all resolutions based on GFDL MOM6-example main branch update on 20201022 * change executable permissions for CMakeLists.txt * chmod 644 to 6 files Dom pointed out * chmod for CMakeLists.txt and tests/compile.sh * change baseline directpory to 20201202 in rt.sh * Update CICE, Move regression test input outside baseline directory (ufs-community#270) *Updates CICE to most recent develop branch of NOAA-EMC * Sets n_aero (number of aerosols) in ice_in_template to 0. * removes trailing whitespace from ice_in * moves regression test input outside baseline directory (ufs-weather PR ufs-community#312) Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com> Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com> * Revert change to .gitmodules and update submodule pointer for fv3atm Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com> Co-authored-by: jiandewang <jiande.wang@noaa.gov> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
…er updates and bugfixes (NCAR#52)
…CAR#55) Code is identical to original/current code in the authoritative repository (NOAA-PSD, branch master)
* Add regression tests with stochastic land perturbations for suites FV3_GSD_v0 and FV3_GSD_noah Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
…perturbed variables (NCAR#61) * Updates to regression tests fv3_ccpp_gsd_lndp and fv3_ccpp_gsd_noah_lndp * Bug fix for tests/parm/ccpp_gsd_sar.nml.IN
* Updates to stochastic_physics_wrapper (ufs-community#280) Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> * Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T (ufs-community#304) Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms). The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc). * Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290) * point MOM6 to new branch which corresponding to GFDL 20201022 commit * modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM6 code as this version of MOM6 contains some file deletion, new files being added and renaming of files * manually set MOM6 parameters in order to retain origonal results for 0.25x0.25 resolution * update MOM6 to include Bugfix for mom6solo to be built * modify compile.sh to allow mom6solo compiling * modify MOM_input_template for all resolutions based on GFDL MOM6-example main branch update on 20201022 * change executable permissions for CMakeLists.txt * chmod 644 to 6 files Dom pointed out * chmod for CMakeLists.txt and tests/compile.sh * change baseline directpory to 20201202 in rt.sh * Update CICE, Move regression test input outside baseline directory (ufs-community#270) *Updates CICE to most recent develop branch of NOAA-EMC * Sets n_aero (number of aerosols) in ice_in_template to 0. * removes trailing whitespace from ice_in * moves regression test input outside baseline directory (ufs-weather PR ufs-community#312) Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com> Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com> * Updates to build for JEDI linking/control, add wcoss2 (ufs-community#295) * Build on wcoss2 (acorn) * Use -march=core-avx2 instead of -xCORE-AVX2 on wcoss2 * Updates to build for JEDI linking/control * Removed unnecessary include files and INLINE POST setting * Updated to address PR suggestions. * Add rt_acorn.conf. Change /lfs/h2 to /lfs/h1. * Update .gitmodules and submodule pointer for fv3atm for code review and testing * regression test results * Updated .gitmodules and removed extraneous file * Fixed .gitmodules and updated pointer for FV3 * Updated pointer to NEMS repo Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> * Final-final GFS v16 updates / restart reproducibility bugfixes (ufs-community#325) * Update .gitmodules and submodule pointer for fv3atm for code review and testing * Add GFS v16 beta restart test, update stochastics test * Update regression test baseline date tag to 20201214; skip-ci * tests/rt.conf: bugfix, add missing 'fv3' to new stochy tests; skip-ci * Regression test logs for gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci * Run GFS v16beta tests also on wcoss; regression test logs for wcoss; skip-ci * Regression test logs for cheyenne.intel and cheyenne.gnu * Revert change to .gitmodules and update submodule pointer for fv3atm * Add optional bulk flux calculation in ufs-datm (ufs-community#266) * Update NEMS DATM and CMEPS to allow the optional bulk flux formulation; add two tests using the option * Update top level CMakeList.txt to have compile flags for MOM6 and CICE6 identical for ufs-cpld and ufs-datm * Add optional configuration variable to nems.configure to specify the directory where CMEPS will write restarts * Adds cheyenne tasking variables to default_vars and sets WW3_COMP to cheyenne for platform cheyenne.intel *NOTE: Baselines develop-20201215 exist on all platforms, regression tests were run against exactly that baseline on all systems except cheyenne.intel. On cheyenne.intel the tests were run against 20201214, and this baseline is identical to 20201215 (as per "diff -r develop-20201214 develop-20201215"). Co-authors: @DusanJovic-NOAA @aerorahul @JessicaMeixner-NOAA skip-ci * Add 2 new tests for DATM-MOM6-CICE6 application (ufs-community#332) * Add the following 2 tests: datm_restart_cfsr, datm_debug_cfsr * Add wcoss_dell_p3.log. * Add Hera log, Orion log, wcoss_dell_p3 log. * RRTMGP and Thompson MP coupling (ufs-community#323) * Feature branch with RRTMGP and Thompson MP * Updated FV3/ccpp-physics. Added namelist and configuration for RRTMGP RTs using GSD physics. * Updated FV3 * Update physics in FV3 * Updated baselines in rt.sh * Updated RT logs. Updated FV3 physics submodule pointer. * Updated FV3 hash and .gitmodules * Regression test log for PR ufs-community#323 for jet.intel (ufs-community#336) * Update modules with hpc-stack v1.1.0 (ufs-community#319) * Update modules with hpc-stack v1.1.0 * Minor bug fixes to CCPP UGWP Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> * Replace old regional SDF with FV3_GFS_v15_thompson_mynn (ufs-community#333) * Replace old FV3_GFS_2017_gfdlmp_regional SDF for regional tests with FV3_GFS_v15_thompson_mynn. * Final path to IC's and new results. Also, input.nml updated. * Update RegressionTests_wcoss_dell_p3.log * Update RegressionTests_wcoss_cray.log * Update RegressionTests_hera.intel.log * Update RegressionTests_jet.intel.log * Update RegressionTests_orion.intel.log * Update RegressionTests_cheyenne* logs. * Update RegressionTests_hera.gnu.log * Feature/ww3update (ufs-community#334) This updates the WW3 submodule pointer to point to the top of the WW3 develop branch. The path to WW3 inputs is changed to input-data-20201201/WW3_input_data_20201207/ * Remove IPD (step 1) (ufs-community#331) Make CCPP=Y the default in tests/compile.sh. Remove CCPP=Y from tests/rt*.conf and adjust formatting. Update submodule pointer for MOM6 to include PR ufs-community#341 ("Update MOM6 to GFDL's 20201218 commit") Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3) Fix broken utest (see ufs-community#348) * Update the format of rt.conf (ufs-community#349) Update the format of MACHINES column in rt.conf (and other .conf files). This column can be either empty, which means a test will run on all supported machines, or start with - or + sign to exclude or include specified machines explicitly. * Add checkpoint restarts for ufs-cpld (ufs-community#342) * Adds 3 checkpoint restart tests for the ufs-cpld model * Drops the existing c92mx025 restart test * Adds cheyenne.intel as tested configuration for ufs-cpld and ufs-datm * Fixes instances of srf_data* in various fv3_conf files * add frac grid input, update and add additional cpld tests (ufs-community#354) * Updates FV3_input_frac to add both benchmark dates and L127 files * Adds additional tests and restart tests for coupled model * Sets all cpld tests to use frac grid input by default * Removes all instances of USE_LA_LI2016=True except for benchmark+wave configurations * Remove unnecessary SIMD instruction sets for Jet, first round of cleanup in rt.conf, initialize cld_amt to zero for regional runs (dycore) (ufs-community#353) * Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake * First cleanup of regression test config tests/rt.conf * tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5 * Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files * Remove tests/rt_acorn.conf and run GFS v15p2 and GFS v16beta DEBUG tests on all platforms * Implementation of CCPP timestep_init and timestep_final phases (ufs-community#337) * Update .gitmodules and submodule pointer for fv3atm for code review and testing * Update submodule pointer for fv3atm; skip-ci * Don't try to compile all suites in DEBUG mode on cheyenne.intel, weird bug on compute nodes; skip-ci * Don't try to compile all suites in DEBUG mode on wcoss_cray; skip-ci * Regression test logs for cheyenne.gnu, cheyenne.intel, gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci * Don't try to compile all suites in DEBUG mode on wcoss_dell_p3; skip-ci * Regression test logs for wcoss_cray and wcoss_dell_p3 * Revert change to .gitmodules and update submodule pointer for fv3atm * Update CMEPS (ufs-community#345) * Update CMEPS for recent changes, including addition of new run "post" run phases to eliminate redundant mapping, multiple ice sheet capability and ocn->land ice dynamic mapping * Add a new test fv3_gfs_v16_RRTMGP_c192L127 Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com> * Remove IPD steps 3 and 5 (ufs-community#357) Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake * First cleanup of regression test config tests/rt.conf * tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5; skip-ci * Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files * Update usage in rt.sh, add modulefiles/jet.intel/fv3_debug; skip-ci * CCPP is default in cmake build * Add debug modulefiles for linux.gnu and macosx.gnu * Update submodule pointer for fv3atm * Change logic in CMakeLists.txt and tests/compile.sh so that 32BIT=ON automatically sets DYN32=ON; skip-ci * Move logic to set DYN32 - depending on 32BIT setting - to fv3atm * Remove -DCCPP=ON from tests/compile.sh; update submodule pointer for fv3atm; skip-ci * point fv3 to EMC develop branch (ufs-community#377) * update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (ufs-community#378) * update CMEPS, fix character length error for gnu compile * add Dusan's fix for rt_utils.sh * update cpl gfsv16 tests, replace seaice_newland.grb with global_slmask.t1534.3072.1536.grb, recover input.mom6.nml.IN, update input directory, update global thread and decomp tests, update fdiag for global control * point to Dustins rrtmgp fix branch * update input directory Co-authored-by: denise.worthen <Denise.Worthen@noaa.gov> Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com> * Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (ufs-community#386) * Update .gitmodules and submodule pointer for fv3atm for gsl/develop branch * RUC ice for gsl/develop (replaces NCAR#47) (NCAR#49)Implementation of RUC LSM ice model in CCPP * Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop * Add kice=9 to tests/tests/fv3_ccpp_rap and tests/tests/fv3_ccpp_hrrr * Change NEW_BASELINE directory for gsl/develop to avoid conflicts with development work on the authoritative branches * Add KICE=9 to tests/tests/fv3_ccpp_gsd_unified_ugwp and tests/tests/fv3_ccpp_gsd_drag_suite_unified_ugwp * Revert change to .gitmodules and update submodule pointer for fv3atm * Update gsl/develop from develop 2020/12/08 (NCAR#50) * Updates to stochastic_physics_wrapper (ufs-community#280) Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model * Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T (ufs-community#304) Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms). The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc). * Land stochastic perturbations (NCAR#57) * dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (ufs-community#369) * Update fv3atm * update ccpp control test forecast length to 24h * remove rename command * Add CI related changes * Update RT logs * Update RT log files * Add the gaea RT log file * Update the point of fv3atm * Update fv3atm Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com> Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov> Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com> * MOM6 bugfixes, GFDL update, update CDMBGWD settings; fix for restart reproducibility (without waves) when USE_LA_LI2016=True, sign error on fprec passed to ocean, GFDL update, resolution dependent cdmbgwd settings (ufs-community#379) * implements two MOM6 bugfixes in the NUOPC MOM6 cap to allow restart reproducibility when USE_LA_LI2016=True and to change the sign of the latent heat flux associated with frozen precipitation (fprec) exported to MOM6 * updates MOM6 to include the GFDL 20210120 main branch which contains EMC's wave coupling code, alone with some minor code standardization and documentation * updates the cdmbgwd namelist settings for FV3 standalone tests at C96 and implements resolution dependent values for ufs-cpld tests Co-authored-by: Ali <ali.abdolali@noaa.gov> * Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (ufs-community#384) * Update .gitmodules and submodule pointers for fv3atm and NEMS * Remove Python 2.7 support from top-level CMakeLists.txt * Reduce forecast length of test fv3_ccpp_gfs_v16_RRTMGP_c192L127 from 24h to 12h * Rename v16beta to v16 everywhere except the public release documentation * Bugfixes and missing changes * Remove 'export CCPP_LIB_DIR=ccpp/lib' from all regression tests * Update regression test baseline date tag to 20210128; skip-ci * Update ecflow-python environment on cheyenne and jet; skip-ci * Update CMEPS for HAFS integration; add datm and coupled-model tests on Gaea (ufs-community#401) * Add HAFS support in NOAA-EMC/CMEPS * Add coupled and datm tests for Gaea.intel Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com> Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> * Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2) (ufs-community#407) * Regression test logs for all tier=1 platforms * updates FMS to 2020.04.01 (ufs-community#392) * updates FMS to 2020.04.01 * fixes fms_files.cmake * removes extra horiz_interp * Workaround for FMS 2020.04.01 for Cheyenne with GNU 9.1.0, incl. regression test log Co-authored-by: Mikyung Lee <mlee@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> * add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (ufs-community#399) *Implements an optional setting in the cpld and datm nems.configure files to specify whether the MOM6 cap should use a mesh or a grid *Adds configurable settings for min_seaice to gfs_physics_nml and dz_min to fv_core_nml. * UGWP v0 v1 combined (ufs-community#396) - combines the changes in PRs ufs-community#360 and ufs-community#382 - adds three regression tests `fv3_ccpp_gfsv16_ugwpv1 `, `fv3_ccpp_gfsv16_ugwpv1_warmstart` and `fv3_ccpp_gfsv16_ugwpv1_debug` - contains updates and bugfixes for `nc_compare.py` and the CI tests from @MinsukJi-NOAA - update Python3 environment on jet.intel, gaea.intel, cheyenne.{intel,gnu} - turn off (again) test `fv3_ccpp_decomp` on jet.intel, this test didn't work in the past, but recently it "passed", because the error checking with `nc_compare.py` failed silently and we didn't notice it Co-authored-by: valery.yudin <valery.yudin@noaa.gov> Co-authored-by: Michael Toy <michael.toy@noaa.gov> Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov> * Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (ufs-community#419)" (ufs-community#421) * Add one regional regression test in DEBUG mode. * Update .gitmodules and submodule pointer for fv3atm for code review and testing * Update regression tests from GFSv15+Thompson to GFSv16+Thompson * Combine several COMPILE lines in tests/rt.conf and tests/rt_gnu.conf * Regression test log for cheyenne.{gnu,intel},gaea.intel, hera.gnu, jet.intel,hera.intel,orion.intel;wcoss_cray and wcoss_dell_p3; Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com> Co-authored-by: jiandewang <jiande.wang@noaa.gov> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com> Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com> Co-authored-by: BinLi-NOAA <bin.li@noaa.gov> Co-authored-by: dustinswales <dustin.swales@noaa.gov> Co-authored-by: Kyle Gerheiser <3209794+kgerheiser@users.noreply.github.com> Co-authored-by: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com> Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com> Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com> Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com> Co-authored-by: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com> Co-authored-by: Ali <ali.abdolali@noaa.gov> Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: MiKyung Lee <58964324+mlee03@users.noreply.github.com> Co-authored-by: valery.yudin <valery.yudin@noaa.gov> Co-authored-by: Michael Toy <michael.toy@noaa.gov> Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
…NCAR#64) * Update submodule pointer for fv3atm
…ter_20210316 Update gsl/develop from develop 20210316
…m/SamuelTrahanNOAA/ufs-weather-model into feature/per-timestep-pgr-like-wrf
…fv3atm for code review and testing
…r-model into update_gsl_develop_from_develop_20210331
… and stochastic_physics
…elop_20210331 Update gsl/develop from develop 2021/03/31
…v3_gsd_diag3d_debug
Turn on the printout of the WRF noise parameter for regression test fv3_gsd_diag3d_debug
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
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Ready for reviews and upstream merges |
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I forgot to run ORT on the new test. Running now. |
@SamuelTrahanNOAA Is it possible for you to conduct thread, decomposition, restart and debug test for the |
grantfirl
reviewed
May 17, 2022
| @@ -186,21 +206,22 @@ | |||
| imfdeepcnv = @[IMFDEEPCNV] | |||
| imfshalcnv = @[IMFSHALCNV] | |||
| imp_physics = @[IMP_PHYSICS] | |||
| ! Yes, really, I mean it. Stop changing the iopt settings too. | |||
There was a problem hiding this comment.
Does this repo use the CODEOWNERS functionality? If so, it might make sense to add @SamuelTrahanNOAA to this file to review any changes to it?
grantfirl
approved these changes
May 17, 2022
It does fail ORT. We will be skipping ORT for now to commit, and @SamuelTrahanNOAA can create a PR for any changes. I was running: |
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@BrianCurtis-NOAA Can you confirm that only the decomposition test is failing? All others should pass (they do for the existing RAP regression test). |
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That test uses the FV3_HRRR suite, which generally fails debug tests. Even the WRF-based HRRR had that problem. I am certain the threading test will work, but I have not tried decomp or restart. |
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The FV3_HRRR suite is known to not work in debug mode. It is impossible for me to fix that in this PR. |
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The smoke restart test is failing because fv3_conf/rrfs_warm_run.IN does not know how to restart from another test. |
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The 2thread and decomp tests will fail because there are hard-coded INPES and JNPES in test/tests/rrfs_smoke_conus13km_hrrr_warm. You need new _decomp and _2threads versions. |
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Let's get the commits started. |
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@SamuelTrahanNOAA fv3atm was merged. Please revert .gitmodules and update FV3 hash. |
Done. |
junwang-noaa
approved these changes
May 17, 2022
SamuelTrahanNOAA
added a commit
to NOAA-GSL/ufs-weather-model
that referenced
this pull request
May 19, 2022
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: BinLi-NOAA <bin.li@noaa.gov> * 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 <dusan.jovic@noaa.gov> * 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 <climbfuji@ymail.com> Co-authored-by: climbfuji <dom.heinzeller@icloud.com> * 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 <jiande.wang@noaa.gov> * 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 <david.huber@noaa.gov> Co-authored-by: Bin Liu <Bin.Liu@noaa.gov> * 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 <Samuel.Trahan@noaa.gov> * 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 <gerhard.j.theurich@noaa.gov > * 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 <ted.mansell@noaa.gov> Co-authored-by: Dom Heinzeller <heinzell@ucar.edu> * 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 <bin.liu@noaa.gov> * 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. * Feature: NSSL Microphysics support (ufs-community#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) (ufs-community#1071) updates all p8 tests to the p8b settings, which includes GOCART Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov> * Split CCPP finalize into physics_finalize and (framework) finalize, fix CCPP's metadata2html.py (ufs-community#1061) * add a cdeps test using GFSv16 input data (ufs-community#1070) * CMAKE for WW3 (ufs-community#1089) * Use WW3 CMake build Co-authored-by: kgerheiser <kgerheiser@icloud.com> * Add 'valid time' variable using ISO string format (ufs-community#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 (ufs-community#1084) * Add hi-res regional test on small domain * Fix Lambert Conformal Conic mapping in the write component on the southern hemisphere (ufs-community#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 <57227195+MinsukJi-NOAA@users.noreply.github.com> * Rectify total number of Thompson MP species and add UFS-Aerosols to S2S and S2SW (ufs-community#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 (ufs-community#1136) Co-authored-by: jiandewang <jiande.wang@noaa.gov> Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: DusanJovic-NOAA <dusan.jovic@noaa.gov> * update submodule pointer for fv3atm * Update fms to 2021.04 (ufs-community#1135) * Update fms to 2021.04 * Add RT for ocean IAU * Update documentation Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com> Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com> * land surface upgrades for p8 (ufs-community#1095) * reset the Noah-MP default options for those well tested * P8c: Added capability for cdmbgwd(1) to scale GSL blocking drag (ufs-community#1110) * Update ESMF to version 8.3.0bs09 (ufs-community#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 <jong.kim@noaa.gov> Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> * 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 ufs-community#881) (ufs-community#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 (ufs-community#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 <raffaele.montuoro@noaa.gov> Co-authored-by: jiandewang <jiande.wang@noaa.gov> * Radiation changes for prototype 8 (ufs-community#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 (ufs-community#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 <daniel.rosen@noaa.gov> Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov> Co-authored-by: uturuncoglu <turuncu@ucar.edu> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov> Co-authored-by: A-Kyle <kyle.ahern@noaa.gov> * fv3atm: Split GFS_typedefs.F90, rename CCPP_interstitial, import ccpp_t from ccpp_types; contains bug fix for WW3 debug (ufs-community#1130) Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> * Close MOM6 1deg at j=1; Update input-data for P8c (ufs-community#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 (ufs-community#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 (ufs-community#1176) * point to one_scheme_to_one_file PR branch (ufs-community#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 (ufs-community#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 (ufs-community#1156) Co-authored-by: Yunheng Wang * Update CMEPS; Add gocart userguide (was ufs-community#1182) (ufs-community#1189) * Update CMEPS submodule * Add GOCART documentation Co-authored-by: Li Pan <Li.Pan@noaa.gov> * Combine PROD and REPRO build options into 'Release' build type (ufs-community#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 (ufs-community#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 (ufs-community#1196) * add NoahMP opt_trs to namelist * Updated namelist settings related to NoahMP scheme, Thompson scheme and RRTMGP (issue ufs-community#1173 and ufs-community#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 (ufs-community#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 <57227195+MinsukJi-NOAA@users.noreply.github.com> * NSSL ccpp-physics bugfixes and new ccpp-framework debugging feature (ufs-community#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 <brian.curtis@noaa.gov> * [AutoRT] hera.intel Job Completed. on-behalf-of @ufs-community <brian.curtis@noaa.gov> * [AutoRT] cheyenne.intel Job Completed. on-behalf-of @ufs-community <brian.curtis@noaa.gov> * WCOSS Dell P3 tests passed * Correct argument passing within mynn edmf * [AutoRT] gaea.intel Job Completed. on-behalf-of @ufs-community <brian.curtis@noaa.gov> * [AutoRT] cheyenne.gnu Job Completed. on-behalf-of @ufs-community <brian.curtis@noaa.gov> * Orion RT Passed * [AutoRT] jet.intel Job Completed. on-behalf-of @ufs-community <brian.curtis@noaa.gov> * Point to NOAA-EMC develop for FV3 * merge gsl institutional fork (ufs-community#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 <48258889+DusanJovic-NOAA@users.noreply.github.com> Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: BinLi-NOAA <bin.li@noaa.gov> Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> Co-authored-by: Grant Firl <grant.firl@noaa.gov> Co-authored-by: Dom Heinzeller <climbfuji@ymail.com> Co-authored-by: mzhangw <mzhangw@gmail.com> Co-authored-by: jiandewang <jiande.wang@noaa.gov> Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: SMoorthi-emc <47667426+SMoorthi-emc@users.noreply.github.com> Co-authored-by: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Bin Liu <Bin.Liu@noaa.gov> Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com> Co-authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov > Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com> Co-authored-by: Ted Mansell <ted.mansell@noaa.gov> Co-authored-by: Dom Heinzeller <heinzell@ucar.edu> Co-authored-by: Jeff Whitaker <jswhit@fastmail.fm> Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com> Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov> Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: MatthewPyle-NOAA <48285220+MatthewPyle-NOAA@users.noreply.github.com> Co-authored-by: Jessica Meixner <jessica.meixner@noaa.gov> Co-authored-by: kgerheiser <kgerheiser@icloud.com> Co-authored-by: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com> Co-authored-by: joeolson42 <Joseph.B.Olson@noaa.gov> Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com> Co-authored-by: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Co-authored-by: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> Co-authored-by: JONG KIM <jong.kim@noaa.gov> Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> Co-authored-by: Brian Curtis <64433609+BrianCurtis-NOAA@users.noreply.github.com> Co-authored-by: dustinswales <dustin.swales@noaa.gov> Co-authored-by: Daniel Rosen <daniel.rosen@noaa.gov> Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov> Co-authored-by: uturuncoglu <turuncu@ucar.edu> Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov> Co-authored-by: A-Kyle <kyle.ahern@noaa.gov> Co-authored-by: ClaraDraper-NOAA <33430543+ClaraDraper-NOAA@users.noreply.github.com> Co-authored-by: Li Pan <Li.Pan@noaa.gov>
16 tasks
SamuelTrahanNOAA
added a commit
to NOAA-GSL/ufs-weather-model
that referenced
this pull request
Jun 27, 2022
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
* 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 <dusan.jovic@noaa.gov>
* 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 <climbfuji@ymail.com>
Co-authored-by: climbfuji <dom.heinzeller@icloud.com>
* 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 <jiande.wang@noaa.gov>
* 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 <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <gerhard.j.theurich@noaa.gov >
* 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 <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
* 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 <bin.liu@noaa.gov>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
* 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 <dusan.jovic@noaa.gov>
* 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 <climbfuji@ymail.com>
Co-authored-by: climbfuji <dom.heinzeller@icloud.com>
* 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 <jiande.wang@noaa.gov>
* 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 <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <gerhard.j.theurich@noaa.gov >
* 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 <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
* 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 <bin.liu@noaa.gov>
* 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 <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Grant Firl <grant.firl@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: mzhangw <mzhangw@gmail.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com>
Co-authored-by: SMoorthi-emc <47667426+SMoorthi-emc@users.noreply.github.com>
Co-authored-by: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
Co-authored-by: Samuel Trahan <Samuel.Trahan@noaa.gov>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov >
Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Co-authored-by: Ted Mansell <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
Co-authored-by: Jeff Whitaker <jswhit@fastmail.fm>
Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com>
Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>
Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com>
Co-authored-by: MatthewPyle-NOAA <48285220+MatthewPyle-NOAA@users.noreply.github.com>
* 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 <Samuel.Trahan@noaa.gov>
* p8b (with aerosols) (#1071)
updates all p8 tests to the p8b settings, which includes GOCART
Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>
* 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 <kgerheiser@icloud.com>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
* 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 <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: DusanJovic-NOAA <dusan.jovic@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
* 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 <jong.kim@noaa.gov>
Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>
* 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 <raffaele.montuoro@noaa.gov>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
* 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 <daniel.rosen@noaa.gov>
Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov>
Co-authored-by: uturuncoglu <turuncu@ucar.edu>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov>
Co-authored-by: A-Kyle <kyle.ahern@noaa.gov>
* 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 <Jessica.Meixner@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <Li.Pan@noaa.gov>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
* 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 <brian.curtis@noaa.gov>
* [AutoRT] hera.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* [AutoRT] cheyenne.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* WCOSS Dell P3 tests passed
* Correct argument passing within mynn edmf
* [AutoRT] gaea.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* [AutoRT] cheyenne.gnu Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* Orion RT Passed
* [AutoRT] jet.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
* 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 <dusan.jovic@noaa.gov>
* 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 <climbfuji@ymail.com>
Co-authored-by: climbfuji <dom.heinzeller@icloud.com>
* 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 <jiande.wang@noaa.gov>
* 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 <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
* 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 <Samuel.Trahan@noaa.gov>
* 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 <gerhard.j.theurich@noaa.gov >
* 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 <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
* 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 <bin.liu@noaa.gov>
* 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 <raffaele.montuoro@noaa.gov>
* 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 <kgerheiser@icloud.com>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
* 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 <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: DusanJovic-NOAA <dusan.jovic@noaa.gov>
* 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 <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
* 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 <jong.kim@noaa.gov>
Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>
* 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 <raffaele.montuoro@noaa.gov>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
* 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 <daniel.rosen@noaa.gov>
Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov>
Co-authored-by: uturuncoglu <turuncu@ucar.edu>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov>
Co-authored-by: A-Kyle <kyle.ahern@noaa.gov>
* 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 <Jessica.Meixner@noaa.gov>
* 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 <Li.Pan@noaa.gov>
* 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 <57227195+MinsukJi-NOAA@users.noreply.github.com>
* 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 <brian.curtis@noaa.gov>
* [AutoRT] hera.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* [AutoRT] cheyenne.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* WCOSS Dell P3 tests passed
* Correct argument passing within mynn edmf
* [AutoRT] gaea.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* [AutoRT] cheyenne.gnu Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* Orion RT Passed
* [AutoRT] jet.intel Job Completed.
on-behalf-of @ufs-community <brian.curtis@noaa.gov>
* 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 <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Grant Firl <grant.firl@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: mzhangw <mzhangw@gmail.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: SMoorthi-emc <47667426+SMoorthi-emc@users.noreply.github.com>
Co-authored-by: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov >
Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Co-authored-by: Ted Mansell <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
Co-authored-by: Jeff Whitaker <jswhit@fastmail.fm>
Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com>
Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>
Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com>
Co-authored-by: MatthewPyle-NOAA <48285220+MatthewPyle-NOAA@users.noreply.github.com>
Co-authored-by: Jessica Meixner <jessica.meixner@noaa.gov>
Co-authored-by: kgerheiser <kgerheiser@icloud.com>
Co-authored-by: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com>
Co-authored-by: joeolson42 <Joseph.B.Olson@noaa.gov>
Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com>
Co-authored-by: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
Co-authored-by: JONG KIM <jong.kim@noaa.gov>
Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>
Co-authored-by: Brian Curtis <64433609+BrianCurtis-NOAA@users.noreply.github.com>
Co-authored-by: dustinswales <dustin.swales@noaa.gov>
Co-authored-by: Daniel Rosen <daniel.rosen@noaa.gov>
Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov>
Co-authored-by: uturuncoglu <turuncu@ucar.edu>
Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov>
Co-authored-by: A-Kyle <kyle.ahern@noaa.gov>
Co-authored-by: ClaraDraper-NOAA <33430543+ClaraDraper-NOAA@users.noreply.github.com>
Co-authored-by: Li Pan <Li.Pan@noaa.gov>
* 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…
This was referenced Aug 11, 2022
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PR Checklist
This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model wiki if you are unsure how to do this.
This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR
An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR
are specified below.
Results for one or more of the regression tests change and the reasons for the changes are understood and explained below.
New or updated input data is required by this PR. If checked, please work with the code managers to update input data sets on all platforms.
/scratch2/BMC/wrfruc/RT/NEMSfv3gfs/input-data-20220414+smoke/FV3_input_data_conus13km/INPUTdust12m_data.nc,SMOKE_GBBEPx_data.nc, andemi_data.ncDescription
Syncs the gsl/develop branch from the GSL institutional fork with the ufs-community develop branch. This includes surface layer, PBL, gravity wave drag, smoke, and other improvements from GSL RRFS and global model development; and Rocoto fault tolerance changes to the rt_utils.sh.
Detailed changelog:
start, snow on land or on ice is initialized in io/FV3GFS_io.F90. In case of
a warm start, these variables are carried along.
Issue(s) addressed
Testing
This was tested in several global and regional model parallels over the last few months. Regression tests are run for hera.intel, hera.gnu, and jet.intel. There's a new regression test, and results will change.
Dependencies
NCAR/ccpp-physics#911
NOAA-EMC/fv3atm#526