GFDL to main (Jan 2022) #1556

marshallward · 2022-01-31T04:36:37Z

This PR includes many new features, bugfixes, and code refactors.

The following parameter defaults have been changed:

INTERNAL_WAVE_SPEED_BETTER_EST (now .true.)
EPBL_MLD_BISECTION (now .false.)
BBL_USE_EOS (now set to the value of USE_EOS)

The test suite is expected to report a regression due to
INTERNAL_WAVE_SPEED_BETTER_EST; we recommend that this fail-test be ignored, which will allow future tests to use the new default parameters.

Individual regression tests at other labs should not change after accounting for these new parameter values.

Several deprecated parameters have also been eliminated. None were known to be
in active use.

Features

Bugfixes

Refactor

Infrastructure

Contributors

Added the new runtime option MEKE_ADVECTION_BUG and corrected a bug in the calculation of the vertically integrated transport for the advection of the MEKE field when MEKE_ADVECTION_FACTOR > 0. The default is to fix the bug, so answers can change in some cases by default, and in those cases there are changes to the MOM_parameter_doc files, but this option is not widely used and there are no answer changes in the MOM6-examples test suite. This PR addresses MOM6 issue mom-ocean#1465, which can be closed once this PR is merged into dev/gfdl.

Added a runtime flag, BAROTROPIC_TIDAL_SAL_BUG, to fix a sign error in the tidal self-attraction and loading anomalies in the barotropic solver when tides are enabled. The default is to keep the previous bug so that answers do not change, but this default will be changed after solutions have been corrected. This commit partly addresses MOM6 issue mom-ocean#1496, but it should only be considered to be properly handled once the default has been changed to avoid this bug. This commit will change the MOM_parameter_doc files in cases where this bug matters, but by default all answers are bitwise identical.

…ugfix (+*)Fix MEKE advection bug

+Add BAROTROPIC_TIDAL_SAL_BUG to fix a tide bug

* first draft API based on Luyu's code * fixed various errors * Code for particles in MOM.F90 * moved particles_run into dynamics step * added particles_end * Fixed particle time * Fixed some documentation * Further documentation edits * converted pointers to allocatables in particles_gridded * Remove trailing space * Further doxygen tweaks * another trailing space * removed set_time Co-authored-by: Cory Spencer Jones <spencerjones@login4.cluster>

Esmg docs

FMS mpp domain creation is done in the `clone_MD_to_d2D` function, and currently an IO domain is always created within the MPP domain. This has caused problems with single-PE runs in FMS1, where the `write_field` logic was not able to reach the part which removes halo data if an IO domain was present, and halo data was being written to the restart files. This issue arose when `PARALLEL_RESTARTFILES` was set to `True` for single-PE tests. This does not appear to be a problem with FMS2, and no action is needed by the FMS team.

@Hallberg-NOAA

* Revert "Implement changes suggested by @Hallberg-NOAA" This reverts commit 8f4af3d. * Revert "*Corrected the clock as seen by diabatic processes" This reverts commit bc6c6e6. * Revert "*Use rho_ref in finite volume PGF density calcs" This reverts commit 48e90d0. * Update of MOM6 code to allow SPEAR to reproduce previous answers. Updates MOM code to dev/gfdl as of 2/7/2019 (6dd6f52) and reverts 3 answer changing modifications. Update produced by git revert 8f4af3d git add src/tracer/MOM_neutral_diffusion.F90 git revert --continue git revert bc6c6e6 git add src/core/MOM.F90 git revert --continue git revert 48e90d0 git add src/equation_of_state/MOM_EOS.F90 git revert --continue Some conflict resolution was needed. * Optional use of differing restoring piston velocities for temp and salt * Correction to ePBL code to mitigate blowup. Also "corrects" some spelling differences in variables (MStar vs mstar) * add MJHarrison-GFDL salt_flux_add_fix to SPEAR codeset from https://github.com/MJHarrison-GFDL/MOM6/compare/salt_flux_add_fix * Added ability to change remapping scheme. Added call for parameter REMAPPING_SCHEME to allow changes to be made. Previously was hardwired to PLM. Call for MOM_grid_int was issing a global_indexing=F argument Tests indicated that oda clocks were being called out of order and crashing the test, so I commented them out. * Removed timers, Changes name for REMAPPING_SCHEME parameter Changes REMAPPING_SCHEME to ODA_REMAPPING_SCHEME Removed timers that were causing blowups * Adds documentation for ODA_remapping_scheme Changes second argument to get_param calls to the module name. Co-authored-by: Matthew Harrison <Matthew.Harrison@noaa.gov>

NOTE: Initial submission included 4 parameters. `PARALLEL_RESTARTFILES` was dropped after an issue was detected. Full commit log history below. * +*Change defaults for 4 parameters to better values Updated the defaults of 4 run-time parameters (INTERNAL_WAVE_SPEED_BETTER_EST, PARALLEL_RESTARTFILES, EPBL_MLD_BISECTION, and BBL_USE_EOS) to more appropriate values. In each case, the previous default was simply the older setting, and not the better recommendation. It also adds logic determining whether SIMPLE_TKE_TO_KD does anything, and only log its setting if it does. These default changes were discussed by the MOM6 consortium as a whole in June, 2021 and were widely agreed to. In addition this commit removes the old obsoleted runtime parameter ORIG_MLD_ITERATION, and obsoletes the runtime parameter LARGE_FILE_SUPPORT, and it adds comments describing several real variables and their units. Because this changes several default values, it will change answers unless these parameters are explicitly set in the MOM_input files. However, because MOM6-examples PR #344 does set these values to their old defaults where they are used, no answers are changed in the MOM6-examples regression suite, although there are changes to the MOM_parameter_doc files. * +Reverted default for PARALLEL_RESTARTFILES Reverted the default for PARALLEL_RESTARTFILES to False because the TC restart testing was having problems with this set to True. This is surprising because PARALLEL_RESTARTFILES = True has been used in production runs for many years now without any indication that MOM6 fails to reproduce across restarts in this mode, so this could be an issue with the TC testing. In the mean time, reverting this default will allow the other changes to be accepted while this curious behavior is explored separately. Several comments related to PARALLEL_RESTARTFILES were also updated for consistency. All answers are bitwise identical.

Add the new runtime parameter FATAL_INCONSISTENT_RESTART_TIME, which if true causes the model to compare the restart time read from a restart file with any value provided as a time_in to MOM_initialize_state and issue a fatal error if they differ. In ocean-only mode, this input time is read from a ocean_solo.res file, following FMS behavior. The default value simply uses the specified time, replicating the previous behavior. If set to true, this would prevent a problem with the time-history that recently occurred in a series of high-resolution runs that were shared between several groups, where the nominal times were repeated. All answers are bitwise identical, but many MOM_parameter_doc files have a new entry.

* +(*)Fix bug when RES_SCALE_MEKE_VISC = True Fix a bug that can lead to segmentation faults when RES_SCALE_MEKE_VISC is true, as noted in MOM6 issue mom-ocean#1464, and add better error handling to detect related problems. The refactoring that is a part of this may also avoid some problems with optimized code even when RES_SCALE_MEKE_VISC it false, as described in MOM6 issue mom-ocean#1463. In addition, logic was added so that the value of RES_SCALE_MEKE_VISC is only logged if USE_MEKE is true. All answers are bitwise identical in cases that worked, including the MOM6-examples test suite, but there are some changes in the MOM_parameter_doc files, due to an irrelevant parameter no longer being logged. * (*)Initialize CS%res_scale_MEKE Initialize the logical element res_scale_MEKE in the hor_visc_CS even if there is no Laplacian viscosity, so that a self-consistency test does not use an initialized value. Also improved some comments. All answers are bitwise identical for all cases that successfully ran before, including in all cases in the MOM6-examples test suite.

Made 37 optional arguments that are always present in calls into non-optional arguments to routines in the src/core directory. Many of these are pointer arguments related to things like open boundary conditions, so if these types are not to be used, they are simply not allocated. In several cases, this required the order of the arguments to be shifted around, but the various types of the arguments should prevent the model from compiling if the calls (e.g., in user-modified code that is not in the github repository) are not changed equivalently. Also eliminated 3 internal arguments in MOM_barotropic.F90 that are always hard-coded to the same values (the maximize argument to BT_cont_to_face_areas()) or are never used (the guess arguments to uhbt_to_ubt() and vhbt_to_vbt()), along with the code that they would exercise. All answers and output are bitwise identical.

Refactored solo_driver/MOM_driver.F90 to move logically self-contained blocks of code into separate subroutines within this file to improve the readability of the code and to reduce the number of global variables. This started out as an exercise to explore the use of the F2008 block / end block construct to reduce the scope of variables, but the code ended up being cleaner just using traditional subroutines contained in this file. All answers are bitwise identical and all output files are unaltered.

+Make 37 optional arguments in src/core mandatory

Main to dev

Made 44 previously optional just_read_params arguments into mandatory arguments and renamed them just_read to avoid duplicated variables. This change should be minimally disruptive, as these optional arguments were always being provided. Some argument documentation blocks were also reformatted or the comments in them were corrected. All answers are bitwise identical, but some arguments have changed.

Cleaned up 27 falsely optional or unused arguments in the vertical parameterization code, and related changes. This includes: - Eliminating the symmetrize arguments to set_viscous_BBL and set_viscous_ML, which are now effectively always true. - Making the Waves and OBC pointer arguments mandatory in several routines where they were always being supplied. These are pointers, so the test of whether they should be used can be based on whether they are associated. - Adding error messages about unassociated Waves types that would be used. - Eliminating the unused Waves argument to KPP_init. - Eliminating unused arguments that energetic_PBL inherited from the bulk mixed layer code, and simplified some disabled debugging code. - Making the optics argument to opacity_end mandatory. - Making the h argument to get_Langmuir_Number mandatory and rearranged the arguments to this routine to put the optional arguments last, following the practice elsewhere in the MOM6 code. Also standardized the case of several variables in the MOM_wave_interface.F90 code to facilitate searches. - Eliminating the unused US argument to CoriolisStokes. All answers are bitwise identical, and no output is changed.

This patch uses the FMS2 `file_exists` function when using the FMS2 infra. Previously, the FMS1 version of this function was being used. This patch also removes the `mpp_domain` and `no_domain` arguments from the direct `file_exist` calls, which were not used by any known MOM6 configurations. (Nor would we expect them to be, since explicit references to FMS should not exist outside of the infra layer.) Since FMS2 does not use these arguments, their removal also creates a more meaningful interface between the two frameworks. Motivation: An issue with the FMS1 `file_exists` under the FMS2 infra was discovered in the UFS model on Hera. It was only reproducible in submitted jobs, and not for interactive jobs, and only with the GCC 9.2 compiler. (Other GCC versions were not tested.) One potential explanation is that it is related to the `save` attribute of the domain pointer, `d_ptr`. In the case above, `d_ptr` pointed to the MOM input domain for the failed cases. For the other working cases, `d_ptr` pointed to a `NULL()` value and behavior was normal. It is possible that `d_ptr` is inconsisently updated when FMS1 and FMS2 IO operations are used together, which should probably be considered undefined behavior.

Eliminated the unused optional OBC argument to write_energy() and several unused optional arguments to wave_speed() and wave_speeds() that are set instead via arguments to wave_speed_init() that store these values in a wave_speed_CS type. Also made the optional row_scale argument to tridiag_det() and the tracer_CSp argument to write_energy() that were always present in calls into mandatory arguments. All answers are bitwise identical, and solutions do not change.

FMS1: Don't create IO domains for single-PE domain

Modified create_file to always specify that the threading will be for a single PE to do the writing to a single file if there is only a single ocean PE, to avoid some incorrect behavior inside of the FMS IO modules. This can fix restart problems in some single-processor cases with an inconsistent setting of the optional threading argument, but in all cases that ran correctly before, all answers are bitwise identical.

JohnSteffen-NOAA · 2022-02-07T17:50:57Z

Hello @jiandewang @marshallward ,

We have a regional (HAT10), ocean-only configuration of MOM6 that is cold started using ocean BC/IC generated from RTOFS and atmospheric forcing from GFS. The test case is a 24-hour run beginning on Jan. 1 2020 12Z that is performed on Orion. The original run directory has read access and can be found here,

/work/noaa/hwrf/save/jsteff/mom6/MOM6-NOAA-EMC/ocean_only/OBC3_HAT10_IC_newHSK

And model output fields are in ./out1_newHSK

I cloned the read_2dvar_dimfix branch from Marshall and compiled/run MOM6 using the same FMS and mkmf as our original run. The model runs successfully and produces reasonable output fields, however, they are not bitwise identical to our original test run output. The run directory for the read_2dvar_dimfix branch is here,

/work/noaa/hwrf/save/jsteff/mom6/MOM6-NOAA-EMC-testPR/ocean_only/OBC3_HAT10_IC_newHSK

And output is in ./out1/

Please let me know if I can provide additional details about our MOM6 configuration.

jiandewang · 2022-02-07T18:09:25Z

@JohnSteffen-NOAA there are three parameter's default value being changed in this PR, I will help you sort that out.

JohnSteffen-NOAA · 2022-02-07T20:13:26Z

@jiandewang @marshallward,
I added two default parameters to my MOM_input, as suggested by Jiande.

INTERNAL_WAVE_SPEED_BETTER_EST = False
EPBL_MLD_BISECTION = True

After rerunning the test, the 2d output is bitwise identical to the original run.

jiandewang · 2022-02-08T15:13:14Z

@marshallward since UFS and HAT10 all worked fine, I think you can merge your read-var2d branch into the PR branch

The read_variable_2d function was previously configured to only run if the start and nread arrays matched the size of the field they were accessing. This was incompatible with the history of the function, which had previously required a fourth time axis (of one record), then was later modified to not require this axis. As a result, there are now files in use both with and without a time axis. This patch relaxes this check to ensure that the read is quasi-2d, i.e. the first two axes can read a segment of a 2d field, but will now reshape the start and nread arrays to match the field being read. Some additional checks are also added to ensure that it only reads one 2d slice.

marshallward · 2022-02-08T17:49:03Z

Thanks @jiandewang @JohnSteffen-NOAA for testing the patch.
I have merged the PR into the candidate branch.

abozec

COAPS approves these changes

jiandewang · 2022-02-08T21:47:28Z

approve from EMC

src/parameterizations/vertical/MOM_diabatic_driver.F90

Pointers to the diabatic driver's energetic PBL field are now only associated when `use_energetic_PBL` is true. The `energetic_PBL` field was also renamed to `ePBL` to avoid potential conflict with the `energetic_PBL` subroutine. Thanks to Alper Altuntas for detecting this issue and the proposed fix. Co-Authored-By: Alper Altuntas <alperaltuntas@gmail.com>

jiandewang · 2022-02-16T23:04:27Z

@marshallward : John and I re-ran the system in EMC, they are fine.

marshallward · 2022-02-17T13:58:04Z

Thanks @jiandewang. Can you also click the approval button for the PR? (If it's not on this page, then you can find in the "Files changed" tab).

alperaltuntas

NCAR tests are passing. I am noting here that we also needed to set MEKE_ADVECTION_BUG = True to get bitwise identical results.

marshallward · 2022-02-17T20:07:22Z

Thanks @alperaltuntas , that should have been mentioned in the PR log. (It was the very first commit!) Same with BAROTROPIC_TIDAL_SAL_BUG and possibly others.

marshallward · 2022-02-17T21:11:02Z

All groups have now approved the PR, so I will merge this now. (With a merge commit this time!)

I will have to apply admin override due to the answer changes. We are exploring some user-configurable override options for future PRs.

A big thanks to everyone for their testing and verification work.

…M6#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

… PR 1058); update MOM6 (was PR 1060) (#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

@MicroTed

* Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (ufs-community#931) * Add UFS driver, a copy of two fortran files from the NEMS repository. Remove NEMS submodule. * Update CMEPS for current escomp/master. Implement the ability to write mediator history files for ATM on tiles rather than mesh * Update CDEPS component. The updated CDEPS includes code updates for GFS v16 data mode. * Operation requirement test (ORT) for: - cpld_control_p7 thread and decomposition tests - cpld_bmark_p7 thread and decomposition tests - Due to the wave component in these tests, restart and debug do not work Co-authored-by: Minsuk Ji <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. * 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>

@MicroTed

* Merge ufs-community develop into gsl/develop (#119) * Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (ufs-community#931) * Add UFS driver, a copy of two fortran files from the NEMS repository. Remove NEMS submodule. * Update CMEPS for current escomp/master. Implement the ability to write mediator history files for ATM on tiles rather than mesh * Update CDEPS component. The updated CDEPS includes code updates for GFS v16 data mode. * Operation requirement test (ORT) for: - cpld_control_p7 thread and decomposition tests - cpld_bmark_p7 thread and decomposition tests - Due to the wave component in these tests, restart and debug do not work Co-authored-by: Minsuk Ji <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. * 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> * Update to top of FV3 to get latest ccpp-physics codeowners (#123) * FV3 submodule: merge gsl/develop into RRFS_dev * Hera gnu tests passed. * Hera intel tests passed. * jet tests passed * Put a comment back in the FV3/ccpp/physics submodule. * point to head of FV3 RRFS_dev branch Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> 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: Hannah C Barnes <38660891+hannahcbarnes@users.noreply.github.com>

* update GEOS-MOM6 cMakeLists.txt to work with the updates proposed in m… * update defaults

@MicroTed

* Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition. (ufs-community#931) * Add UFS driver, a copy of two fortran files from the NEMS repository. Remove NEMS submodule. * Update CMEPS for current escomp/master. Implement the ability to write mediator history files for ATM on tiles rather than mesh * Update CDEPS component. The updated CDEPS includes code updates for GFS v16 data mode. * Operation requirement test (ORT) for: - cpld_control_p7 thread and decomposition tests - cpld_bmark_p7 thread and decomposition tests - Due to the wave component in these tests, restart and debug do not work Co-authored-by: Minsuk Ji <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>

* 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…

Hallberg-NOAA and others added 30 commits October 1, 2021 19:49

Merge branch 'dev/gfdl' into MEKE_advection_bugfix

e4cdaaf

Merge pull request mom-ocean#1506 from Hallberg-NOAA/MEKE_advection_b…

a384fcc

…ugfix (+*)Fix MEKE advection bug

Merge branch 'dev/gfdl' into tidal_SAL_bugfix

780919f

Merge pull request mom-ocean#1508 from Hallberg-NOAA/tidal_SAL_bugfix

7d808b5

+Add BAROTROPIC_TIDAL_SAL_BUG to fix a tide bug

adds missing _ (mom-ocean#1519)

ce5595f

Working on boundary layer docs.

b08efb8

Done with EPBL docs?

5adf763

Merge pull request mom-ocean#1510 from ESMG/esmg-docs

e2da693

Esmg docs

Merge branch 'dev/gfdl' into opt_args_in_core

1fb283b

Merge pull request mom-ocean#1523 from Hallberg-NOAA/opt_args_in_core

e291d32

+Make 37 optional arguments in src/core mandatory

Merge branch 'main' into main_to_dev

ba01cea

Merge pull request mom-ocean#1529 from marshallward/main_to_dev

5d82809

Main to dev

fix low mode in tidal_mixing

ee3b92f

Merge branch 'dev/gfdl' into no_1pe_io_layout

2f91303

Merge pull request mom-ocean#1522 from marshallward/no_1pe_io_layout

1700498

FMS1: Don't create IO domains for single-PE domain

abozec approved these changes Feb 8, 2022

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jiandewang approved these changes Feb 17, 2022

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marshallward merged commit 6f6d4d6 into mom-ocean:main Feb 17, 2022

alperaltuntas mentioned this pull request Feb 18, 2022

Merge with latest main (2022 feb17) NCAR/MOM6#211

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marshallward mentioned this pull request Feb 18, 2022

Main to dev NOAA-GFDL/MOM6#71

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This was referenced Feb 19, 2022

update MOM6 to its main branch commit (20220217) NOAA-EMC/MOM6#84

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update MOM6 to its main branch 20220217 commit ufs-community/ufs-weather-model#1059

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sanAkel mentioned this pull request Mar 22, 2022

Update MOM6 after https://github.com/mom-ocean/MOM6/pull/1556 is merged GEOS-ESM/GEOS_OceanGridComp#2

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sanAkel added a commit to GEOS-ESM/GEOS_OceanGridComp that referenced this pull request Mar 22, 2022

Update MOM6 after mom-ocean/MOM6#1556 is merged (#2)

2ae923b

* update GEOS-MOM6 cMakeLists.txt to work with the updates proposed in m… * update defaults

adcroft deleted the dev-gfdl-main-candidate-2022-01-29 branch December 7, 2022 22:15

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GFDL to main (Jan 2022) #1556

GFDL to main (Jan 2022) #1556

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GFDL to main (Jan 2022) #1556

GFDL to main (Jan 2022) #1556

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marshallward commented Jan 31, 2022

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