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Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations #386

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merged 20 commits into from
Jan 22, 2021
Merged

Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations #386

merged 20 commits into from
Jan 22, 2021

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@climbfuji climbfuji commented Jan 20, 2021 •
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Description

This PR contains changes required for the updates to ccpp-physics:

  • set number of ice layers (kice) for sfc_sice (2; default) and RUC ice(9), set flag to apply land surface perturbations at every time step (as in WRF) or atfhcyc` hours (as for GFS)
  • regression tests for GSD physics with both Noah LSM and RUC LSM using the extended land surface perturbations (currently exercised in rt_ccpp_dev.conf)
  • bugfixes for GSD SAR regression tests and MYNN sfclayer (fixes crashes with GNU compiler)

Testing

The updated code compiles on macOS with both clang+gfortran and gcc+gfortran.

At first, regression tests will be run against existing baselines on Hera with Intel and GNU to confirm that only the expected regression tests change results.

  • GNU: all tests pass except the following, as expected (but they both run to completion)
fv3_ccpp_rrfs_v1beta 012 failed in check_result
fv3_ccpp_gsd 009 failed in check_result

rt_hera_gnu.log
rt_hera_gnu_fail_test.log

  • Intel: all tests pass except the following, as expected (but they all run to completion)
fv3_ccpp_rap 040 failed in check_result
fv3_ccpp_rrfs_v1beta 044 failed in check_result
fv3_ccpp_hrrr 041 failed in check_result
fv3_ccpp_gsd 039 failed in check_result
fv3_ccpp_lndp 014 failed in check_result
fv3_ccpp_gsd_debug 062 failed in check_result
fv3_ccpp_rrfs_v1beta_debug 066 failed in check_result
fv3_ccpp_gsd_diag3d_debug 063 failed in check_result

rt_hera_intel.log
rt_hera_intel_fail_test.log

Next, new baselines will be created and regression testing will be carried out on all tier-1 platforms except Jet, which is under extended maintenance 01/20-01/22.

Regression tests passed on cheyenne.{gnu,intel}, hera.{gnu,intel}, gaea.intel, orion.intel, wcoss_dell_p3 and wcoss_cray; logs updated in the PR.

Dependencies

NOAA-PSL/stochastic_physics#36
NCAR/ccpp-physics#558
NOAA-EMC/fv3atm#239
#386

climbfuji and others added 9 commits November 25, 2020 13:33
@climbfuji
Update .gitmodules and submodule pointer for fv3atm for gsl/develop b…
ff98902 
…ranch
@DomHeinzeller @climbfuji
RUC ice for gsl/develop (replaces ufs-community#47) (ufs-community#49)
d4de9e6 
Implementation of RUC LSM ice model in CCPP

* Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop

* Add kice=9 to tests/tests/fv3_ccpp_rap and tests/tests/fv3_ccpp_hrrr

* Change NEW_BASELINE directory for gsl/develop to avoid conflicts with development work on the authoritative branches

* Add KICE=9 to tests/tests/fv3_ccpp_gsd_unified_ugwp and tests/tests/fv3_ccpp_gsd_drag_suite_unified_ugwp

* Revert change to .gitmodules and update submodule pointer for fv3atm

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
@climbfuji @pjpegion
@jiandewang @DeniseWorthen @DusanJovic-NOAA
Update gsl/develop from develop 2020/12/08 (ufs-community#50)
7a249f2 
* Updates to stochastic_physics_wrapper (ufs-community#280)

Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (ufs-community#304)

Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms).

The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc).

* Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290)

* point MOM6 to new branch which corresponding to GFDL 20201022 commit
* modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM6 code as this version of MOM6 contains some file deletion, new files being added and renaming of files
* manually set MOM6 parameters in order to retain origonal results for 0.25x0.25 resolution
* update MOM6 to include Bugfix for mom6solo to be built
* modify compile.sh to allow mom6solo compiling
* modify MOM_input_template for all resolutions based on GFDL MOM6-example main branch update on 20201022
* change executable permissions for CMakeLists.txt
* chmod 644 to 6 files Dom pointed out
* chmod for CMakeLists.txt and tests/compile.sh
* change baseline directpory to 20201202 in rt.sh

* Update CICE, Move regression test input outside baseline directory (ufs-community#270)

*Updates CICE to most recent develop branch of NOAA-EMC
* Sets n_aero (number of aerosols) in ice_in_template to 0.
* removes trailing whitespace from ice_in
* moves regression test input outside baseline directory (ufs-weather PR ufs-community#312)

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

* Revert change to .gitmodules and update submodule pointer for fv3atm

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
@climbfuji
Update submodule pointer for fv3atm / ccpp-physics - MYNN surface lay…
d5fa4c1 
…er updates and bugfixes (ufs-community#52)
@climbfuji
Update stochastic_physics submodule to point to NOAA-GSL gsl/develop (u…
57a8258 
…fs-community#55)

Code is identical to original/current code in the authoritative repository (NOAA-PSD, branch master)
@DomHeinzeller @climbfuji
Land stochastic perturbations (ufs-community#57)
72d48f3 
* Add regression tests with stochastic land perturbations for suites FV3_GSD_v0 and FV3_GSD_noah

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
@climbfuji
Stochastic land perturbations: add roughness length over land to the …
77f56a4 
…perturbed variables (ufs-community#61)

* Updates to regression tests fv3_ccpp_gsd_lndp and fv3_ccpp_gsd_noah_lndp
* Bug fix for tests/parm/ccpp_gsd_sar.nml.IN
@climbfuji
Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…
0315aa2 
…r-model into gsl/develop
@climbfuji
Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…
94ad00e 
…r-model into update_develop_from_gsl_develop
This was referenced Jan 20, 2021
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@climbfuji climbfuji marked this pull request as ready for review January 20, 2021 17:57
@climbfuji climbfuji added the Baseline Updates Current baselines will be updated. label Jan 20, 2021
@climbfuji climbfuji added the Waiting for Reviews The PR is waiting for reviews from associated component PR's. label Jan 20, 2021
@junwang-noaa junwang-noaa mentioned this pull request Jan 21, 2021
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junwang-noaa approved these changes Jan 22, 2021
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Please update fv3 submodule.

@climbfuji climbfuji added the Ready for Commit Queue The PR is ready for the Commit Queue. All checkboxes in PR template have been checked. label Jan 22, 2021
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@junwang-noaa @DusanJovic-NOAA this is ready for commit, please check again. I think we do not need to wait for the CI tests, since they are still broken without the updates from @MinsukJi-NOAA, but please correct me if I am wrong. Thanks!

@junwang-noaa junwang-noaa merged commit ea8a7aa into ufs-community:develop Jan 22, 2021
DomHeinzeller pushed a commit to NOAA-GSL/ufs-weather-model that referenced this pull request Feb 23, 2021
@climbfuji @pjpegion
@jiandewang @DeniseWorthen @DusanJovic-NOAA @mark-a-potts @binli2337 @dustinswales @kgerheiser @RatkoVasic-NOAA @aliabdolali @junwang-noaa @XiaqiongZhou-NOAA @mlee03 @ValeryYudin-NOAA @mdtoyNOAA @MinsukJi-NOAA
Update gsl develop from master (#63)
56e9901 
* Updates to stochastic_physics_wrapper (ufs-community#280)

Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (ufs-community#304)

Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms).

The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc).

* Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290)

* point MOM6 to new branch which corresponding to GFDL 20201022 commit
* modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM6 code as this version of MOM6 contains some file deletion, new files being added and renaming of files
* manually set MOM6 parameters in order to retain origonal results for 0.25x0.25 resolution
* update MOM6 to include Bugfix for mom6solo to be built
* modify compile.sh to allow mom6solo compiling
* modify MOM_input_template for all resolutions based on GFDL MOM6-example main branch update on 20201022
* change executable permissions for CMakeLists.txt
* chmod 644 to 6 files Dom pointed out
* chmod for CMakeLists.txt and tests/compile.sh
* change baseline directpory to 20201202 in rt.sh

* Update CICE, Move regression test input outside baseline directory (ufs-community#270)

*Updates CICE to most recent develop branch of NOAA-EMC
* Sets n_aero (number of aerosols) in ice_in_template to 0.
* removes trailing whitespace from ice_in
* moves regression test input outside baseline directory (ufs-weather PR ufs-community#312)

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

* Updates to build for JEDI linking/control, add wcoss2 (ufs-community#295)

* Build on wcoss2 (acorn)
* Use -march=core-avx2 instead of -xCORE-AVX2 on wcoss2
* Updates to build for JEDI linking/control
* Removed unnecessary include files and INLINE POST setting
* Updated to address PR suggestions.
* Add rt_acorn.conf. Change /lfs/h2 to /lfs/h1.
* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* regression test results
* Updated .gitmodules and removed extraneous file
* Fixed .gitmodules and updated pointer for FV3
* Updated pointer to NEMS repo
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Final-final GFS v16 updates / restart reproducibility bugfixes (ufs-community#325)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Add GFS v16 beta restart test, update stochastics test
* Update regression test baseline date tag to 20201214; skip-ci
* tests/rt.conf: bugfix, add missing 'fv3' to new stochy tests; skip-ci
* Regression test logs for gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci
* Run GFS v16beta tests also on wcoss; regression test logs for wcoss; skip-ci
* Regression test logs for cheyenne.intel and cheyenne.gnu
* Revert change to .gitmodules and update submodule pointer for fv3atm

* Add optional bulk flux calculation in ufs-datm (ufs-community#266)


* Update NEMS DATM and CMEPS to allow the optional bulk flux formulation; add two tests using the option
* Update top level CMakeList.txt to have compile flags for MOM6 and CICE6 identical for ufs-cpld and ufs-datm
* Add optional configuration variable to nems.configure to specify the directory where CMEPS will write restarts
* Adds cheyenne tasking variables to default_vars and sets WW3_COMP to cheyenne for platform cheyenne.intel 

*NOTE: Baselines develop-20201215 exist on all platforms, regression tests were run against exactly that baseline on all systems except cheyenne.intel. On cheyenne.intel the tests were run against 20201214, and this baseline is identical to 20201215 (as per "diff -r develop-20201214 develop-20201215").

Co-authors:
@DusanJovic-NOAA
@aerorahul
@JessicaMeixner-NOAA

skip-ci

* Add 2 new tests for DATM-MOM6-CICE6 application (ufs-community#332)

* Add the following 2 tests: datm_restart_cfsr, datm_debug_cfsr
* Add wcoss_dell_p3.log.
* Add Hera log, Orion log, wcoss_dell_p3 log.

* RRTMGP and Thompson MP coupling (ufs-community#323)

* Feature branch with RRTMGP and Thompson MP
* Updated FV3/ccpp-physics. Added namelist and configuration for RRTMGP RTs using GSD physics.
* Updated FV3
* Update physics in FV3
* Updated baselines in rt.sh
* Updated RT logs. Updated FV3 physics submodule pointer.
* Updated FV3 hash and .gitmodules

* Regression test log for PR ufs-community#323 for jet.intel (ufs-community#336)

* Update modules with hpc-stack v1.1.0 (ufs-community#319)

* Update modules with hpc-stack v1.1.0
* Minor bug fixes to CCPP UGWP

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Replace old regional SDF with FV3_GFS_v15_thompson_mynn (ufs-community#333)

* Replace old FV3_GFS_2017_gfdlmp_regional SDF for regional tests with FV3_GFS_v15_thompson_mynn.
* Final path to IC's and new results.  Also, input.nml updated.
* Update RegressionTests_wcoss_dell_p3.log
* Update RegressionTests_wcoss_cray.log
* Update RegressionTests_hera.intel.log
* Update RegressionTests_jet.intel.log
* Update RegressionTests_orion.intel.log
* Update RegressionTests_cheyenne* logs.
* Update RegressionTests_hera.gnu.log

* Feature/ww3update (ufs-community#334)

This updates the WW3 submodule pointer to point to the top of the WW3 develop branch.
The path to WW3 inputs is changed to input-data-20201201/WW3_input_data_20201207/

* Remove IPD (step 1) (ufs-community#331)

Make CCPP=Y the default in tests/compile.sh. Remove CCPP=Y from tests/rt*.conf and adjust formatting.
Update submodule pointer for MOM6 to include PR ufs-community#341 ("Update MOM6 to GFDL's 20201218 commit")
Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3)
Fix broken utest (see ufs-community#348)

* Update the format of rt.conf (ufs-community#349)

Update the format of MACHINES column in rt.conf (and other .conf files). This column can be either empty, which means a test will run on all supported machines, or start with - or + sign to exclude or include specified machines explicitly.

* Add checkpoint restarts for ufs-cpld (ufs-community#342)


* Adds 3 checkpoint restart tests for the ufs-cpld model
* Drops the existing c92mx025 restart test
* Adds cheyenne.intel as tested configuration for ufs-cpld and ufs-datm
* Fixes instances of srf_data* in various fv3_conf files

* add frac grid input, update and add additional cpld tests (ufs-community#354)


* Updates FV3_input_frac to add both benchmark dates and L127 files
* Adds additional tests and restart tests for coupled model
* Sets all cpld tests to use frac grid input by default
* Removes all instances of  USE_LA_LI2016=True except for benchmark+wave configurations

* Remove unnecessary SIMD instruction sets for Jet, first round of cleanup in rt.conf, initialize cld_amt to zero for regional runs (dycore) (ufs-community#353)

* Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake
* First cleanup of regression test config tests/rt.conf
* tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5
* Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files
* Remove tests/rt_acorn.conf and run GFS v15p2 and GFS v16beta DEBUG tests on all platforms

* Implementation of CCPP timestep_init and timestep_final phases (ufs-community#337)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Update submodule pointer for fv3atm; skip-ci
* Don't try to compile all suites in DEBUG mode on cheyenne.intel, weird bug on compute nodes; skip-ci
* Don't try to compile all suites in DEBUG mode on wcoss_cray; skip-ci
* Regression test logs for cheyenne.gnu, cheyenne.intel, gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci
* Don't try to compile all suites in DEBUG mode on wcoss_dell_p3; skip-ci
* Regression test logs for wcoss_cray and wcoss_dell_p3
* Revert change to .gitmodules and update submodule pointer for fv3atm

* Update CMEPS  (ufs-community#345)


* Update CMEPS for recent changes, including addition of new run "post" run phases to eliminate redundant mapping, multiple ice sheet capability and ocn->land ice dynamic mapping
* Add a new test fv3_gfs_v16_RRTMGP_c192L127

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Remove IPD steps 3 and 5 (ufs-community#357)

Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake
* First cleanup of regression test config tests/rt.conf
* tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5; skip-ci
* Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files
* Update usage in rt.sh, add modulefiles/jet.intel/fv3_debug; skip-ci
* CCPP is default in cmake build
* Add debug modulefiles for linux.gnu and macosx.gnu
* Update submodule pointer for fv3atm
* Change logic in CMakeLists.txt and tests/compile.sh so that 32BIT=ON automatically sets DYN32=ON; skip-ci
* Move logic to set DYN32 - depending on 32BIT setting - to fv3atm
* Remove -DCCPP=ON from tests/compile.sh; update submodule pointer for fv3atm; skip-ci

* point fv3 to EMC develop branch (ufs-community#377)

* update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (ufs-community#378)

* update CMEPS, fix character length error for gnu compile
* add Dusan's fix for rt_utils.sh
* update cpl gfsv16 tests, replace seaice_newland.grb with global_slmask.t1534.3072.1536.grb, recover input.mom6.nml.IN, update input directory, update global thread and decomp tests, update fdiag for global control
* point to Dustins rrtmgp fix branch
* update input directory

Co-authored-by: denise.worthen <Denise.Worthen@noaa.gov>
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (ufs-community#386)

* Update .gitmodules and submodule pointer for fv3atm for gsl/develop branch
* RUC ice for gsl/develop (replaces #47) (#49)Implementation of RUC LSM ice model in CCPP
* Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop
* Add kice=9 to tests/tests/fv3_ccpp_rap and tests/tests/fv3_ccpp_hrrr
* Change NEW_BASELINE directory for gsl/develop to avoid conflicts with development work on the authoritative branches
* Add KICE=9 to tests/tests/fv3_ccpp_gsd_unified_ugwp and tests/tests/fv3_ccpp_gsd_drag_suite_unified_ugwp
* Revert change to .gitmodules and update submodule pointer for fv3atm
* Update gsl/develop from develop 2020/12/08 (#50)
* Updates to stochastic_physics_wrapper (ufs-community#280)
Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model
* Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (ufs-community#304)
Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms).
The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc).
* Land stochastic perturbations (#57)

* dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (ufs-community#369)

* Update fv3atm
* update ccpp control test forecast length to 24h
* remove rename command
* Add CI related changes
* Update RT logs
* Update RT log files
* Add the gaea RT log file
* Update the point of fv3atm
* Update fv3atm
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>

* MOM6 bugfixes, GFDL update, update CDMBGWD settings; fix for restart reproducibility (without waves) when USE_LA_LI2016=True, sign error on fprec passed to ocean, GFDL update, resolution dependent cdmbgwd settings (ufs-community#379)


* implements two MOM6 bugfixes in the NUOPC MOM6 cap to allow restart reproducibility when USE_LA_LI2016=True and to change the sign of the latent heat flux associated with frozen precipitation (fprec) exported to MOM6

* updates MOM6 to include the GFDL 20210120 main branch which contains EMC's wave coupling code, alone with some minor code standardization and documentation

* updates the cdmbgwd namelist settings for FV3 standalone tests at C96 and implements resolution dependent values for ufs-cpld tests

Co-authored-by: Ali <ali.abdolali@noaa.gov>

* Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (ufs-community#384)

* Update .gitmodules and submodule pointers for fv3atm and NEMS
* Remove Python 2.7 support from top-level CMakeLists.txt
* Reduce forecast length of test fv3_ccpp_gfs_v16_RRTMGP_c192L127 from 24h to 12h
* Rename v16beta to v16 everywhere except the public release documentation
* Bugfixes and missing changes
* Remove 'export CCPP_LIB_DIR=ccpp/lib' from all regression tests
* Update regression test baseline date tag to 20210128; skip-ci
* Update ecflow-python environment on cheyenne and jet; skip-ci

* Update CMEPS for HAFS integration; add datm and coupled-model tests on Gaea (ufs-community#401)


* Add HAFS support in NOAA-EMC/CMEPS 
* Add coupled and datm tests for Gaea.intel

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov>

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2)  (ufs-community#407)

* Regression test logs for all tier=1 platforms

* updates FMS to 2020.04.01 (ufs-community#392)

* updates FMS to 2020.04.01
* fixes fms_files.cmake
* removes extra horiz_interp
* Workaround for FMS 2020.04.01 for Cheyenne with GNU 9.1.0, incl. regression test log
Co-authored-by: Mikyung Lee <mlee@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (ufs-community#399)

*Implements an optional setting in the cpld and datm nems.configure files to specify whether the MOM6 cap should use a mesh or a grid

*Adds configurable settings for min_seaice to gfs_physics_nml and dz_min to fv_core_nml.

* UGWP v0 v1 combined (ufs-community#396)

- combines the changes in PRs ufs-community#360 and ufs-community#382
- adds three regression tests `fv3_ccpp_gfsv16_ugwpv1 `, `fv3_ccpp_gfsv16_ugwpv1_warmstart` and `fv3_ccpp_gfsv16_ugwpv1_debug`
- contains updates and bugfixes for `nc_compare.py` and the CI tests from @MinsukJi-NOAA 
- update Python3 environment on jet.intel, gaea.intel, cheyenne.{intel,gnu}
- turn off (again) test `fv3_ccpp_decomp` on jet.intel, this test didn't work in the past, but recently it "passed", because the error checking with `nc_compare.py` failed silently and we didn't notice it

Co-authored-by: valery.yudin <valery.yudin@noaa.gov>
Co-authored-by: Michael Toy <michael.toy@noaa.gov>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>

* Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (ufs-community#419)" (ufs-community#421)

* Add one regional regression test in DEBUG mode.
* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Update regression tests from GFSv15+Thompson to GFSv16+Thompson
* Combine several COMPILE lines in tests/rt.conf and tests/rt_gnu.conf
* Regression test log for cheyenne.{gnu,intel},gaea.intel, hera.gnu, jet.intel,hera.intel,orion.intel;wcoss_cray and wcoss_dell_p3;

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
Co-authored-by: dustinswales <dustin.swales@noaa.gov>
Co-authored-by: Kyle Gerheiser <3209794+kgerheiser@users.noreply.github.com>
Co-authored-by: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com>
Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com>
Co-authored-by: Ali <ali.abdolali@noaa.gov>
Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov>
Co-authored-by: MiKyung Lee <58964324+mlee03@users.noreply.github.com>
Co-authored-by: valery.yudin <valery.yudin@noaa.gov>
Co-authored-by: Michael Toy <michael.toy@noaa.gov>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
AnningCheng-NOAA added a commit to AnningCheng-NOAA/ufs-weather-model that referenced this pull request Mar 8, 2021
@AnningCheng-NOAA
Merge remote-tracking branch 'upstream/develop' into merra2
e6bc1e4 
* upstream/develop:
  update MOM6 to GFDL 20210224 main branch commit (ufs-community#439)
  Add GNU and Cheyenne Support to Automated RT (ufs-community#444)
  Move Noah MP init to CCPP and update Noah MP regression tests, ice flux init bug fix in CCPP (ufs-community#425)
  Feature/rt automation (ufs-community#403)
  Update ccpp-physics. Make RRTMGP thread safe (ufs-community#418)
  Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (ufs-community#419)" (ufs-community#421)
  UGWP v0 v1 combined (ufs-community#396)
  add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (ufs-community#399)
  updates FMS to 2020.04.01 (ufs-community#392)
  Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2)  (ufs-community#407)
  Update CMEPS for HAFS integration; add datm and coupled-model tests on Gaea (ufs-community#401)
  Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (ufs-community#384)
  MOM6 bugfixes, GFDL update, update CDMBGWD settings; fix for restart reproducibility (without waves) when USE_LA_LI2016=True, sign error on fprec passed to ocean, GFDL update, resolution dependent cdmbgwd settings (ufs-community#379)
  dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (ufs-community#369)
  Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (ufs-community#386)
  update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (ufs-community#378)
  point fv3 to EMC develop branch (ufs-community#377)
  Remove IPD steps 3 and 5 (ufs-community#357)
  Update CMEPS  (ufs-community#345)
  Implementation of CCPP timestep_init and timestep_final phases (ufs-community#337)
  Remove unnecessary SIMD instruction sets for Jet, first round of cleanup in rt.conf, initialize cld_amt to zero for regional runs (dycore) (ufs-community#353)
  add frac grid input, update and add additional cpld tests (ufs-community#354)
  Add checkpoint restarts for ufs-cpld (ufs-community#342)
  Update the format of rt.conf (ufs-community#349)
  Remove IPD (step 1) (ufs-community#331)
  Feature/ww3update (ufs-community#334)
  Replace old regional SDF with FV3_GFS_v15_thompson_mynn (ufs-community#333)
  Update modules with hpc-stack v1.1.0 (ufs-community#319)
  Regression test log for PR ufs-community#323 for jet.intel (ufs-community#336)
  RRTMGP and Thompson MP coupling (ufs-community#323)
  Add 2 new tests for DATM-MOM6-CICE6 application (ufs-community#332)
  Add optional bulk flux calculation in ufs-datm (ufs-community#266)
  Final-final GFS v16 updates / restart reproducibility bugfixes (ufs-community#325)
  Updates to build for JEDI linking/control, add wcoss2 (ufs-community#295)
  Update CICE, Move regression test input outside baseline directory (ufs-community#270)
  Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290)
  Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (ufs-community#304)
  Updates to stochastic_physics_wrapper (ufs-community#280)
  Update develop from gsd/develop 2020/11/20: Unified gravity wave drag, updates to other GSL physics (ufs-community#297)
  Fix to allow quilting with non-factors for layout (ufs-community#250)
  rt update (ufs-community#261)
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@junwang-noaa junwang-noaa junwang-noaa approved these changes

@DusanJovic-NOAA DusanJovic-NOAA DusanJovic-NOAA approved these changes

@pjpegion pjpegion Awaiting requested review from pjpegion

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@climbfuji @junwang-noaa @DusanJovic-NOAA @DomHeinzeller