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coupled: use tiled fix files and oro data #331

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JessicaMeixner-NOAA opened this issue Jun 1, 2021 · 21 comments · Fixed by #373
Closed

coupled: use tiled fix files and oro data #331

JessicaMeixner-NOAA opened this issue Jun 1, 2021 · 21 comments · Fixed by #373
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@KateFriedman-NOAA
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coupled Issues related to the coupled branch
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Prototype 7

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@JessicaMeixner-NOAA
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New tiled fix files and oro data have been staged on Mars here: /gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix_NEW

We need to use the new oro data and tiled fix files in the feature/coupled-crow workflow. An example of how this is used can be seen in the ufs-weather-model rt tests: cpld_bmarkfrac_wave_v16_noahmp
@JessicaMeixner-NOAA JessicaMeixner-NOAA added the coupled Issues related to the coupled branch label Jun 1, 2021
@JessicaMeixner-NOAA
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@KateFriedman-NOAA where is the corresponding fix_NEW on hera?

@KateFriedman-NOAA
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@JessicaMeixner-NOAA It wasn't on Hera yet, just Mars. I am rsyncing it to the following location on Hera now:

/scratch1/NCEPDEV/global/glopara/fix_NEW

Give it half an hour to an hour for all files to arrive.

@KateFriedman-NOAA
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The fix_NEW set is complete on Hera now @JessicaMeixner-NOAA . I'll sync the Hera one with the WCOSS-Mars one as we make changes.

@JessicaMeixner-NOAA
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JessicaMeixner-NOAA commented Jun 16, 2021 •
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I deleted the comment about the ugwd fix files to keep things clean.

While I believe the functionality of using the different oro data existed before, the code commit that brought in using it in the coupled tests in ufs-weather-model was on may 25, 2021 commit: ufs-community/ufs-weather-model@c622d7d There is a bug fix that is needed, but it can be run without the bug fix using the tiled file. The bug fix is already in the p7a and p7b branches and will eventually get back to the develop branch soon.

See the cpld_bmarkfrac_wave_v16_noahmp tests for an example of how the titled fix files are used.

@KateFriedman-NOAA KateFriedman-NOAA self-assigned this Jun 16, 2021
@JessicaMeixner-NOAA JessicaMeixner-NOAA added this to the Prototype 7 milestone Jun 22, 2021
@JessicaMeixner-NOAA
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The part of the code that copies in the tiled fix files in the rt.sh system is here https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/fv3_conf/cpld_bmark_tiled_run.IN#L16-L26 and here https://github.com/ufs-community/ufs-weather-model/blob/release/P7b/tests/tests/cpld_bmark_wave_v16_noahmp_nsst#L135-L145
which I believe should be replacing parts of the global-workflow I believe here: https://github.com/NOAA-EMC/global-workflow/blob/feature/coupled-crow/ush/forecast_postdet.sh#L292-L321
as well as updating the link script to point to the new fix files.

@JessicaMeixner-NOAA
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Remaining items for this issue are:

  • have feature/coupled-crow point to new fix files "fix_NEW" in the link script
  • in the forecast run script, either link the new oro and other fix tiled files to the run directory that are on tiles (this is done in rt script here: https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/fv3_conf/cpld_bmark_tiled_run.IN#L33-L40 ) and/or update the input.nml definitions that are denoting where tiled fix files are. In rt.sh these variables are set as:
    export FNALBC="'C384.snowfree_albedo.tileX.nc',"
    export FNALBC2="'C384.facsf.tileX.nc',"
    export FNTG3C="'C384.substrate_temperature.tileX.nc',"
    export FNVEGC="'C384.vegetation_greenness.tileX.nc',"
    export FNVETC="'C384.vegetation_type.tileX.nc',"
    export FNSOTC="'C384.soil_type.tileX.nc',"
    export FNSMCC="'global_soilmgldas.statsgo.t766.1536.768.grb',"
    export FNVMNC="'C384.vegetation_greenness.tileX.nc',"
    export FNVMXC="'C384.vegetation_greenness.tileX.nc',"
    export FNSLPC="'C384.slope_type.tileX.nc',"
    export FNABSC="'C384.maximum_snow_albedo.tileX.nc',"
    (which should replace what is here I believe: https://github.com/NOAA-EMC/global-workflow/blob/feature/coupled-crow/ush/forecast_postdet.sh#L292-L321

If more information is needed please let me know

@WalterKolczynski-NOAA
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Remaining items for this issue are:

  • have feature/coupled-crow point to new fix files "fix_NEW" in the link script
  • in the forecast run script, either link the new oro and other fix tiled files to the run directory that are on tiles (this is done in rt script here: https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/fv3_conf/cpld_bmark_tiled_run.IN#L33-L40 ) and/or update the input.nml definitions that are denoting where tiled fix files are. In rt.sh these variables are set as:
    export FNALBC="'C384.snowfree_albedo.tileX.nc',"
    export FNALBC2="'C384.facsf.tileX.nc',"
    export FNTG3C="'C384.substrate_temperature.tileX.nc',"
    export FNVEGC="'C384.vegetation_greenness.tileX.nc',"
    export FNVETC="'C384.vegetation_type.tileX.nc',"
    export FNSOTC="'C384.soil_type.tileX.nc',"
    export FNSMCC="'global_soilmgldas.statsgo.t766.1536.768.grb',"
    export FNVMNC="'C384.vegetation_greenness.tileX.nc',"
    export FNVMXC="'C384.vegetation_greenness.tileX.nc',"
    export FNSLPC="'C384.slope_type.tileX.nc',"
    export FNABSC="'C384.maximum_snow_albedo.tileX.nc',"
    (which should replace what is here I believe: https://github.com/NOAA-EMC/global-workflow/blob/feature/coupled-crow/ush/forecast_postdet.sh#L292-L321

If more information is needed please let me know

So all of these are already defined, and the files in fix_am use a different naming convention. Unless fix_am needs to be updated and hasn't yet.

@WalterKolczynski-NOAA
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WalterKolczynski-NOAA commented Jul 16, 2021 •
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Looks like the FV3_fix_tiled files need to be brought over to fix_am (or a new fix_am_tiled) under fix_NEW.

/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs/input-data-20210614/FV3_fix_tiled/

@WalterKolczynski-NOAA
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Nevermind, I found them. They are hiding deep in fracoro

@WalterKolczynski-NOAA
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@yangfanglin

In the forecast script, we have a check on FNALBC, FNVETC, FNSOTC, and FNABSC to use the highest resolution available if the files of the given resolution are not available. Will that still work with the new tile data, or does it need to match exactly? I need to know whether I should remove it or update it to use C3072 as a fallback.

Existing code:

# If the appropriate resolution fix file is not present, use the highest resolution available (T1534)
[[ ! -f $FNALBC ]] && FNALBC="$FIX_AM/global_snowfree_albedo.bosu.t1534.3072.1536.rg.grb"
[[ ! -f $FNVETC ]] && FNVETC="$FIX_AM/global_vegtype.igbp.t1534.3072.1536.rg.grb"
[[ ! -f $FNSOTC ]] && FNSOTC="$FIX_AM/global_soiltype.statsgo.t1534.3072.1536.rg.grb"
[[ ! -f $FNABSC ]] && FNABSC="$FIX_AM/global_mxsnoalb.uariz.t1534.3072.1536.rg.grb"
[[ ! -f $FNSMCC ]] && FNSMCC="$FIX_AM/global_soilmgldas.statsgo.t1534.3072.1536.grb"

Code if the fallback still works:

# If the appropriate resolution fix file is not present, use the highest resolution available (C3072)
[[ ! -f $FNALBC ]] && FNALBC="${FIX_SFC}/C3072.snowfree_albedo.tileX.nc"
[[ ! -f $FNVETC ]] && FNVETC="${FIX_SFC}/C3072.vegetation_type.tileX.nc"
[[ ! -f $FNSOTC ]] && FNSOTC="${FIX_SFC}/C3072.soil_type.tileX.nc"
[[ ! -f $FNABSC ]] && FNABSC="${FIX_SFC}/C3072.maximum_snow_albedo.tileX.nc"
[[ ! -f $FNSMCC ]] && FNSMCC="$FIX_AM/global_soilmgldas.statsgo.t1534.3072.1536.grb"

@SMoorthi-emc
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SMoorthi-emc commented Jul 18, 2021 via email

@yangfanglin
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yangfanglin commented Jul 18, 2021 via email

@SMoorthi-emc
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SMoorthi-emc commented Jul 18, 2021 via email

@yangfanglin
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@HelinWei-NOAA @barlage Mike and Helin, do you have a version of the VIIRS veg type data on the Gaussian grid, similar to global_vegtype.igbp.t1534.3072.1536.rg.grb ? We also need the fix files on the tiles for on C1152 and C3072 grids. @shan.sun@noaa.gov @GeorgeGayno-NOAA Can you generate fractional oro datasets for the C1152 and C3072 resolutions ?

@GeorgeGayno-NOAA
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@yangfanglin Why do you need the VIIRS veg type data on the Gaussian grid?

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yangfanglin commented Jul 19, 2021 via email

@SMoorthi-emc
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SMoorthi-emc commented Jul 19, 2021 via email

@yangfanglin
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yangfanglin commented Jul 19, 2021 via email

@GeorgeGayno-NOAA
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George, In case one wants to *experiment *the model at a resolution different from the standard settings of C48. C96, C192 C384, C768, C1152 and C3072, the fix files on the Gaussian grid at the "highest" resolution can always be used as a backup without creating files on the tiles. Fanglin

If anyone wants to test a non-standard resolution, they would need to set up their grid using these UFS_UTILS scripts:
https://github.com/NOAA-EMC/UFS_UTILS/tree/develop/driver_scripts

And these scripts create the 'grid', orography and surface fields. I just ran them for a global C100 grid, and they worked.

@yangfanglin
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@GeorgeGayno-NOAA That is great to know. BTW, has the fractional grid option been built in these driver scripts ? If the answer is yes, could you please make the fix files on the tiles for C1152 and C3072 grids ? They are still missing from the "FIX" archive.

@WalterKolczynski-NOAA
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Can all of this be taken to a new issue somewhere? My original question has been answered, and almost everything after that would be about fix directory maintenance or other changes outside the purview of this issue.

WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Jul 24, 2021
@WalterKolczynski-NOAA
Update to tiled fix files, UGWD v1, NOAH-MP
3c56751 
Updates model to use tiled fix files. Fix directory is updated to the
fix_NEW location.

Adds the ability to use UGWD v1. Since this capability is tied to the
CCPP suite used, the sutie definition file is grepped to determine whether
UGWD is active. Otherwise, gwd_opt 1 is used. Either way, the appropriate
namelist settings are added to input.nml. For v1, the necessary fix files
are also linked to the run directory. If additional options are supported
in the future, there will need to be more sophisicated parsing.

Adds the ability to use Noah-MP. Like UGWD, this is dictated by the CCPP
suite used, so the suite definition file is grepped to determine whether
to use Noah (lsm=1) or Noah-MP (lsm=2).

Additional CCPP suites are added to allow for the new options.

The two non-fractional coupled cases are updated to use a CCPP suite using
both UGWD v1 and Noah-MP. The two aerosol cases are updated to a suite using
UGWD v1 (there does not appear to be an atm-only suite that has both).

There is also a minor change to the UFS build script to remove any existing
UFS build directory. This prevents problems when attempting to build a
different app after one has already been built.

Closes: NOAA-EMC#331, NOAA-EMC#346
Merged
@WalterKolczynski-NOAA WalterKolczynski-NOAA linked a pull request Jul 24, 2021 that will close this issue
Update to tiled fix files, UGWD v1, NOAH-MP #373
Merged
WalterKolczynski-NOAA added a commit that referenced this issue Jul 27, 2021
@WalterKolczynski-NOAA
Update to tiled fix files, UGWD v1, NOAH-MP (#373)
dbc28c4 
* Update to tiled fix files, UGWD v1, NOAH-MP

Updates model to use tiled fix files. Fix directory is updated to the
fix_NEW location.

Adds the ability to use UGWD v1. Since this capability is tied to the
CCPP suite used, the sutie definition file is grepped to determine whether
UGWD is active. Otherwise, gwd_opt 1 is used. Either way, the appropriate
namelist settings are added to input.nml. For v1, the necessary fix files
are also linked to the run directory. If additional options are supported
in the future, there will need to be more sophisicated parsing.

Adds the ability to use Noah-MP. Like UGWD, this is dictated by the CCPP
suite used, so the suite definition file is grepped to determine whether
to use Noah (lsm=1) or Noah-MP (lsm=2).

Additional CCPP suites are added to allow for the new options.

The two non-fractional coupled cases are updated to use a CCPP suite using
both UGWD v1 and Noah-MP. The two aerosol cases are updated to a suite using
UGWD v1 (there does not appear to be an atm-only suite that has both).

There is also a minor change to the UFS build script to remove any existing
UFS build directory. This prevents problems when attempting to build a
different app after one has already been built.

Closes: #331, #346
WalterKolczynski-NOAA added a commit that referenced this issue Jul 28, 2021
@WalterKolczynski-NOAA
Update to MERRA2 aerosol climatology (#380)
ef419a6 
* Update to tiled fix files, UGWD v1, NOAH-MP

Updates model to use tiled fix files. Fix directory is updated to the
fix_NEW location.

Adds the ability to use UGWD v1. Since this capability is tied to the
CCPP suite used, the sutie definition file is grepped to determine whether
UGWD is active. Otherwise, gwd_opt 1 is used. Either way, the appropriate
namelist settings are added to input.nml. For v1, the necessary fix files
are also linked to the run directory. If additional options are supported
in the future, there will need to be more sophisicated parsing.

Adds the ability to use Noah-MP. Like UGWD, this is dictated by the CCPP
suite used, so the suite definition file is grepped to determine whether
to use Noah (lsm=1) or Noah-MP (lsm=2).

Additional CCPP suites are added to allow for the new options.

The two non-fractional coupled cases are updated to use a CCPP suite using
both UGWD v1 and Noah-MP. The two aerosol cases are updated to a suite using
UGWD v1 (there does not appear to be an atm-only suite that has both).

There is also a minor change to the UFS build script to remove any existing
UFS build directory. This prevents problems when attempting to build a
different app after one has already been built.

Closes: #331, #346

* Ensure CCPP_SUITE is set and suite file exists

Previously there was no guarantee that CCPP_SUITE was set before it
was used in forecast_postdet.sh. The suite how has a default value if
it is not set. A default later in the execution chain is removed, as
CCPP_SUITE is now guaranteed to be set beforehand. The default is also
updated to FV3_GFS_v16.

There is also now a check to ensure the suite file is present inside
the UFS directory before trying to determine settings from it.

Refs: #346

* Update to MERRA2 aerosol climatology

Adds the capability to use MERRA2 aerosol climatology and makes it
the default.

An addition to the diag table is required. Rather than continue the
proliferation of diag tables to produce one specifically for coupled
and MERRA2, the existing diag table from the MERRA2 update in devleop
is pared down to just the additional fields introduced. This is then
appended to the main diag table if necessary.

Also corrected a related issue in the CROW forecast config. While
IAER and several other similar settings were already present in the
schema, the values were hard-coded in the forecast config instead of
using the value set. The script now correctly uses the values set by
the configuration system. The default for IAER is changed to 1011 for
MERRA2.

Refs: #379
zhanglikate pushed a commit to zhanglikate/global-workflow that referenced this issue Oct 6, 2022
@climbfuji
Remove IPD (step 1) (NOAA-EMC#331)
cfe6ed2 
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 NOAA-EMC#341 ("Update MOM6 to GFDL's 20201218 commit")
Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3)
Fix broken utest (see NOAA-EMC#348)
zhanglikate pushed a commit to zhanglikate/global-workflow that referenced this issue Oct 6, 2022
@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 (NOAA-EMC#63)
56e9901 
* Updates to stochastic_physics_wrapper (NOAA-EMC#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  (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 NOAA-EMC#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 (#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 NOAA-EMC#323 for jet.intel (NOAA-EMC#336)

* Update modules with hpc-stack v1.1.0 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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) (NOAA-EMC#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 NOAA-EMC#341 ("Update MOM6 to GFDL's 20201218 commit")
Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3)
Fix broken utest (see NOAA-EMC#348)

* Update the format of rt.conf (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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) (NOAA-EMC#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 (NOAA-EMC#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  (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#377)

* update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (NOAA-EMC#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 (NOAA-EMC#386)

* Update .gitmodules and submodule pointer for fv3atm for gsl/develop branch
* RUC ice for gsl/develop (replaces NOAA-EMC#47) (NOAA-EMC#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 (NOAA-EMC#50)
* Updates to stochastic_physics_wrapper (NOAA-EMC#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  (NOAA-EMC#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 (NOAA-EMC#57)

* dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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)  (NOAA-EMC#407)

* Regression test logs for all tier=1 platforms

* updates FMS to 2020.04.01 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#396)

- combines the changes in PRs NOAA-EMC#360 and NOAA-EMC#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. (NOAA-EMC#419)" (NOAA-EMC#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>
kayeekayee pushed a commit to kayeekayee/global-workflow that referenced this issue May 30, 2024
@climbfuji @dustinswales
@ericaligo-NOAA @DomHeinzeller
Add extended diagnostic output from Thompson MP, includes "Add option…
20883ed 
…al scaling to RRTMGP flux adjustment" (NOAA-EMC#319), bug fix in several suite definition files (NOAA-EMC#331)

Adds a set of dedicated 3d arrays for extended diagnostic output from Thompon MP, and a logical flag that controls allocating, outputting and resetting these arrays. This work is based on @ericaligo-NOAA 's code changes.

The flag to reset the extended diagnostics from Thompson MP is - for the UFS - currently tied to avg_max_length, which is used to reset maximum hourly fields (the corresponding reset variable is renamed to make its purpose clear).

Include the changes in NOAA-EMC#319, "Add optional scaling to RRTMGP flux adjustment".

Important: Fixed bugs in several suite definition files that were missing the call to GFS_radiation_surface:

* suite_FV3_GFS_v15_thompson_mynn_RRTMGP.xml
* suite_FV3_GFS_v16_coupled_noahmp.xml
* suite_FV3_GFS_v16_coupled_nsstNoahmp.xml
* suite_FV3_RRFS_v1alpha.xml

Co-authored-by: Dustin Swales <dustin.swales@noaa.gov>
Co-authored-by: Eric Aligo <eric.aligo@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>
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Update to tiled fix files, UGWD v1, NOAH-MP WalterKolczynski-NOAA/global-workflow
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@JessicaMeixner-NOAA @WalterKolczynski-NOAA @KateFriedman-NOAA @yangfanglin @SMoorthi-emc @GeorgeGayno-NOAA