update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model #453

XuLi-NOAA · 2021-03-08T16:39:24Z

Description

Incorporation the changes in fv3atm and ccpp/physics for the NSST model in the coupled system .
See issue #350

fv3atm changes: see NOAA-EMC/fv3atm#219

Reduce the initialized warm layer thickness to be 20 m when the NSST model is cold start in FV3 io.
Add one ccpp suite: suite_FV3_GFS_v15p2_couplednsst.xml
Include the change in ccpp/physics submodule (see NCAR/ccpp-physics#537).

ccpp/physics changes: see NCAR/ccpp-physics#537

Three changes in this issue and a bug fix

(1) Scheme-A to Scheme-A.1 in ccpp/physics
The cooling effect is removed from the formula to determine Tf
(2) Apply a safeguard to tref in sfc_nst_pre_run
(3) Reduce z_w_max from 30 m to 20 in ccpp/physics and FV3/io

A bug fix in ccpp physics related to NSST model in the coupled mode

The new baseline results are at: /scratch1/NCEPDEV/stmp4/Xu.Li/FV3_RT/REGRESSION_TEST_INTEL, the new baseline has been generated since the changes alter the results related to the NSST model.
There is no library update.

The results are as expected.

Issue(s) addressed

Testing

A new test, cpld_control_nsst has been generated and included in the regression tests, the added ccpp suite, suite_FV3_GFS_v15p2_couplednsst.xml, has been added in rt.conf

The regression tests have been done on Hera by:

./rt.sh -ce >baseline_new
./rt.sh -me

Dependencies

The update of ufs-weather-model depends on the update in FV3, which depends on the updates in ccpp/physics.

junwang-noaa · 2021-03-08T16:44:08Z

Please update your title to be more specific, e,g, what feature/updates are in the PR. Also please answer the questions in the PR template, do not delete them.

XuLi-NOAA · 2021-03-08T18:02:51Z

Please update your title to be more specific, e,g, what feature/updates are in the PR. Also please answer the questions in the PR template, do not delete them.

I modified the PR by following the template but not sure how deal with the dependency part. How to find which PRs are before me?

junwang-noaa · 2021-03-08T18:34:08Z

No, the dependency of PRs means which subcomponent PRs (e.g. fv3, ccpp) are associated with your ufs-weather-model PR, these PRs need to be committed before the ufs-weather-model PR is merged. It is not the ufs-weather-model PRs that are committed before yours.

…

On Mon, Mar 8, 2021 at 1:03 PM XuLi-NOAA ***@***.***> wrote: Please update your title to be more specific, e,g, what feature/updates are in the PR. Also please answer the questions in the PR template, do not delete them. I modified the PR by following the template but not sure how deal with the dependency part. How to find which PRs are before me? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#453 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI7D6TISE4G4HS5QNQFEM23TCUGNZANCNFSM4YZXATHQ> .

BrianCurtis-NOAA · 2021-03-09T21:33:36Z

Does this PR link with any ufs-weather-model issues that have been created?

XuLi-NOAA · 2021-03-10T14:47:54Z

Yes, see the description.

…

On Tue, Mar 9, 2021 at 4:33 PM BrianCurtis-NOAA ***@***.***> wrote: Does this PR link with any ufs-weather-model issues that have been created? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#453 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANEMLJWKNZ646ADR6YX26YLTC2A3DANCNFSM4YZXATHQ> .

BrianCurtis-NOAA · 2021-03-10T15:25:01Z

Yes, see the description.
…
On Tue, Mar 9, 2021 at 4:33 PM BrianCurtis-NOAA @.***> wrote: Does this PR link with any ufs-weather-model issues that have been created? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#453 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANEMLJWKNZ646ADR6YX26YLTC2A3DANCNFSM4YZXATHQ .

Thanks! I did miss it. I edited it to say "Closes #" so that the merge of this pull request closes that issue.

XuLi-NOAA · 2021-03-10T15:31:09Z

Yes, see the description.
…
On Tue, Mar 9, 2021 at 4:33 PM BrianCurtis-NOAA @.***> wrote: Does this PR link with any ufs-weather-model issues that have been created? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#453 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANEMLJWKNZ646ADR6YX26YLTC2A3DANCNFSM4YZXATHQ .

Thanks! I did miss it. I edited it to say "Closes #" so that the merge of this pull request closes that issue.

Thanks! I just modified the description to make it clearer.

XuLi-NOAA · 2021-03-10T15:32:21Z

Anybody can tell me what do the failures of the Build mean showing above?

MinsukJi-NOAA · 2021-03-10T15:45:49Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

XuLi-NOAA · 2021-03-10T16:16:55Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

I have updated to the newest version in my regression tests, which went through smoothly (on hera).
No idea what these failures came from (or who did it).

MinsukJi-NOAA · 2021-03-10T16:40:58Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

I have updated to the newest version in my regression tests, which went through smoothly (on hera).
No idea what these failures came from (or who did it).

If you referring to the Pull Request Tests, they are automatic tests run by GitHub Actions CI in the ufs-weather-model repository.

XuLi-NOAA · 2021-03-15T16:49:12Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

I have updated to the newest version in my regression tests, which went through smoothly (on hera).
No idea what these failures came from (or who did it).

If you referring to the Pull Request Tests, they are automatic tests run by GitHub Actions CI in the ufs-weather-model repository.

XuLi-NOAA · 2021-03-15T16:51:35Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

I have updated to the newest version in my regression tests, which went through smoothly (on hera).
No idea what these failures came from (or who did it).

If you referring to the Pull Request Tests, they are automatic tests run by GitHub Actions CI in the ufs-weather-model repository.

The automatic tests run failure needs to be fixed or not at this stage?

MinsukJi-NOAA · 2021-03-15T16:54:41Z

@XuLi-NOAA , could you try updating the ufs-weather-model to the latest?

I have updated to the newest version in my regression tests, which went through smoothly (on hera).
No idea what these failures came from (or who did it).

If you referring to the Pull Request Tests, they are automatic tests run by GitHub Actions CI in the ufs-weather-model repository.

The automatic tests run failure needs to be fixed or not at this stage?

My understanding is that, if automatic tests fails, it needs to be fixed before going to the next stage.

DeniseWorthen · 2021-03-16T16:18:04Z

@XuLi-NOAA Could you please edit the title of this PR to describe what you are implementing? Perhaps "implement the NSST model in the coupled system"

Also, there is no associated test file for ufs-weather-model included. You mention that cpld_control_nsst has been added and suite_FV3_GFS_v15p2_couplednsst.xml added to rt.conf but neither changes are in your PR.

SMoorthi-emc · 2021-03-16T16:20:14Z

NSST model is already in both uncoupled and coupled system. This is supposed to fix some issues, specifically related to coupling.

DeniseWorthen · 2021-03-16T16:26:14Z

If I did not suggest a good title, that is fine. But something more descriptive than update with fv3 & ccpp/physics updates

…_nsst, to test an added ccpp suite, suite_FV3_GFS_v15p2_couplednsst.xml

XuLi-NOAA · 2021-03-16T17:03:44Z

If I did not suggest a good title, that is fine. But something more descriptive than update with fv3 & ccpp/physics updates

@DeniseWorthen @SMoorthi-emc: I just push the branch to dial with the add of a new regression test, cpld_control_nsst. I planned to do it latter since a new rt will be run any way after merging with the updated master.

DeniseWorthen · 2021-03-16T17:04:30Z

tests/rt.sh

@@ -242,7 +242,7 @@ elif [[ $MACHINE_ID = hera.* ]]; then
  QUEUE=batch
  COMPILE_QUEUE=batch

-  #ACCNR=fv3-cpu
+  ACCNR=da-cpu


Please revert these two changes to ACCNR.

Please revert these two changes to ACCNR.

Will do in the final push, and that's why I didn't push it earlier. Thanks!

binli2337 · 2021-03-23T14:36:30Z

@XuLi-NOAA Please update your branch with the latest changes in the develop branch.

binli2337 · 2021-03-24T17:45:56Z

@XuLi-NOAA , Please revise tests/rt.conf (between line 136 and line 149).

binli2337 · 2021-03-25T12:24:39Z

@XuLi-NOAA ,Please resolve the conflict in rt.conf (starting from line 136).

XuLi-NOAA · 2021-03-25T12:55:45Z

@XuLi-NOAA ,Please resolve the conflict in rt.conf (starting from line 136).

@binli2337 : Done and thanks!

…l on in the coupled model (Replace PR #453) (#483) * point to fv3 branch * Add one more test cpld_control_nsst to test added ccpp suite (FV3_GFS_v15p2_couplednsst) * Modify rt.conf to add FV3_GFS_v15p2_couplednsst * Modify rt.conf to add a new test, cpld_bmarkfrac_v16_nsst, remove test cpld_control_nsst * Modify tests/tests/cpld_bmarkfrac_v16_nsst: 1. cpld_bmarkfrac_v16 to cpld_bmarkfrac_v16_nsst. 2. export NSTF_NAME=2,1,0,0,0 to export nstf_name=2,1,0,0,0. * Modify input.benchmark_v16.nml.IN & cpld_bmarkfrac_v16_nsst for a consistent definition of nstf_name namelist * Modify cpld_bmarkfrac_v16_nsst by moving the NSTF_NAME to the namelist field updates section * RegressionTests_orion.intel.log of the rt run and BL_DATE=20210406 in rt.sh * RT JOBS PASSED: hera.intel. Log file uploaded. * run-ci, commit 7 RegressionTest log files * Push RegressionTests_wcoss_dell_p3.log Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>

* First test * Change branch name * github event name... * change to tests/ci dir * change repo name * print out stderr * try recursive checkout * checkout myself * in a hurry * fetch owner id * Make setup depend on prcheck * update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model (Replace PR ufs-community#453) (ufs-community#483) * point to fv3 branch * Add one more test cpld_control_nsst to test added ccpp suite (FV3_GFS_v15p2_couplednsst) * Modify rt.conf to add FV3_GFS_v15p2_couplednsst * Modify rt.conf to add a new test, cpld_bmarkfrac_v16_nsst, remove test cpld_control_nsst * Modify tests/tests/cpld_bmarkfrac_v16_nsst: 1. cpld_bmarkfrac_v16 to cpld_bmarkfrac_v16_nsst. 2. export NSTF_NAME=2,1,0,0,0 to export nstf_name=2,1,0,0,0. * Modify input.benchmark_v16.nml.IN & cpld_bmarkfrac_v16_nsst for a consistent definition of nstf_name namelist * Modify cpld_bmarkfrac_v16_nsst by moving the NSTF_NAME to the namelist field updates section * RegressionTests_orion.intel.log of the rt run and BL_DATE=20210406 in rt.sh * RT JOBS PASSED: hera.intel. Log file uploaded. * run-ci, commit 7 RegressionTest log files * Push RegressionTests_wcoss_dell_p3.log Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> * remove develop * quiet git commands. run-ci * Update CMEPS for latest ESCOMP/master; Update PIO to 2.5.2; Refactor modules (ufs-community#492) * update ufs for CMEPS master with PIO changes * update pio to 2.5.2 across platforms * replace variable SUITE_NAME with CCPP_SUITE * Merge remote-tracking branch 'DusanJovic/module_common' into feature/updcmeps * switch to h-nems area on jet Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> * debug this again... * debug again * debug continues * missed repo field * remove debug related texts * remove -x flag. run-ci * reduce sleep time * diag * diag2 * Fix pr_uid * diag again Co-authored-by: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* First test * Change branch name * github event name... * change to tests/ci dir * change repo name * print out stderr * try recursive checkout * checkout myself * in a hurry * fetch owner id * Make setup depend on prcheck * update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model (Replace PR ufs-community#453) (ufs-community#483) * point to fv3 branch * Add one more test cpld_control_nsst to test added ccpp suite (FV3_GFS_v15p2_couplednsst) * Modify rt.conf to add FV3_GFS_v15p2_couplednsst * Modify rt.conf to add a new test, cpld_bmarkfrac_v16_nsst, remove test cpld_control_nsst * Modify tests/tests/cpld_bmarkfrac_v16_nsst: 1. cpld_bmarkfrac_v16 to cpld_bmarkfrac_v16_nsst. 2. export NSTF_NAME=2,1,0,0,0 to export nstf_name=2,1,0,0,0. * Modify input.benchmark_v16.nml.IN & cpld_bmarkfrac_v16_nsst for a consistent definition of nstf_name namelist * Modify cpld_bmarkfrac_v16_nsst by moving the NSTF_NAME to the namelist field updates section * RegressionTests_orion.intel.log of the rt run and BL_DATE=20210406 in rt.sh * RT JOBS PASSED: hera.intel. Log file uploaded. * run-ci, commit 7 RegressionTest log files * Push RegressionTests_wcoss_dell_p3.log Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> * remove develop * quiet git commands. run-ci * Update CMEPS for latest ESCOMP/master; Update PIO to 2.5.2; Refactor modules (ufs-community#492) * update ufs for CMEPS master with PIO changes * update pio to 2.5.2 across platforms * replace variable SUITE_NAME with CCPP_SUITE * Merge remote-tracking branch 'DusanJovic/module_common' into feature/updcmeps * switch to h-nems area on jet Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> * debug this again... * debug again * debug continues * missed repo field * remove debug related texts * remove -x flag. run-ci * reduce sleep time * diag * diag2 * Fix pr_uid * diag again * still debugging * lets see if this works * use context as main yml key Co-authored-by: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* First test * Change branch name * github event name... * change to tests/ci dir * change repo name * print out stderr * try recursive checkout * checkout myself * in a hurry * fetch owner id * Make setup depend on prcheck * update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model (Replace PR ufs-community#453) (ufs-community#483) * point to fv3 branch * Add one more test cpld_control_nsst to test added ccpp suite (FV3_GFS_v15p2_couplednsst) * Modify rt.conf to add FV3_GFS_v15p2_couplednsst * Modify rt.conf to add a new test, cpld_bmarkfrac_v16_nsst, remove test cpld_control_nsst * Modify tests/tests/cpld_bmarkfrac_v16_nsst: 1. cpld_bmarkfrac_v16 to cpld_bmarkfrac_v16_nsst. 2. export NSTF_NAME=2,1,0,0,0 to export nstf_name=2,1,0,0,0. * Modify input.benchmark_v16.nml.IN & cpld_bmarkfrac_v16_nsst for a consistent definition of nstf_name namelist * Modify cpld_bmarkfrac_v16_nsst by moving the NSTF_NAME to the namelist field updates section * RegressionTests_orion.intel.log of the rt run and BL_DATE=20210406 in rt.sh * RT JOBS PASSED: hera.intel. Log file uploaded. * run-ci, commit 7 RegressionTest log files * Push RegressionTests_wcoss_dell_p3.log Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> * remove develop * quiet git commands. run-ci * Update CMEPS for latest ESCOMP/master; Update PIO to 2.5.2; Refactor modules (ufs-community#492) * update ufs for CMEPS master with PIO changes * update pio to 2.5.2 across platforms * replace variable SUITE_NAME with CCPP_SUITE * Merge remote-tracking branch 'DusanJovic/module_common' into feature/updcmeps * switch to h-nems area on jet Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov> * debug this again... * debug again * debug continues * missed repo field * remove debug related texts * remove -x flag. run-ci * reduce sleep time * diag * diag2 * Fix pr_uid * diag again * still debugging * lets see if this works * use context as main yml key * Try pull request now. run-ci * minor change. run-ci * typo fix * debug 1 * debug2 * minor mods. run-ci * check another dir * sleep * sigh * sigh2 * increase time again * test again Co-authored-by: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Co-authored-by: Brian Curtis <brian.curtis@noaa.gov> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov> Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* update submodule pointer for regression testing of ccpp-physics#812

update with fv3 merge

a39e138

BrianCurtis-NOAA added the Triaged label Mar 10, 2021

DeniseWorthen added the Baseline Updates Current baselines will be updated. label Mar 14, 2021

XuLi-NOAA changed the title ~~update with fv3 merge~~ update with fv3 & ccpp/physics updates Mar 15, 2021

XuLi-NOAA closed this Mar 15, 2021

XuLi-NOAA reopened this Mar 15, 2021

junwang-noaa requested review from climbfuji, SMoorthi-emc and junwang-noaa March 16, 2021 01:02

SMoorthi-emc approved these changes Mar 16, 2021

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Modifcations to tun the rt, including adding a new test: cpld_control…

8d708a9

…_nsst, to test an added ccpp suite, suite_FV3_GFS_v15p2_couplednsst.xml

XuLi-NOAA changed the title ~~update with fv3 & ccpp/physics updates~~ update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model Mar 16, 2021

DeniseWorthen reviewed Mar 16, 2021

View reviewed changes

binli2337 self-requested a review March 23, 2021 14:36

binli2337 assigned binli2337 and XuLi-NOAA Mar 24, 2021

XuLi-NOAA added 2 commits March 24, 2021 12:31

Merge remote-tracking branch 'upstream/develop' into feature/ufs-nst

da7506a

merge to the develop branch in ufs-weather-model

a6b7225

Resolve conflict in rt.sh

4bbb2ab

binli2337 mentioned this pull request Mar 26, 2021

update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model (Replace PR #453) #483

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XuLi-NOAA closed this Mar 26, 2021

XuLi-NOAA deleted the feature/ufs-nst branch April 16, 2021 03:20

pjpegion pushed a commit to NOAA-PSL/ufs-weather-model that referenced this pull request Apr 4, 2023

Wrapper for ccpp-physics ufs-community#812 (ufs-community#453)

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* update submodule pointer for regression testing of ccpp-physics#812

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update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model #453

update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model #453

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update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model #453

update with fv3 & ccpp/physics updates in order to turn the NSST model on in the coupled model #453

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