(1) update MOM6 to its main branch 20220902 commit (2) update GNU to include s2swa tests #1401

jiandewang · 2022-09-07T01:18:10Z

PR Checklist

This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model wiki if you are unsure how to do this.
This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR
An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR
are specified below.
Results for one or more of the regression tests change and the reasons for the changes are understood and explained below.
the SPPT temperature limiter calculation method is being changed, thus the stochastic test case will require new baseline
New or updated input data is required by this PR. If checked, please work with the code managers to update input data sets on all platforms.

Instructions: All subsequent sections of text should be filled in as appropriate.

The information provided below allows the code managers to understand the changes relevant to this PR, whether those changes are in the ufs-weather-model repository or in a subcomponent repository. Ufs-weather-model code managers will use the information provided to add any applicable labels, assign reviewers and place it in the Commit Queue. Once the PR is in the Commit Queue, it is the PR owner's responsibility to keep the PR up-to-date with the develop branch of ufs-weather-model.

Description

Provide a detailed description of what this PR does. What bug does it fix, or what feature does it add? Is a change of answers expected from this PR? Are any library updates included in this PR (modulefiles etc.)?
update MOM6 to its main branch 20220902 commit, this is originally based on dev-emc-candidate-20220828 to MOM6 main branch but with minor modification on SPPT temperature limiter

Issue(s) addressed

UFS #1400 and MOM6 issue NOAA-EMC/MOM6#103
MOM6 PR NOAA-EMC/MOM6#104
Link the issues to be closed with this PR, whether in this repository, or in another repository.
(Remember, issues must always be created before starting work on a PR branch!)

fixes update MOM6 to main branch 20220902 commit #1400 and MOM6 issue update MOM6 to its main branch 20220902 commit NOAA-EMC/MOM6#103

Testing

How were these changes tested? What compilers / HPCs was it tested with? Are the changes covered by regression tests? (If not, why? Do new tests need to be added?) Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)

Dependencies

waiting on update to MOM6 main 20220902 commit NOAA-EMC/MOM6#104

jkbk2004 · 2022-09-12T16:16:01Z

@jiandewang we can start working on the pr. can we combine in #1388 ?

DeniseWorthen · 2022-09-12T16:21:09Z

@jiandewang once you update your branch, I will make a PR to add the S2SWA test for GNU (script level changes only).

jiandewang · 2022-09-12T16:23:28Z

@DeniseWorthen just updated my branch

jiandewang · 2022-09-12T16:23:58Z

@jiandewang we can start working on the pr. can we combine in #1388 ?

yes we can combine them

jkbk2004 · 2022-09-12T18:52:07Z

@jiandewang we can start working on the pr. can we combine in #1388 ?

yes we can combine them

@jiandewang #1388 needs only changes in rt_gnu.conf. I think its possible to manually add in but @DeniseWorthen will you create pr to jiande's branch?

DeniseWorthen · 2022-09-12T18:55:58Z

I made a PR to @jiandewang UWM branch a couple of hours ago.

Feature/adds2swa gnutests

jiandewang · 2022-09-12T18:59:25Z

just saw that, merged.
Do I need to launch rt.sh on wcoss2 manually ?

jkbk2004 · 2022-09-12T19:02:47Z

@jiandewang thanks! I will add new BL_DATE and start testing RT runs on RDHPCs. @BrianCurtis-NOAA will test on wcoss2

BrianCurtis-NOAA · 2022-09-12T20:05:08Z

WCOSS2 on baseline creation: Failed test hafs_regional_atm_wav (test 073) walltime 1813 exceeded limit 1800.

on-behalf-of @ufs-community <brian.curtis@noaa.gov>

BrianCurtis-NOAA · 2022-09-12T23:57:29Z

Automated RT Failure Notification
Machine: orion
Compiler: intel
Job: BL
[BL] Repo location: /work/noaa/nems/emc.nemspara/autort/pr/1048155862/20220912180010/ufs-weather-model
[BL] Error: Test compile_017 failed in run_compile failed
[BL] Error: Test compile_018 failed in run_compile failed
Please make changes and add the following label back: orion-intel-BL

jiandewang · 2022-09-13T15:18:38Z

MOM6 PR merged, let me know when it's time to switch submodule in UFS

jiandewang · 2022-09-13T15:24:21Z

sounds like we need to create issue to hafs team. But I am able to clone on other machines. `From https://github.com/NOAA-EMC/HYCOM-src

branch 09bdf00e500d99e2b8811c0571258f86c14efc30 -> FETCH_HEAD
Submodule path 'HYCOM-interface/HYCOM': checked out '09bdf00e500d99e2b8811c0571258f86c14efc30''

my fresh clone for the branch of this PR shows
-b7e077699ca1054104cc93342a038941346bef04 FV3/upp/sorc/ncep_post.fd/post_gtg.fd
a342b1b215c3d915948b1220843f9b30ea159401 GOCART (rt-v5_29_1_BPL91_1-exRT4-453-ga342b1b)
+8d247021484c5cb7f8ded897c1e2020c028ef7e9 HYCOM-interface/HYCOM (2.3.01-52-g8d24702)
where does "09bdf00e5" come from ?

jiandewang · 2022-09-13T15:30:27Z

sounds like we need to create issue to hafs team. But I am able to clone on other machines. `From https://github.com/NOAA-EMC/HYCOM-src

branch 09bdf00e500d99e2b8811c0571258f86c14efc30 -> FETCH_HEAD
Submodule path 'HYCOM-interface/HYCOM': checked out '09bdf00e500d99e2b8811c0571258f86c14efc30''

my fresh clone for the branch of this PR shows -b7e077699ca1054104cc93342a038941346bef04 FV3/upp/sorc/ncep_post.fd/post_gtg.fd a342b1b215c3d915948b1220843f9b30ea159401 GOCART (rt-v5_29_1_BPL91_1-exRT4-453-ga342b1b) +8d247021484c5cb7f8ded897c1e2020c028ef7e9 HYCOM-interface/HYCOM (2.3.01-52-g8d24702) where does "09bdf00e5" come from ?

now I see
Submodule path 'HYCOM-interface/HYCOM': checked out '09bdf00e500d99e2b8811c0571258f86c14efc30'
seems github is having issue at this moment, I just cloned on HERA and tried git submodule status --recursive and got the following:
e22724738fd104327fee7c3c7ffc805ccabd619f FV3/upp (upp_v10.2.0-9-ge227247)
b7e077699ca1054104cc93342a038941346bef04 FV3/upp/sorc/ncep_post.fd/post_gtg.fd
fatal: not a git repository: '.git'
fatal: failed to recurse into submodule 'sorc/ncep_post.fd/post_gtg.fd'
fatal: failed to recurse into submodule 'upp'
fatal: failed to recurse into submodule 'FV3'

BrianCurtis-NOAA · 2022-09-13T15:33:17Z

@jiandewang Should HYCOM in UFS be at the HEAD of the emc/develop branch?

jiandewang · 2022-09-13T15:37:09Z

@jiandewang Should HYCOM in UFS be at the HEAD of the emc/develop branch?

yes, this is what's inside .gitmodules
[submodule "HYCOM"]
path = HYCOM-interface/HYCOM
url = https://github.com/NOAA-EMC/HYCOM-src
branch = emc/develop

and my fresh clone for the above is

emc/develop 8d24702 Add hybthn to blkdat.input

jiandewang · 2022-09-13T15:47:59Z

can someone repeat what I just did:
147 11:40 git clone https://github.com/jiandewang/ufs-weather-model
148 11:40 cd ufs-weather-model/
149 11:40 git branch -a
150 11:40 git checkout feature/update-MOM6-20220902
151 11:40 git submodule update --init --recursive

cd HYCOM-interface/HYCOM
git branch -v

what I got is

(HEAD detached at 09bdf00) 09bdf00 Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (Update ufs-weather-model/develop with changes from gmtb/develop as of 2019/10/16 #1)
emc/develop 8d24702 Add hybthn to blkdat.input

it should point to emc.develop, not the HEAD
so something has been changed on HYCOM during the past couple of days (maybe someone used forced push ?)

my cloned directory on HERA: /scratch1/NCEPDEV/climate/Jiande.Wang/MOM6-update/MOM6-update-20220902/Final/ufs-weather-model

during the submodule update --init --recursive, it had
From https://github.com/NOAA-EMC/HYCOM-src

branch 09bdf00e500d99e2b8811c0571258f86c14efc30 -> FETCH_HEAD
this shouldn't be there

I also cloned the ufs develop branch, and got the same thing

jkbk2004 · 2022-09-13T16:12:43Z

can someone repeat what I just did: 147 11:40 git clone https://github.com/jiandewang/ufs-weather-model 148 11:40 cd ufs-weather-model/ 149 11:40 git branch -a 150 11:40 git checkout feature/update-MOM6-20220902 151 11:40 git submodule update --init --recursive

cd HYCOM-interface/HYCOM git branch -v

what I got is

(HEAD detached at 09bdf00) 09bdf00 Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (Update ufs-weather-model/develop with changes from gmtb/develop as of 2019/10/16 #1)
emc/develop 8d24702 Add hybthn to blkdat.input

it should point to emc.develop, not the HEAD so something has been changed on HYCOM during the past couple of days (maybe someone used forced push ?)

my cloned directory on HERA: /scratch1/NCEPDEV/climate/Jiande.Wang/MOM6-update/MOM6-update-20220902/Final/ufs-weather-model

during the submodule update --init --recursive, it had From https://github.com/NOAA-EMC/HYCOM-src

branch 09bdf00e500d99e2b8811c0571258f86c14efc30 -> FETCH_HEAD
this shouldn't be there

I also cloned the ufs develop branch, and got the same thing

Yes, I see the same on other machines. BTW, we need to use 'module load git/2.28.0' on orion.

jkbk2004 · 2022-09-13T16:45:15Z

I checked out a ufs-wm hash around early June.
'-09bdf00e500d99e2b8811c0571258f86c14efc30 HYCOM-interface/HYCOM'
Same hycom hash was used then. I think we are ok to merge this pr. We just need to make sure about hycom hash with hafs team.

BrianCurtis-NOAA · 2022-09-13T16:49:14Z

Please hold while we track down this HYCOM issue.

DeniseWorthen · 2022-09-13T16:49:25Z

The hycom hash should not have changed. Brian and I have checked w/ Bin Liu. The emc/develop branch in our fork was updated---and we're not clear why. Please don't merge until we can straighten this out. The issue is that we cannot find the hash 09bdf00 currently in emc/develop.

For instance: git clone https://github.com/NOAA-EMC/HYCOM-src.git
git checkout 09bdf00e50
error: pathspec '09bdf00e50' did not match any file(s) known to git

DusanJovic-NOAA · 2022-09-13T17:41:57Z

The last event in NOAA-EMC/HYCOM-src repo that changed the HEAD of the emc/develop branch from 09bdf00 to 8d24702 was:

[
  {
    "id": "23923922315",
    "type": "PushEvent",
    "actor": {
      "id": 11394126,
      "login": "aerorahul",
      "display_login": "aerorahul",
      "gravatar_id": "",
      "url": "https://api.github.com/users/aerorahul",
      "avatar_url": "https://avatars.githubusercontent.com/u/11394126?"
    },
    "repo": {
      "id": 389701838,
      "name": "NOAA-EMC/HYCOM-src",
      "url": "https://api.github.com/repos/NOAA-EMC/HYCOM-src"
    },
    "payload": {
      "push_id": 10978986151,
      "size": 66,
      "distinct_size": 1,
      "ref": "refs/heads/emc/develop",
      "head": "8d247021484c5cb7f8ded897c1e2020c028ef7e9",
      "before": "09bdf00e500d99e2b8811c0571258f86c14efc30",
      "commits": [
        {
          "sha": "8c5cc444f5065d5fd8c74582db95c360e0e4a99f",
          "author": {
            "email": "33480590+TillRasmussen@users.noreply.github.com",
            "name": "TRasmussen"
          },
          "message": "Merge pull request #2 from HYCOM/master\n\nUpdate from upstream",
          "distinct": false,
          "url": "https://api.github.com/repos/NOAA-EMC/HYCOM-src/commits/8c5cc444f5065d5fd8c74582db95c360e0e4a99f"
        },
        . . .
      ]
    },
    "public": true,
    "created_at": "2022-09-09T19:58:45Z",
    "org": {
      "id": 37810995,
      "login": "NOAA-EMC",
      "gravatar_id": "",
      "url": "https://api.github.com/orgs/NOAA-EMC",
      "avatar_url": "https://avatars.githubusercontent.com/u/37810995?"
    }
  },
  . . .
]

jkbk2004 · 2022-09-13T17:52:51Z

The last event in NOAA-EMC/HYCOM-src repo that changed the HEAD of the emc/develop branch from 09bdf00 to 8d24702 was:

[
  {
    "id": "23923922315",
    "type": "PushEvent",
    "actor": {
      "id": 11394126,
      "login": "aerorahul",
      "display_login": "aerorahul",
      "gravatar_id": "",
      "url": "https://api.github.com/users/aerorahul",
      "avatar_url": "https://avatars.githubusercontent.com/u/11394126?"
    },
    "repo": {
      "id": 389701838,
      "name": "NOAA-EMC/HYCOM-src",
      "url": "https://api.github.com/repos/NOAA-EMC/HYCOM-src"
    },
    "payload": {
      "push_id": 10978986151,
      "size": 66,
      "distinct_size": 1,
      "ref": "refs/heads/emc/develop",
      "head": "8d247021484c5cb7f8ded897c1e2020c028ef7e9",
      "before": "09bdf00e500d99e2b8811c0571258f86c14efc30",
      "commits": [
        {
          "sha": "8c5cc444f5065d5fd8c74582db95c360e0e4a99f",
          "author": {
            "email": "33480590+TillRasmussen@users.noreply.github.com",
            "name": "TRasmussen"
          },
          "message": "Merge pull request #2 from HYCOM/master\n\nUpdate from upstream",
          "distinct": false,
          "url": "https://api.github.com/repos/NOAA-EMC/HYCOM-src/commits/8c5cc444f5065d5fd8c74582db95c360e0e4a99f"
        },
        . . .
      ]
    },
    "public": true,
    "created_at": "2022-09-09T19:58:45Z",
    "org": {
      "id": 37810995,
      "login": "NOAA-EMC",
      "gravatar_id": "",
      "url": "https://api.github.com/orgs/NOAA-EMC",
      "avatar_url": "https://avatars.githubusercontent.com/u/37810995?"
    }
  },
  . . .
]

Looks like coaps people from fsu

DeniseWorthen · 2022-09-13T17:57:25Z

@jkbk2004 The FSU folks do not have write permission to the emc fork. Only Bin Liu, Rahul, Jun, Dan Rosen and "the bot" have write permission.

jkbk2004 · 2022-09-13T18:07:48Z

@DeniseWorthen so we need to ask hafs to come with urgent pr to sync up hycom, right? But it sounds like they need to evaluate hycom code changes first.

DeniseWorthen · 2022-09-13T18:11:59Z

@jkbk2004 We do not want to update the hycom hash in our fork. Bin Liu will make a force push back to our emc fork to recover our history.

BinLiu-NOAA · 2022-09-13T18:32:26Z

The commit hash of 09bdf00 has now been forced pushed and restored in NOAA-EMC HYCOM-src fork.
https://github.com/NOAA-EMC/HYCOM-src

jiandewang · 2022-09-13T18:40:44Z

just made a fresh clone, this is what I have now for HYCOM:

(HEAD detached at 09bdf00) 09bdf00 Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (Update ufs-weather-model/develop with changes from gmtb/develop as of 2019/10/16 #1)
emc/develop 09bdf00 Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (Update ufs-weather-model/develop with changes from gmtb/develop as of 2019/10/16 #1)

is it suppose to point to emc/develop ?

UFS code location: /scratch1/NCEPDEV/climate/Jiande.Wang/MOM6-update/MOM6-update-20220902/Final/ufs-weather-model/

DeniseWorthen · 2022-09-13T18:57:34Z

@jiandewang When I do a fresh checkout of UWM, I get the hash for Hycom as 09bdf00. That is our current hash in the develop branch of UWM. The commit message for that hash is "Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (#1)".

jkbk2004 · 2022-09-13T19:02:22Z

I checked hycom source codes that we used to test against fresh clone. All looks good.

jiandewang · 2022-09-13T19:04:26Z

@jiandewang When I do a fresh checkout of UWM, I get the hash for Hycom as 09bdf00. That is our current hash in the develop branch of UWM. The commit message for that hash is "Add :: symbol to read from nems.configure.Required for ESMF 8bs20+. (#1)".

yes I got the same thing. What puzzled me is the location of the *
if you do a git branch -v under HYCOM-interface/HYCOM

(HEAD detached at 09bdf00) 09bdf00
emc/develop 09bdf00 Add :: symbol

what I mean is the * should located on emc/develop (note here * is showing as dot, but if you do on one of the machine, you will see the *)

jiandewang · 2022-09-13T19:05:41Z

I checked hycom source codes that we used to test against fresh clone. All looks good.

let me know when it's the time to do submodule switch

jkbk2004 · 2022-09-13T19:09:05Z

I checked hycom source codes that we used to test against fresh clone. All looks good.

let me know when it's the time to do submodule switch
@jiandewang please, go ahead to update submodule pointer and revert branch on gitmodules.

jiandewang · 2022-09-13T19:20:34Z

MOM6 submodule switched

DeniseWorthen and others added 3 commits August 26, 2022 20:25

update GNU to include s2swa tests

047e651

Merge branch 'ufs-community:develop' into feature/adds2swa_gnutests

994d92d

switch to MOM6 testing branch

cc2bb6c

Merge branch 'ufs-community:develop' into feature/adds2swa_gnutests

aa90e6e

Merge branch 'ufs-community:develop' into feature/update-MOM6-20220902

818865a

Merge pull request #4 from DeniseWorthen/feature/adds2swa_gnutests

b517576

Feature/adds2swa gnutests

add new BL_DATE

9c2faf2

jkbk2004 added Baseline Updates Current baselines will be updated. hera-gnu-BL labels Sep 12, 2022

BrianCurtis-NOAA removed hera-gnu-BL labels Sep 12, 2022

[AutoRT] hera.gnu Job Completed.

46ae1a8

on-behalf-of @ufs-community <brian.curtis@noaa.gov>

jkbk2004 added gaea-intel-BL labels Sep 12, 2022

BrianCurtis-NOAA removed gaea-intel-BL labels Sep 12, 2022

[AutoRT] hera.intel Job Completed.

a57e609

on-behalf-of @ufs-community <brian.curtis@noaa.gov>

revert MOM6 submodule

ad9b784

DeniseWorthen approved these changes Sep 13, 2022

View reviewed changes

binli2337 approved these changes Sep 13, 2022

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jkbk2004 approved these changes Sep 13, 2022

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jkbk2004 merged commit 1bba232 into ufs-community:develop Sep 13, 2022

DeniseWorthen mentioned this pull request Sep 13, 2022

update GNU to include s2swa tests #1388

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(1) update MOM6 to its main branch 20220902 commit (2) update GNU to include s2swa tests #1401

(1) update MOM6 to its main branch 20220902 commit (2) update GNU to include s2swa tests #1401

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(1) update MOM6 to its main branch 20220902 commit (2) update GNU to include s2swa tests #1401

(1) update MOM6 to its main branch 20220902 commit (2) update GNU to include s2swa tests #1401

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