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@ekluzek ekluzek commented Nov 11, 2025

Description of changes

Update submodules to cesm3_0_alpha07h levels. And bring in a few things beyond that level with useful things to bring in. cesm3_0_alpha07h is going to become cesm3_0_beta07 shortly at this point.

An important part of this is the git-fleximod update to v1.1.1 which brings in a nice formatting update to the status option. And an important bug fix where running git-fleximod could overwrite changes in the submodules in your clone.

Specific notes

Contributors other than yourself, if any: @billsacks @wwieder

CTSM Issues Fixed (include github issue #):
Fixes #3599
Fixes #3483 (actually fixed in the previous Carbon isotope PR's)

Are answers expected to change (and if so in what way)? No

Any User Interface Changes (namelist or namelist defaults changes)? No

Does this create a need to change or add documentation? Did you do so? No No

Testing performed, if any: will run aux_clm, ctsm_sci and fates on Derecho/Izumi

…ght be useful, as well as a cmeps branch which will be useful and to test that it works in aux_clm
@ekluzek ekluzek added this to the cesm3_0_beta08 milestone Nov 11, 2025
@ekluzek ekluzek self-assigned this Nov 11, 2025
@ekluzek ekluzek added enhancement new capability or improved behavior of existing capability code health improving internal code structure to make easier to maintain (sustainability) labels Nov 11, 2025
@ekluzek ekluzek added the bfb bit-for-bit label Nov 11, 2025
@github-project-automation github-project-automation bot moved this to Ready to start (or start again) in CTSM: Upcoming tags Nov 13, 2025
@wwieder wwieder moved this from Ready to start (or start again) to In progress - master in CTSM: Upcoming tags Nov 13, 2025
@wwieder wwieder moved this from In progress - master to In progress - b4b-dev in CTSM: Upcoming tags Nov 13, 2025
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wwieder commented Nov 13, 2025

@ekluzek, since this is ready to go and going to b4b dev, can you just go ahead a merge this when you're ready. I've put it to the top of the b4b upcoming tags that are in progress.

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ekluzek commented Nov 22, 2025

Actually, I've been running into issues here, so it isn't ready to go.

One issue is that the CISM tag changes answers, so we'll bring it in seperately.

…rs, because of the change in the 4km GRIS grid
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ekluzek commented Nov 22, 2025

These tests showed a change in answers because of CISM:

ERI_D.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningModeLDust
ERP_D_Ld5.f10_f10_mg37.I1850Clm50BgcCropG.derecho_gnu.clm-glcMEC_changeFlags
ERP_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam6LndTuningMode
ERP_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningModeLDust
ERP_D_Ld9.ne30pg3_t232.IHistClm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningModeLDust
ERP_P256x2_D_Ld5.f19_g17_gris4.I1850Clm50BgcCropG.derecho_intel.clm-glcMEC_increase
ERP_P64x2_D_Ld10.f10_f10_mg37.IHistClm50SpG.derecho_intel.clm-glcMEC_decrease--clm-nofireemis
ERP_P64x2_Ld396.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings             EXPECTED POSSIBILITY
ERS_D_Ld12.f10_f10_mg37.I1850Clm50BgcCropG.derecho_intel.clm-glcMEC_spunup_inc_dec_bgc
ERS_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode
ERS_Ly3_P64x2.f10_f10_mg37.IHistClm50BgcCropG.derecho_intel.clm-cropMonthOutput
SMS_Lm1.ne30pg3_t232.I1850Clm60BgcCropCrujraG.derecho_intel.clm-clm60cam7LndTuningMode
SMS_Lm1.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode
SMS_Ly3.f10_f10_mg37.I1850Clm50SpG.derecho_intel.clm-glcMEC_long--clm-nofireemis

And one failing test that's unexpected:

ERR_Ld7.f10_f10_mg37.IHistClm60BgcCrop.derecho_gnu.drv-interim_restart (NLCOMP RUN)

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ekluzek commented Nov 22, 2025

This is also updated to a cime based off of cime6.1.137, as updated to cime6.1.142 had cases die in setup, which look like is due to the namelist case change that comes in with cime6.1.138.

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This is also updated to a cime based off of cime6.1.137, as updated to cime6.1.142 had cases die in setup, which look like is due to the namelist case change that comes in with cime6.1.138.

@ekluzek - can you tell me what failures you're seeing that appear due to cime6.1.138? That was a CIME tag that I made, so if you're seeing issues with it, I'd like to understand these and look into them. (I'm wondering if there's some externals difference between what you're testing and what I tested with, or if there's some issue that turns up in some test cases that I didn't see in my more limited testing of that change?)

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ekluzek commented Nov 23, 2025

@ekluzek - can you tell me what failures you're seeing that appear due to cime6.1.138? That was a CIME tag that I made, so if you're seeing issues with it, I'd like to understand these and look into them.

Thanks for asking @billsacks . My comment came early enough that I hadn't narrowed down exactly what was going on. But from looking at cime tags I was most suspicious of that one. And tried the one before it which has also been in CESM testing and found it to work. I also found I needed a cime change on a branch I had -- but I thought my testing problems also had something else going on besides that. But I'm going back a little more carefully I updated my branch to 6.1.137 and found it to work. And it worked with an update to 6.1.143 as well. At least for the one test I did.

So bottom line is that 6.1.137 looks to be fine right now. But I might learn something new after I run all the testing.

Sorry for laying blame on your tag when it was something else. I did that before I had absolutely verified it, but it was my guess at the time

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@ekluzek - okay, thanks for the follow-up. I'm glad to hear that it looks like cime6.1.138 is probably okay: that turned out to be a trickier set of changes than I had originally anticipated, so I'm really hoping that these changes haven't caused some new subtle issue that would add even more trickiness! Do let me know if you are seeing some issues with it in full testing.

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ekluzek commented Nov 24, 2025

There are 22 tests on Derecho that are still in the queue. And several unexpected fails to look into:

ERI_D_Ld9.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_intel.clm-FatesColdSatPhenCamLndTuningMode      (NLCOMP RUN)
(COMPARE_base_hybrid)
ERP_D_Ld5.f10_f10_mg37.I1850Clm50BgcCropG.derecho_gnu.clm-glcMEC_changeFlags    (NLCOMP RUN)
ERP_P256x2_D_Ld5.f19_g17_gris4.I1850Clm50BgcCropG.derecho_intel.clm-glcMEC_increase     (NLCOMP RUN)
ERP_P64x2_D_Ld10.f10_f10_mg37.IHistClm50SpG.derecho_intel.clm-glcMEC_decrease--clm-nofireemis   (NLCOMP RUN)
ERR_Ld7.f10_f10_mg37.IHistClm60BgcCrop.derecho_gnu.drv-interim_restart  (NLCOMP RUN)
ERS_D_Ld12.f10_f10_mg37.I1850Clm50BgcCropG.derecho_intel.clm-glcMEC_spunup_inc_dec_bgc  (NLCOMP RUN)
ERS_Ly3_P64x2.f10_f10_mg37.IHistClm50BgcCropG.derecho_intel.clm-cropMonthOutput (NLCOMP RUN)
LII2FINIDATAREAS_D_P256x2_Ld1.f09_t232.I1850Clm60BgcCrop.derecho_intel.clm-default--clm-matrixcnOn_ignore_warnings  (NLCOMP RUN)
PEM_D_Ld20.5x5_amazon.I2000Clm50FatesRs.derecho_intel.clm-FatesColdSeedDisp     (NLCOMP COMPARE_base_modpes TPUTCOMP)
REP_P64x2_Ld396.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings    (NLCOMP COMPARE_base_rep2
SMS_Ly3.f10_f10_mg37.I1850Clm50SpG.derecho_intel.clm-glcMEC_long--clm-nofireemis        (NLCOMP RUN)

One Izumi, all of the tests failed at runtime, so that needs to be figured out as well.

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ekluzek commented Nov 30, 2025

Most of the fails are due to a dependency between the latest CISM and ccs_config. So I need to back up ccs_config a little bit to 1.0.61 in order to work with the older cism.

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ekluzek commented Nov 30, 2025

The ERR test fails because it's looking for the wrong cpl rpointer file. The LIIFINIDATAREAS test fails as it can't find bare soil, which is wierd. FATES SeedDisp test fails with a difference in two seed fields. The top ERI test fails with a floating invalid in taking the difference between mlai2t(:,1) vs. mlai2t(:,2) at the end or readMonthlyVegetation.

So the ERR test has to do with the cmeps update for rpointer file handling. I'm not sure about the other two.

@ekluzek ekluzek changed the title Update submodules to cesm3_0_alpha07g levels b4b: Update submodules to cesm3_0_alpha07g levels Dec 1, 2025
5796799a6 Bump to 1.1.1
8b1259b8b Merge pull request ESCOMP#90 from ESMCI/add_doctests
bf8ab4832 remove CI pylint test
5a3bc5296 update wrapt
53d434cfa update wrapt
edc3d24f2 update wrapt
2743863dd update wrapt
912e30985 update wrapt
34432fd19 update wrapt
df8ec2b67 more updates
4093354eb update pre-commit-hooks
95aee9eb6 update pre-commit-hooks
a38f5c742 update pre-commit-hooks
5e4a1234c update pre-commit-hooks
074c63a76 update pre-commit-hooks
ce6957e09 update pre-commit-hooks
19e077004 update pre-commit-hooks
2b16d9d3c update pre-commit-hooks
c8ee10dd3 update pre-commit-hooks
7fc5fad92 fix doctest in cli.py
6ca52ff46 add more doctests
5a6fd5a48 add more doctests
301168779 add doctests to workflow
c68eec463 add pre-commit test to workflow
309d98645 pre-commit cleanup
6d1216245 add some doctests
493940fcc Merge pull request ESCOMP#89 from ESMCI/fix/overwrite_local_mod
cb8c95bb2 fix the 3rd test
86590829b add a test of 3rd scenario
351a2399d add a test of 2nd scenario
b901ff535 add a test
1c8b80582 remove commented code
eab580b5a fix issue with overwritting local mods
9d0d74a0d Bump to 1.1.0
bce9bf76e Merge pull request ESCOMP#87 from billsacks/fix_modified_output
a8d24c0d1 Fix imports to hopefully work in automated testing
9d63e762e Normalize whitespace in tests
7f4b9a470 Fix alignment of tree indicators
74ef626d9 Allow suppressing details of local mods in status output
7642150c4 Indent child submodules with a nice tree-like output
f40536830 Fix status output when there are local modifications
d4ebd3998 Bump to 1.0.3
f4d1647a4 Merge pull request ESCOMP#85 from nusbaume/hash_fetch
5ae52f677 Fetch full history if 'fxtag' is a hash.
22026d29b Merge pull request ESCOMP#81 from ESMCI/fxtag_documentation_update
1ab63bc78 update doc to correct fxtag
5a406d3ac Bump to 1.0.2
e15942e7f Merge pull request ESCOMP#78 from ESMCI/py38_compatibility_better_warnings
5d3af8015 cleanup
4652bc3ac add test
01e297552 improve handling of tag not found
0ca1644c5 improve tag not found error message
67a0ca91b remove commented code
2deb85249 fix issue in find_root_dir
49ed14d01 fix help option
b07e1bd93 py 3.8 compatibility
cbf30d854 Bump to 1.0.1
5f54da7fb Merge pull request ESCOMP#76 from ESMCI/fix_sparse_restore
c24b726ea response to copilot review
3bc940457 fix issue 75 sparse checkout restore
8d3cdea1d Bump to 1.0.0
695811bf2 add README.md to distribution
5f7a322b0 Merge pull request ESCOMP#73 from alperaltuntas/async_clone
13845fc74 implement asynchronous submodule update
2be5073ad Merge pull request ESCOMP#71 from ESMCI/fix_test_issue_update_flag
9597cc68f use file if defined
7027a4297 append README.md to help contents
98599dc90 add README.md contents to help
5f05c45c1 Bump to 0.9.4
574d2b0e3 Merge pull request ESCOMP#68 from ESMCI/fix_nonfleximod_submodule_checkout
004194fd4 if not fxtag is available tag=hash

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 5796799a6c414bed35bb473fab0e5b6c2257a950
…ubmodules_cesm30alpha07g

I'm not sure why but it created conflicts, which I resolved by accepting
incoming. I didn't find a way to batch doing that, so did it in VS Code
for each file.

 Conflicts:
	.lib/git-fleximod/git_fleximod/cli.py
	.lib/git-fleximod/git_fleximod/git_fleximod.py
	.lib/git-fleximod/git_fleximod/gitinterface.py
	.lib/git-fleximod/git_fleximod/submodule.py
	.lib/git-fleximod/pyproject.toml
	.lib/git-fleximod/tbump.toml
	.lib/git-fleximod/tests/conftest.py
	.lib/git-fleximod/tests/test_c_required.py
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ekluzek commented Dec 3, 2025

From the CSEG meeting yesterday there are some status readability changes for gitr-fleximod in v1.1.0 and a fix to a problem from v1.0.1 in v1.1.1 so we should also update it. We currently have v1.0.2 so we especially want to bring that fix in. The problem will overwrite changes in submodules with modified code, so an especially bad one.

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@ekluzek I could approve, but I am not familiar with these codes:

  • seems like git-fleximod stuff mostly
  • also do you need a new line in .git-blame-ignore-revs, because I sense that many of the mods are due to reformatting by black or lint

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A follow-up thought:
Do we allow submodule updates merged to b4b-dev? Does testing confirm that this is b4b?

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ekluzek commented Dec 3, 2025

A follow-up thought:
Do we allow submodule updates merged to b4b-dev? Does testing confirm that this is b4b?

Good questions. We have allowed submodule updates on b4b-dev, but with extra testing. The changes are extensive enough that we could make this a tag on master though. So far my testing has shown that this is b4b.

Also the changes to git-fleximod dominate -- but that's just because git-fleximod is a subtree. It's actually just updating it to v1.1.1 so not really something for us to look at the differences in detail.

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ekluzek commented Dec 3, 2025

@ekluzek I could approve, but I am not familiar with these codes:

  • seems like git-fleximod stuff mostly
  • also do you need a new line in .git-blame-ignore-revs, because I sense that many of the mods are due to reformatting by black or lint

The first one I talk about above. So neither of us need to know much about git-fleximod.

We don't need new lines in the git blame ignore because the black format commits are only for git-fleximod and don't apply to general CTSM code where we do want to track the black commits.

@ekluzek ekluzek changed the title b4b: Update submodules to cesm3_0_alpha07g levels b4b: Update submodules to cesm3_0_beta07 levels Dec 4, 2025
@ekluzek ekluzek added the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Dec 4, 2025
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ekluzek commented Dec 4, 2025

I've sent all the testing for Derecho/Izumi: aux_clm, fates, ctsm_sci. So far it looks fine, but a few more need to finish

One test failed, but I think this is expected:

ERI_Ld9.f09_t232.I2000Clm60BgcCropCrujra.derecho_intel.clm-default

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ekluzek commented Dec 4, 2025

It looks like the ERI test is just a reappearance of this problem that was dealt with on the alpha ctsm5.4 branch, because the IC file is from ctsm5.4.

#3576 (comment)

So I'm calling this handled for the purpose of this PR.

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