Update submodules to ones that are based on cesm3_0_alpha04a #2853

ekluzek · 2024-10-30T17:30:46Z

Description of changes

Update the submodules to something close to cesm3_0_alpha04a. I needed to update cime and ccs_config beyond to get the PF Unit testing working.

Specific notes

Remove mct from submodules
Add mpi-serial to submodules
Update the PF unit testing to use the full ESMF library (which will enable wider testing), this also required bringing in NetCDF and PIO libraries which we shouldn't actively use but may allow us to do fewer stub modules for I/O.

Contributors other than yourself, if any: @jedwards4b

CTSM Issues Fixed (include github issue #):
Fixes #2640
Fixes #2375
Finishes resolving #2294

Are answers expected to change (and if so in what way)?
I'm actually not sure yet, I think possibly compsets with active CISM might

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 do regular and ctsm_sci
So far done PF UNIT testing and testing of two simple cases
I haven't tested this for LILIC and I wonder if it will fail

…requires PIO and NetCDF as a result

…ated beyond it as needed by PF UNIT testing, and ccs_config just updated to one beyond the previous one used by CTSM

…cesm30b04submodules

…nd share forward, and remove mct

ekluzek · 2024-10-30T17:33:07Z

@billsacks and @jedwards4b could you review this for the cmake changes I made for the PF unit testing? I learned more about cmake as a result of getting this to work, but I'd like to have it reviewed by the two of you with more knowledge/skill in using cmake.

jedwards4b

I would remove the lines in CMakeLists.txt that you have commented out, but otherwise LGTM.

billsacks

Thanks for getting this working @ekluzek! A couple of questions here....

src/CMakeLists.txt

ekluzek · 2024-10-30T21:35:26Z

OK, my suspicion about LILAC was correct, running the LILAC test I get a fail:

    Case dir: /glade/work/erik/ctsm_worktrees/external_updates/cime/scripts/LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac.20241030_152038_a3kydm
    Errors were:
        Building test for LILACSMOKE in directory /glade/work/erik/ctsm_worktrees/external_updates/cime/scripts/LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac.20241030_152038_a3kydm
        Traceback (most recent call last):
          File "/glade/work/erik/ctsm_worktrees/external_updates/cime/scripts/LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac.20241030_152038_a3kydm/./case.build", line 267, in <module>
            _main_func(__doc__)
          File "/glade/work/erik/ctsm_worktrees/external_updates/cime/scripts/LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac.20241030_152038_a3kydm/./case.build", line 226, in _main_func
            test = find_system_test(testname, case)(case)
          File "/glade/work/erik/ctsm_worktrees/external_updates/cime/CIME/utils.py", line 2272, in find_system_test
            mod = import_module(path)
          File "/glade/u/apps/derecho/23.09/opt/._view/yazo4iwystz7p2hxu5ukzrw3xa24ksen/lib/python3.10/importlib/__init__.py", line 126, in import_module
            return _bootstrap._gcd_import(name[level:], package, level)
          File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
          File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
          File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
          File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
          File "<frozen importlib._bootstrap_external>", line 883, in exec_module
          File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
          File "/glade/work/erik/ctsm_worktrees/external_updates/cime_config/SystemTests/lilacsmoke.py", line 28, in <module>
            from CIME.utils import run_cmd, run_cmd_no_fail, symlink_force, new_lid, safe_copy, append_testlog
        ImportError: cannot import name 'append_testlog' from 'CIME.utils' (/glade/work/erik/ctsm_worktrees/external_updates/cime/CIME/utils.py)

Waiting for tests to finish
FAIL LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac (phase SHAREDLIB_BUILD)
    Case dir: /glade/work/erik/ctsm_worktrees/external_updates/cime/scripts/LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.derecho_intel.clm-lilac.20241030_152038_a3kydm
Due to presence of batch system, create_test will exit before tests are complete.
To force create_test to wait for full completion, use --wait
test-scheduler took 7.439677476882935 seconds

… what's going on based on code review

ekluzek · 2024-10-31T19:44:06Z

I've fixed the LILAC problem between a minor update, and something I need to add to cime:

ESMCI/cime#4703

Now, I'm wondering what will happen with run_neon?

billsacks

Thanks for your explanations to my questions, @ekluzek ! I'm satisfied with this now.

…o CIME.status

…lid driver option

…m30b04submodules

ekluzek · 2024-11-04T18:06:01Z

Answers for aux_clm were identical on Derecho, but 36 tests on Izumi show answer changes that appear to be roundoff, but propagate in some fields:

ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput
ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC
ERI_D_Ld9_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-reduceOutput
ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm50Bgc.izumi_nag.clm-ciso
ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso
ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso--clm-matrixcnOn
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-flexCN_FUN
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-flexCN_FUN--clm-matrixcnOn
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-luna
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-noFUN_flexCN
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-noFUN_flexCN--clm-matrixcnOn
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-reduceOutput
ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-o3lombardozzi2015
ERP_D_Ld9.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-clm60cam7LndTuningModeLDust
ERP_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart
ERP_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart--clm-matrixcnOn_ignore_warnings
ERS_D.f10_f10_mg37.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup
ERS_D.f10_f10_mg37.I1850Clm60Sp.izumi_nag.clm-ExcessIceStreams
ERS_D_Ld5.f10_f10_mg37.I2000Clm50Fates.izumi_nag.clm-FatesCold
SMS.f10_f10_mg37.I2000Clm50BgcCrop.izumi_gnu.clm-crop
SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only
SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.izumi_gnu.clm-crop
SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.izumi_nag.clm-crop
SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd
SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-datm_bias_correct_cruv7
SMS_D_Ld3.f10_f10_mg37.I2000Clm60Bgc.izumi_nag.clm-HillslopeD
SMS_D_Ld5.f10_f10_mg37.I1850Clm45BgcCrop.izumi_nag.clm-crop
SMS_D_Ld5.f10_f10_mg37.I2000Clm50BgcCrop.izumi_nag.clm-irrig_alternate
SMS_D_Ld5.f10_f10_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesCold
SMS_D_Ld5.f45_f45_mg37.I2000Clm60Fates.izumi_nag.clm-FatesCold
SMS_D_Ld65.f10_f10_mg37.I2000Clm60BgcCrop.izumi_nag.clm-FireLi2024GSWP
SMS_D_Ld65.f10_f10_mg37.IHistClm60BgcCrop.izumi_nag.clm-cropMonthOutput--clm-RxCropCalsAdaptGGCMI
SMS_D_P48x1_Ld5.f10_f10_mg37.I2000Clm50BgcCrop.izumi_nag.clm-irrig_spunup
SMS_Ld5_D_P48x1.f10_f10_mg37.IHistClm50Bgc.izumi_nag.clm-monthly
SMS_Ld5_D_P48x1.f10_f10_mg37.IHistClm60Bgc.izumi_nag.clm-decStart
SMS_Ln9.f10_f10_mg37.I1850Clm45Bgc.izumi_gnu.clm-clm45cam4LndTuningModeZDustSoilErod

The mpi-serial tests are failing at the build step as well:

ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate (SHAREDLIB_BUILD NLCOMP)
ERS_D_Ld7_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropRs.izumi_intel.clm-decStart1851_noinitial (SHAREDLIB_BUILD NLCOMP)
ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold (SHAREDLIB_BUILD NLCOMP)
ERS_Lm13.f10_f10_mg37.I1850Clm60Bgc.izumi_intel.clm-monthly_matrixcn_fast_spinup (NLCOMP RUN)
ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-cropMonthlyNoinitial (SHAREDLIB_BUILD NLCOMP)
ERS_Lm40_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial (SHAREDLIB_BUILD NLCOMP)
ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial (SHAREDLIB_BUILD NLCOMP)
ERS_Ly20_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial (SHAREDLIB_BUILD NLCOMP)
ERS_Ly20_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial--clm-matrixcnOn (SHAREDLIB_BUILD NLCOMP)
ERS_Ly3_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_gnu.clm-cropMonthOutput (SHAREDLIB_BUILD NLCOMP)
ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-ciso_monthly (SHAREDLIB_BUILD NLCOMP)
ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-ciso_monthly--clm-matrixcnOn (SHAREDLIB_BUILD NLCOMP)
ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_intel.clm-cropMonthOutput (SHAREDLIB_BUILD NLCOMP)
ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_intel.clm-cropMonthOutput--clm-matrixcnOn_ignore_warnings (SHAREDLIB_BUILD NLCOMP)
SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA (SHAREDLIB_BUILD NLCOMP)
SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsROA (SHAREDLIB_BUILD NLCOMP)
SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_nag.clm-ptsRLA (SHAREDLIB_BUILD NLCOMP)
SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput (SHAREDLIB_BUILD NLCOMP)
SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60FatesRs.izumi_nag.clm-FatesCold (SHAREDLIB_BUILD NLCOMP)
SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL (SHAREDLIB_BUILD NLCOMP)
SMS_Ld5_Mmpi-serial.1x1_brazil.IHistClm60Bgc.izumi_gnu.clm-mimics (SHAREDLIB_BUILD NLCOMP)
SMS_Ly3_Mmpi-serial.1x1_numaIA.I2000Clm50BgcDvCropQianRs.izumi_gnu.clm-ignor_warn_cropMonthOutputColdStart (SHAREDLIB_BUILD NLCOMP)
SMS_Ly5_Mmpi-serial.1x1_brazil.IHistClm50BgcQianRs.izumi_intel.clm-newton_krylov_spinup (SHAREDLIB_BUILD NLCOMP)
SMS_Ly5_Mmpi-serial.1x1_smallvilleIA.IHistClm60BgcCropQianRs.izumi_gnu.clm-gregorian_cropMonthOutput (SHAREDLIB_BUILD NLCOMP)
SSPMATRIXCN_Ly5_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-ciso_monthly (SHAREDLIB_BUILD NLCOMP)

ekluzek · 2024-11-05T00:14:11Z

It looks like mpi-serial works up to the following set of submodules:

ccs_config_cesm1.0.0
cime6.0.249
share1.0.19
cmeps0.14.17
(Note, cdeps and pio are the latest versions used in this PR, not the previous ctsm5.3.009 ones)

Beyond that it starts breaking. The set I should use together to get working are the cesm3_0_alpha02a externals:

ccs_config_cesm1.0.0
cime6.1.0
share1.1.2
cmeps1.0.2

cesm3_0_alpha03b has the next set of important updates for ccs_config and cime. The next set of updates are the recent ones that were important in getting PFunit tests to work.

NOTE: The top set is still showing changes to answers on Izumi, so the change in answers must be between the ctsm5.3.009 externals and the ones listed above.

jedwards4b · 2024-11-05T14:59:39Z

Hi Erik,

I found that the configure script was not included in the mpi-serial distribution, I have added it in ESMCI/mpi-serial#30. I think that this will allow you to update to the latest tags.

ekluzek · 2024-11-05T16:48:52Z

Excellent, thanks @jedwards4b!

Yeah, that is one of the things I saw, I thought it might be generated as part of the build process. But, obviously not. Thanks for figuring that out. I"ll try with that branch and make sure it works.

ekluzek added 7 commits October 30, 2024 01:47

Get the PF UNIT tests working using the full ESMF library which also …

721ce0e

…requires PIO and NetCDF as a result

Update submodules to something towards cesm3_0_alpha04a with cime upd…

31070e6

…ated beyond it as needed by PF UNIT testing, and ccs_config just updated to one beyond the previous one used by CTSM

Merge branch 'cesm3_0_beta04_changes' of github.com:ESCOMP/CTSM into …

4a3a6d7

…cesm30b04submodules

Match cesm3_0_alpha04a submodules closer, move ccs_config back one, a…

326d8dd

…nd share forward, and remove mct

Update git submodule directories

c3a4d8b

Delete mct as no longer needed

c0d4080

Update ccs_config as required for the build with this version of cime

d7cb182

ekluzek added enhancement new capability or improved behavior of existing capability priority: high High priority to fix/merge soon, e.g., because it is a problem in important configurations code health improving internal code structure to make easier to maintain (sustainability) labels Oct 30, 2024

ekluzek added this to the cesm3_0_beta05 milestone Oct 30, 2024

ekluzek self-assigned this Oct 30, 2024

ekluzek requested review from jedwards4b and billsacks October 30, 2024 17:31

jedwards4b approved these changes Oct 30, 2024

View reviewed changes

billsacks reviewed Oct 30, 2024

View reviewed changes

src/CMakeLists.txt Outdated Show resolved Hide resolved

src/CMakeLists.txt Show resolved Hide resolved

Remove commented out code and log message and add some comments about…

f472f6d

… what's going on based on code review

billsacks approved these changes Oct 31, 2024

View reviewed changes

CIME update at cime6.1.11 requires moving CIME.utils append_testlog t…

1c60312

…o CIME.status

This was linked to issues Nov 1, 2024

use of mct_mod is deprecated #2294

Open

Update submodules to cesm3_0_beta04 versions #2640

Open

Add a comment to note that MCTID is just the component ID number

94dccba

This was linked to issues Nov 1, 2024

Stop building esmf_wrf_timemgr for unit tests; instead use the actual ESMF library #2375

Open

LILAC option in build-namelist for --driver doesn't correctly test that lnd_frac is set #2857

Closed

ekluzek added 3 commits November 2, 2024 01:04

Add test for valid driver option

ae600d5

Some adjustments to make lilac clearer, also add checking for an inva…

d38b3a5

…lid driver option

Merge remote-tracking branch 'escomp/cesm3_0_beta04_changes' into ces…

eba0edb

…m30b04submodules

ekluzek added 2 commits November 2, 2024 02:14

Update ccs_config

933abae

Merge commit '933abaeac' into cesm30b04submodules

ed27a50

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Update submodules to ones that are based on cesm3_0_alpha04a #2853

Update submodules to ones that are based on cesm3_0_alpha04a #2853

ekluzek commented Oct 30, 2024 •

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ekluzek commented Nov 5, 2024

Update submodules to ones that are based on cesm3_0_alpha04a #2853

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Update submodules to ones that are based on cesm3_0_alpha04a #2853

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ekluzek commented Oct 30, 2024 • edited Loading

Description of changes

Specific notes

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