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Merge tag 'ctsm5.3.043' into merge-master-20250509
Merge b4bdev 20250509 Updates to the b4b-dev branch since its last merge to master (PRs ESCOMP#3091 ESCOMP#3092), as shown by git log: - Merge pull request Update docs infrastructure ESCOMP#2809 from samsrabin/update-docs-builder-2 Update docs infrastructure - Merge pull request Update externals to cesm3_0_alpha06c ESCOMP#3106 from ekluzek/update_to_alpha06c Update externals to cesm3_0_alpha06c - Merge pull request User control over snow thermal conductivity scheme over glaciers ESCOMP#3072 from wwieder/JordanGlacier User control over snow thermal conductivity scheme over glaciers
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‎.gitmodules‎

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[submodule "fates"]
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path = src/fates
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url = https://github.com/NGEET/fates
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fxtag = sci.1.82.3_api.39.0.0
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fxtag = sci.1.83.1_api.39.0.0
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fxrequired = AlwaysRequired
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# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
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fxDONOTUSEurl = https://github.com/NGEET/fates

‎bld/namelist_files/namelist_definition_ctsm.xml‎

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</entry>
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<entry id="fates_electron_transport_model" type="char*256" category="physics"
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group="elm_inparm" valid_values="FvCB1980,JohnsonBerry2021" value="FvCB1980">
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group="clm_inparm" valid_values="FvCB1980,JohnsonBerry2021" value="FvCB1980">
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Set the FATES electron transport model to either Johnson-Berry 2021 or
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Farquhar von Caemmerer and Berry 1980 (FvCB1980).
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</entry>
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<entry id="fates_radiation_model" type="char*256" category="physics"

‎cime_config/testdefs/ExpectedTestFails.xml‎

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</phase>
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</test>
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<test name="PEM_D_Ld20.f10_f10_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdSeedDisp">
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<phase name="COMPARE_base_modpes">
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<test name="PEM_D_Ld20.5x5_amazon.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdSeedDisp">
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<phase name="RUN">
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<status>FAIL</status>
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<issue>FATES#1089</issue>
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<issue>#3097</issue>
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</phase>
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</test>
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‎cime_config/testdefs/testlist_clm.xml‎

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<option name="comment">Ensure functionality of the tree damage option in FATES</option>
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</options>
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</test>
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<test name="ERS_D_Ld20" grid="f45_f45_mg37" compset="I2000Clm60FatesRs" testmods="clm/FatesColdElecTransJB">
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<machines>
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<machine name="derecho" compiler="gnu" category="fates"/>
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</machines>
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<options>
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<option name="wallclock">00:20:00</option>
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<option name="comment">Ensure functionality of the JohnsonBerry2021 option in FATES</option>
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</options>
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</test>
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<test name="ERI_D_Ld20" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTwoStream">
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<machines>
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<machine name="derecho" compiler="intel" category="fates"/>

‎cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm‎

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hist_ndens = 1
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hist_fincl1 = 'FATES_TLONGTERM',
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'FATES_TGROWTH','FATES_SEEDS_IN_GRIDCELL_PF','FATES_SEEDS_OUT_GRIDCELL_PF','FATES_NCL_AP',
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'FATES_NPATCH_AP','FATES_VEGC_AP','FATES_SECONDARY_ANTHRODISTAGE_AP','FATES_SECONDARY_AREA_AP',
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'FATES_NPATCH_AP','FATES_VEGC_AP','FATES_SECONDARY_AREA_ANTHRO_AP','FATES_SECONDARY_AREA_AP',
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'FATES_FUEL_AMOUNT_APFC','FATES_STOREC_TF_USTORY_SZPF','FATES_STOREC_TF_CANOPY_SZPF',
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'FATES_CROWNAREA_CLLL','FATES_ABOVEGROUND_MORT_SZPF',
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'FATES_ABOVEGROUND_PROD_SZPF','FATES_NPLANT_SZAP','FATES_NPLANT_CANOPY_SZAP',
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'FATES_PARSUN_CL','FATES_PARSHA_CL','FATES_LAISUN_CLLL','FATES_LAISHA_CLLL','FATES_LAISUN_CLLLPF',
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'FATES_LAISHA_CLLLPF','FATES_PARPROF_DIR_CLLLPF','FATES_PARPROF_DIF_CLLLPF','FATES_LAISUN_CL','FATES_LAISHA_CL',
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'FATES_PARPROF_DIR_CLLL','FATES_PARPROF_DIF_CLLL','FATES_NET_C_UPTAKE_CLLL','FATES_CROWNFRAC_CLLLPF',
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'FATES_LBLAYER_COND_AP','FATES_STOMATAL_COND_AP','FATES_TLONGTERM','FATES_PRIMARY_AREA_AP','FATES_NPP_LU',
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'FATES_GPP_LU'
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'FATES_LBLAYER_COND_AP','FATES_STOMATAL_COND_AP','FATES_TLONGTERM','FATES_PRIMARY_AREA_AP','FATES_NPP_LU','FATES_GPP_LU',
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'FATES_SEED_BANK_PF','FATES_UNGERM_SEED_BANK_PF','FATES_SEEDLING_POOL_PF','FATES_SEEDS_IN_PF','FATES_SEEDS_IN_LOCAL_PF',
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'FATES_SAPWOOD_AREA_SZPF','FATES_CANOPYAREA','FATES_NCL','FATES_PATCHAREA','FATES_PRIMARY_AREA','FATES_SCORCH_HEIGHT_PF',
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'FATES_SECONDARY_AREA_ANTHRO','FATES_SECONDARY_AREA','FATES_ZSTAR'

‎cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/include_user_mods‎

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../FatesCold

‎cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/user_nl_clm‎

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fates_electron_transport_model='JohnsonBerry2021'

‎doc/ChangeLog‎

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===============================================================
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Tag name: ctsm5.3.043
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Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
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Date: Fri 09 May 2025 12:28:17 PM MDT
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One-line Summary: Merge b4b-dev
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Purpose and description of changes
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----------------------------------
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Updates to the b4b-dev branch since its last merge to master (PRs #3091 #3092), as shown by git log:
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- Merge pull request Update docs infrastructure #2809 from samsrabin/update-docs-builder-2
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Update docs infrastructure
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- Merge pull request Update externals to cesm3_0_alpha06c #3106 from ekluzek/update_to_alpha06c
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Update externals to cesm3_0_alpha06c
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- Merge pull request User control over snow thermal conductivity scheme over glaciers #3072 from wwieder/JordanGlacier
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User control over snow thermal conductivity scheme over glaciers
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Significant changes to scientifically-supported configurations
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--------------------------------------------------------------
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Does this tag change answers significantly for any of the following physics configurations?
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(Details of any changes will be given in the "Answer changes" section below.)
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[Put an [X] in the box for any configuration with significant answer changes.]
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[ ] clm6_0
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[ ] clm5_0
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[ ] ctsm5_0-nwp
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[ ] clm4_5
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Bugs fixed
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----------
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List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
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Resolves #2818 Update doc-builder
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Resolves #3098 st-archive issues in ctsm5.3.041
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Resolves #3071 Opt to use Jordan1991 over glacier land
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Resolves #3080 Lake snow thermal conductivity hard coded to Jordan
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Notes of particular relevance for users
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---------------------------------------
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Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
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Introduce user control over snow thermal conductivity scheme over glaciers
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Changes to documentation:
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#2809 updates docs infrastructure
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Testing summary:
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----------------
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[PASS means all tests PASS; OK means tests PASS other than expected fails.]
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regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
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derecho ----- OK
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izumi ------- OK
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Answer changes
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--------------
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Changes answers relative to baseline: No
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Other details
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-------------
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List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
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#3106 updates submodules to cesm3_0_alpha06c
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Pull Requests that document the changes (include PR ids):
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https://github.com/ESCOMP/ctsm/pull/3123
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===============================================================
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===============================================================
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Tag name: ctsm5.3.042
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Originator(s): glemieux (Gregory Lemieux, LBNL, [email protected])
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Date: Thu May 8 16:15:48 MDT 2025
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One-line Summary: Update FATES tag, tests and address namelist option bug
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Purpose and description of changes
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----------------------------------
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This pull request updates the FatesColdAllVars test list due to changes in the FATES
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history output associated with ngeet/fates#1252, which is coordinated with this update.
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A bug in which the incorrect control variable was being sent to FATES for a recently
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added namelist options has been addressed. The NEON-FATES-NIWO tests have also been
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addressed through the update of the FATES tag which includes fixes brought in with
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ngeet/fates#1376.
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Significant changes to scientifically-supported configurations
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--------------------------------------------------------------
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Does this tag change answers significantly for any of the following physics configurations?
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(Details of any changes will be given in the "Answer changes" section below.)
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[Put an [X] in the box for any configuration with significant answer changes.]
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[ ] clm6_0
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[ ] clm5_0
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[ ] ctsm5_0-nwp
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[ ] clm4_5
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Bugs fixed
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----------
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List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
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- [Issue #3052: Update FatesColdAllVars history output with recent additions](https://github.com/ESCOMP/CTSM/issues/3052)
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- [Issue #3038: NEON-FATES-NIWO test in aux_clm fails RUN](https://github.com/ESCOMP/CTSM/issues/3038)
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- [Issue #3062: Incorrect value being set for FATES electron transport namelist option](https://github.com/ESCOMP/CTSM/issues/3062)
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Notes of particular relevance for developers:
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---------------------------------------------
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Changes to tests or testing:
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The PEM seed dispersal test is now failing RUN, where it was previously failing COMPARE_base_modpes.
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This has been added to the expected failures and has been documented in a new issue, [#3097](https://github.com/ESCOMP/CTSM/issues/3097).
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This issue is associated with updates that came in previously with ctsm5.3.041.
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Testing summary:
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----------------
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regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
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derecho ----- OK
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izumi ------- OK
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fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
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derecho ----- OK
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izumi ------- OK
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Notes:
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- All tests resulted in expected st_archive exception due to known issue [#3098](https://github.com/ESCOMP/CTSM/issues/3098)
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- Due to permission issues, the izumi aux_clm tests were run against ctsm5.3.040 baselines. This was deemed acceptable since ctsm5.3.041 is a b4b tag
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Answer changes
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--------------
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Changes answers relative to baseline: Yes, but only for FATES tests
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This is due to updating the fates tag which includes a number of bug fixes and science updates
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Other details
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-------------
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List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
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fates: sci.1.82.3_api.39.0.0 -> sci.1.83.1_api.39.0.0
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Pull Requests that document the changes (include PR ids):
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(https://github.com/ESCOMP/ctsm/pull)
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https://github.com/ESCOMP/CTSM/pull/3058
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https://github.com/ESCOMP/CTSM/pull/3063
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https://github.com/NGEET/fates/pull/1252
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https://github.com/NGEET/fates/pull/1376
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===============================================================
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===============================================================
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Tag name: ctsm5.3.041
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Originator(s): samrabin (Sam Rabin, UCAR/TSS)
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Date: Fri Apr 25 08:02:37 MDT 2025

‎doc/ChangeSum‎

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Tag Who Date Summary
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============================================================================================================================
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ctsm5.3.043 slevis 05/09/2025 Merge b4b-dev
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ctsm5.3.042 glemieux 05/08/2025 Update FATES tag, tests and address namelist option bug
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ctsm5.3.041 samrabin 04/25/2025 Merge b4b-dev to master
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ctsm5.3.040 samrabin 04/15/2025 Update ctsm_pylib to 3.13.2
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ctsm5.3.039 afoster 04/14/2025 Create driver data structure for SP mode

‎src/fates‎

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