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ctsm5.3.020: Merge b4b-dev 2025-01-16 #2938

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merged 50 commits into from
Jan 17, 2025
Merged

ctsm5.3.020: Merge b4b-dev 2025-01-16 #2938

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e15789d
Delete unused hist_add_subscript method (no references in the CTSM repo)
johnpaulalex Jun 14, 2023
ecdddf3
Remove data only used by hist_add_subscript
johnpaulalex Jun 21, 2023
b85efc1
Doc that masterlist's actflag is only set for primary history tape in…
johnpaulalex Jun 21, 2023
a3a25a5
Merge branch 'master' into remove_unused
ekluzek Aug 10, 2023
89e9f32
Update WhatsNewInCTSM5.3.md
samsrabin Sep 25, 2024
a5506fc
First stab at the submodules needed for the rpointer changes, this do…
ekluzek Dec 5, 2024
5d8a23d
Update to latest cime with a new rpointer fix
ekluzek Dec 5, 2024
63fef2f
Merge branch 'add_timestamp_to_rpointers' into cesm3_0_beta05_submodules
ekluzek Dec 5, 2024
c0bca6b
Merge remote-tracking branch 'jedwards4b/add_timestamp_to_rpointers' …
ekluzek Dec 17, 2024
dd534e8
Update for cdeps
ekluzek Dec 17, 2024
20a8772
Merge tag 'ctsm5.3.016' into cesm3_0_beta05_submodules
ekluzek Dec 21, 2024
e06a33c
Update to latest from cesm3_0_alpha05c planned tags page, the cime up…
ekluzek Dec 21, 2024
fe0ec28
Code review responces, timemgr_restart is NO longer done instead of t…
ekluzek Dec 21, 2024
3b8c132
Add comments about the ordering of the stop and restart alarms
ekluzek Dec 21, 2024
f10b014
Merge tag 'branch_tags/tmp-241219.n01.ctsm5.3.016' into merge-master-…
slevis-lmwg Dec 30, 2024
d4855ca
Merge pull request #2918 from slevis-lmwg/merge-master-20241230
slevis-lmwg Dec 30, 2024
f6bf737
Update submodules to latest slated for the cesm3_0_beta05 tag
ekluzek Jan 4, 2025
1a7b773
Merge branch 'b4b-dev' into cesm3_0_beta05_submodules
ekluzek Jan 4, 2025
cbe6109
Back up mosart and rtm, so it doesn't bring in answer changes
ekluzek Jan 5, 2025
2fbbae4
Merge branch 'cesm3_0_beta05_submodules' of github.com:ekluzek/CTSM i…
ekluzek Jan 5, 2025
adebf76
Update cime with a fix for SSP issues
ekluzek Jan 6, 2025
730bebe
Changes to get the LILACSMOKE test to work. Pass current time down to…
ekluzek Jan 6, 2025
193f844
Bug fix for izumi nag tests to pass
slevis-lmwg Jan 7, 2025
d59162c
Merge pull request #2926 from slevis-lmwg/fix_izumi_nag_in_b4bdev
ekluzek Jan 7, 2025
a322e75
Fix the mizuRoute tag, and bring in one more cime update for SRCROOT …
ekluzek Jan 9, 2025
b78e56a
Merge branch 'cesm3_0_beta05_submodules' of github.com:ekluzek/CTSM i…
ekluzek Jan 9, 2025
d19a679
Add submodule directory updates
ekluzek Jan 9, 2025
1224d97
Merge remote-tracking branch 'escomp/b4b-dev' into cesm3_0_beta05_sub…
ekluzek Jan 9, 2025
b867a3e
Merge tag 'ctsm5.3.017' into b4b-dev
ekluzek Jan 13, 2025
9c4d3dc
Merge pull request #2931 from ekluzek/update_to_17
ekluzek Jan 13, 2025
7b88335
Merge remote-tracking branch 'escomp/b4b-dev' into cesm3_0_beta05_sub…
ekluzek Jan 13, 2025
680833a
Merge pull request #2912 from ekluzek/cesm3_0_beta05_submodules
ekluzek Jan 14, 2025
24660a7
Merge branch 'b4b-dev' into remove_unused
ekluzek Jan 15, 2025
0d44483
Merge remote-tracking branch 'escomp/b4b-dev' into remove_unused
ekluzek Jan 15, 2025
6fddf3c
Merge pull request #2022 from johnpaulalex/remove_unused
ekluzek Jan 15, 2025
de32263
Merge remote-tracking branch 'escomp/b4b-dev' into hist_doc_master
ekluzek Jan 15, 2025
2dca24c
Merge pull request #2035 from johnpaulalex/hist_doc_master
ekluzek Jan 16, 2025
6e2f046
Merge pull request #2789 from samsrabin/update-ctsm53-release-notes
ekluzek Jan 16, 2025
0b74069
Remove expected build failures related to mpi-serial (issue 2916)
samsrabin Jan 16, 2025
598b546
Add aux_clm_mpi_serial test suite.
samsrabin Jan 16, 2025
d93f8a8
Add an expected failure due to ESCOMP/CTSM#2913.
samsrabin Jan 16, 2025
0ec2493
Merge pull request #2937 from samsrabin/mpi-serial-test-tweaks
samsrabin Jan 16, 2025
6d1a0e0
[BROKEN] Merge tag 'ctsm5.3.019' into merge-b4bdev-20250116
samsrabin Jan 16, 2025
c9e2ca8
Fix conflicts in lilac/lnd_comp_esmf.F90 with 019 version.
samsrabin Jan 16, 2025
031407c
lilac/lnd_comp_esmf.F90: Switch stop/restart alarm order.
samsrabin Jan 16, 2025
6194751
Update MOSART and RTM to fix nag build error.
samsrabin Jan 16, 2025
b427fc9
Remove two expected failures due to issue ESCOMP/CTSM#2914.
samsrabin Jan 17, 2025
bf65082
Remove an expected failure due to ESCOMP/CTSM#2905.
samsrabin Jan 17, 2025
bc03504
Remove failures expected due to ESCOMP/CTSM#2454.
samsrabin Jan 17, 2025
ff2ac19
Update ChangeLog/ChangeSum.
samsrabin Jan 17, 2025
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12 changes: 6 additions & 6 deletions .gitmodules
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
[submodule "cism"]
path = components/cism
url = https://github.com/ESCOMP/CISM-wrapper
fxtag = cismwrap_2_2_002
fxtag = cismwrap_2_2_005
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
Expand All @@ -60,31 +60,31 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
[submodule "mizuRoute"]
path = components/mizuRoute
url = https://github.com/ESCOMP/mizuRoute
fxtag = cesm-coupling.n02_v2.1.3
fxtag = cesm-coupling.n03_v2.2.0
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute

[submodule "ccs_config"]
path = ccs_config
url = https://github.com/ESMCI/ccs_config_cesm.git
fxtag = ccs_config_cesm1.0.10
fxtag = ccs_config_cesm1.0.16
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git

[submodule "cime"]
path = cime
url = https://github.com/ESMCI/cime
fxtag = cime6.1.49
fxtag = cime6.1.59
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESMCI/cime

[submodule "cmeps"]
path = components/cmeps
url = https://github.com/ESCOMP/CMEPS.git
fxtag = cmeps1.0.32
fxtag = cmeps1.0.33
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
Expand All @@ -100,7 +100,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
[submodule "share"]
path = share
url = https://github.com/ESCOMP/CESM_share
fxtag = share1.1.6
fxtag = share1.1.7
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
Expand Down
63 changes: 29 additions & 34 deletions WhatsNewInCTSM5.3.md
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@@ -1,53 +1,48 @@
Purpose and description of changes since ctsm5.2.005
----------------------------------------------------
# What's new in CTSM 5.3 (tag `ctsm5.3.0`)

Bring in updates needed for the CESM3.0 science capability/functionality "chill". Most importantly bringing
in: CN Matrix to speed up spinup for the BGC model, updated surface datasets, updated Leung 2023 dust emissions,
explicit Air Conditioning for the Urban model, updates to crop calendars. For clm6_0 physics these options are now
default turned on in addition to Sturm snow, and excess ice.
## Purpose and description of changes since CTSM 5.2 (tag `ctsm5.2.005`)
- Adds CN Matrix method to speed up spinup for the BGC model.
- Updates surface datasets.
- Brings in new Leung 2023 dust emissions.
- Adds explicit air conditioning for the urban model.
- Updates crop calendars.
- Updates fire model with various improvements, including default parameterization against climate reanalysis from CRU-JRA instead of GSWP.
- FATES compsets can now be run with transient land use.

Changes to CTSM Infrastructure:
===============================
These changes were needed ahead of the CESM3 capability/functionality "chill". For `clm6_0` physics these options are now turned on by default, in addition to Sturm snow and excess ice.

- manage_externals removed and replaced by git-fleximod
- Ability to handle CAM7 in LND_TUNING_MODE
## Changes to CTSM infrastructure
- `manage_externals` removed and replaced by `git-fleximod`
- Ability to handle CAM7 in `LND_TUNING_MODE`

Changes to CTSM Answers:
========================
## Changes to CTSM answers

Changes to defaults for clm6_0 physics:
Changes to defaults for `clm6_0` physics:
- Urban explicit A/C turned on
- Snow thermal conductivity is now Sturm_1997
- New IC file for f09 1850
- Snow thermal conductivity method is now `Sturm_1997`
- New initial conditions file for f09 ("1-degree") 1850, with more in progress
- New crop calendars
- Dust emissions is now Leung_2023
- Dust emissions method is now `Leung_2023`
- Excess ice is turned on
- Updates to MEGAN for BVOC's
- Updates to MEGAN for BVOCs
- Updates to BGC fire method

Changes for all physics versions:

- Parameter files updated
- FATES parameter file updated
- Glacier region 1 is now undefined
- Update in FATES transient Land use
- Update in FATES transient land use
- Pass active glacier (CISM) runoff directly to river model (MOSART)
- Add the option for using matrix for Carbon/Nitrogen BGC spinup
- Add the option for using Matrix CN method for Carbon/Nitrogen BGC spinup

New surface datasets:
=====================
## New surface datasets

- With new surface datasets the following GLC fields have region "1" set to UNSET:
glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
- With new surface datasets the following GLC fields have region "1" set to UNSET: glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
- Updates to allow creating transient landuse timeseries files going back to 1700.
- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should.
- Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
- Add version to the surface datasets.
- Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
- Remove VIC fields from surface datasets.

New input datasets to mksurfdata_esmf:
======================================

- Updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
- Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should.
- Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid.
- Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version.
- Remove the `--hires_pft` option from `mksurfdata_esmf` as we don't have the datasets for it.
- Remove `VIC` fields from surface datasets.
- Updates to input datasets in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (crop fire peak month, peatland fraction), and the glacier behavior dataset.

2 changes: 1 addition & 1 deletion ccs_config
Open in desktop
Submodule ccs_config updated 11 files
+0 −664 component_grids_mct.xml
+0 −59 config_grids_mct.xml
+12 −3 machines/Depends.intel-oneapi
+17 −0 machines/Depends.nvhpc
+3 −4 machines/cmake_macros/cray.cmake
+0 −1 machines/cmake_macros/intel-oneapi.cmake
+63 −0 machines/cmake_macros/intel-oneapi.cmake
+1 −1 machines/derecho/config_batch.xml
+2 −0 machines/derecho/config_machines.xml
+0 −1,220 maps_mct.xml
+0 −1,261 modelgrid_aliases_mct.xml
+6 −3 modelgrid_aliases_nuopc.xml
2 changes: 1 addition & 1 deletion cime
Open in desktop
Submodule cime updated 19 files
+7 −7 .github/workflows/testing.yml
+37 −13 CIME/SystemTests/system_tests_common.py
+2 −2 CIME/Tools/code_checker
+2 −2 CIME/Tools/xmlconvertors/config_pes_converter.py
+9 −10 CIME/Tools/xmlconvertors/grid_xml_converter.py
+3 −3 CIME/case/case_clone.py
+1 −1 CIME/case/case_run.py
+5 −3 CIME/case/case_submit.py
+2 −4 CIME/code_checker.py
+18 −20 CIME/compare_namelists.py
+3 −0 CIME/hist_utils.py
+159 −110 CIME/namelist.py
+8 −2 CIME/status.py
+6 −11 CIME/test_status.py
+23 −3 CIME/tests/test_unit_system_tests_mvk.py
+1 −1 CIME/utils.py
+1 −1 CIME/wait_for_tests.py
+2 −4 docker/Dockerfile
+1 −0 docker/cime.yaml
195 changes: 7 additions & 188 deletions cime_config/testdefs/ExpectedTestFails.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -187,212 +187,31 @@
</phase>
</test>

<test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
<test name="SSP_Ld4.f09_g17.I1850Clm50BgcCrop.derecho_intel.clm-ciso_rtmColdSSP">
<phase name="RUN">
<status>FAIL</status>
<issue>#2310</issue>
<issue>#2913</issue>
</phase>
</test>

<test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM">
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2310</issue>
</phase>
<test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
<phase name="RUN">
<status>FAIL</status>
<issue>#2310</issue>
</phase>
</test>


<!--- Izumi mpi-serial tests failing for me -->

<test name='ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_D_Ld7_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropRs.izumi_intel.clm-decStart1851_noinitial' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ld1200_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ld1600_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ld600_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-cropMonthlyNoinitial' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly20_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly20_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-cropMonthlyNoinitial--clm-matrixcnOn' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly3_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_gnu.clm-cropMonthOutput' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-ciso_monthly' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.izumi_gnu.clm-ciso_monthly--clm-matrixcnOn' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_intel.clm-cropMonthOutput' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianRs.izumi_intel.clm-cropMonthOutput--clm-matrixcnOn_ignore_warnings' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsROA' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_nag.clm-ptsRLA' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60FatesRs.izumi_nag.clm-FatesCold' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_Ld5_Mmpi-serial.1x1_brazil.IHistClm60Bgc.izumi_gnu.clm-mimics' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_Ly3_Mmpi-serial.1x1_numaIA.I2000Clm50BgcDvCropQianRs.izumi_gnu.clm-ignor_warn_cropMonthOutputColdStart' >
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
</phase>
</test>


<test name='SMS_Ly5_Mmpi-serial.1x1_brazil.IHistClm50BgcQianRs.izumi_intel.clm-newton_krylov_spinup' >
<test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM">
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
<issue>#2916</issue>
<issue>#2310</issue>
</phase>
</test>


<test name='SMS_Ly5_Mmpi-serial.1x1_smallvilleIA.IHistClm60BgcCropQianRs.izumi_gnu.clm-gregorian_cropMonthOutput' >
<phase name="SHAREDLIB_BUILD">
<phase name="RUN">
<status>FAIL</status>
<issue>#2916</issue>
<issue>#2310</issue>
</phase>
</test>

<!-- End of Izumi mpi-serial tests failing -->

<test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
<phase name="SHAREDLIB_BUILD">
<status>FAIL</status>
Expand Down
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