Merge branch 'cesm3.0-alphabranch' for cesm3_0_alpha05d

ESCOMP · Jan 29, 2025 · c7048db · c7048db
2 parents fe48b0f + ce4a9f6
commit c7048db
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Showing 8 changed files with 145 additions and 42 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -30,7 +30,7 @@
         path = ccs_config
         url = https://github.com/ESMCI/ccs_config_cesm.git
         fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
-        fxtag = ccs_config_cesm1.0.16
+        fxtag = ccs_config_cesm1.0.19
         fxrequired = ToplevelRequired
 
 [submodule "cime"]
@@ -66,7 +66,7 @@
         url = https://github.com/ESCOMP/CTSM
         fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
         fxrequired = ToplevelRequired
-        fxtag = ctsm5.3.016
+        fxtag = ctsm5.3.017
 
 [submodule "cice"]
         path = components/cice
@@ -80,7 +80,7 @@
         url = https://github.com/ESCOMP/MOM_interface
         fxDONOTUSEurl = https://github.com/ESCOMP/MOM_interface
         fxrequired = ToplevelRequired
-        fxtag = mi_241122
+        fxtag = mi_250128
 
 [submodule "cism"]
         path = components/cism
@@ -129,7 +129,7 @@
         url = https://github.com/ESCOMP/MOSART
         fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
         fxrequired = ToplevelRequired
-        fxtag = mosart1.1.06
+        fxtag = mosart1.1.07
 
 [submodule "parallelio"]
         path = libraries/parallelio
@@ -157,4 +157,4 @@
         url = https://github.com/NCAR/CUPiD.git
         fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
         fxrequired = ToplevelRequired
-        fxtag = v0.1.2
+        fxtag = v0.1.4
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,106 @@
+==============================================================
+Tag name: cesm3_0_alpha05d
+Originator(s): CSEG
+Date: 28th January 2024
+One-line Summary: MOM and CTSM updates
+
+ccs_config              https://github.com/ESMCI/ccs_config_cesm/tree/ccs_config_cesm1.0.19   **
+cime                    https://github.com/ESMCI/cime/tree/cime6.1.56                         --
+components/fms          https://github.com/ESCOMP/FMS_interface/tree/fi_240822                --
+share                   https://github.com/ESCOMP/CESM_share/tree/share1.1.7                  --
+components/cam          https://github.com/ESCOMP/CAM/cam6_4_048                              --
+components/clm          https://github.com/ESCOMP/ctsm/tree/ctsm5.3.017                       **
+components/cice         https://github.com/ESCOMP/CESM_CICE/tree/cesm3_cice6_6_0_1            --
+components/mom          https://github.com/ESCOMP/MOM_interface/mi_250128                     **
+components/cism         https://github.com/ESCOMP/cism-wrapper/tree/cismwrap_2_2_005          --
+components/cdeps        https://github.com/ESCOMP/CDEPS/tree/cdeps1.0.61                      --
+components/cmeps        https://github.com/ESCOMP/CMEPS/tree/cmeps1.0.33                      --
+components/rtm          https://github.com/ESCOMP/rtm/tree/rtm1_0_84                          --
+components/ww3          https://github.com/ESCOMP/WW3-CESM/tree/main_0.0.16                   --
+components/mizuroute    https://github.com/ESCOMP/mizuRoute/tree/cesm-coupling.n03_v2.3.0     --
+components/mosart       https://github.com/ESCOMP/mosart/tree/mosart1_1_07                    **
+libraries/mpi-serial    https://github.com/ESMCI/mpi-serial/tree/MPIserial_2.5.0              --
+libraries/parallelio    https://github.com/NCAR/ParallilIO/tree/pio2_6_3                      --
+tools/CUPiD             https://github.com/NCAR/CUPiD/tree/v0.1.4                             **
+
+
+ccs_config
+    Alper Altuntas 2025-01-08 - ccs_config_cesm1.0.19 - ccs_config (cesm3_0_alpha05d)
+    https://github.com/ESMCI/ccs_config_cesm/tags/ccs_config_cesm1.0.18
+
+    ccs_config_cesm1.0.19: Fix typo, sm ~> nnsm
+    ccs_config_cesm1.0.18: Update JRA to tx2_3v2 Mapping File
+
+
+    James Edwards 2025-01-07 - ccs_config_cesm1.0.17 - ccs_config (cesm3_0_alpha05d)
+    https://github.com/ESMCI/ccs_config_cesm/tags/ccs_config_cesm1.0.17
+
+    Adds cupid workflow
+
+
+clm
+    Erik Kluzek 2025-01-08 - ctsm5.3.017 - components/clm (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/ctsm/tags/branch_tags/tmp-241219.n04.ctsm5.3.016
+
+    Identical to tmp-241219.n03.ctsm5.3.016
+    but on CTSM master
+
+
+    Erik Kluzek 2025-01-08 - branch_tags/tmp-241219.n03.ctsm5.3.016 - components/clm (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/ctsm/tags/branch_tags/tmp-241219.n03.ctsm5.3.016
+
+    Fixes an important problem to the new nfix_method
+    found by the nag compiler
+
+
+    Erik Kluzek 2025-01-08 - branch_tags/tmp-241219.n02.ctsm5.3.016 - components/clm (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/ctsm/tags/branch_tags/tmp-241219.n02.ctsm5.3.016
+
+    Small FATES update, only changes answers for FatesHydro tests
+
+
+    Erik Kluzek 2025-01-08 - branch_tags/tmp-241219.n01.ctsm5.3.016 - components/clm (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/ctsm/tags/branch_tags/tmp-241219.n01.ctsm5.3.016
+
+    Merge of b4b-dev to master
+
+    Adds a new namelist option for an alternative curve
+    for the FUN module. This should be turned on
+    for coupled testing.
+
+    Set nfix_method='Bytnerowicz' for coupled simulations.
+
+
+CUPiD
+    Michael Levy 2025-01-15 - v0.1.4 - tools/CUPiD (cesm3_0_alpha05d)
+    https://github.com/NCAR/CUPiD/tags/v0.1.4
+
+    - Fix bug in time series import
+    - Update seaice notebook in key metrics
+    - Move obs data to common directory
+
+
+    Michael Levy 2025-01-07 - v0.1.3 - tools/CUPiD (cesm3_0_alpha05d)
+    https://github.com/NCAR/CUPiD/tags/v0.1.3
+
+    Updates to scripts that generate config files for CESM workflow
+
+
+mom
+    Alper Altuntas 2025-01-08 - mi_250128 - components/mom (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/MOM_interface/tags/mi_2501xx
+
+    bug fixes and parameter changes
+
+
+mosart
+    Erik Kluzek 2025-01-07 - mosart1.1.07 - components/mosart (cesm3_0_alpha05d)
+    https://github.com/ESCOMP/mosart/tags/mosart1.1.07
+
+    Simple fix for NAG compiler on Izumi
+
+
+
 ==============================================================
 Tag name: cesm3_0_alpha05c
 Originator(s): CSEG

diff --git a/ccs_config b/ccs_config
diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml
@@ -46,12 +46,12 @@
 	<comment></comment>
 	<ntasks>
 	  <ntasks_atm>5400</ntasks_atm>
-	  <ntasks_lnd>1816</ntasks_lnd>
-	  <ntasks_rof>1816</ntasks_rof>
-	  <ntasks_ice>3584</ntasks_ice>
-	  <ntasks_ocn>488</ntasks_ocn>
+	  <ntasks_lnd>2456</ntasks_lnd>
+	  <ntasks_rof>2456</ntasks_rof>
+	  <ntasks_ice>2944</ntasks_ice>
+	  <ntasks_ocn>680</ntasks_ocn>
 	  <ntasks_glc>4</ntasks_glc>
-	  <ntasks_wav>1</ntasks_wav>
+	  <ntasks_wav>64</ntasks_wav>
 	  <ntasks_cpl>5400</ntasks_cpl>
 	</ntasks>
 	<nthrds>
@@ -66,12 +66,12 @@
 	</nthrds>
 	<rootpe>
 	  <rootpe_atm>0</rootpe_atm>
-	  <rootpe_lnd>3584</rootpe_lnd>
-	  <rootpe_rof>3584</rootpe_rof>
+	  <rootpe_lnd>2944</rootpe_lnd>
+	  <rootpe_rof>2944</rootpe_rof>
 	  <rootpe_ice>0</rootpe_ice>
 	  <rootpe_ocn>5400</rootpe_ocn>
 	  <rootpe_glc>0</rootpe_glc>
-	  <rootpe_wav>0</rootpe_wav>
+	  <rootpe_wav>6080</rootpe_wav>
 	  <rootpe_cpl>0</rootpe_cpl>
 	</rootpe>
       </pes>
@@ -109,15 +109,15 @@
 	</rootpe>
       </pes> -->
       <pes pesize="XL" compset="CAM.*%LT.*MOM6(?!.*%MARBL-BIO)">
-	<comment>20 ypd/ 7100 pe-hrs/simyr expected</comment>
+	<comment>18 ypd/ 8530 pe-hrs/simyr expected</comment>
   	<ntasks>
 	  <ntasks_atm>5400</ntasks_atm>
-	  <ntasks_lnd>1792</ntasks_lnd>
-	  <ntasks_rof>1792</ntasks_rof>
-	  <ntasks_ice>3608</ntasks_ice>
-	  <ntasks_ocn>612</ntasks_ocn>
-	  <ntasks_glc>4</ntasks_glc>
-	  <ntasks_wav>1</ntasks_wav>
+	  <ntasks_lnd>2624</ntasks_lnd>
+	  <ntasks_rof>2624</ntasks_rof>
+	  <ntasks_ice>2776</ntasks_ice>
+	  <ntasks_ocn>896</ntasks_ocn>
+	  <ntasks_glc>104</ntasks_glc>
+	  <ntasks_wav>104</ntasks_wav>
 	  <ntasks_cpl>5400</ntasks_cpl>
 	</ntasks>
 	<nthrds>
@@ -134,8 +134,8 @@
 	  <rootpe_atm>0</rootpe_atm>
 	  <rootpe_lnd>0</rootpe_lnd>
 	  <rootpe_rof>0</rootpe_rof>
-	  <rootpe_ice>1792</rootpe_ice>
-	  <rootpe_ocn>5404</rootpe_ocn>
+	  <rootpe_ice>2624</rootpe_ice>
+	  <rootpe_ocn>5504</rootpe_ocn>
 	  <rootpe_glc>5400</rootpe_glc>
 	  <rootpe_wav>5400</rootpe_wav>
 	  <rootpe_cpl>0</rootpe_cpl>
@@ -215,12 +215,12 @@
 	<comment>13.9 ypd/ 5300 pe-hrs/simyr expected</comment>
 	<ntasks>
 	  <ntasks_atm>2700</ntasks_atm>
-	  <ntasks_lnd>896</ntasks_lnd>
-	  <ntasks_rof>32</ntasks_rof>
+	  <ntasks_lnd>1280</ntasks_lnd>
+	  <ntasks_rof>1280</ntasks_rof>
 	  <ntasks_ice>1772</ntasks_ice>
-	  <ntasks_ocn>372</ntasks_ocn>
-	  <ntasks_glc>32</ntasks_glc>
-	  <ntasks_wav>32</ntasks_wav>
+	  <ntasks_ocn>640</ntasks_ocn>
+	  <ntasks_glc>116</ntasks_glc>
+	  <ntasks_wav>116</ntasks_wav>
 	  <ntasks_cpl>2700</ntasks_cpl>
 	</ntasks>
 	<nthrds>
@@ -237,10 +237,10 @@
 	  <rootpe_atm>0</rootpe_atm>
 	  <rootpe_lnd>0</rootpe_lnd>
 	  <rootpe_rof>896</rootpe_rof>
-	  <rootpe_ice>928</rootpe_ice>
-	  <rootpe_ocn>2700</rootpe_ocn>
-	  <rootpe_glc>896</rootpe_glc>
-	  <rootpe_wav>896</rootpe_wav>
+	  <rootpe_ice>1280</rootpe_ice>
+	  <rootpe_ocn>2816</rootpe_ocn>
+	  <rootpe_glc>2700</rootpe_glc>
+	  <rootpe_wav>2700</rootpe_wav>
 	  <rootpe_cpl>0</rootpe_cpl>
 	</rootpe>
       </pes>
@@ -281,10 +281,10 @@
 	<comment>10 ypd/ 5500 pe-hrs/simyr expected</comment>
 	<ntasks>
 	  <ntasks_atm>1920</ntasks_atm>
-	  <ntasks_lnd>640</ntasks_lnd>
+	  <ntasks_lnd>1152</ntasks_lnd>
 	  <ntasks_rof>512</ntasks_rof>
-	  <ntasks_ice>1152</ntasks_ice>
-	  <ntasks_ocn>384</ntasks_ocn>
+	  <ntasks_ice>768</ntasks_ice>
+	  <ntasks_ocn>512</ntasks_ocn>
 	  <ntasks_glc>64</ntasks_glc>
 	  <ntasks_wav>64</ntasks_wav>
 	  <ntasks_cpl>1920</ntasks_cpl>
@@ -303,10 +303,10 @@
 	  <rootpe_atm>0</rootpe_atm>
 	  <rootpe_lnd>0</rootpe_lnd>
 	  <rootpe_rof>0</rootpe_rof>
-	  <rootpe_ice>704</rootpe_ice>
+	  <rootpe_ice>1152</rootpe_ice>
 	  <rootpe_ocn>1920</rootpe_ocn>
-	  <rootpe_glc>1856</rootpe_glc>
-	  <rootpe_wav>1792</rootpe_wav>
+	  <rootpe_glc>2496</rootpe_glc>
+	  <rootpe_wav>2432</rootpe_wav>
 	  <rootpe_cpl>0</rootpe_cpl>
 	</rootpe>
       </pes>

diff --git a/components/clm b/components/clm
diff --git a/components/mom b/components/mom
diff --git a/components/mosart b/components/mosart
diff --git a/tools/CUPiD b/tools/CUPiD
+2 −2		machines/casper/config_machines.xml
+14 −0		machines/config_workflow.xml
+2 −0		machines/derecho/config_machines.xml
+47 −0		machines/template.cupid
+2 −2		maps_nuopc.xml
+1 −1		.gitmodules
+3 −1		bld/CLMBuildNamelist.pm
+5 −4		bld/namelist_files/namelist_defaults_ctsm.xml
+5 −0		bld/namelist_files/namelist_definition_ctsm.xml
+8 −1		cime_config/testdefs/ExpectedTestFails.xml
+9 −0		cime_config/testdefs/testlist_clm.xml
+0 −8		cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
+0 −1		cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
+1 −1		cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+1 −1		cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+1 −0		cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/include_user_mods
+2 −0		cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/user_nl_clm
+313 −0		doc/ChangeLog
+4 −0		doc/ChangeSum
+142 −21		src/biogeochem/CNFUNMod.F90
+1 −1		src/fates
+2 −0		src/main/controlMod.F90
+5 −8		.github/workflows/general-ci-tests.yml
+1 −1		MOM6
+29 −40		cime_config/MOM_RPS/FType_diag_table.py
+20 −0		cime_config/config_component.xml
+6 −281		cime_config/config_pes.xml
+1 −1		cime_config/testdefs/testlist_mom.xml
+109 −57		param_templates/MOM_input.yaml
+21 −8		param_templates/diag_table.yaml
+4 −1		param_templates/input_data_list.yaml
+98 −53		param_templates/json/MOM_input.json
+73 −17		param_templates/json/diag_table.json
+5 −1		param_templates/json/input_data_list.json
+286 −267		docs/ChangeLog.md
+1 −1		src/riverroute/mosart_driver.F90
+1 −1		src/riverroute/mosart_restfile.F90
+3 −10		src/riverroute/mosart_timemanager.F90
+1 −0		.github/PULL_REQUEST_TEMPLATE.md
+10 −8		cupid/run_timeseries.py
+1 −1		cupid/timeseries.py
+23 −17		examples/coupled_model/config.yml
+17 −20		examples/key_metrics/config.yml
+18 −27		helper_scripts/generate_adf_config_file.py
+29 −6		helper_scripts/generate_cupid_config_for_cesm_case.py
+1 −1		nblibrary/atm/Global_PSL_NMSE_compare_obs_lens.ipynb
+4 −1		nblibrary/atm/averaging_utils.py
+20 −9		nblibrary/glc/Greenland_SMB_visual_compare_obs.ipynb
+320 −0		nblibrary/ice/Hemis_seaice_visual_compare_contour.ipynb
+777 −0		nblibrary/ice/Hemis_seaice_visual_compare_obs_lens.ipynb
+0 −42		nblibrary/ice/cice_vars.yml
+53 −0		nblibrary/ice/cice_vars_full.yml
+3 −3		nblibrary/ice/plot_diff.py
+0 −564		nblibrary/ice/seaice.ipynb
+2 −2		nblibrary/ice/vect_diff.py
+117 −22		nblibrary/lnd/Global_TerrestrialCouplingIndex_VisualCompareObs.ipynb