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cam6_4_089: Update externals to match alpha06f and bring in timestamped rpointer files #1303

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cam6_4_089: Update externals to match alpha06f and bring in timestamped rpointer files #1303

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2102355
update to handle timestamped rpointer files
jedwards4b Apr 14, 2025
9955683
corrections for st_archive tests
jedwards4b Apr 14, 2025
a5743ca
make consistant with model code
jedwards4b Apr 16, 2025
c6b35c0
Merge remote-tracking branch 'jim/st_archive_fix' into cam_rpointer
cacraigucar Apr 25, 2025
716f9eb
Update externals to match alpha06f
cacraigucar Apr 25, 2025
209ce88
Update externals
cacraigucar Apr 25, 2025
5921174
Add missing external
cacraigucar Apr 25, 2025
c785e9d
Update externals one more time
cacraigucar Apr 25, 2025
c856298
Update .gitmodules
cacraigucar Apr 25, 2025
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24 changes: 12 additions & 12 deletions .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@
fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git

[submodule "pumas"]
path = src/physics/pumas
url = https://github.com/ESCOMP/PUMAS
path = src/physics/pumas
url = https://github.com/ESCOMP/PUMAS
fxrequired = AlwaysRequired
fxtag = pumas_cam-release_v1.38
fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
Expand Down Expand Up @@ -116,21 +116,21 @@
[submodule "cism"]
path = components/cism
url = https://github.com/ESCOMP/CISM-wrapper
fxtag = cismwrap_2_2_005
fxtag = cismwrap_2_2_006
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper

[submodule "rtm"]
path = components/rtm
url = https://github.com/ESCOMP/RTM
fxtag = rtm1_0_84
fxtag = rtm1_0_86
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/RTM

[submodule "mosart"]
path = components/mosart
url = https://github.com/ESCOMP/MOSART
fxtag = mosart1.1.07
fxtag = mosart1.1.08
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

Expand All @@ -144,28 +144,28 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
[submodule "ccs_config"]
path = ccs_config
url = https://github.com/ESMCI/ccs_config_cesm.git
fxtag = ccs_config_cesm1.0.39
fxtag = ccs_config_cesm1.0.40
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git

[submodule "cime"]
path = cime
url = https://github.com/ESMCI/cime
fxtag = cime6.1.72
fxtag = cime6.1.92
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESMCI/cime

[submodule "cmeps"]
path = components/cmeps
url = https://github.com/ESCOMP/CMEPS.git
fxtag = cmeps1.0.39
fxtag = cmeps1.0.47
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git

[submodule "cdeps"]
path = components/cdeps
url = https://github.com/ESCOMP/CDEPS.git
fxtag = cdeps1.0.69
fxtag = cdeps1.0.73
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git

Expand All @@ -179,7 +179,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
[submodule "parallelio"]
path = libraries/parallelio
url = https://github.com/NCAR/ParallelIO
fxtag = pio2_6_3
fxtag = pio2_6_4
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/NCAR/ParallelIO

Expand All @@ -193,14 +193,14 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
[submodule "clm"]
path = components/clm
url = https://github.com/ESCOMP/CTSM
fxtag = ctsm5.3.017
fxtag = ctsm5.3.029
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CTSM

[submodule "fms"]
path = libraries/FMS
url = https://github.com/ESCOMP/FMS_interface
fxtag = fi_240828
fxtag = fi_250411
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface

Expand Down
2 changes: 1 addition & 1 deletion ccs_config
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Submodule ccs_config updated 4 files
+14 −13 machines/casper/gnu_casper.cmake
+14 −13 machines/casper/nvhpc_casper.cmake
+4 −13 machines/derecho/gnu_derecho.cmake
+4 −13 machines/derecho/nvhpc_derecho.cmake
2 changes: 1 addition & 1 deletion cime
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Submodule cime updated 35 files
+1 −0 .git-blame-ignore-revs
+15 −5 CIME/SystemTests/err.py
+23 −13 CIME/SystemTests/system_tests_common.py
+1 −1 CIME/Tools/Makefile
+2 −2 CIME/Tools/standard_script_setup.py
+2 −1 CIME/XML/compsets.py
+13 −15 CIME/XML/env_batch.py
+200 −23 CIME/XML/machines.py
+34 −7 CIME/bless_test_results.py
+2 −5 CIME/build.py
+3 −2 CIME/build_scripts/buildlib.mpi-serial
+1 −1 CIME/case/case.py
+49 −32 CIME/case/case_st_archive.py
+1 −1 CIME/case/case_submit.py
+7 −5 CIME/case/check_input_data.py
+3 −4 CIME/data/config/xml_schemas/config_machines_version3.xsd
+57 −57 CIME/get_tests.py
+1 −0 CIME/hist_utils.py
+1 −1 CIME/non_py/cprnc
+40 −58 CIME/scripts/query_config.py
+1 −1 CIME/tests/base.py
+4 −4 CIME/tests/test_sys_bless_tests_results.py
+1 −1 CIME/tests/test_sys_build_system.py
+20 −20 CIME/tests/test_sys_cime_case.py
+1 −1 CIME/tests/test_sys_full_system.py
+1 −1 CIME/tests/test_sys_save_timings.py
+1 −1 CIME/tests/test_sys_single_submit.py
+21 −23 CIME/tests/test_sys_test_scheduler.py
+11 −11 CIME/tests/test_unit_baselines_performance.py
+26 −1 CIME/tests/test_unit_bless_test_results.py
+4 −4 CIME/tests/test_unit_case.py
+17 −17 CIME/tests/test_unit_system_tests.py
+2 −2 CIME/tests/test_unit_xml_grids.py
+183 −1 CIME/tests/test_unit_xml_machines.py
+51 −41 CIME/utils.py
8 changes: 5 additions & 3 deletions cime_config/config_archive.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,14 @@
<hist_file_extension>e</hist_file_extension>
<rest_history_varname>nhfil</rest_history_varname>
<rpointer>
<rpointer_file>rpointer.atm$NINST_STRING</rpointer_file>
<rpointer_file>rpointer.cam$NINST_STRING.$DATENAME</rpointer_file>
<rpointer_content>$CASE.cam$NINST_STRING.r.$DATENAME.nc </rpointer_content>
</rpointer>
<test_file_names>
<tfile disposition="copy">rpointer.atm</tfile>
<tfile disposition="copy">rpointer.atm_9999</tfile>
<tfile disposition="copy">rpointer.cam.1976-01-01-00000</tfile>
<tfile disposition="copy">rpointer.cam_9999.1976-01-01-00000</tfile>
<tfile disposition="ignore">rpointer.cam.1976-02-01-00000</tfile>
<tfile disposition="ignore">rpointer.cam_9999.1976-01-02-00000</tfile>
<tfile disposition="copy">casename.cam.r.1976-01-01-00000.nc</tfile>
<tfile disposition="copy">casename.cam.rh4.1976-01-01-00000.nc</tfile>
<tfile disposition="move">casename.cam.h0.1976-01-01-00000.nc</tfile>
Expand Down
2 changes: 1 addition & 1 deletion components/cdeps
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Submodule cdeps updated 7 files
+5 −0 cime_config/stream_cdeps.py
+31 −1 datm/cime_config/buildnml
+1 −1 datm/cime_config/namelist_definition_datm.xml
+73 −133 datm/cime_config/stream_definition_datm.xml
+30 −0 datm/cime_config/testdefs/testlist_datm.xml
+10 −10 datm/datm_datamode_clmncep_mod.F90
+1 −0 share/CMakeLists.txt
2 changes: 1 addition & 1 deletion components/cism
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Submodule cism updated 2 files
+0 −84 CODE_OF_CONDUCT.md
+9 −0 ChangeLog
2 changes: 1 addition & 1 deletion components/clm
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Submodule clm updated 79 files
+6 −0 .git-blame-ignore-revs
+10 −0 .gitignore
+9 −9 .gitmodules
+0 −107 CODE_OF_CONDUCT.md
+107 −52 WhatsNewInCTSM5.3.md
+17 −5 bld/CLMBuildNamelist.pm
+51 −35 bld/namelist_files/namelist_defaults_ctsm.xml
+60 −2 bld/namelist_files/namelist_definition_ctsm.xml
+6 −2 bld/unit_testers/build-namelist_test.pl
+1 −1 ccs_config
+1 −1 cime
+8 −6 cime_config/SystemTests/rxcropmaturity.py
+6 −0 cime_config/SystemTests/rxcropmaturityinst.py
+6 −0 cime_config/SystemTests/rxcropmaturityskipgeninst.py
+1 −4 cime_config/SystemTests/ssp.py
+52 −68 cime_config/SystemTests/sspmatrixcn.py
+20 −0 cime_config/config_tests.xml
+1 −249 cime_config/testdefs/ExpectedTestFails.xml
+345 −289 cime_config/testdefs/testlist_clm.xml
+3 −2 cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
+0 −8 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands
+1 −1 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm
+0 −8 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands
+2 −2 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm
+1 −1 cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+1 −1 components/cism
+1 −1 components/cmeps
+1 −1 components/mizuRoute
+1 −1 components/mosart
+1 −1 components/rtm
+973 −1 doc/ChangeLog
+12 −0 doc/ChangeSum
+3 −1 parse_cime.cs.status
+2 −1 python/ctsm/crop_calendars/convert_axis_time2gs.py
+1 −0 python/ctsm/crop_calendars/cropcal_figs_module.py
+41 −21 python/ctsm/crop_calendars/cropcal_module.py
+44 −6 python/ctsm/crop_calendars/cropcal_utils.py
+12 −1 python/ctsm/crop_calendars/generate_gdds.py
+21 −9 python/ctsm/crop_calendars/generate_gdds_functions.py
+3 −1 python/ctsm/crop_calendars/import_ds.py
+10 −0 python/ctsm/path_utils.py
+4 −82 python/ctsm/site_and_regional/neon_site.py
+41 −0 python/ctsm/site_and_regional/plumber_site.py
+109 −37 python/ctsm/site_and_regional/run_tower.py
+75 −38 python/ctsm/site_and_regional/tower_arg_parse.py
+70 −25 python/ctsm/site_and_regional/tower_site.py
+3 −3 python/ctsm/test/test_sys_modify_singlept_site_neon.py
+0 −71 python/ctsm/test/test_sys_run_neon.py
+213 −0 python/ctsm/test/test_sys_run_tower.py
+0 −76 python/ctsm/test/test_unit_neon_arg_parse.py
+1 −1 python/ctsm/test/test_unit_neon_site.py
+5 −5 python/ctsm/test/test_unit_run_tower.py
+185 −0 python/ctsm/test/test_unit_sspmatrix.py
+107 −0 python/ctsm/test/test_unit_tower_arg_parse.py
+12 −0 python/ctsm/utils.py
+1 −1 share
+1 −13 src/biogeochem/CNPhenologyMod.F90
+2 −2 src/biogeochem/CNVegetationFacade.F90
+1 −1 src/biogeochem/CropType.F90
+1 −1 src/biogeochem/dynCNDVMod.F90
+1 −1 src/biogeophys/SoilTemperatureMod.F90
+9 −5 src/biogeophys/UrbBuildTempOleson2015Mod.F90
+114 −130 src/cpl/lilac/lnd_comp_esmf.F90
+88 −95 src/cpl/nuopc/lnd_comp_nuopc.F90
+1 −1 src/fates
+1 −1 src/init_interp/initInterp.F90
+23 −25 src/main/clm_driver.F90
+11 −0 src/main/clm_varctl.F90
+35 −0 src/main/controlMod.F90
+65 −61 src/main/histFileMod.F90
+2 −3 src/soilbiogeochem/CNSoilMatrixMod.F90
+1 −4 src/unit_test_shr/unittestTimeManagerMod.F90
+2 −1 src/utils/AnnualFluxDribbler.F90
+20 −18 src/utils/clm_time_manager.F90
+115 −23 src/utils/clmfates_interfaceMod.F90
+4 −4 src/utils/test/clm_time_manager_test/test_clm_time_manager.pf
+171 −0 tools/contrib/remove_duplicate_tests.py
+107 −0 tools/contrib/test_rxcropmaturity_python.sh
+5 −5 tools/site_and_regional/run_tower
2 changes: 1 addition & 1 deletion components/cmeps
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Submodule cmeps updated 16 files
+2 −2 .github/workflows/extbuild.yml
+3 −3 .github/workflows/srt.yml
+4 −3 cime_config/config_archive.xml
+1 −0 cime_config/config_component_cesm.xml
+3 −3 cime_config/namelist_definition_drv.xml
+22 −2 mediator/esmFldsExchange_cesm_mod.F90
+32 −0 mediator/esmFldsExchange_ufs_mod.F90
+2 −2 mediator/med.F90
+31 −12 mediator/med_diag_mod.F90
+4 −2 mediator/med_internalstate_mod.F90
+133 −86 mediator/med_map_mod.F90
+15 −6 mediator/med_phases_history_mod.F90
+1 −1 mediator/med_phases_ocnalb_mod.F90
+29 −2 mediator/med_phases_restart_mod.F90
+8 −0 ufs/ccpp/data/MED_typedefs.F90
+20 −0 ufs/ccpp/data/MED_typedefs.meta
2 changes: 1 addition & 1 deletion components/mosart
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Submodule mosart updated 3 files
+20 −0 docs/ChangeLog.md
+2 −4 src/cpl/nuopc/rof_import_export.F90
+13 −7 src/riverroute/mosart_histfile.F90
2 changes: 1 addition & 1 deletion components/rtm
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Submodule rtm updated 4 files
+1 −0 cime_config/testdefs/testlist_rtm.xml
+31 −0 docs/ChangeLog.md
+13 −7 src/riverroute/RtmHistFile.F90
+1 −1 src/riverroute/RtmRestFile.F90
2 changes: 1 addition & 1 deletion libraries/FMS
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Submodule FMS updated 2 files
+1 −1 .gitmodules
+1 −1 src
2 changes: 1 addition & 1 deletion libraries/parallelio
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Submodule parallelio updated 10 files
+3 −0 .github/actions/buildhdf5/action.yml
+9 −11 .github/actions/intelcompilers/action.yml
+2 −2 .github/workflows/autotools.yml
+0 −131 .github/workflows/intel.yml
+0 −77 .github/workflows/withspack.yml
+12 −12 CMakeLists.txt
+4 −4 configure.ac
+24 −8 src/clib/pio_darray_int.c
+7 −15 src/clib/pio_rearrange.c
+3 −3 src/flib/pio_nf.F90