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add timestamp to rpointer files #2757

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add timestamp to rpointer files #2757

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9f07cf9
add timestamps to rpointer files
jedwards4b Sep 26, 2024
887ceb8
Merge tag 'ctsm5.3.0' into add_timestamp_to_rpointers
jedwards4b Sep 27, 2024
cddf7e7
Merge tag 'ctsm5.3.002' into add_timestamp_to_rpointers
jedwards4b Sep 30, 2024
718bd41
reverse initialization of alarm_stop and alarm_restart
jedwards4b Oct 17, 2024
45fb774
Merge branch 'master' into add_timestamp_to_rpointers
ekluzek Dec 4, 2024
ee5261a
This is my understanding of the submodules that need to be used with …
ekluzek Dec 5, 2024
277384b
Another cime submodule update regarding rpointer things
ekluzek Dec 5, 2024
66b680d
Fix a syntax error that nag caught
ekluzek Dec 6, 2024
9a96642
Update cmeps, cime, share submodules to fix some testing issues
ekluzek Dec 9, 2024
bd06342
Update cmeps, cime, share submodules to fix some testing issues
ekluzek Dec 9, 2024
35dcfb4
Change tagname for share tag
ekluzek Dec 10, 2024
f2f1039
Move usermods_dirs under a clm subdirectory due to a change in cime i…
ekluzek Dec 11, 2024
3341540
Add the clm directory when the usermods_Dirs directory is referenced
ekluzek Dec 11, 2024
ae9986f
More change of usermods dirs to be under the clm subdir
ekluzek Dec 11, 2024
6e5b1b8
Correct path to NEON/PLUMBER2 user_mods_dirs
ekluzek Dec 11, 2024
acd2266
More usermods_dir corrections
ekluzek Dec 11, 2024
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6 changes: 3 additions & 3 deletions .gitmodules
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Expand Up @@ -76,15 +76,15 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
[submodule "cime"]
path = cime
url = https://github.com/ESMCI/cime
fxtag = cime6.1.37
fxtag = cime6.1.49
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 = cmeps1.0.16
fxtag = cmeps1.0.31
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 = share1.1.2
fxtag = share1.1.6
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
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4 changes: 2 additions & 2 deletions README
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Expand Up @@ -126,9 +126,9 @@ cime_config/config_tests.xml ----- Define CTSM specific tests
cime_config/config_pes.xml ------- Define Processor layouts for various CTSM grids and compsets
cime_config/testdefs ------------- Directory for specification of CTSM testing
cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail
cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs
cime_config/usermods_dirs/clm ---- Directories of sets of user-modification subdirs
(These are directories that add specific user modifications to
simulations created using "cime/scripts/create_newcase --user-mods-dir".)
simulations created using "cime/scripts/create_newcase --user-mods-dir clm/*)

tools/mksurfdata_esmf --------- Directory to build program to create surface dataset
at any resolution.
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4 changes: 2 additions & 2 deletions bld/unit_testers/build-namelist_test.pl
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Expand Up @@ -368,7 +368,7 @@ sub cat_and_create_namelistinfile {
my $phys = "clm6_0";
$mode = "-phys $phys";
&make_config_cache($phys);
my $neondir = "../../cime_config/usermods_dirs/NEON";
my $neondir = "../../cime_config/usermods_dirs/clm/NEON";
foreach my $site ( "ABBY", "BLAN", "CPER", "DEJU", "GRSM", "HEAL", "KONA", "LENO", "NIWO",
"ONAQ", "PUUM", "SERC", "SRER", "TALL", "TREE", "WOOD", "BARR", "BONA",
"DCFS", "DELA", "GUAN", "JERC", "KONZ", "MLBS", "NOGP", "ORNL", "RMNP",
Expand Down Expand Up @@ -421,7 +421,7 @@ sub cat_and_create_namelistinfile {
my $phys = "clm6_0";
$mode = "-phys $phys";
&make_config_cache($phys);
my $plumdir = "../../cime_config/usermods_dirs/PLUMBER2";
my $plumdir = "../../cime_config/usermods_dirs/clm/PLUMBER2";
foreach my $site (
"AR-SLu", "AU-Emr", "AU-TTE", "CA-NS1", "CA-SF3", "CN-HaM", "DE-Obe", "ES-ES1", "FR-Gri", "IE-Dri", "IT-LMa", "IT-SRo", "RU-Fyo", "US-Aud", "US-Ho1", "US-Ne2", "US-Syv", "ZM-Mon",
"AT-Neu", "AU-Gin", "AU-Tum", "CA-NS2", "CH-Cha", "CN-Qia", "DE-Seh", "ES-ES2", "FR-Hes", "IT-Amp", "IT-Mal", "JP-SMF", "RU-Zot", "US-Bar", "US-KS2", "US-Ne3", "US-Ton",
Expand Down
2 changes: 1 addition & 1 deletion cime
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Submodule cime updated 38 files
+4 −0 .github/workflows/testing.yml
+1 −1 CIME/BuildTools/configure.py
+33 −6 CIME/SystemTests/eri.py
+6 −7 CIME/SystemTests/err.py
+6 −0 CIME/SystemTests/ers.py
+222 −92 CIME/SystemTests/mvk.py
+6 −0 CIME/SystemTests/restart_tests.py
+80 −9 CIME/SystemTests/system_tests_common.py
+81 −0 CIME/SystemTests/test_mods.py
+112 −30 CIME/XML/env_batch.py
+18 −0 CIME/XML/generic_xml.py
+16 −13 CIME/case/case.py
+10 −1 CIME/case/case_run.py
+63 −45 CIME/case/case_st_archive.py
+4 −3 CIME/case/case_submit.py
+6 −1 CIME/case/check_input_data.py
+95 −33 CIME/config.py
+1 −3 CIME/data/config/config_tests.xml
+0 −8 CIME/data/config/xml_schemas/config_machines_version3.xsd
+1 −1 CIME/data/config/xml_schemas/config_workflow.xsd
+9 −0 CIME/get_timing.py
+8 −1 CIME/hist_utils.py
+43 −14 CIME/namelist.py
+1 −1 CIME/non_py/cprnc
+12 −26 CIME/test_scheduler.py
+87 −14 CIME/tests/test_sys_test_scheduler.py
+1 −11 CIME/tests/test_unit_case_setup.py
+15 −3 CIME/tests/test_unit_system_tests.py
+710 −0 CIME/tests/test_unit_system_tests_mvk.py
+165 −2 CIME/tests/test_unit_xml_env_batch.py
+1 −0 CIME/tests/test_unit_xml_tests.py
+12 −0 CIME/tests/utils.py
+9 −5 CIME/utils.py
+1 −2 CIME/wait_for_tests.py
+1 −0 doc/requirements.txt
+2 −1 doc/source/conf.py
+237 −52 doc/source/users_guide/testing.rst
+1 −0 test-requirements.txt
18 changes: 9 additions & 9 deletions cime_config/config_component.xml
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Expand Up @@ -355,15 +355,15 @@
<valid_values></valid_values>
<default_value></default_value>
<values match="last">
<value compset="_CLM60%[^_]*FATES-SP[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
<value compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*FATES-SP[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/fates_sp</value>
<value compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
</values>
<group>run_component_ctsm</group>
<file>env_case.xml</file>
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2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods
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@@ -1,2 +1,2 @@
../monthly
../../../../usermods_dirs/output_sp_exice
../../../../usermods_dirs/clm/output_sp_exice
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods
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@@ -1 +1 @@
../../../../usermods_dirs/cmip6_deck
../../../../usermods_dirs/clm/cmip6_deck
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods
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@@ -1 +1 @@
../../../../usermods_dirs/lilac
../../../../usermods_dirs/clm/lilac
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README
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@@ -1,6 +1,6 @@
slevis 2022/2/1:
This testmod tests the newton_krylov_spinup usermod found in
cime_config/usermods_dirs/newton_krylov_spinup
cime_config/usermods_dirs/clm/newton_krylov_spinup
combined with the mimics testmod.

By default this usermod runs for 20 yrs and writes a history file at that
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2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods
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@@ -1,2 +1,2 @@
../mimics
../../../../usermods_dirs/newton_krylov_spinup
../../../../usermods_dirs/clm/newton_krylov_spinup
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods
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../../../../usermods_dirs/output_bgc_highfreq
../../../../usermods_dirs/clm/output_bgc_highfreq
../basic
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods
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../../../../usermods_dirs/output_crop_highfreq
../../../../usermods_dirs/clm/output_crop_highfreq
../basic
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods
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../CLM1PTStartDate
../../../../usermods_dirs/output_sp_highfreq
../../../../usermods_dirs/clm/output_sp_highfreq
../basic
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Expand Up @@ -2,7 +2,7 @@

Use these user mods as you would any other user_mods, e.g.:

`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm60Fates --run-unsupported --user-mods-dir /glade/work/$user/CTSM/cime_config/usermods_dirs/NEON/FATES/ABBY`
`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm60Fates --run-unsupported --user-mods-dir clm/NEON/FATES/ABBY`

## Note on crop sites KONA and STER

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