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Merge tag 'ctsm5.3.048' into doc-builder-podman-support
Automatically publish docs to this repo
2 parents 096549f + a2782b4 commit a13fca6

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-84
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10 files changed

+348
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‎bld/CLMBuildNamelist.pm‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4044,11 +4044,11 @@ sub setup_logic_dry_deposition {
40444044
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
40454045
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
40464046
}
4047-
if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
4047+
if ( &value_is_true( $nl_flags->{'use_fates'}) ) {
40484048
foreach my $var ( @list ) {
40494049
if ( defined($nl->get_value($var)) ) {
4050-
$log->warning("DryDeposition $var is being set and can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
4051-
" Use the '--no-drydep' option when '-bgc fates' is activated");
4050+
$log->fatal_error("DryDeposition $var is being set and can NOT be on when FATES is also on.\n" .
4051+
" Use the '--no-drydep' option when '-bgc fates' is activated");
40524052
}
40534053
}
40544054
}
@@ -4171,8 +4171,8 @@ sub setup_logic_megan {
41714171
defined($nl->get_value('megan_factors_file')) ) {
41724172
check_megan_spec( $opts, $nl, $definition );
41734173
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
4174-
$log->warning("MEGAN can NOT be on when FATES is also on.\n" .
4175-
" Use the '-no-megan' option when '-bgc fates' is activated");
4174+
$log->fatal_error("MEGAN can NOT be on when FATES is also on.\n" .
4175+
" Use the '-no-megan' option when '-bgc fates' is activated");
41764176
}
41774177
}
41784178
}

‎cime_config/config_archive.xml‎

Lines changed: 6 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -8,14 +8,12 @@
88
<hist_file_extension>e</hist_file_extension>
99
<rest_history_varname>locfnh</rest_history_varname>
1010
<rpointer>
11-
<rpointer_file>rpointer.lnd$NINST_STRING.$DATENAME</rpointer_file>
11+
<rpointer_file>rpointer.lnd$NINST_STRING</rpointer_file>
1212
<rpointer_content>./$CASE.clm2$NINST_STRING.r.$DATENAME.nc</rpointer_content>
1313
</rpointer>
1414
<test_file_names>
15-
<tfile disposition="copy">rpointer.lnd.1976-01-01-00000</tfile>
16-
<tfile disposition="copy">rpointer.lnd_9999.1976-01-01-00000</tfile>
17-
<tfile disposition="ignore">rpointer.lnd.0000-01-01-00000</tfile>
18-
<tfile disposition="ignore">rpointer.lnd_9999.1976-01-03-00000</tfile>
15+
<tfile disposition="copy">rpointer.lnd</tfile>
16+
<tfile disposition="copy">rpointer.lnd_9999</tfile>
1917
<tfile disposition="copy">casename.clm2.r.1976-01-01-00000.nc</tfile>
2018
<tfile disposition="copy">casename.clm2.rh4.1976-01-01-00000.nc</tfile>
2119
<tfile disposition="move">casename.clm2.h0.1976-01-01-00000.nc</tfile>
@@ -34,14 +32,12 @@
3432
<hist_file_extension>e</hist_file_extension>
3533
<rest_history_varname>locfnh</rest_history_varname>
3634
<rpointer>
37-
<rpointer_file>rpointer.lnd$NINST_STRING.$DATENAME</rpointer_file>
35+
<rpointer_file>rpointer.lnd$NINST_STRING</rpointer_file>
3836
<rpointer_content>./$CASE.ctsm$NINST_STRING.r.$DATENAME.nc</rpointer_content>
3937
</rpointer>
4038
<test_file_names>
41-
<tfile disposition="copy">rpointer.lnd.1976-01-01-00000</tfile>
42-
<tfile disposition="copy">rpointer.lnd_9999.1976-01-01-00000</tfile>
43-
<tfile disposition="ignore">rpointer.lnd.0000-01-01-00000</tfile>
44-
<tfile disposition="ignore">rpointer.lnd_9999.1976-01-03-00000</tfile>
39+
<tfile disposition="copy">rpointer.lnd</tfile>
40+
<tfile disposition="copy">rpointer.lnd_9999</tfile>
4541
<tfile disposition="copy">casename.ctsm.r.1976-01-01-00000.nc</tfile>
4642
<tfile disposition="copy">casename.ctsm.rh4.1976-01-01-00000.nc</tfile>
4743
<tfile disposition="move">casename.ctsm.h0.1976-01-01-00000.nc</tfile>

‎cime_config/testdefs/testlist_clm.xml‎

Lines changed: 19 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -3779,24 +3779,25 @@
37793779
<option name="comment">Test with DEBUG on for FatesSP mode, NOTE: FatesSp has the largest difference in CTSM code for any FATES mode</option>
37803780
</options>
37813781
</test>
3782-
<test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdDryDepSatPhen">
3783-
<machines>
3784-
<machine name="derecho" compiler="gnu" category="aux_clm"/>
3785-
</machines>
3786-
<options>
3787-
<option name="wallclock">00:20:00</option>
3788-
<option name="comment">Run a test with dry deposition on and FATES-SP</option>
3789-
</options>
3790-
</test>
3791-
<test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdMeganSatPhen">
3792-
<machines>
3793-
<machine name="derecho" compiler="gnu" category="aux_clm"/>
3794-
</machines>
3795-
<options>
3796-
<option name="wallclock">00:20:00</option>
3797-
<option name="comment">Run a test with MEGAN on and FATES-SP</option>
3798-
</options>
3799-
</test>
3782+
<!-- DISABLING UNTIL COMPATIBLE (RGK 051925) https://github.com/ESCOMP/CTSM/issues/1784
3783+
<test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdDryDepSatPhen">
3784+
<machines>
3785+
<machine name="derecho" compiler="gnu" category="aux_clm"/>
3786+
</machines>
3787+
<options>
3788+
<option name="wallclock">00:20:00</option>
3789+
<option name="comment">Run a test with dry deposition on and FATES-SP</option>
3790+
</options>
3791+
</test>
3792+
<test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdMeganSatPhen">
3793+
<machines>
3794+
<machine name="derecho" compiler="gnu" category="aux_clm"/>
3795+
</machines>
3796+
<options>
3797+
<option name="wallclock">00:20:00</option>
3798+
<option name="comment">Run a test with MEGAN on and FATES-SP</option>
3799+
</options>
3800+
</test> -->
38003801

38013802
<test name="SMS_D_Ld3" grid="f09_g17" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
38023803
<machines>

‎doc/ChangeLog‎

Lines changed: 228 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,232 @@
11
===============================================================
2+
Tag name: ctsm5.3.048
3+
Originator(s): samrabin (Sam Rabin, UCAR/TSS)
4+
Date: Mon May 26 18:30:59 MDT 2025
5+
One-line Summary: Automatically publish docs to this repo
6+
7+
Purpose and description of changes
8+
----------------------------------
9+
10+
Enables automatic publication of documentation to this repo's GitHub Pages, making ctsm-docs repo obsolete. Also updates documentation documentation.
11+
12+
13+
Significant changes to scientifically-supported configurations
14+
--------------------------------------------------------------
15+
16+
Does this tag change answers significantly for any of the following physics configurations?
17+
(Details of any changes will be given in the "Answer changes" section below.)
18+
19+
[ ] clm6_0
20+
21+
[ ] clm5_0
22+
23+
[ ] ctsm5_0-nwp
24+
25+
[ ] clm4_5
26+
27+
28+
Bugs fixed
29+
----------
30+
31+
List of CTSM issues fixed (include CTSM Issue # and description):
32+
- [Issue #2541: Some links in User's Guide sidebar are broken](https://github.com/ESCOMP/CTSM/issues/2541)
33+
- [Issue #2839: Automatically publish updated docs](https://github.com/ESCOMP/CTSM/issues/2839)
34+
- [Issue #3121: Fix capital letter in doc filenames](https://github.com/ESCOMP/CTSM/issues/3121)
35+
36+
Notes of particular relevance for users
37+
---------------------------------------
38+
39+
Changes to documentation:
40+
- Canonical URL for User's Guide and Tech Note will be changing from https://escomp.github.io/ctsm-docs to https://escomp.github.io/ctsm.
41+
- Updates to "Working with the CTSM documentation" section
42+
43+
44+
Notes of particular relevance for developers:
45+
---------------------------------------------
46+
47+
We're going to get rid of the ctsm-docs repo!
48+
49+
50+
Testing summary:
51+
----------------
52+
53+
None, as no code is changing aside from the documentation infrastructure, which is tested in GitHub Workflows.
54+
55+
Other details
56+
-------------
57+
58+
List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
59+
- doc-builder
60+
61+
Pull Requests that document the changes (include PR ids):
62+
- [Pull Request #3146: ctsm5.3.048: Automatically publish docs to this repo by samsrabin](https://github.com/ESCOMP/CTSM/pull/3146/files)
63+
64+
===============================================================
65+
===============================================================
66+
Tag name: ctsm5.3.047
67+
Originator(s): samrabin (Sam Rabin, UCAR/TSS)
68+
Date: Mon May 26 16:30:10 MDT 2025
69+
One-line Summary: Merge b4b-dev to master
70+
71+
Purpose and description of changes
72+
----------------------------------
73+
74+
Merge b4b-dev to master. Includes PRs:
75+
- [Pull Request #3056: QOL improvements in mksurfdata_esmf makefile by samsrabin](https://github.com/ESCOMP/CTSM/pull/3056)
76+
- [Pull Request #3100: Fix Longitude comparison error for regional subset_data by samsrabin](https://github.com/ESCOMP/CTSM/pull/3100)
77+
- [Pull Request #3122: Fix a couple of things in documentation conf.py by samsrabin](https://github.com/ESCOMP/CTSM/pull/3122)
78+
- [Pull Request #3128: Fix ctsm-docs container version tagging by samsrabin](https://github.com/ESCOMP/CTSM/pull/3128)
79+
- [Pull Request #3138: Don't build docs for ChangeLog/Sum by samsrabin](https://github.com/ESCOMP/CTSM/pull/3138)
80+
- [Pull Request #3143: Don't run workflows on plain tag creation by samsrabin](https://github.com/ESCOMP/CTSM/pull/3143)
81+
- [Pull Request #3144: Add docs issue template by samsrabin](https://github.com/ESCOMP/CTSM/pull/3144)
82+
83+
Significant changes to scientifically-supported configurations
84+
--------------------------------------------------------------
85+
86+
Does this tag change answers significantly for any of the following physics configurations?
87+
(Details of any changes will be given in the "Answer changes" section below.)
88+
89+
[ ] clm6_0
90+
91+
[ ] clm5_0
92+
93+
[ ] ctsm5_0-nwp
94+
95+
[ ] clm4_5
96+
97+
98+
Bugs fixed
99+
----------
100+
101+
List of CTSM issues fixed (include CTSM Issue # and description):
102+
- [Issue #3093: subset_data: Longitude comparison error](https://github.com/ESCOMP/CTSM/issues/3093)
103+
- [Issue #3126: Increment docs container version](https://github.com/ESCOMP/CTSM/issues/3126)
104+
- [Issue #3142: Workflows run on new tags even w/o file changes](https://github.com/ESCOMP/CTSM/issues/3142)
105+
106+
107+
Testing summary:
108+
----------------
109+
110+
111+
[PASS means all tests PASS; OK means tests PASS other than expected fails.]
112+
113+
build-namelist tests (if CLMBuildNamelist.pm has changed):
114+
115+
derecho - PASS
116+
117+
python testing (if python code has changed; see instructions in python/README.md; document testing done):
118+
119+
derecho - PASS
120+
121+
regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
122+
123+
derecho ----- OK
124+
izumi ------- OK
125+
126+
127+
Other details
128+
-------------
129+
130+
Pull Requests that document the changes (include PR ids):
131+
- [Pull Request #3154: Merge b4b-dev 2025-05-24 by samsrabin](https://github.com/ESCOMP/CTSM/pull/3154)
132+
133+
===============================================================
134+
===============================================================
135+
Tag name: ctsm5.3.046
136+
Originator(s): rgknox (Ryan Knox)
137+
Date: Mon 26 May 2025 02:45:52 AM MDT
138+
One-line Summary: For FATES set itype to ispval and a few unused variables to nan to help prevent future problems
139+
140+
Purpose and description of changes
141+
----------------------------------
142+
143+
144+
On FATES patches, there should be no notion of pft associated with the patch, and therefore patch%itype should always be invalid.
145+
Even for FATES-SP, the patch should be associated with the FATES pft, which is not associated with itype. In this set of changes,
146+
itype is set to spval on fates patches. This will help prevent bugs in the future, because its use in a fates context should trigger
147+
errors, particularly in debug mode.
148+
149+
When FATES with itype tset o ispval which when used in DEBUG mode will show up as a bounds overflow.
150+
For example in issue 2932, where the use of Meier 2022 was turned on in FATES and shouldn't have been.
151+
152+
For FATES also set the fields downreg, leafn, froot, and croot t NaN, so when used in DEBUG mode their use will result in a floting
153+
point exception.
154+
155+
156+
Significant changes to scientifically-supported configurations
157+
--------------------------------------------------------------
158+
159+
Does this tag change answers significantly for any of the following physics configurations?
160+
(Details of any changes will be given in the "Answer changes" section below.)
161+
162+
[Put an [X] in the box for any configuration with significant answer changes.]
163+
164+
[ ] clm6_0
165+
166+
[ ] clm5_0
167+
168+
[ ] ctsm5_0-nwp
169+
170+
[ ] clm4_5
171+
172+
173+
Bugs fixed
174+
----------
175+
176+
List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
177+
Fixed #2933 -- setting patch%itype to invalid for FATES patches
178+
179+
Notes of particular relevance for users
180+
---------------------------------------
181+
182+
Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
183+
Dissallow drydep or MEGAN for all FATES types including FatesSp and die with
184+
a fatal_error, rather than a warning
185+
186+
Notes of particular relevance for developers:
187+
---------------------------------------------
188+
189+
Caveats for developers (e.g., code that is duplicated that requires double maintenance):
190+
Unfrtunately setting itype doesn't fix all possible problems with
191+
See discussin #2149
192+
193+
Changes to tests or testing:
194+
Disable FatesSp drydep and MEGAN tests
195+
196+
Testing summary: regular fates
197+
----------------
198+
[PASS means all tests PASS; OK means tests PASS other than expected fails.]
199+
200+
build-namelist tests (if CLMBuildNamelist.pm has changed):
201+
202+
derecho - OK
203+
204+
python testing (if python code has changed; see instructions in python/README.md; document testing done):
205+
206+
derecho - PASS
207+
208+
regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
209+
210+
derecho ----- OK
211+
izumi ------- OK
212+
213+
If the tag used for baseline comparisons was NOT the previous tag, note that here:
214+
215+
216+
Answer changes
217+
--------------
218+
219+
Changes answers relative to baseline: No bit-fr-bit
220+
221+
Other details
222+
-------------
223+
224+
Pull Requests that document the changes (include PR ids):
225+
(https://github.com/ESCOMP/ctsm/pull)
226+
https://github.com/ESCOMP/CTSM/pull/2935
227+
228+
===============================================================
229+
===============================================================
2230
Tag name: ctsm5.3.045
3231
Originator(s): glemieux (Gregory Lemieux, LBNL, [email protected])
4232
Date: Tue May 20 11:56:15 MDT 2025

‎doc/ChangeSum‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,8 @@
11
Tag Who Date Summary
22
============================================================================================================================
3+
ctsm5.3.048 samrabin 05/26/2025 Automatically publish docs to this repo
4+
ctsm5.3.047 samrabin 05/26/2025 Merge b4b-dev to master
5+
ctsm5.3.046 rgknox 05/26/2025 For FATES set itype to ispval and a few unused variables to nan to help prevent future problems
36
ctsm5.3.045 glemieux 05/20/2025 FATES default parameter update for API 40
47
ctsm5.3.044 slevis 05/14/2025 Introduce time-evolving LEAFCN_TARGET as function of leafcn param
58
ctsm5.3.043 slevis 05/09/2025 Merge b4b-dev

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