Merge remote-tracking branch 'upstream/master' into noresm

NorESMhub · Jan 25, 2024 · e8c5a94 · e8c5a94
2 parents a5b9683 + a73a170
commit e8c5a94
Show file tree

Hide file tree

Showing 17 changed files with 1,170 additions and 665 deletions.
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -21,6 +21,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 025d5e7c2e80263717fb029101d65cbbf261c3c4
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
@@ -0,0 +1,23 @@
+name: Auto Assign to Project(s)
+
+on:
+  issues:
+    types: [opened, labeled]
+  pull_request:
+    types: [opened, labeled]
+  issue_comment:
+    types: [created]
+
+jobs:
+  assign_high_priority:
+    runs-on: ubuntu-latest
+    name: Assign to High Priority project
+    steps:
+    - name: Assign issues and pull requests with `priority: high` label to project 25
+      uses: srggrs/assign-one-project-github-action@1.3.1
+      if: |
+        contains(github.event.issue.labels.*.name, 'priority: high') ||
+        contains(github.event.pull_request.labels.*.name, 'priority: high')
+      with:
+        project: 'https://github.com/ESCOMP/CTSM/projects/25'
+        column_name: 'Needs triage'
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1571,6 +1571,7 @@ sub process_namelist_inline_logic {
   setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_start_type($opts, $nl_flags, $nl);
   setup_logic_decomp_performance($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_roughness_methods($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_snicar_methods($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl,  $envxml_ref);
@@ -1636,7 +1637,7 @@ sub process_namelist_inline_logic {
   ###############################
   # namelist group: tillage     #
   ###############################
-  setup_logic_tillage($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 
   ###############################
   # namelist group: ch4par_in   #
@@ -2002,6 +2003,25 @@ sub setup_logic_decomp_performance {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_roughness_methods {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method',
+              'phys'=>$nl_flags->{'phys'} );
+
+  my $var = remove_leading_and_trailing_quotes( $nl->get_value("z0param_method") );
+  if ( $var ne "Meier2022" && $var ne "ZengWang2007" ) {
+    $log->fatal_error("$var is incorrect entry for the namelist variable z0param_method; expected Meier2022 or ZengWang2007");
+  }
+  my $phys = $physv->as_string();
+  if ( $phys eq "clm4_5" || $phys eq "clm5_0" ) {
+    if ( $var eq "Meier2022" ) {
+      $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm5_1 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file");
+    }
+  }
+}
+#-------------------------------------------------------------------------------
+
 sub setup_logic_snicar_methods {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -2242,6 +2262,7 @@ sub setup_logic_crop_inparm {
                  'use_crop'=>$nl->get_value('use_crop') );
 
      my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_residue_removal_frac' );
      if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
         $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
      }
@@ -2254,10 +2275,13 @@ sub setup_logic_crop_inparm {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_tillage {
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode',
+              'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() );
 
   my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) );
-  if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) {
+  if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl_flags->{'use_crop'}) ) {
       $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." );
   }
 }

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -499,6 +499,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- ================================================================== -->
 
 <z0param_method>ZengWang2007</z0param_method>
+<z0param_method phys="clm5_1">Meier2022</z0param_method>
 
 <use_z0m_snowmelt z0param_method="Meier2022" >.true.</use_z0m_snowmelt>
 <use_z0m_snowmelt >.false.</use_z0m_snowmelt>
@@ -554,6 +555,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_grainproduct use_crop=".true." phys="clm5_1" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
 
 <crop_residue_removal_frac>0.d+0</crop_residue_removal_frac>
+<crop_residue_removal_frac phys="clm5_1">0.5d00</crop_residue_removal_frac>
 
 <!-- Crop model options -->
 <baset_mapping           use_crop=".true." phys="clm4_5" >constant</baset_mapping>
@@ -2813,6 +2815,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <!-- =========================================  -->
 
 <tillage_mode>off</tillage_mode>
+<tillage_mode use_crop=".true." phys="clm5_1">low</tillage_mode>
+
 <use_original_tillage_phases>.false.</use_original_tillage_phases>
 <max_tillage_depth>0.26d00</max_tillage_depth>
 

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -228,4 +228,25 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
+  </test>
+
 </expectedFails>
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -3437,6 +3437,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,162 @@
 ===============================================================
+Tag name: ctsm5.1.dev166
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), samrabin (Sam Rabin)
+Date: Wed 24 Jan 2024 05:39:41 PM MST
+One-line Summary: BFB merge tag
+
+Purpose and description of changes
+----------------------------------
+
+ #2315 @TeaganKing Refactoring run_neon for PLUMBER2 part1
+ #2213 @samsrabin Automatically assign high priority items to project 25
+ #2330 @samsrabin Add Izumi version of the aux_clm unit testing
+ #2326 @samsrabin run_sys_tests: Check Python environment for FatesColdTwoStream tests
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+CTSM issues fixed (include CTSM Issue #):
+ Fixes #2315
+ Fixes #2213
+ Fixes #2330
+ Fixes #2326
+
+Known bugs introduced in this tag (include issue #):
+ - New feature coming in with #2213 where user will receive email from
+ github when pushing to their remote:
+ "Run failed: .github/workflows/assign-to-project.yml"
+ - New feature that also affects older tags: The izumi FatesColdTwoStream
+ test submitted from ./run_sys_tests will fail at CREATE_NEWCASE unless users
+ introduce "module load lang/python/3.7.0" in their .bash_profile.
+ Longterm solution discussed in #2335. The test also works when submitted
+ manually with ./create_test.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ #2315 New unit tests for arg_parse and NeonSite
+ #2330 New test in aux_clm that does unit testing on izumi because unit
+       testing does not work on derecho, yet
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - OK, pylint gives long list of warnings (expected)
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+Changes answers relative to baseline: No
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2334
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev165
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), oleson (Keith Oleson), samrabin (Sam Rabin)
+Date: Fri 19 Jan 2024 06:40:36 PM MST
+One-line Summary: Turn Meier2022, tillage, and residue removal on for ctsm5.1, fix #2212
+
+Purpose and description of changes
+----------------------------------
+
+Answer-changing merge-tag:
+- Turn Meier2022 on for ctsm5.1. Had turned off temporarily while fixing a bug.
+- Bring in Urban answer fix #2212.
+- Turn tillage and residue removal on for ctsm5.1.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[x] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+CTSM issues fixed (include CTSM Issue #):
+Fixes #2212
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+- Making Meier2022 the default for ctsm5.1 again.
+- Making tillage low by default for ctsm5.1.
+- Making residue removal 0.5 by default for ctsm5.1.
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES
+
+  [ If a tag changes answers relative to baseline comparison the
+    following should be filled in (otherwise remove this section).
+    And always remove these three lines and parts that don't apply. ]
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: ALL
+    - what platforms/compilers: ALL
+    - nature of change:i
+ clm45 and clm50: larger than roundoff
+ clm51: possibly climate changing
+        Effect of Meier2022 was documented here: https://github.com/NCAR/LMWG_dev/issues/38
+        Effect of tillage and residue removal may require an Answer Changing Tag simulation
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2323
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev164
 Originator(s): rgknox (Ryan Knox)
 Date: Wed 17 Jan 2024 12:38:18 PM MST

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,7 +1,9 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev166 multiple 01/24/2024 BFB merge tag
+    ctsm5.1.dev165   slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212
     ctsm5.1.dev164   rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream
-    ctsm5.1.dev163      sam 01/10/2024 Add tillage and residue removal
+    ctsm5.1.dev163 samrabin 01/10/2024 Add tillage and residue removal
     ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files
     ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation
     ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1