Merge tag 'ctsm5.3.012' into merge-b4bdev-20241125

Fates fuel refactor

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.3_api.36.1.0
+fxtag = sci.1.79.3_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

bld/CLMBuildNamelist.pm

@@ -2588,12 +2588,9 @@ sub setup_logic_initial_conditions {
   my $finidat = $nl->get_value($var);
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
-    if (defined $finidat ) {
-      $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
+    if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
+      $log->fatal_error("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incompatible with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
-      $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );
-      my $group = $definition->get_group_name($var);
-      $nl->set_variable_value($group, $var, "' '" );
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                 $var, 'val'=>"' '", 'no_abspath'=>1);

bld/unit_testers/build-namelist_test.pl

@@ -1314,10 +1314,6 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
-     "coldwfinidat"              =>{ options=>"-envxml_dir . -clm_start_type cold",
-                                     namelst=>"finidat = 'testfile.nc'",
-                                     phys=>"clm5_0",
-                                   },
      "bgcspin_w_suplnitro"       =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup on",
                                      namelst=>"suplnitro='ALL'",
                                      phys=>"clm5_0",
@@ -1398,6 +1394,56 @@ sub cat_and_create_namelistinfile {
    system( "cat $tempfile" );
 }
 
+print "\n===============================================================================\n";
+print "Ensure cold starts with finidat are handled properly \n";
+print "=================================================================================\n";
+
+my %coldwfinidat = (
+     "bgc"   => { options=>"-envxml_dir . -clm_start_type cold",
+                  namelst=>"finidat = 'testfile.nc'",
+                  phys=>"clm5_0",
+                  expected_fail=>1,
+                },
+     "fates" => { options=>"-envxml_dir . -clm_start_type cold -bgc fates -no-megan",
+                  namelst=>"finidat = 'testfile.nc', use_fates = .true.",
+                  phys=>"clm5_0",
+                  expected_fail=>0,
+                },
+);
+my $finidat;
+foreach my $key ( keys(%coldwfinidat) ) {
+   print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst", "expected_fail" ) {
+      if ( not exists $coldwfinidat{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for coldwfinidat $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
+   &make_config_cache($coldwfinidat{$key}{"phys"});
+   my $options  = $coldwfinidat{$key}{"options"};
+   my $namelist = $coldwfinidat{$key}{"namelst"};
+   my $expected_fail = $coldwfinidat{$key}{"expected_fail"};
+   my %settings;
+   &make_env_run( %settings );
+
+   # Should fail if expected to, pass otherwise
+   eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+   is( $? eq 0, $expected_fail eq 0, "coldwfinidat $key run");
+
+   if ( $expected_fail ) {
+      # Now run with -ignore_warnings and make sure it still doesn't work
+      $options .= " -ignore_warnings";
+      eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+      isnt( $?, 0, "coldwfinidat $key run -ignore_warnings" );
+   } else {
+      # Check that finidat was correctly set
+      $finidat = `grep finidat lnd_in`;
+      ok ( $finidat =~ "testfile.nc", "coldwfinidat $key finidat? $finidat" );
+   }
+}
+
 #
 # Loop over all physics versions
 #

cime_config/testdefs/ExpectedTestFails.xml

@@ -180,6 +180,10 @@
       <status>FAIL</status>
       <issue>#2454</issue>
     </phase>
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
   </test>
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
@@ -188,6 +192,13 @@
       <issue>#2454</issue>
     </phase>
   </test>
+
+  <test name="ERS_Ld60.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdST3">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2867</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
@@ -270,21 +281,22 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
+  <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>
+
+  <!-- izumi nag failures -->
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
-    <phase name="COMPARE_base_rest">
+  <test name="SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only">
+    <phase name="RUN">
       <status>FAIL</status>
-      <issue>#2325</issue>
+      <issue>#2861</issue>
     </phase>
   </test>
 
-  <!-- izumi nag failures -->
   <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
     <phase name="RUN">
       <status>FAIL</status>
@@ -334,6 +346,12 @@
     </phase>
   </test>
 
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_intel.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
@@ -348,6 +366,29 @@
       <issue>#2810</issue>
     </phase>
   </test>
+
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELLO">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
 
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 

cime_config/testdefs/testlist_clm.xml

@@ -2679,7 +2679,7 @@
       <option name="comment"  >5x5_amazon grid with FATES and latest CLM</option>
     </options>
   </test>
-  <test name="ERS_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="ERS_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
@@ -2688,7 +2688,7 @@
       <option name="comment"  >This test should be converted to an ERP test once the PEM version of this test is passing COMPARE_base_modpes. Also change to 5x5_amazon once ccs_config updated to allow it</option>
     </options>
   </test>
-  <test name="PEM_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="PEM_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>

cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm

@@ -1 +1,2 @@
 use_fates_ed_st3= .true.
+hist_fexcl1 = 'FATES_ERROR_EL'

doc/ChangeLog

@@ -1,4 +1,149 @@
 ===============================================================
+Tag name: ctsm5.3.012
+Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
+Date: Wed 13 Nov 2024 09:53:51 AM MST
+One-line Summary: update fates tag
+
+Purpose and description of changes
+----------------------------------
+
+Updates FATES tag to latest fates main (sci.1.79.3_api.37.0.0), and updates API to go
+along with latest FATES update to refactor it's fire equations
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+
+
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests:
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+Round-off differences for FATES compsets where fire is active.
+NLCOMP differences for some FATES compsets
+
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2782: Fates fuel refactor (https://github.com/ESCOMP/CTSM/pull/2782)
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.011
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, [email protected])
+Date: Mon Nov 11 17:55:57 MST 2024
+One-line Summary: Improve handling of cold-start finidat
+
+Purpose and description of changes
+----------------------------------
+
+This PR changes things so that:
+
+1. Cold-start FATES runs with finidat specified will not require -ignore_warnings, and the supplied finidat will actually be obeyed.
+2. Cold-start non-FATES runs will not be allowed, even with -ignore_warnings.
+
+
+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.)
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List of CTSM issues fixed:
+- Resolves ESCOMP/CTSM#2856: FATES will never start from specified finidat (https://github.com/ESCOMP/CTSM/issues/2856)
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Changes to tests or testing:
+Adds three fates suite tests to expected fails:
+- ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold
+- SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro
+- ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests:
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES cold-start runs with finidat
+    - what platforms/compilers: All
+    - nature of change: new climate
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2870: Fix handling of finidat with cold starts (https://github.com/ESCOMP/CTSM/pull/2870)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.010
 Originator(s): afoster (Adrianna Foster)
 Date: Sat Nov  9 12:54:18 MST 2024

doc/ChangeSum

@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.012  afoster 11/13/2024 update fates tag
+       ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev
        ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests
        ctsm5.3.008   olyson 10/14/2024 PPE change to sa_leaf in CanopyFluxesMod.F90