Merge remote-tracking branch 'escomp/master' into deadveg

slevis resolved conflicts: doc/ChangeLog doc/ChangeSum
olyson · Mar 13, 2024 · 6126bf2 · 6126bf2
2 parents 89b037b + 55f2cf3
commit 6126bf2
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -30,3 +30,4 @@ d866510188d26d51bcd6d37239283db690af7e82
 8a168bb0895f4f2421608dd2589398e13a6663e6
 183fc26a6691bbdf87f515dc47924a64be3ced9b
 6fccf682eaf718615407d9bacdd3903b8786a03d
+2500534eb0a83cc3aff94b30fb62e915054030bf
diff --git a/Externals.cfg b/Externals.cfg
@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_96
+tag = cismwrap_2_1_97
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_78
+tag = rtm1_0_79
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_48
+tag = mosart1_0_49
 required = True
 
 [mizuRoute]
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.84
+tag = ccs_config_cesm0.0.92
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.175
+tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.14.43
+tag = cmeps0.14.50
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.24
+tag = cdeps1.0.28
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.17
+tag = share1.0.18
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -98,4 +98,4 @@ tag = v1.0.8
 required = False
 
 [externals_description]
-schema_version = 1.0.0
+schema_version = 1.0.0
diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.71.0_api.33.0.0
+repo_url = https://github.com/rgknox/fates
+tag = sci.1.72.2_api.34.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -784,7 +784,8 @@ sub setup_cmdl_fates_mode {
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
-                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
+                      "fates_parteh_mode","use_fates_tree_damage","fates_history_dimlevel","fates_seeddisp_cadence",
+		      "use_fates_luh","fluh_timeseries" );
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
           if ( defined($nl->get_value($var)) ) {
@@ -4438,7 +4439,8 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
-                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
+                       "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
+		       "use_fates_luh","fates_history_dimlevel" );
         foreach my $var ( @list ) {
  	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
                       'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -2786,7 +2786,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_luh                 use_fates=".true.">.false.</use_fates_luh>
 <fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
 <fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
-
+<fates_history_dimlevel        use_fates=".true.">2,2</fates_history_dimlevel>
 <use_fates_nocomp              use_fates=".true." use_fates_sp=".true.">.true.</use_fates_nocomp>
 <use_fates_nocomp              use_fates=".true."                      >.false.</use_fates_nocomp>
 <use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true.">.true.</use_fates_fixed_biogeog>

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -777,6 +777,19 @@ Full pathname to the inventory initialization control file.
 (Only relevant if FATES is on).
 </entry>
 
+<entry id="fates_history_dimlevel" type="integer(2)" category="physics"
+       group="clm_inparm" valid_values="0,1,2" >
+  Setting for what types of FATES history to be allocate and
+  calculated at the dynamics timestep (1st integer) and the
+  model timestep (2nd integer). This must be consistent with
+  hist_fincl*, ie output variables must not be listed if the
+  output level is not enabled.
+  0 = no fates history variables are calculated or allocated
+  1 = only time x space (3d) fates history variables allowed
+  2 = multiplexed dimensioned fates history is also allowed
+  (Only relevant if FATES is on)
+</entry>
+
 <!-- This may eventually migrate to the dynamic_subgrid group-->
 <entry id="use_fates_luh" type="logical" category="physics"
        group="clm_inparm" valid_values="" >

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1999;
+my $ntests = 1549;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1353;
+   $ntests += 907;
 }
 plan( tests=>$ntests );
 
@@ -190,8 +190,7 @@ sub cat_and_create_namelistinfile {
 &make_config_cache($phys);
 
 my $DOMFILE = "$inputdata_rootdir/atm/datm7/domain.lnd.T31_gx3v7.090928.nc";
-my $real_par_file = "user_nl_ctsm_real_parameters";
-my $bldnml = "../build-namelist -verbose -csmdata $inputdata_rootdir -configuration clm -structure standard -glc_nec 10 -no-note -output_reals $real_par_file";
+my $bldnml = "../build-namelist -verbose -csmdata $inputdata_rootdir -configuration clm -structure standard -glc_nec 10 -no-note";
 if ( $opts{'test'} ) {
    $bldnml .= " -test";
 }
@@ -201,7 +200,7 @@ sub cat_and_create_namelistinfile {
   system( "/bin/rm $tempfile" );
 }
 
-my @files = ( "lnd_in", $tempfile, $real_par_file );
+my @files = ( "lnd_in", $tempfile );
 my $cwd = `pwd`;
 chomp( $cwd );
 my $cfiles = NMLTest::CompFiles->new( $cwd, @files );
@@ -269,13 +268,11 @@ sub cat_and_create_namelistinfile {
       $cfiles->copyfiles( "most_options", $mode );
    # Compare to default
       $cfiles->doNOTdodiffonfile( "lnd_in",    "default", $mode );
-      $cfiles->doNOTdodiffonfile( "$real_par_file", "default", $mode );
       $cfiles->doNOTdodiffonfile( "$tempfile", "default", $mode );
       $cfiles->comparefiles( "default", $mode );
    # Compare to baseline
    if ( defined($opts{'compare'}) ) {
       $cfiles->dodiffonfile(      "lnd_in",    "most_options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "most_options", $mode );
       $cfiles->doNOTdodiffonfile( "$tempfile", "most_options", $mode );
       $cfiles->comparefiles( "most_options", $mode, $opts{'compare'} );
    }
@@ -358,7 +355,6 @@ sub cat_and_create_namelistinfile {
       }
       if ( defined($opts{'compare'}) ) {
          $cfiles->doNOTdodiffonfile( "$tempfile", "$base_options $options", $mode );
-         $cfiles->dodiffonfile( "$real_par_file", "$base_options $options", $mode );
          $cfiles->comparefiles( "$base_options $options", $mode, $opts{'compare'} );
       }
       if ( defined($opts{'generate'}) ) {
@@ -408,7 +404,6 @@ sub cat_and_create_namelistinfile {
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
       $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -445,7 +440,6 @@ sub cat_and_create_namelistinfile {
       if ( defined($opts{'compare'}) ) {
          $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
          $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
-         $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
          $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
       }
       if ( defined($opts{'generate'}) ) {
@@ -486,7 +480,6 @@ sub cat_and_create_namelistinfile {
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
       $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1388,7 +1381,6 @@ sub cat_and_create_namelistinfile {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
 
@@ -1473,7 +1465,6 @@ sub cat_and_create_namelistinfile {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1547,7 +1538,6 @@ sub cat_and_create_namelistinfile {
    $cfiles->shownmldiff( "default", "standard" );
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-      $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
       $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
    }
    if ( defined($opts{'generate'}) ) {
@@ -1574,7 +1564,6 @@ sub cat_and_create_namelistinfile {
       $cfiles->shownmldiff( "default", "standard" );
       if ( defined($opts{'compare'}) ) {
          $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
-         $cfiles->dodiffonfile( "$real_par_file", "$options", $mode );
          $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
       }
       if ( defined($opts{'generate'}) ) {
@@ -1757,7 +1746,6 @@ sub cleanup {
   my $type = shift;
 
   print "Cleanup files created\n";
-  system( "/bin/rm env_run.xml $real_par_file" );
   if ( defined($type) ) {
      if ( $type eq "config" ) {
         system( "/bin/rm config_cache.xml" );

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -29,12 +29,6 @@
 
 
   <!-- cesm3_dev test suite failures -->
-  <test name="ERP_D_Ld9.ne30pg3_t232.IHistClm51BgcCrop.derecho_intel.clm-clm51cam6LndTuningMode">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2268</issue>
-    </phase>
-  </test>
 
   <!-- aux_clm test suite failures -->
   <test name="SMS_D_Ld1_Mmpi-serial_Vmct.f45_f45_mg37.I2000Clm50SpRs.izumi_gnu.clm-ptsRLA">
@@ -58,41 +52,6 @@
     </phase>
   </test>
 
-  <test name="FUNITCTSM_P1x1.f10_f10_mg37.I2000Clm50Sp.derecho_intel">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#131</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm50FatesRs.derecho_intel.clm-FatesCold">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm51FatesRs.derecho_intel.clm-FatesCold">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.derecho_intel.clm-ptsRLA">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Lm1_Mmpi-serial.CLM_USRDAT.I1PtClm50SpRs.derecho_intel.clm-USUMB_nuopc">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.derecho_gnu.clm-default--clm-NEON-NIWO">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -199,20 +158,6 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesCold">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdHydro">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/ccs_config_cesm#130</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdPRT2">
     <phase name="RUN">
       <status>PEND</status>