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

olyson · Oct 14, 2024 · 0464237 · 0464237
2 parents 6c7ecf6 + 6d8dad8
commit 0464237
Show file tree

Hide file tree

Showing 74 changed files with 1,338 additions and 1,146 deletions.
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -51,3 +51,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
+f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
diff --git a/.gitmodules b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.2_api.36.0.0
+fxtag = sci.1.78.3_api.36.1.0
 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

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -2756,6 +2756,12 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
         $log->fatal_error("$useinitvar is being set for you but a $var was not found, so $useinitvar, init_interp_attributes, and finidat must not be set correctly for this configuration in the namelist_default file" );
      }
   }
+
+  # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
+  if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
+     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values from initial conditions, even if the initial conditions (finidat) file has hillslope information. If you are sure you want this behaviour, add -ignore_warnings to CLM_BLDNML_OPTS.")
+  }
+
 } # end initial conditions
 
 #-------------------------------------------------------------------------------
@@ -3630,6 +3636,10 @@ sub setup_logic_hillslope {
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
       $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
   }
+  my $hillslope_file = $nl->get_value('hillslope_file');
+  if ( &value_is_true($use_hillslope) && ( ! defined($hillslope_file) ) ) {
+    $log->fatal_error("You must provide hillslope_file if use_hillslope is .true.\n" );
+  }
 }
 
 #-------------------------------------------------------------------------------

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -962,6 +962,11 @@ Full pathname datafile with fates parameters
 Full pathname of surface data file.
 </entry>
 
+<entry id="hillslope_file" type="char*256"     category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname of hillslope data file.
+</entry>
+
 <entry id="fsnowoptics" type="char*256" category="datasets" 
        input_pathname="abs" group="clm_inparm" valid_values="" >
 SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3994;
+my $ntests = 3997;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2437;
@@ -1287,6 +1287,13 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for failtest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($failtest{$key}{"phys"});
    my $options  = $failtest{$key}{"options"};
    my $namelist = $failtest{$key}{"namelst"};
@@ -1359,9 +1366,21 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      phys=>"clm6_0",
                                    },
+     "hillslope with init_interp"=>{ options=>"--res 10x15 --bgc bgc --envxml_dir .",
+                                     namelst=>"use_init_interp=.true.,use_hillslope=.true.,hillslope_file='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
                );
 foreach my $key ( keys(%warntest) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $warntest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for warntest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($warntest{$key}{"phys"});
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
@@ -1591,6 +1610,14 @@ sub cat_and_create_namelistinfile {
 
 foreach my $key ( keys(%finidat_files) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "atm_forc", "res", "bgc", "crop", "use_case", "start_ymd", "namelist" ) {
+      if ( not exists $finidat_files{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for finidat_file $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    my $phys = $finidat_files{$key}{'phys'};
    print "physics = $phys\n";
    &make_config_cache($phys);

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -16,7 +16,7 @@
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
     <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm5.0:</desc>
     <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
-    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
+    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
 
     <desc option="SP-VIC"          >Satellite phenology with VIC hydrology:</desc>
@@ -371,6 +371,10 @@
       <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>
     </values>
     <group>run_component_ctsm</group>
     <file>env_case.xml</file>

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -200,13 +200,21 @@
     <alias>I1850Clm50BgcCropCmip6</alias>
     <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I1850Clm60BgcCropCmip6</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <!-- Primarily for testing the CMIP6WACCMDECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
   <compset>
     <alias>I1850Clm50BgcCropCmip6waccm</alias>
     <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I1850Clm60BgcCropCmip6waccm</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <!-- clm5_0 (CMIP6) version with BGC-Crop and CRU forcing -->
   <compset>

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -37,6 +37,50 @@
   </test>
 
   <!-- aux_clm test suite failures -->
+  <test name="SMS_Ld2_D_PS.f09_g17.I1850Clm50BgcCropCmip6.derecho_intel.clm-basic_interp">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+  <test name="ERS_Ly3.f10_f10_mg37.I1850Clm50BgcCropCmip6.derecho_intel.clm-basic">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+  <test name="SMS_Lm1.f10_f10_mg37.I1850Clm50BgcCropCmip6waccm.derecho_gnu.clm-basic">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2787</issue>
+      <comment>The issue shows how to fix it.</comment>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-default--clm-NEON-HARV--clm-matrixcnOn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+  <test name="SMS_D.1x1_brazil.I1850Clm60BgcCrop.derecho_gnu.clm-mimics_matrixcn">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2780</issue>
+      <comment>Crashes in the matrix solver.</comment>
+    </phase>
+  </test>
+
   <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="BASELINE">
       <status>FAIL</status>
@@ -51,6 +95,13 @@
       <comment>This failure relates to the preceding ERP failure.</comment>
     </phase>
   </test>
+  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
+    <phase name="BASELINE">
+      <status>FAIL</status>
+      <issue>#2619</issue>
+      <comment>This failure relates to the preceding ERP failure.</comment>
+    </phase>
+  </test>
 
   <test name="PEM_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode">
     <phase name="COMPARE_base_modpes">
@@ -84,6 +135,17 @@
     </phase>
   </test>
 
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2310</issue>
+    </phase>
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2310</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -120,6 +182,13 @@
     </phase>
   </test>
 
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
+    <phase name="CREATE_NEWCASE">
+      <status>FAIL</status>
+      <issue>#2454</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">
       <status>FAIL</status>
@@ -194,13 +263,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld5.5x5_amazon.I1850Clm51Bgc.derecho_gnu.clm-HillslopeC">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2423</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
@@ -229,6 +291,13 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm51Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1732,7 +1732,7 @@
       <option name="comment"       >Repeat ERS_Ly20_Mmpi-serial...cropMonthlyNoinitial test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic">
+  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1773,7 +1773,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">02:30:00</option>
       <option name="comment"  >Repeat ERS_Ly5_P128x1...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>
@@ -1987,7 +1987,7 @@
       <option name="comment"  >Simple test to make sure the basic Fates-SP compset works"</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -1996,7 +1996,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2431,7 +2431,7 @@
       <option name="comment"  >include a production intel test of Clm45</option>
     </options>
   </test>
-  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
+  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic_interp">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -3262,7 +3262,7 @@
       <option name="comment">12 month exact restart FATES single site debug test covering anthropogenic fire ignition mode.</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6waccm" testmods="clm/basic">
+  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6waccm" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prealpha"/>
@@ -3511,23 +3511,24 @@
     </options>
   </test>
 
-  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment">Serial test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 
-  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">Add a non-FATES test to aux_clm for 5x5_amazon that fails because of the ccs_config issue, can remove once this passes</option>
+      <option name="comment">Parallel test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
@@ -0,0 +1,8 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates
+FATESPARAMFILE=$CASEDIR/fates_params_hydrograsstempfix.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_allom_smode --val 1 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
@@ -2,6 +2,7 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
+fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.nc'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./xmlchange CLM_BLDNML_OPTS="-i-clm_demand -flanduse_timeseries" --append
+./xmlchange CLM_BLDNML_OPTS="-clm_demand flanduse_timeseries" --append