Update submodules to ones that are based on cesm3_0_alpha04a

.gitmodules

@@ -60,67 +60,67 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n02_v2.1.2
+fxtag = cesm-coupling.n02_v2.1.3
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.0
+fxtag = ccs_config_cesm1.0.10
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.0.246
+fxtag = cime6.1.37
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps0.14.77
+fxtag = cmeps1.0.16
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.48
+fxtag = cdeps1.0.53
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.0.19
+fxtag = share1.1.2
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
-[submodule "mct"]
-path = libraries/mct
-url = https://github.com/MCSclimate/MCT
-fxtag = MCT_2.11.0
-fxrequired = ToplevelRequired
-# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/MCSclimate/MCT
-
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_2
+fxtag = pio2_6_3
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
+[submodule "mpi-serial"]
+path = libraries/mpi-serial
+url = https://github.com/ESMCI/mpi-serial
+fxtag = MPIserial_2.5.1
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial
+
 [submodule "doc-builder"]
 path = doc/doc-builder
 url = https://github.com/ESMCI/doc-builder

bld/CLMBuildNamelist.pm

@@ -71,7 +71,7 @@ REQUIRED OPTIONS
                               (if read they allow user_nl_clm and CLM_BLDNML_OPTS to expand
                                variables [for example to use \$DIN_LOC_ROOT])
                               (default current directory)
-     -lnd_frac "domainfile"   Land fraction file (the input domain file) (needed for LILAC)
+     -lnd_frac "domainfile"   Land fraction file (the input domain file) (only needed with --lilac option)
      -res "resolution"        Specify horizontal grid.  Use nlatxnlon for spectral grids;
                               dlatxdlon for fv grids (dlat and dlon are the grid cell size
                               in degrees for latitude and longitude respectively)
@@ -1994,7 +1994,7 @@ sub setup_logic_lnd_frac {
                      "env variables) AND fatmlndfrac on namelist");
        }
        if ( $opts->{$var} =~ /UNSET/ ) {
-          $log->fatal_error("-lnd_frac was set as UNSET in the CTSM build-namelist set it with the env variables: LND_DOMAIN_PATH/LND_DOMAIN_FILE.");
+          $log->fatal_error("-lnd_frac was set as UNSET in the CTSM build-namelist, it's required with the --lilac option");
        }
        my $lnd_frac = SetupTools::expand_xml_var( $opts->{$var}, $envxml_ref);
        add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fatmlndfrc','val'=>$lnd_frac );
@@ -2004,20 +2004,22 @@ sub setup_logic_lnd_frac {
      if (defined $nl->get_value('fatmlndfrc')) {
        # do nothing - use value provided by config_grid.xml and clm.cpl7.template
      } else {
-       $log->fatal_error("fatmlndfrc was NOT sent into CLM build-namelist.");
+       $log->fatal_error("fatmlndfrc was NOT sent into CLM build-namelist, it is required for the --lilac option.");
      }
   #
   # For the NUOPC driver neither lnd_frac nor fatmlndfrc need to be set
   #
-  } else {
+  } elsif ($opts->{'driver'} eq "nuopc" ) {
      if ( defined($opts->{$var}) ) {
        if ( $opts->{$var} !~ /UNSET/ ) {
-          $log->fatal_error("$var should NOT be set for the NUOPC driver as it is unused" );
+          $log->fatal_error("$var should NOT be set for the NUOPC driver as it is unused (only used by the --lilac option)" );
        }
      }
      if ( defined($nl->get_value('fatmlndfrc')) ) {
        $log->fatal_error("fatmlndfrac should NOT be set in the namelist for the NUOPC driver as it is unused" );
      }
+  } else {
+       $log->fatal_error("Input --driver type of $opts->{'driver'} is an invalid option. Correct this in xml variable COMP_iINTERFACE in your case" );
   }
 }
 
@@ -2762,7 +2764,7 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
   # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
   if ( &value_is_true($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
 

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 = 3229;
+my $ntests = 3263;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2437;
@@ -473,7 +473,7 @@ sub cat_and_create_namelistinfile {
 print "\n===============================================================================\n";
 print "Test some CAM specific setups for special grids \n";
 print "=================================================================================\n";
-foreach my $phys ( "clm4_5", "clm5_0" ) {
+foreach my $phys ( "clm4_5", "clm5_0", "clm6_0" ) {
    $mode = "-phys $phys";
    &make_config_cache($phys);
    foreach my $options (
@@ -485,7 +485,7 @@ sub cat_and_create_namelistinfile {
                       "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 2000_control  -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0",
                       "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam7.0",
                       "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0",
-                      "-res 1x1_brazil -no-megan -use_case 2000_control -lnd_tuning_mode ${phys}_CRUv7",
+                      "-res 1x1_brazil -no-megan -use_case 2000_control -lnd_tuning_mode ${phys}_GSWP3v1",
                       "-res C96 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0",
                       "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0",
                      ) {
@@ -906,7 +906,7 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"h2osfcflag=0",
                                      phys=>"clm5_0",
                                    },
-     "45bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm5_0_GSWP3  -envxml_dir .",
+     "45bad lnd_tuning_mode value" =>{ options=>"-lnd_tuning_mode clm5_0_GSWP3v1  -envxml_dir .",
                                      namelst=>"",
                                      phys=>"clm4_5",
                                    },
@@ -946,6 +946,10 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"",
                                      phys=>"clm6_0",
                                    },
+     "driver is invalid"         =>{ options=>"-driver invalid_name -envxml_dir .",
+                                     namelst=>"",
+                                     phys=>"clm6_0",
+                                   },
      "lnd_frac not set but lilac"=>{ options=>"-driver nuopc -lilac -envxml_dir . -lnd_frac UNSET",
                                      namelst=>"fsurdat='surfdata.nc'",
                                      phys=>"clm6_0",

cime_config/SystemTests/lilacsmoke.py

@@ -25,7 +25,8 @@
 import shutil
 
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
-from CIME.utils import run_cmd, run_cmd_no_fail, symlink_force, new_lid, safe_copy, append_testlog
+from CIME.utils import run_cmd, run_cmd_no_fail, symlink_force, new_lid, safe_copy
+from CIME.status import append_testlog
 from CIME.build import post_build
 from CIME.test_status import (
     NAMELIST_PHASE,

cime_config/SystemTests/sspmatrixcn.py

@@ -22,7 +22,7 @@
     sys.path.append(os.path.join(CIMEROOT, "scripts", "lib"))
     sys.path.append(os.path.join(CIMEROOT, "scripts"))
 else:
-    from CIME.utils import append_testlog
+    from CIME.status import append_testlog
 
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon

cime_config/testdefs/ExpectedTestFails.xml

@@ -138,6 +138,13 @@
     </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>#2310</issue>
+    </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>
@@ -291,71 +298,6 @@
     </phase>
   </test>
 
-  <!-- izumi nag failures -->
-
-  <test name="SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_nag.clm-ptsRLA">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60FatesRs.izumi_nag.clm-FatesCold">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
-  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </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">
       <status>FAIL</status>
@@ -370,22 +312,6 @@
     </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>