ESCOMP · ekluzek · May 18, 2021 · Mar 30, 2021 · Mar 30, 2021 · Mar 30, 2021
diff --git a/Externals.cfg b/Externals.cfg
@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cism2_1_78
+tag = cismwrap_2_1_83
 externals = Externals_CISM.cfg
 required = True
 
@@ -37,21 +37,22 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.42_a01
+tag = cime5.8.47
 required = True
 
 [cmeps]
 local_path = cime/src/drivers/nuopc/
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
-tag = v0.9.0
+tag = cmeps0.13.2
 required = True
 
 [cdeps]
 local_path = components/cdeps
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
-tag = v0.6.0
+tag = cdeps0.12.4
+externals = Externals_CDEPS.cfg
 required = True
 
 [doc-builder]

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -84,6 +84,31 @@ sub make_config_cache {
    $fh->close();
 }
 
+sub cat_and_create_namelistinfile {
+#
+# Concatenate the user_nl_clm files together and turn it into a namelist input file
+# that can be read in by build-namelist
+#
+   my ($file1, $file2, $outfile) = @_;
+
+   my $fh    = IO::File->new($file1,   '<') or die "can't open file: $file1";
+   my $outfh = IO::File->new($outfile, '>') or die "can't open file: $outfile";
+   print $outfh "&clm_settings\n\n";
+   while ( my $line = <$fh> ) {
+     print $outfh " $line";
+   }
+   $fh->close();
+   if ( defined($file2) ) {
+      my $fh    = IO::File->new($file2,   '<') or die "can't open file: $file2";
+      while ( my $line = <$fh> ) {
+        print $outfh " $line";
+      }
+   }
+   print $outfh "\n/\n";
+   $fh->close();
+   $outfh->close();
+}
+
 #
 # Process command-line options.
 #
@@ -138,9 +163,9 @@ sub make_config_cache {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1552;
+my $ntests = 1740;
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1044;
+   $ntests += 1185;
 }
 plan( tests=>$ntests );
 
@@ -323,6 +348,56 @@ sub make_config_cache {
    }
    &cleanup();
 }
+print "\n===============================================================================\n";
+print "Test the NEON sites\n";
+print "=================================================================================\n";
+my $phys = "clm5_1";
+$mode = "-phys $phys";
+&make_config_cache($phys);
+my $neondir      = "../../cime_config/usermods_dirs/NEON";
+foreach my $site ( "ABBY", "BLAN", "CPER", "DEJU", "GRSM", "HEAL", "KONA", "LENO", "NIWO", 
+                   "ONAQ", "PUUM", "SERC", "SRER", "TALL", "TREE", "WOOD", "BARR", "BONA", 
+                   "DCFS", "DELA", "GUAN", "JERC", "KONZ", "MLBS", "NOGP", "ORNL", "RMNP", 
+                   "SJER", "STEI", "TEAK", "UKFS", "WREF", "BART", "CLBJ", "DSNY", "HARV", 
+                   "JORN", "LAJA", "MOAB", "OAES", "OSBS", "SCBI", "SOAP", "STER", "TOOL", 
+                   "UNDE", "YELL" 
+ ) {
+   &make_env_run();
+   #
+   # Concatonate  default usermods and specific sitetogether expanding env variables while doing that
+   # 
+   if ( ! -d "$neondir/$site" ) {
+      print "NEON directory is not there: $neondir/$site\n";
+      die "ERROR:: NEON site does not exist: $site\n";
+   }
+   my $neondefaultfile = "$neondir/defaults/user_nl_clm";
+   my $neonsitefile = "$neondir/$site/user_nl_clm";
+   if ( ! -f $neonsitefile )  {
+      $neonsitefile = undef;
+   }
+   $ENV{'NEONSITE'} = $site;
+   my $namelistfile = "temp.namelistinfile_$site";
+   &cat_and_create_namelistinfile( $neondefaultfile, $neonsitefile, $namelistfile );
+   #
+   # Now run  the site
+   # 
+   my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2000 -infile $namelistfile";
+   eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
+   is( $@, '', "options: $options" );
+   $cfiles->checkfilesexist( "$options", $mode );
+   $cfiles->shownmldiff( "default", $mode );
+   if ( defined($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'}) ) {
+      $cfiles->copyfiles( "$options", $mode );
+   }
+   system( "/bin/rm $namelistfile" );
+   &cleanup();
+}
 
 print "\n===============================================================================\n";
 print "Test some CAM specific setups for special grids \n";

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -288,7 +288,20 @@
     <desc>User mods to apply to specific compset matches. </desc>
   </entry>
 
-  <help>
+  <entry id="NEONSITE">                                                                                    
+    <type>char</type>
+    <valid_values>                                                                                      
+      ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD,
+      BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF,
+      BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL
+    </valid_values>                                                                                        
+    <default_value/>                                                                                       
+    <group>run_component_ctsm</group>                                                                      
+    <file>env_run.xml</file>                                                                               
+    <desc>Name of site for NEON tower data</desc>                                                          
+  </entry>                                                                                                 
+
+<help>
     =========================================
     CLM naming conventions
     =========================================

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -36,6 +36,16 @@
 
 <!-- I single point forcing -->
 
+  <compset>
+    <alias>I1PtClm51Bgc</alias>
+    <lname>2000_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
+  <compset>
+    <alias>IHist1PtClm51Bgc</alias>
+    <lname>HIST_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>I1PtClm51SpRs</alias>
     <lname>2000_DATM%1PT_CLM51%SP_SICE_SOCN_SROF_SGLC_SWAV</lname>

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -30,38 +30,31 @@
 
   <!-- aux_clm test suite failures -->
 
-  <test name="ERS_Ln12.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>#1117</issue>
-    </phase>
-  </test>
-
   <test name="DAE_N2_D_Lh12_Vnuopc.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_intel.clm-DA_multidrv">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>ESCOMP/CMEPS#175</issue>
     </phase>
   </test>
 
-  <test name="SMS_D_Lm1_Mmpi-serial_Vnuopc.CLM_USRDAT.I1PtClm50SpRs.cheyenne_intel.clm-USUMB">
-    <phase name="RUN">
+  <test name="ERI_D_Ld9_P48x1_Vnuopc.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC">
+    <phase name="MODEL_BUILD">
       <status>FAIL</status>
-      <issue>ESMCI/cime#3905</issue>
+      <issue>ESMCI/cime#3915</issue>
     </phase>
   </test>
 
-  <test name="SMS_D_Lm1_Mmpi-serial.CLM_USRDAT.I1PtClm50SpRs.cheyenne_intel.clm-USUMB">
-    <phase name="SUBMIT">
+  <test name="ERS_D_Mmpi-serial_Ld5_Vnuopc.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesColdDef">
+    <phase name="MODEL_BUILD">
       <status>FAIL</status>
-      <issue>ESMCI/cime#3905</issue>
+      <issue>ESMCI/cime#3970</issue>
     </phase>
   </test>
 
-  <test name="ERI_D_Ld9_P48x1_Vnuopc.f10_f10_mg37.I2000Clm50Sp.izumi_nag.clm-SNICARFRC">
+  <test name="SMS_D_Vnuopc_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-NEON_NIWO">
     <phase name="MODEL_BUILD">
       <status>FAIL</status>
-      <issue>ESMCI/cime#3915</issue>
+      <issue>ESMCI/cime#3970</issue>
     </phase>
   </test>
 
@@ -86,20 +79,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Vnuopc.f10_f10_mg37.I2000Clm50BgcCrop.izumi_pgi.clm-crop">
-    <phase name="BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/cime#3496</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Vnuopc.f10_f10_mg37.I2000Clm51BgcCrop.izumi_pgi.clm-crop">
-    <phase name="BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/cime#3496</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates">

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -948,7 +948,7 @@
       <option name="comment"  >include a debug test with flooding on</option>
     </options>
   </test>
-  <test name="ERP_P180x2_D_Ld5" grid="f19_g17_gl4" compset="I1850Clm50BgcCropG" testmods="clm/default">
+  <test name="ERP_P180x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="prealpha"/>
@@ -957,7 +957,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P180x2_D_Ld5" grid="f19_g17_gl4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
+  <test name="ERP_P180x2_D_Ld5" grid="f19_g17_gris4" compset="I1850Clm50BgcCropG" testmods="clm/glcMEC_increase">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1157,7 +1157,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="ERS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -1191,7 +1191,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRs" testmods="clm/default">
+  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
@@ -1200,7 +1200,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1521,23 +1521,23 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
@@ -1662,7 +1662,7 @@
       <option name="comment"  >include a nag debug test of Clm45BgcCrop</option>
     </options>
   </test>
-  <test name="SMS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="SMS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="prebeta"/>
@@ -1672,17 +1672,29 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="SMS_D_Lm1_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm50SpRs" testmods="clm/USUMB">
+  <test name="SMS_D_Vnuopc_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON_NIWO">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Add at least one test of a NEON site</option>
+    </options>
+  </test>
+  <test name="SMS_D_Lm1_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm50SpRs" testmods="clm/USUMB_mct">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
       <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >This is a test of a generic tower site under MCT</option>
     </options>
   </test>
-  <test name="SMS_D_Lm1_Mmpi-serial_Vnuopc" grid="CLM_USRDAT" compset="I1PtClm50SpRs" testmods="clm/USUMB">
+  <test name="SMS_D_Lm1_Mmpi-serial_Vnuopc" grid="CLM_USRDAT" compset="I1PtClm50SpRs" testmods="clm/USUMB_nuopc">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1754,7 +1766,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/default">
+  <test name="SMS_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>

diff --git a/cime_config/testdefs/testmods_dirs/clm/CLM1PTStartDate/shell_commands b/cime_config/testdefs/testmods_dirs/clm/CLM1PTStartDate/shell_commands
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+if   [ "`./xmlquery ATM_GRID --value`" == "1x1_vancouverCAN"  ]; then
+  # Go one day in, so don't have to set the TOD as well
+  ./xmlchange RUN_STARTDATE="1992-08-13"
+elif [ "`./xmlquery ATM_GRID --value`" == "1x1_mexicocityMEX" ]; then
+  # Go one day in, so don't have to set the TOD as well
+  ./xmlchange RUN_STARTDATE="1993-12-02"
+elif [ "`./xmlquery ATM_GRID --value`" == "1x1_urbanc_alpha"  ]; then
+  # Go one day in, so don't have to set the TOD as well
+  ./xmlchange RUN_STARTDATE="0001-08-13"
+#
+# Otherwise let this be set by the specific site
+#
+fi
+
diff --git a/cime_config/testdefs/testmods_dirs/clm/NEON_NIWO/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/NEON_NIWO/include_user_mods
@@ -0,0 +1 @@
+../../../../usermods_dirs/NEON/NIWO
diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/include_user_mods
@@ -0,0 +1 @@
+../CLM1PTStartDate
diff --git a/...fs/testmods_dirs/clm/USUMB/shell_commands → ...estmods_dirs/clm/USUMB_mct/shell_commands b/...fs/testmods_dirs/clm/USUMB/shell_commands → ...estmods_dirs/clm/USUMB_mct/shell_commands
diff --git a/...tdefs/testmods_dirs/clm/USUMB/user_nl_clm → ...s/testmods_dirs/clm/USUMB_mct/user_nl_clm b/...tdefs/testmods_dirs/clm/USUMB/user_nl_clm → ...s/testmods_dirs/clm/USUMB_mct/user_nl_clm
diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/include_user_mods
@@ -0,0 +1 @@
+../CLM1PTStartDate