Merge ctsm1.0.dev105 tag into fates_main_api

Externals.cfg

@@ -30,7 +30,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.23_a01
+tag = cime5.8.28
 externals = ../Externals_cime.cfg
 required = True
 

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.42.0_api.14.0.0
+tag = sci.1.42.4_api.14.0.0
 required = True
 
 [PTCLM]

Externals_cime.cfg

@@ -1,9 +1,23 @@
 [cmeps]
-hash = 386e1631a6a1e1900700c3a04d693df8692c9420
+hash = 9376b87
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = src/drivers/nuopc/
 required = True
 
+[fox]
+hash = 0ed59c1
+protocol = git
+repo_url = https://github.com/ESMCI/fox.git
+local_path = src/externals/fox
+required = True
+
+[cdeps]
+hash = 8e77759
+protocol = git
+repo_url = https://github.com/ESCOMP/CDEPS.git
+local_path = src/components/cdeps
+required = True
+
 [externals_description]
 schema_version = 1.0.0

bld/CLMBuildNamelist.pm

@@ -35,7 +35,7 @@ use File::Basename qw(dirname);
 use English;
 use Getopt::Long;
 use IO::File;
-use File::Glob ':glob';
+use File::Glob ':bsd_glob';
 
 #-------------------------------------------------------------------------------
 #
@@ -189,7 +189,6 @@ OPTIONS
                                form \$CASEDIR/user_nl_clm/user_nl_clm_????)
      -inputdata "filepath"    Writes out a list containing pathnames for required input datasets in
                               file specified.
-     -l_ncpl "LND_NCPL"       Number of CLM coupling time-steps in a day.
      -lnd_tuning_mode "value" Use the parameters tuned for the given configuration (CLM version and atmospheric forcing)
      -mask "landmask"         Type of land-mask (default, navy, gx3v5, gx1v5 etc.)
                               "-mask list" to list valid land masks.
@@ -255,7 +254,6 @@ sub process_commandline {
                help                  => 0,
                glc_nec               => "default",
                light_res             => "default",
-               l_ncpl                => undef,
                lnd_tuning_mode       => "default",
                lnd_frac              => undef,
                dir                   => "$cwd",
@@ -307,7 +305,6 @@ sub process_commandline {
              "infile=s"                  => \$opts{'infile'},
              "lnd_frac=s"                => \$opts{'lnd_frac'},
              "lnd_tuning_mode=s"         => \$opts{'lnd_tuning_mode'},
-             "l_ncpl=i"                  => \$opts{'l_ncpl'},
              "inputdata=s"               => \$opts{'inputdata'},
              "mask=s"                    => \$opts{'mask'},
              "namelist=s"                => \$opts{'namelist'},
@@ -477,7 +474,7 @@ sub read_envxml_case_files {
   my %envxml = ();
   if ( defined($opts->{'envxml_dir'}) ) {
       (-d $opts->{'envxml_dir'})  or  $log->fatal_error( "envxml_dir is not a directory" );
-      my @files = glob( $opts->{'envxml_dir'}."/env_*xml" );
+      my @files = bsd_glob( $opts->{'envxml_dir'}."/env_*xml" );
       ($#files >= 0)              or  $log->fatal_error( "there are no env_*xml files in the envxml_dir" );
       foreach my $file (@files) {
           $log->verbose_message( "Open env.xml file: $file" );
@@ -1198,7 +1195,16 @@ sub setup_cmdl_run_type {
   my $val;
   my $var = "clm_start_type";
   my $ic_date = $nl->get_value('start_ymd');
-  my $st_year = int( $ic_date / 10000);
+  my $st_year;
+  if ( defined($ic_date) ) {
+     $st_year = int( $ic_date / 10000);
+  } else {
+    $st_year = $nl_flags->{'sim_year'};
+    $ic_date = $st_year *10000 + 101;
+    my $date = 'start_ymd';
+    my $group = $definition->get_group_name($date);
+    $nl->set_variable_value($group, $date, $ic_date );
+  }
   if (defined $opts->{$var}) {
     if ($opts->{$var} eq "default" ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
@@ -1214,6 +1220,7 @@ sub setup_cmdl_run_type {
                   'sim_year'=>$st_year );
   }
   $nl_flags->{'clm_start_type'} = $nl->get_value($var);
+  $nl_flags->{'st_year'}        = $st_year;
 }
 
 #-------------------------------------------------------------------------------
@@ -1396,9 +1403,6 @@ sub process_namelist_commandline_clm_usr_name {
         $nvars++;
       }
     }
-    if ( $nvars == 0 ) {
-      $log->message("setting clm_usr_name -- but did NOT find any user datasets: $opts->{'clm_usr_name'}", $opts);
-    }
     # Go through all variables and expand any XML env settings in them
     expand_xml_variables_in_namelist( $nl_usrfile, $envxml_ref );
     # Merge input values into namelist.  Previously specified values have higher precedence
@@ -1440,7 +1444,7 @@ sub process_namelist_commandline_use_case {
       my $val = $uc_defaults->get_value($var, \%settings );
 
       if ( defined($val) ) {
-        $log->message("CLM adding use_case $opts->{'use_case'} defaults for var '$var' with val '$val'");
+        $log->verbose_message("CLM adding use_case $opts->{'use_case'} defaults for var '$var' with val '$val'");
 
         add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl_usecase, $var, 'val'=>$val);
       }
@@ -1488,7 +1492,6 @@ sub process_namelist_inline_logic {
   setup_logic_co2_type($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_start_type($opts, $nl_flags, $nl);
-  setup_logic_delta_time($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_decomp_performance($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl,  $envxml_ref);
@@ -1864,28 +1867,6 @@ sub setup_logic_start_type {
 
 #-------------------------------------------------------------------------------
 
-sub setup_logic_delta_time {
-  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
-
-  if ( defined($opts->{'l_ncpl'}) ) {
-    my $l_ncpl = $opts->{'l_ncpl'};
-    if ( $l_ncpl <= 0 ) {
-      $log->fatal_error("bad value for -l_ncpl option.");
-    }
-    my $val = ( 3600 * 24 ) / $l_ncpl;
-    my $dtime = $nl->get_value('dtime');
-    if ( ! defined($dtime)  ) {
-      add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtime', 'val'=>$val);
-    } elsif ( $dtime ne $val ) {
-      $log->fatal_error("can NOT set both -l_ncpl option (via LND_NCPL env variable) AND dtime namelist variable.");
-    }
-  } else {
-    add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtime', 'hgrid'=>$nl_flags->{'res'});
-  }
-}
-
-#-------------------------------------------------------------------------------
-
 sub setup_logic_decomp_performance {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -2246,7 +2227,7 @@ sub setup_logic_initial_conditions {
 
   if (not defined $finidat ) {
     my $ic_date = $nl->get_value('start_ymd');
-    my $st_year = int( $ic_date / 10000);
+    my $st_year = $nl_flags->{'st_year'};
     my $nofail = 1;
     my %settings;
     $settings{'hgrid'}   = $nl_flags->{'res'};
@@ -2304,47 +2285,67 @@ sub setup_logic_initial_conditions {
           #}
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_sim_years" );
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_how_close" );
+          #
+          # Figure out which sim_year has a usable finidat file that is closest to the desired one
+          #
           my $close = $nl->get_value("init_interp_how_close");
-          foreach my $sim_yr ( split( /,/, $nl->get_value("init_interp_sim_years") )) {
+          my $closest_sim_year = undef;
+          my @sim_years = split( /,/, $nl->get_value("init_interp_sim_years") );
+SIMYR:    foreach my $sim_yr ( @sim_years ) {
              my $how_close = undef;
              if ( $nl_flags->{'sim_year'} eq "PtVg" ) {
                 $how_close = abs(1850 - $sim_yr);
+             # EBK 07/20/2020 -- This makes sure the sim_year matched is based on the sim-year
+             #                   rather than  the start year.
+             #} elsif ( $nl_flags->{'flanduse_timeseries'} eq "null" ) {
+             #   $how_close = abs($nl_flags->{'sim_year'} - $sim_yr);
              } else {
                 $how_close = abs($st_year - $sim_yr);
              }
-             if ( ($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close) ) {
-                $close = $how_close;
+             if ( ($sim_yr == $sim_years[-1]) || (($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close)) ) {
+                my $group = $definition->get_group_name($useinitvar);
                 $settings{'sim_year'} = $sim_yr;
+                $settings{$useinitvar} = $defaults->get_value($useinitvar, \%settings);
+                if ( ! defined($settings{$useinitvar}) ) {
+                   $settings{$useinitvar} = $use_init_interp_default;
+                }
+                if ( &value_is_true($settings{$useinitvar}) ) {
+
+                   if ( ($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close) ) {
+                      $close = $how_close;
+                      $closest_sim_year = $sim_yr;
+                   }
+                }
              }
-          } 
+          }    # SIMYR:
+          $settings{'sim_year'} = $closest_sim_year;
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar,
-                     'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(),
-                     'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
-                     'use_fates'=>$nl_flags->{'use_fates'} );
+                      'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(),
+                      'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},
+                      'use_fates'=>$nl_flags->{'use_fates'} );
           $settings{$useinitvar} = $nl->get_value($useinitvar);
-          if ( $try > 1 ) {
-             my $group = $definition->get_group_name($useinitvar);
-             $nl->set_variable_value($group, $useinitvar, $use_init_interp_default );
-          }
-          if ( &value_is_true($nl->get_value($useinitvar) ) ) {
-
-             add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes",
-                        'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, 
-                        'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'},
-                        'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},'nofail'=>1 );
-             my $attributes_string = remove_leading_and_trailing_quotes($nl->get_value("init_interp_attributes"));
+          if ( ! &value_is_true($nl->get_value($useinitvar) ) ) {
+             if ( $nl_flags->{'clm_start_type'} =~ /startup/  ) {
+                $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true");
+             }
+          } else {
+             my $stat = add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes",
+                                 'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, 
+                                 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'},
+                                 'hgrid'=>$nl_flags->{'res'}, 
+                                 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'nofail'=>1 );
+             if ( $stat ) {
+                $log->fatal_error("$useinitvar is NOT synchronized with init_interp_attributes");
+             }
+             my $attributes = $nl->get_value("init_interp_attributes");
+             my $attributes_string = remove_leading_and_trailing_quotes($attributes);
              foreach my $pair ( split( /\s/, $attributes_string) ) {
-                if ( $pair =~ /^([a-z_]+)=([a-z._0-9]+)$/ ) {
+                if ( $pair =~ /^([a-z_]+)=([a-zA-Z._0-9]+)$/ ) {
                    $settings{$1} = $2;
                 } else {
-                   $log->fatal_error("Problem interpreting init_interp_attributes");
+                   $log->fatal_error("Problem interpreting init_interp_attributes: $pair");
                 }
              }
-          } else {
-             if ( $nl_flags->{'clm_start_type'} =~ /startup/  ) {
-                $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true");
-             }
-             $try = $done;
           }
        } else {
          $try = $done
@@ -3973,7 +3974,7 @@ sub add_default {
         }
       }
       else {
-        return;
+        return( 1 );
       }
     }
 
@@ -4008,6 +4009,7 @@ sub add_default {
     # set the value in the namelist
     $nl->set_variable_value($group, $var, $val);
   }
+  return( 0 );
 
 }
 
@@ -4202,7 +4204,7 @@ sub validate_options {
            # create the @expect array by listing the files in $use_case_dir
            # and strip off the ".xml" part of the filename
            @expect = ();
-           my @files = glob("$opts->{'use_case_dir'}/*.xml");
+           my @files = bsd_glob("$opts->{'use_case_dir'}/*.xml");
            foreach my $file (@files) {
                $file =~ m{.*/(.*)\.xml};
                &check_use_case_name( $1 );
@@ -4216,7 +4218,7 @@ sub validate_options {
         } else {
            print "Use cases are:...\n\n";
            my @ucases;
-           foreach my $file( sort( glob($opts->{'use_case_dir'}."/*.xml") ) ) {
+           foreach my $file( sort( bsd_glob($opts->{'use_case_dir'}."/*.xml") ) ) {
               my $use_case;
               if ( $file =~ /\/([^\/]+)\.xml$/ ) {
                  &check_use_case_name( $1 );