Merge pull request #1182 from rosiealice/SP_api

FATES SP api

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.46.2_api.16.1.0
+tag = sci.1.47.0_api.17.0.0
 required = True
 
 [PTCLM]

bld/namelist_files/namelist_definition_ctsm.xml

@@ -659,6 +659,17 @@ Toggle to turn on fixed biogeography mode
 (Only relevant if FATES is on)
 </entry>
 
+<entry id="use_fates_nocomp" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">                                        
+Toggle to turn on no competition mode (only relevant if FATES is being used).                  
+</entry>
+
+
+<entry id="use_fates_sp" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">                                                    
+Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used).                        
+</entry>
+
 <entry id="use_fates_logging" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the logging module

bld/unit_testers/build-namelist_test.pl

@@ -23,9 +23,9 @@ sub usage {
 SYNOPSIS
      build-namelist_test.pl [options]
 
-     Test the the CLM build-namelist 
+     Test the the CLM build-namelist
 OPTIONS
-     -help [or -h]                 Print usage to STDOUT.                               
+     -help [or -h]                 Print usage to STDOUT.
      -compare <directory>          Compare namelists for this version to namelists
                                    created by another version.
      -generate                     Leave the namelists in place to do a later compare.
@@ -59,7 +59,7 @@ sub make_env_run {
 EOF
     foreach my $item ( keys(%env_vars) ) {
       print $fh <<EOF;
-<entry id="$item"         value="$env_vars{$item}"  /> 
+<entry id="$item"         value="$env_vars{$item}"  />
 EOF
     }
     print $fh <<EOF;
@@ -135,7 +135,7 @@ sub cat_and_create_namelistinfile {
 my $inputdata_rootdir = undef;
 if (defined($opts{'csmdata'})) {
     $inputdata_rootdir = $opts{'csmdata'};
-} elsif (defined $ENV{'CSMDATA'} ) { 
+} elsif (defined $ENV{'CSMDATA'} ) {
     $inputdata_rootdir = $ENV{'CSMDATA'};
 } else {
    # use yellowstone location as default
@@ -153,7 +153,7 @@ sub cat_and_create_namelistinfile {
    $compGen='compare';
 } elsif ( defined($opts{'compare'} && ($opts{'generate'} eq 1 ))) {
    #_# if compare and generate are both given, use compare
-   $compGen='compare'; 
+   $compGen='compare';
 }
 
 my $ProgName;
@@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1829;
+my $ntests = 1839;
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1245;
+   $ntests += 1251;
 }
 plan( tests=>$ntests );
 
@@ -176,7 +176,7 @@ sub cat_and_create_namelistinfile {
 my $captOut="";  #_# variable to capture Test::More output
 Test::More->builder->output(\$captOut);
 #_# ============================================================
-#_# 
+#_#
 #_# ============================================================
 
 # Check for unparsed arguments
@@ -222,7 +222,7 @@ sub cat_and_create_namelistinfile {
 &make_env_run();
 eval{ system( "$bldnml > $tempfile 2>&1 " ); };
    is( $@, '', "plain build-namelist" );
-   $cfiles->checkfilesexist( "default", $mode ); 
+   $cfiles->checkfilesexist( "default", $mode );
    # Compare to baseline
    if ( defined($opts{'compare'}) ) {
       $cfiles->doNOTdodiffonfile( "$tempfile", "default", $mode );
@@ -236,7 +236,7 @@ sub cat_and_create_namelistinfile {
 $cfiles->copyfiles( "default", $mode );
 &cleanup();
 # Simple test -- run all the list options
-foreach my $options ( "clm_demand", "ssp_rcp",      "res", 
+foreach my $options ( "clm_demand", "ssp_rcp",      "res",
                       "sim_year",   "use_case" ) {
    &make_env_run();
    eval{ system( "$bldnml -${options} list > $tempfile 2>&1 " ); };
@@ -327,7 +327,7 @@ sub cat_and_create_namelistinfile {
                          "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'",
                          "-res 1x1_brazil",
                          "-clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc",
-                         "-envxml_dir . -infile myuser_nl_clm", 
+                         "-envxml_dir . -infile myuser_nl_clm",
                          "-ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop",
                          "-clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'",
                          "-ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop",
@@ -365,17 +365,17 @@ sub cat_and_create_namelistinfile {
 $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" 
+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";
@@ -390,7 +390,7 @@ sub cat_and_create_namelistinfile {
    &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" );
@@ -415,7 +415,7 @@ sub cat_and_create_namelistinfile {
 foreach my $phys ( "clm4_5", "clm5_0" ) {
    $mode = "-phys $phys";
    &make_config_cache($phys);
-   foreach my $options ( 
+   foreach my $options (
                       "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
                       "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
                       "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0",
@@ -452,11 +452,13 @@ sub cat_and_create_namelistinfile {
 $phys = "clm5_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
-foreach my $options ( 
+foreach my $options (
                       "-bgc bgc -use_case 1850-2100_SSP1-2.6_transient -namelist '&a start_ymd=20100101/'",
                       "-bgc sp  -use_case 1850-2100_SSP2-4.5_transient -namelist '&a start_ymd=18501223/'",
                       "-bgc bgc -use_case 1850-2100_SSP3-7.0_transient -namelist '&a start_ymd=20701029/'",
                       "-bgc fates  -use_case 2000_control -no-megan",
+                      "-bgc fates  -use_case 20thC_transient -no-megan",
+                      "-bgc fates  -use_case 1850_control -no-megan -namelist '&a use_fates_sp=T/'",
                       "-bgc sp  -use_case 2000_control -res 0.9x1.25 -namelist '&a use_soil_moisture_streams = T/'",
                       "-bgc bgc -use_case 1850-2100_SSP5-8.5_transient -namelist '&a start_ymd=19101023/'",
                       "-bgc bgc -use_case 2000_control -namelist \"&a fire_method='nofire'/\" -crop",
@@ -490,7 +492,7 @@ sub cat_and_create_namelistinfile {
 my $finidat  = "thing.nc";
 system( "touch $finidat" );
 
-my %failtest = ( 
+my %failtest = (
      "coldstart but with IC file"=>{ options=>"-clm_start_type cold -envxml_dir .",
                                      namelst=>"finidat='$finidat'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -602,7 +604,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "toosmall glc  w trans"     =>{ options=>"-bgc sp  -envxml_dir .",
-                                     namelst=>"toosmall_glacier=10, dyn_transient_pfts=T", 
+                                     namelst=>"toosmall_glacier=10, dyn_transient_pfts=T",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
@@ -968,7 +970,7 @@ sub cat_and_create_namelistinfile {
                                      phys=>"clm5_0",
                                    },
      "usespitfireButNOTFATES"    =>{ options=>"-envxml_dir . -no-megan",
-                                     namelst=>"fates_spitfire_mode>0",
+                                     namelst=>"fates_spitfire_mode=1",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
@@ -992,6 +994,16 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "useFATESSPWONOCOMP"        =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_fates_sp=T,use_fates_nocomp=F",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "useFATESTRANSWdynPFT"      =>{ options=>"-bgc fates -envxml_dir . -use_case 20thC_transient -no-megan",
+                                     namelst=>"do_transient_pfts=T",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "useHYDSTwithFATES"         =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_hydrstress=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1136,7 +1148,7 @@ sub cat_and_create_namelistinfile {
 
 # Warning testing, do things that give warnings, unless -ignore_warnings option is used
 
-my %warntest = ( 
+my %warntest = (
      # Warnings without the -ignore_warnings option given
      "coldwfinidat"              =>{ options=>"-envxml_dir . -clm_start_type cold",
                                      namelst=>"finidat = 'testfile.nc'",
@@ -1481,7 +1493,7 @@ sub cat_and_create_namelistinfile {
   my $mode = "-phys $phys";
   &make_config_cache($phys);
   my @clmoptions = ( "-bgc bgc -envxml_dir .", "-bgc bgc -envxml_dir . -clm_accelerated_spinup=on", "-bgc bgc -envxml_dir . -light_res 360x720",
-                     "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation -ignore_warnings", 
+                     "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation -ignore_warnings",
                      "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000 -namelist '&a start_ymd=18500101/'",
                      "-bgc bgc -envxml_dir . -namelist '&a use_c13=.true.,use_c14=.true.,use_c14_bombspike=.true./'" );
   foreach my $clmopts ( @clmoptions ) {
@@ -1503,7 +1515,7 @@ sub cat_and_create_namelistinfile {
         &cleanup();
      }
   }
-  my @clmoptions = ( "-bgc bgc -envxml_dir .", 
+  my @clmoptions = ( "-bgc bgc -envxml_dir .",
                      "-bgc sp -envxml_dir .", );
   foreach my $clmopts ( @clmoptions ) {
      my @clmres = ( "ne16np4" );
@@ -1545,11 +1557,11 @@ sub cat_and_create_namelistinfile {
   my @clmres = ( "1x1_brazil", "5x5_amazon", "4x5", "1.9x2.5" );
   foreach my $res ( @clmres ) {
      $options = "-res $res -clm_start_type cold";
-     my @edoptions = ( "-use_case 2000_control", 
-                       "-use_case 1850_control", 
-                       "", 
-                       "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"", 
-                       "-clm_accelerated_spinup on" 
+     my @edoptions = ( "-use_case 2000_control",
+                       "-use_case 1850_control",
+                       "",
+                       "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"",
+                       "-clm_accelerated_spinup on"
                      );
      foreach my $edop (@edoptions ) {
         if ( $res eq "5x5_amazon" && ($edop =~ /1850_control/) ) {

cime_config/testdefs/ExpectedTestFails.xml

@@ -53,20 +53,6 @@
 
   <!-- fates test suite failures -->
 
-  <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>NGEET/fates#315</issue>
-    </phase>
-  </test>
-
-  <test name="ERP_Ld9.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-FatesAllVars">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>NGEET/fates#315</issue>
-    </phase>
-  </test>
-
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesLogging">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
@@ -88,13 +74,6 @@
     </phase>
   </test>
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro">
-    <phase name="MEMLEAK">
-      <status>FAIL</status>
-      <issue>NGEET/fates#510</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro">
     <phase name="RUN">
       <status>FAIL</status>
@@ -137,25 +116,25 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro">
+  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro">
     <phase name="RUN">
       <status>FAIL</status>
       <issue>#667</issue>
     </phase>
   </test>
 
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.izumi_nag.clm-FatesHydro">
-    <phase name="RUN">
+  <test name="ERS_D_Lm12.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-Fates_nat_and_anthro_ignitions">
+    <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#667</issue>
     </phase>
   </test>
 
-  <test name="ERS_D_Lm12.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-Fates_nat_and_anthro_ignitions">
+  <test name="ERS_Ld30.f45_f45_mg37.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesReducedComplexSatellitePhenology">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
-      <issue>#667</issue>
+      <issue>#1485</issue>
     </phase>
   </test>
 
-</expectedFails> 
+</expectedFails>

cime_config/testdefs/testlist_clm.xml

@@ -2348,7 +2348,38 @@
       <option name="comment">60 day exact restart test activating FATES prescribed physiology mode on an f45 grid.</option>
     </options>
   </test>
-    <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCru" testmods="clm/FatesReducedComplexFixedBiogeo">
+  <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCru" testmods="clm/FatesReducedComplexFixedBiogeo">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
+    <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCru" testmods="clm/FatesReducedComplexNoComp">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
+  </test>
+  <test name="SMS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCru" testmods="clm/FatesReducedComplexSatellitePhenology">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+      <option name="comment">Temporary smoke test.  This test should be removed once the ERS version of this test passes COMPARE_base_rest</option>
+    </options>
+  </test>
+  <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCru" testmods="clm/FatesReducedComplexSatellitePhenology">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/user_nl_clm

@@ -1 +1 @@
-use_fates_fixed_biogeog=.true.
+use_fates_fixed_biogeog=.true.

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexNoComp/include_user_mods

@@ -0,0 +1 @@
+../FatesColdDef

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexNoComp/user_nl_clm

@@ -0,0 +1 @@
+use_fates_nocomp = .true.

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexSatellitePhenology/include_user_mods

@@ -0,0 +1 @@
+../FatesColdDef

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexSatellitePhenology/user_nl_clm

@@ -0,0 +1,2 @@
+use_fates_sp = .true.
+fates_spitfire_mode = 0