Move plumber2 scripts to python directory

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.72.2_api.34.0.0
+tag = sci.1.73.0_api.35.0.0
 required = True
 
 [externals_description]

bld/CLMBuildNamelist.pm

@@ -4546,6 +4546,10 @@ sub setup_logic_fates {
               if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
                     $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
               }
+              # hydro isn't currently supported to work when FATES SP mode is active
+              if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
+                    $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
+              }
            }
         }
         my $var = "use_fates_inventory_init";

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -480,7 +480,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc</fates_paramfile>
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->

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 = 2511;
+my $ntests = 2513;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 1545;
@@ -1023,6 +1023,16 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm4_5",
                                    },
+     "usespitfireusefatessp"    =>{ options=>"-envxml_dir . --bgc fates",
+                                     namelst=>"fates_spitfire_mode=1,use_fates_sp=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
+     "usefatesspusefateshydro"   =>{ options=>"-envxml_dir . --bgc fates",
+                                     namelst=>"use_fates_sp=.true.,use_fates_planthydro=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_0",
+                                   },
      "useloggingButNOTFATES"     =>{ options=>"-envxml_dir . -no-megan",
                                      namelst=>"use_fates_logging=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

cime_config/testdefs/ExpectedTestFails.xml

@@ -58,13 +58,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.cheyenne_nvhpc.clm-crop">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1733</issue>
-    </phase>
-  </test>
-
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -197,13 +190,6 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesColdHydro">
-    <phase name="COMPARE_base_rest">
-      <status>FAIL</status>
-      <issue>FATES#701</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdHydro">
     <phase name="RUN">
       <status>FAIL</status>
@@ -233,7 +219,7 @@
     </phase>
   </test>
 
-  <test name="PEM_D_Ld15.5x5_amazon.I2000Clm50FatesRs.cheyenne_gnu.clm-FatesColdSeedDisp">
+  <test name="PEM_D_Ld15.f10_f10_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdSeedDisp">
     <phase name="COMPARE_base_modpes">
       <status>FAIL</status>
       <issue>FATES#1089</issue>
@@ -247,31 +233,31 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
-    <phase name="COMPARE_base_rest">
+  <test name="SMS_D_Ld5.5x5_amazon.I1850Clm51Bgc.derecho_gnu.clm-HillslopeC">
+    <phase name="RUN">
       <status>FAIL</status>
-      <issue>#2325</issue>
+      <issue>#2423</issue>
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#2325</issue>
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#2325</issue>
     </phase>
   </test>
 
-  <test name="ERS_Ld30.f45_f45_mg37.I2000Clm60FatesSpCruRsGs.derecho_intel.clm-FatesColdSatPhen">
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
-      <issue>#2478</issue>
+      <issue>#2325</issue>
     </phase>
   </test>
 

cime_config/testdefs/testlist_clm.xml

@@ -2654,24 +2654,24 @@
       <option name="comment"  >5x5_amazon grid with FATES and latest CLM</option>
     </options>
   </test>
-  <test name="ERS_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="ERS_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment"  >This test should be convered to an ERP test once the PEM version of this test is passing COMPARE_base_modpes.</option>
+      <option name="comment"  >This test should be converted to an ERP test once the PEM version of this test is passing COMPARE_base_modpes. Also change to 5x5_amazon once ccs_config updated to allow it</option>
     </options>
   </test>
-  <test name="PEM_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="PEM_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment"  >This checks that the FATES seed dispersal MPI communication is consistent when the PE layout changes.</option>
+      <option name="comment"  >This checks that the FATES seed dispersal MPI communication is consistent when the PE layout changes. Could convert to 5x5_amazon as above</option>
     </options>
   </test>
   <test name="ERS_D_Ld15" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTreeDamage">
@@ -3665,6 +3665,16 @@
     </options>
   </test>
 
+  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </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>
+    </options>
+  </test>
+
   <test name="SMS_D_Ld3" grid="f10_f10_mg37" compset="I2000Clm60Bgc" testmods="clm/HillslopeD">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>

doc/ChangeLog

@@ -1,4 +1,121 @@
 ===============================================================
+Tag name: ctsm5.2.002
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Fri 26 Apr 2024 11:13:46 AM MDT
+One-line Summary: FATES default allometry parameter file update
+
+Purpose and description of changes
+----------------------------------
+
+This updates the default FATES parameter file which includes a number
+of changes:
+
+   - Default global tree pft allometry update
+   - New allometric mode options
+   - New scaling coefficients for alternative leaf maintenance respiration
+   - New switch to control the use of host land model day length scaling factor
+
+This also incorporates some testing additions and clean up, including:
+
+   - Removes cheyenne expected failure tests that have been converted to derecho
+   - Adds a 5x5_amazon test to aux_clm and the expected failures list
+   - Temporarilry converts a fates 5x5_amazon test to f10 test
+   - Adds namelist check and corresponding unit test to make sure fates hydro
+     and fates satellite phenology mode can not be used together
+
+The FATES externals tag is also updated which includes a number of bug fixes
+and the addition of new history output.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   NOTE: FATES hydro mode and FATES satellite phenology mode can not
+	 be used in conjunction as of this API update
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   FATES parameter file default updated to fates_params_api.35.0.0_12pft_c240326.nc
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   A 5x5_amazon smoke test, not using MPI-serial has been added to the test list
+   and list of expected failures to track issue #2423.
+   Out-of-date cheyenne tests on the expected failure list have been removed.
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, only for FATES configurations
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
+
+   The FATES externals update incorporates a number of bug fixes and the new allometry default
+   paramters result in a new scientific baseline.
+
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+   FATES: sci.1.72.2_api.34.0.0 -> sci.1.73.0_api.35.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+#2436 -- FATES API35 parameter file update
+NGEET#1093 -- Update default allometry parameters for tree PFTs
+NGEET#1128 -- New allometric modes
+NGEET#1149 -- Alternative vertical scaling of leaf maintenance respiration
+NGEET#1161 -- Adding day length factor switch
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.001
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Mon 22 Apr 2024 02:10:55 PM MDT

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update
        ctsm5.2.001     erik 04/22/2024 Merge b4b-dev
          ctsm5.2.0     many 04/20/2024 New mksurfdata_esmf tool to create new surface datasets that are in place
     ctsm5.1.dev176  afoster 04/04/2024 Merge b4b-dev