Merge tag 'ctsm5.1.dev097' into hillslope_hydrology

Update ccs_config to fix issue on izumi and maybe elsewhere

Point to latest ccs_config

This fixes an issue I had on izumi where I couldn't run
anything (ESMCI/ccs_config_cesm#45).

Externals.cfg

@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.32
+tag = ccs_config_cesm0.0.36
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,7 +44,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.26
+tag = cime6.0.27
 required = True
 
 [cmeps]

README

@@ -45,6 +45,7 @@ test -------------- CTSM Testing scripts for CTSM offline tools.
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 manage_externals -- Script to manage the external source directories
+manage_python_env - Script to setup the python environment for CTSM python tools using conda
 python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere l
 
 Directory structure only for a CTSM checkout:

bld/CLMBuildNamelist.pm

@@ -863,19 +863,32 @@ sub setup_cmdl_bgc {
      }
   }
   #
+  # Set FATES-SP mode
+  #
+  if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_sp', 'use_fates'=>$nl_flags->{'use_fates'} );
+     if ( &value_is_true($nl->get_value('use_fates_sp')) ) {
+        $nl_flags->{'use_fates_sp'} = ".true.";
+     } else {
+        $nl_flags->{'use_fates_sp'} = ".false.";
+     }
+  } else {
+     $nl_flags->{'use_fates_sp'} = ".false.";
+  }
+  #
   # Determine Soil decomposition method
   #
   my $var = "soil_decomp_method";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} );
+              'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'},
+              'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
   my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( $var ) );
 
   if (      &value_is_true($nl_flags->{'use_cn'}) ) {
      if ( $soil_decomp_method eq "None" ) {
         $log->fatal_error("$var must NOT be None if use_cn is on");
      }
-  } elsif ( &value_is_true($nl_flags->{'use_fates'}) && (not &value_is_true($nl->get_value('use_fates_sp')))  )  {
-     print  "use_fates_sp = ", $nl_flags->{'use_fates_sp'}, "\n";
+  } elsif ( &value_is_true($nl_flags->{'use_fates'}) && (not &value_is_true($nl_flags->{'use_fates_sp'}))  )  {
      if ( $soil_decomp_method eq "None" ) {
         $log->fatal_error("$var must NOT be None if use_fates is on and use_fates_sp is not TRUE");
      }
@@ -4105,12 +4118,6 @@ sub setup_logic_fates {
 
     if (&value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
-        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_sp', 'use_fates'=>$nl_flags->{'use_fates'} );
-        if ( &value_is_true($nl->get_value('use_fates_sp')) ) {
-           $nl_flags->{'use_fates_sp'} = ".true.";
-        } else {
-           $nl_flags->{'use_fates_sp'} = ".false.";
-        }
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp",
                        "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" );

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2538,9 +2538,10 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
 
-<soil_decomp_method use_cn=".true."    >CENTURYKoven2013</soil_decomp_method>
-<soil_decomp_method use_fates=".true." >CENTURYKoven2013</soil_decomp_method>
-<soil_decomp_method                    >None</soil_decomp_method>
+<soil_decomp_method use_cn=".true."                          >CENTURYKoven2013</soil_decomp_method>
+<soil_decomp_method use_fates=".true."                       >CENTURYKoven2013</soil_decomp_method>
+<soil_decomp_method use_fates=".true." use_fates_sp=".true." >None</soil_decomp_method>
+<soil_decomp_method                                          >None</soil_decomp_method>
 
 <use_lch4            soil_decomp_method="None" >.false.</use_lch4>
 <use_lch4                                      >.true.</use_lch4>

cime_config/config_compsets.xml

@@ -224,6 +224,10 @@
     <alias>I2000Clm51FatesSpCruRsGs</alias>
     <lname>2000_DATM%CRUv7_CLM51%FATES-SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I2000Clm51FatesSpRsGs</alias>
+    <lname>2000_DATM%GSWP3v1_CLM51%FATES-SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
   <compset>
     <alias>I2000Clm50FatesCru</alias>
     <lname>2000_DATM%CRUv7_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV</lname>

cime_config/testdefs/ExpectedTestFails.xml

@@ -36,22 +36,11 @@
       <issue>#1733</issue>
     </phase>
   </test>
-  <test name="SMS_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1743</issue>
-    </phase>
-  </test>
-  <test name="DAE_C2_D_Lh12.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_intel.clm-DA_multidrv">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1744</issue>
-    </phase>
-  </test>
-  <test name="DAE_N2_D_Lh12_Vmct.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_intel.clm-DA_multidrv">
-    <phase name="RUN">
+
+  <test name="LILACSMOKE_D_Ld2.f10_f10_mg37.I2000Ctsm50NwpSpAsRs.cheyenne_intel.clm-lilac">
+    <phase name="MODEL_BUILD">
       <status>FAIL</status>
-      <issue>#1744</issue>
+      <issue>#1759</issue>
     </phase>
   </test>
 

cime_config/testdefs/testlist_clm.xml

@@ -1288,6 +1288,15 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test name="SMS" grid="f45_f45_mg37" compset="I2000Clm51FatesSpRsGs" testmods="clm/FatesColdDefReducedComplexSatPhen">
+    <machines>
+      <machine name="cheyenne" compiler="nvhpc" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Simple test to make sure the basic Fates-SP compset works"</option>
+    </options>
+  </test>
   <test name="SMS_D_Ld1_PS" grid="f09_g17" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

cime_config/usermods_dirs/NEON/defaults/shell_commands

@@ -4,3 +4,9 @@
 ./xmlchange CCSM_CO2_PPMV=408.83
 ./xmlchange DATM_PRESAERO=SSP3-7.0
 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2020,DATM_YR_START=2018
+# Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way)
+./xmlchange PIO_TYPENAME=netcdf
+# BD:05/06/2022 - The PIO_REARRANGER_LND value - for global runs, PIO_REARRANGER_LND = 1 is ideal
+#                 and a value of 2 results in slow I/O.  For point runs like these, a value of 1 results in a crash (PIO bug, probably),
+#                 so we explicitly set a value of 2.
+./xmlchange PIO_REARRANGER_LND=2

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -1,7 +1,12 @@
+! Turn FATES-SP mode on
 use_fates_sp = .true.
+! Some settings that will be set when FATES-SP mode is turned on
 soil_decomp_method = 'None'
 use_lch4 = .false.
 fates_spitfire_mode = 0
+use_fates_fixed_biogeog = .true.
+use_fates_nocomp = .true.
+! Turn off a list of fields that are not needed for FATES-SP mode
 hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
               'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
               'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
@@ -31,5 +36,4 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FA
               'FATES_LITTER_AG_FINE_EL', 'FATES_LITTER_BG_FINE_EL', 'FATES_LITTER_BG_CWD_EL', 'FATES_LITTER_AG_CWD_EL',
               'FATES_LITTER_CWD_ELDC', 'FATES_LEAF_ALLOC', 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
               'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC', 'FATES_AUTORESP', 'FATES_GROWTH_RESP',
-              'FATES_LEAFMAINTAR', 'FATES_MAINT_RESP', 'FATES_NPP', 'FATES_NPP_PF',
-              'FATES_c_to_litr_cel_c', 'FATES_c_to_litr_lab_c', 'FATES_c_to_litr_lig_c'
+              'FATES_LEAFMAINTAR', 'FATES_MAINT_RESP', 'FATES_NPP', 'FATES_NPP_PF'

doc/.ChangeLog_template

@@ -31,9 +31,9 @@ Bugs fixed or introduced
 ------------------------
 [Remove any lines that don't apply. Remove entire section if nothing applies.]
 
-Issues fixed (include CTSM Issue #):
+CTSM issues fixed (include CTSM Issue #):
 
-CIME Issues fixed (include issue #):
+Externals issues fixed (include issue #):
 
 Known bugs introduced in this tag (include issue #):
 

doc/.release-ChangeLog_template

@@ -15,8 +15,9 @@ CTSM Master Tag This Corresponds To:
 Summary of changes:
 -------------------
 
-Issues fixed (include CTSM Issue #): [If none, remove this line]
-CIME Issues fixed (include issue #): [If none, remove this line]
+CTSM issues fixed (include CTSM Issue #): [If none, remove this line]
+
+Externals issues fixed (include issue #): [If none, remove this line]
 
 Science changes since: 
 

doc/ChangeLog

@@ -1,4 +1,174 @@
 ===============================================================
+Tag name: ctsm5.1.dev097
+Originator(s): sacks (Bill Sacks)
+Date: Fri May 20 15:30:17 MDT 2022
+One-line Summary: Update ccs_config to fix issue on izumi and maybe elsewhere
+
+Purpose and description of changes
+----------------------------------
+
+Point to latest ccs_config
+
+This fixes an issue I had on izumi where I couldn't run
+anything (https://github.com/ESMCI/ccs_config_cesm/issues/45).
+
+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.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+
+Externals issues fixed (include issue #):
+https://github.com/ESMCI/ccs_config_cesm/issues/45
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- Added LILAC test to the expected fails list (this has been failing for
+  the last 2 tags)
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- PASS
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+- ccs_config: ccs_config_cesm0.0.35 -> ccs_config_cesm0.0.36
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev096
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed May 18 12:44:01 MDT 2022
+One-line Summary: Fix a few glitches from the last tag
+
+Purpose and description of changes
+----------------------------------
+
+Update cime to fix DAE issue
+modify_neon issue
+When FatesSp is on, make soil_decomp None by default
+
+
+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.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+   Fixes #1744 -- DAE tests fail
+   Fixes #1743 -- NEON test failing
+   Fixes #1749 -- cime path
+   Fixes #1752 -- modify_neon script
+
+CIME Issues fixed (include issue #): Fix DAE tests
+
+Known bugs introduced in this tag (include issue #):
+   #1759 -- LILAC test fails
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   manage_python_env is at a prototype stage and not fully developed
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   When use_fates_sp is set -- by default soil_decomp_method will be None
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   Add a simple FatesSp test to aux_clm testlist
+
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    cheyenne - PASS
+
+  tools-tests (test/tools) (if tools have been changed):
+
+    cheyenne - PASS (neon tools)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+    clm_pymods test suite on cheyenne - 
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- PASS
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, ccs_config
+   cime       to cime6.0.27
+   ccs_config to ccs_config_cesm0.035
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #1753 -- Fix modify_singlept_site_neon.py script
+   #1750 -- Correct the path to cime python code
+   #1747 -- Fix a few glitches in last tag
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev095
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Mon May  9 05:02:41 MDT 2022

doc/ChangeSum

@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev097    sacks 05/20/2022 Update ccs_config to fix issue on izumi and maybe elsewhere
+    ctsm5.1.dev096     erik 05/18/2022 Fix a few glitches from the last tag
     ctsm5.1.dev095     erik 05/09/2022 Turn soil BGC off for FATES-SP mode, externals updates, FatesSP user-mod directory and compset
     ctsm5.1.dev094   negins 05/06/2022 subset_data allows zeroing out nonveg landunits without any dompft selected
     ctsm5.1.dev093   slevis 05/03/2022 Modifications for FATES-MIMICS to work