Merge pull request #1411 from jedwards4b/neon_test_rename

fix stop_option=date, move neon niwo test to match user_mods

.config_files.xml

@@ -19,8 +19,8 @@
     <values>
       <value component="clm"       >$SRCROOT</value>
       <value component="ctsm"      >$SRCROOT</value>
-      <value component="dlnd" comp_interface="mct">$CIMEROOT/src/components/data_comps_mct/dlnd</value>
-      <value component="dlnd" comp_interface="nuopc">$CIMEROOT/src/components/cdeps/dlnd</value>
+      <value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
       <value component="slnd"      >$CIMEROOT/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
       <value component="xlnd"      >$CIMEROOT/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>

Externals.cfg

@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_83
+tag = cismwrap_2_1_85
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_76
+tag = rtm1_0_77
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_42
+tag = mosart1_0_43
 required = True
 
 [mizuRoute]
@@ -37,22 +37,50 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.47_a01
+tag = cime6.0.3
 required = True
 
 [cmeps]
-local_path = cime/src/drivers/nuopc/
+tag = cmeps0.13.15
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
-tag = cmeps0.13.2
+local_path = components/cmeps
 required = True
 
 [cdeps]
-local_path = components/cdeps
+tag = cdeps0.12.14
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
-tag = cdeps0.12.11
-externals = Externals_CDEPS.cfg
+local_path = components/cdeps
+externals =  Externals_CDEPS.cfg
+required = True
+
+[cpl7]
+tag = cpl7.0.3
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
+local_path = components/cpl7
+required = True
+
+[share]
+tag = share1.0.2
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_share
+local_path = share
+required = True
+
+[mct]
+tag = MCT_2.11.0
+protocol = git
+repo_url = https://github.com/MCSclimate/MCT
+local_path = libraries/mct
+required = True
+
+[parallelio]
+tag = pio2_5_4
+protocol = git
+repo_url = https://github.com/NCAR/ParallelIO
+local_path = libraries/parallelio
 required = True
 
 [doc-builder]

cime_config/buildnml

@@ -32,7 +32,7 @@ def buildnml(case, caseroot, compname):
 ###############################################################################
     """Build the CTSM namelist """
 
-    # Build the component namelist 
+    # Build the component namelist
     if compname != "ctsm" and compname != "clm":
         raise AttributeError
 
@@ -73,10 +73,10 @@ def buildnml(case, caseroot, compname):
         os.makedirs(ctsmconf)
 
     # -----------------------------------------------------
-    # Create config_cache.xml file 
+    # Create config_cache.xml file
     # -----------------------------------------------------
 
-    # Note that build-namelist utilizes the contents of the config_cache.xml file in 
+    # Note that build-namelist utilizes the contents of the config_cache.xml file in
     # the namelist_defaults.xml file to obtain namelist variables
 
     clm_phys = case.get_value("CLM_PHYSICS_VERSION")
@@ -159,15 +159,15 @@ def buildnml(case, caseroot, compname):
         ignore = "-ignore_ic_date"
 
     tuning = "-lnd_tuning_mode %s "%lnd_tuning_mode
-    
+
     spinup = "-clm_accelerated_spinup %s "%clm_accelerated_spinup
-    
+
     infile = os.path.join(ctsmconf, "namelist")
-    
+
     inputdata_file = os.path.join(caseroot,"Buildconf","ctsm.input_data_list")
-    
+
     lndfrac_file = os.path.join(lnd_domain_path,lnd_domain_file)
-    
+
     config_cache_file = os.path.join(caseroot,"Buildconf", compname+"conf","config_cache.xml")
 
     # -----------------------------------------------------
@@ -191,7 +191,7 @@ def buildnml(case, caseroot, compname):
 
         # If multi-instance case does not have restart file, use
         # single-case restart for each instance
-        rpointer = "rpointer.lnd" 
+        rpointer = "rpointer.lnd"
         if (os.path.isfile(os.path.join(rundir,rpointer)) and
             (not os.path.isfile(os.path.join(rundir,rpointer + inst_string)))):
             shutil.copy(os.path.join(rundir, rpointer),
@@ -234,7 +234,7 @@ def buildnml(case, caseroot, compname):
                    "-configuration %s -structure %s "
                    "-lnd_frac %s -glc_nec %s %s -co2_ppmv %s -co2_type %s -config %s -driver %s "
                    "%s %s %s %s"
-                   %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, 
+                   %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts,
                      nomeg, usecase, lnd_grid, clmusr, start_type, caseroot,
                      configuration, structure,
                      lndfrac_file, glc_nec, glc_use_antarctica_flag, ccsm_co2_ppmv, clm_co2_type, config_cache_file, driver, 

cime_config/testdefs/ExpectedTestFails.xml

@@ -37,20 +37,6 @@
     </phase>
   </test>
 
-  <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#3915</issue>
-    </phase>
-  </test>
-
-  <test name="SMS_D_Ld1_P48x1_Vnuopc.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-af_bias_v7">
-    <phase name="MODEL_BUILD">
-      <status>FAIL</status>
-      <issue>ESMCI/cime#3915</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Ld5_D_P48x1_Vnuopc.f10_f10_mg37.IHistClm51Bgc.izumi_nag.clm-decStart">
     <phase name="RUN">
       <status>FAIL</status>

cime_config/testdefs/testlist_clm.xml

@@ -1432,7 +1432,7 @@
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases, 
+      <option name="comment"  >Run ARCTIC for transient case starting in 1979 as for AMIP CAM cases,
                 (no need to run this high core count test with every tag, but include it in the less frequent ctsm_sci testing)"</option>
     </options>
   </test>
@@ -1680,7 +1680,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="SMS_D_Vnuopc_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON_NIWO">
+  <test name="SMS_D_Vnuopc_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -2422,7 +2422,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
-      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>      
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2442,7 +2442,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="hobart" compiler="nag" category="fates"/>
-      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>      
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2520,16 +2520,6 @@
       </machine>
     </machines>
   </test>
-  <test name="SMS_D_Lm1_Mmpi-serial" grid="1x1_brazil" compset="I2000Clm51Bgc" testmods="clm/localtimeOutput">
-    <machines>
-      <machine name="izumi" compiler="nag" category="aux_clm">
-        <options>
-          <option name="wallclock">00:20:00</option>
-          <option name="comment">A short single-point test for local time output test mods </option>
-        </options>
-      </machine>
-    </machines>
-  </test>
   <test name="SMS_Ly1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/output_sp_highfreq">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm">

cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm

@@ -1,2 +1,6 @@
 calc_human_stress_indices = 'ALL'
 hist_master_list_file = .true.
+
+hist_fincl1   += 'GSSUN:L43200', 'GSSHA:L43200', 'FSDSND:L43200', 'FSRND:L43200', 'FSRSFND:L43200', 
+                 'SSRE_FSRND:L43200', 'FSDSVD:L43200', 'FSDSVI:L43200',
+                 'FSRVD:L43200', 'FSRSFVD:L43200', 'SSRE_FSRVD:L43200'

cime_config/usermods_dirs/NEON/defaults/user_nl_clm

@@ -19,7 +19,7 @@
 !----------------------------------------------------------------------------------
 
 flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_hist_16pfts_Irrig_CMIP6_simyr2000_${NEONSITE}_c210513.nc"
+fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c210720.nc"
 model_year_align_urbantv = 2018
 stream_year_first_urbantv = 2018
 stream_year_last_urbantv = 2019
@@ -29,3 +29,9 @@ stream_year_last_ndep = 2019
 model_year_align_popdens = 2018
 stream_year_first_popdens = 2018
 stream_year_last_popdens = 2019
+stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc'
+! h1 output stream 
+hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI',
+             'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr'
+hist_mfilt(2) = 48
+hist_nhtfrq(2) = 1  

doc/ChangeLog

@@ -1,4 +1,132 @@
 ===============================================================
+Tag name:  ctsm5.1.dev049
+Originator(s):  jedwards4b/erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Mon Jul 26 01:31:04 MDT 2021
+One-line Summary: Update externals, NEON updates, fix stop_option=date, move neon niwo test to match user_mods, local time option
+
+Purpose and description of changes
+----------------------------------
+
+Move the NEON_NIWO test to NEON/NIWO to match the names in usermods. Output particular fields for the NEON
+cases, and use a reduced size dataset for lightning for NEON sites. Update NEON surface datasets with
+new scripts included here. Fix stop option for NUOPC. NEON NIWO test in testlist explicity uses the user-mod
+as well as the defaults testmod.
+
+This script is for modifying the surface dataset at neon sites using data available from the neon server.
+
+Also add the ability to output history fields for a particular time of day (in seconds) with the LXXXXX 
+history averaging option from Ronny Meier.
+
+Externals are updated extensively to the version with cpl7 cime directories split out for CESM.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations? No
+(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 #): #1412
+   Fixes #1412 -- Reduce data requirements for NEON single point sites
+   Fixes #1353 -- Need script to modify NEON surface datasets
+
+CIME Issues fixed (include issue #): #3915
+  Fixes cime/#3915 -- CESM nuopc build fails on izumi_nag
+
+Known bugs introduced in this tag (include issue #):
+  #1437 -- modify_singlept_site_neon.py seems to have trouble finding latest file and creates hidden file for output
+  #1436 -- Need subset_data.py script to be able to run from any directory
+
+Known bugs found since the previous tag (include issue #):
+   #1429 -- Modified NEON surface datasets have errors
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+  NEON cases now download data to $RUNDIR
+
+Changes to the datasets (e.g., parameter, surface or initial files): NEON sufdata
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   Note when you have a test with two testmod directories it won't be able to reduce any deuplication
+   that happens in directories used between the two.
+
+Changes to tests or testing:
+   Test mods in testlists can now include multiple test mod directories and this is used for the NEON test
+
+
+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 (47 tests differ from before because of NEON surface dataset update)
+
+  tools-tests (test/tools) (if tools have been changed):
+
+    cheyenne - OK
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cism, mosart, rtm, cime, cmeps, cdeps (cime split)
+   cism   to cismwrap_2_1_85
+   mosart to mosart1_0_43
+   rtm    to rtm1_0_77
+   cime   to cime6.0.3
+   cmeps  to cmeps0.13.15
+   cdeps  to cdeps0.12.14
+
+   New cime-split externals:
+
+   cpl7.0.3
+   share1.0.2
+   MCT_2.11.0
+   pio2_5_4
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #1411 -- fix stop_option=date, move neon niwo test to match user_mods
+   #1375 -- Script for modifying neon surface dataset 
+   #1374 -- Local solar time option for average flag
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev048
 Originator(s):  slevis (Samuel Levis,SLevis Consulting,303-665-1310)
 Date: Sat Jul 10 11:39:55 MDT 2021