ESCOMP · slevis-lmwg · Jul 9, 2025 · Apr 1, 2024 · Apr 13, 2024 · Apr 17, 2024
diff --git a/cime_config/SystemTests/rxcropmaturityinst.py b/cime_config/SystemTests/rxcropmaturityinst.py
diff --git a/cime_config/SystemTests/rxcropmaturityskipgeninst.py b/cime_config/SystemTests/rxcropmaturityskipgeninst.py
diff --git a/cime_config/config_archive.xml b/cime_config/config_archive.xml
@@ -1,7 +1,8 @@
 <components version="2.0">
   <comp_archive_spec compname="clm" compclass="lnd">
     <rest_file_extension>r</rest_file_extension>
-    <rest_file_extension>rh\d?</rest_file_extension>
+    <rest_file_extension>rh\da</rest_file_extension>
+    <rest_file_extension>rh\di</rest_file_extension>
     <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
     <hist_file_extension>lilac_hi.*\.nc$</hist_file_extension>
     <hist_file_extension>lilac_atm_driver_h\d*.*\.nc$</hist_file_extension>
@@ -13,37 +14,19 @@
     </rpointer>
     <test_file_names>
       <tfile disposition="copy">rpointer.lnd</tfile>
-      <tfile disposition="copy">rpointer.lnd_9999</tfile>
+      <tfile disposition="copy">rpointer.lnd_9999.1976-01-01-00000</tfile>
       <tfile disposition="copy">casename.clm2.r.1976-01-01-00000.nc</tfile>
-      <tfile disposition="copy">casename.clm2.rh4.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.clm2.h0.1976-01-01-00000.nc</tfile>
+      <tfile disposition="copy">casename.clm2.rh4a.1976-01-01-00000.nc</tfile>
+      <tfile disposition="copy">casename.clm2.rh4i.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.clm2.h0a.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.clm2.h0i.1976-01-01-00000.nc</tfile>
       <tfile disposition="move">casename.clm2.lilac_hi.1976-01-01-00000.nc</tfile>
       <tfile disposition="move">casename.clm2.lilac_atm_driver_h0.0001-01.nc</tfile>
-      <tfile disposition="ignore">casename.clm2.h0.1976-01-01-00000.nc.base</tfile>
+      <tfile disposition="ignore">casename.clm2.h0a.1976-01-01-00000.nc.base</tfile>
+      <tfile disposition="ignore">casename.clm2.h0i.1976-01-01-00000.nc.base</tfile>
       <tfile disposition="move">casename.clm2_0002.e.postassim.1976-01-01-00000.nc</tfile>
       <tfile disposition="move">casename.clm2_0002.e.preassim.1976-01-01-00000.nc</tfile>
-      <tfile disposition="ignore">anothercasename.clm2.i.1976-01-01-00000.nc</tfile>
-    </test_file_names>
-  </comp_archive_spec>
-  <comp_archive_spec compname="ctsm" compclass="lnd">
-    <rest_file_extension>r</rest_file_extension>
-    <rest_file_extension>rh\d?</rest_file_extension>
-    <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
-    <hist_file_extension>e</hist_file_extension>
-    <rest_history_varname>locfnh</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer.lnd$NINST_STRING</rpointer_file>
-      <rpointer_content>./$CASE.ctsm$NINST_STRING.r.$DATENAME.nc</rpointer_content>
-    </rpointer>
-    <test_file_names>
-      <tfile disposition="copy">rpointer.lnd</tfile>
-      <tfile disposition="copy">rpointer.lnd_9999</tfile>
-      <tfile disposition="copy">casename.ctsm.r.1976-01-01-00000.nc</tfile>
-      <tfile disposition="copy">casename.ctsm.rh4.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.ctsm.h0.1976-01-01-00000.nc</tfile>
-      <tfile disposition="ignore">casename.ctsm.h0.1976-01-01-00000.nc.base</tfile>
-      <tfile disposition="move">casename.ctsm_0002.e.postassim.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.ctsm_0002.e.preassim.1976-01-01-00000.nc</tfile>
+      <tfile disposition="ignore">anothercasename.clm2.r.1976-01-01-00000.nc</tfile>
     </test_file_names>
   </comp_archive_spec>
 </components>
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
@@ -145,16 +145,6 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
-  <test NAME="RXCROPMATURITYINST">
-    <DESC>As RXCROPMATURITY but ensure instantaneous h1. Can be removed once instantaneous and other variables are on separate files.</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
   <test NAME="RXCROPMATURITYSKIPGEN">
     <DESC>As RXCROPMATURITY but don't actually generate GDDs. Allows short testing with existing GDD inputs.</DESC>
     <INFO_DBUG>1</INFO_DBUG>
@@ -165,16 +155,6 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
-  <test NAME="RXCROPMATURITYSKIPGENINST">
-    <DESC>As RXCROPMATURITYSKIPGEN but ensure instantaneous h1. Can be removed once instantaneous and other variables are on separate files.</DESC>
-    <INFO_DBUG>1</INFO_DBUG>
-    <DOUT_S>FALSE</DOUT_S>
-    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
-    <REST_OPTION>never</REST_OPTION>
-    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
-    <HIST_N>$STOP_N</HIST_N>
-  </test>
-
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -4240,17 +4240,6 @@
     </options>
   </test>
 
-  <test name="RXCROPMATURITYINST_Lm61" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">6:00:00</option>
-      <option name="comment">As RXCROPMATURITY, but ensure that h1 file is instantaneous. Can be removed once instantaneous and other variables are separated onto separate files.</option>
-    </options>
-  </test>
-
   <test name="RXCROPMATURITYSKIPGEN_Ld1097" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -4263,17 +4252,6 @@
     </options>
   </test>
 
-  <test name="RXCROPMATURITYSKIPGENINST_Ld1097" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/cropMonthOutput">
-    <machines>
-      <machine name="derecho" compiler="intel" category="rxcropmaturity"/>
-      <machine name="derecho" compiler="intel" category="crop_calendars"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:45:00</option>
-      <option name="comment">As RXCROPMATURITYSKIPGEN, but ensure that h1 file is instantaneous. Can be removed once instantaneous and other variables are separated onto separate files.</option>
-    </options>
-  </test>
-
   <test name="ERP_D_P64x2_Ld10" grid="f10_f10_mg37" compset="I2000Clm60Bgc" testmods="clm/Hillslope">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -4388,7 +4366,7 @@
       <machine name="derecho" compiler="intel" category="crop_calendars"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:59:00</option>
     </options>
   </test>
 

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,134 @@
 ===============================================================
+Tag name: ctsm5.3.062
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 03 Jul 2025 12:23:00 PM MDT
+One-line Summary: Put instantaneous and non-inst. fields on separate hist files
+
+Purpose and description of changes
+----------------------------------
+ Following ctsm5.3.018 "Change history time to be the middle of the time bounds" the current change intends to prevent confusion associated with the time corresponding to instantaneous history fields by putting them on separate files than non-instantaneous fields. The result is
+ 1) two history files per clm, mosart, and rtm history tape:
+ tape h0 becomes h0a and h0i
+ tape h1 becomes h1a and h1i
+ ...
+ tape hX becomes hXa and hXi
+
+ 2) two history restart files per history restart tape:
+ rh0 becomes rh0a and rh0i
+ rh1 becomes rh1a and rh1i
+ ...
+ rhX becomes rhXa and rhXi
+
+ The clm could and still can handle not generating history (and corresponding history restart) files when empty. The rtm and mosart could not handle not generating empty files. Instead of refactoring rtm and mosart (out of scope), I introduced one active instantaneous field in mosart and one in rtm.
+
+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_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Resolves #1059 Don't allow inst. fields and averaged fields to be on the same history file
+ Resolves ESCOMP/RTM#32
+ Resolves ESCOMP/MOSART#52
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ History tapes have new extensions, e.g. h0 becomes h0a and h0i
+ History restart tapes have new extensions, e.g. rh0 becomes rh0a and rh0i
+
+Changes to documentation:
+ Not, yet:
+ - clm documentation
+ - Adam Phillips' cmip documentation
+
+Substantial timing or memory changes:
+[e.g., check PFS test in the test suite and look at timings, if you
+expect possible significant timing changes]
+
+
+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
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    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: (-c fates-sci.1.84.0_api.40.0.0-ctsm5.3.061 -g fates-sci.1.84.0_api.40.0.0-ctsm5.3.062)
+    derecho ----- OK
+    izumi ------- OK
+
+  any other testing (give details below):
+
+  ctsm_sci (-c ctsm_sci-ctsm5.3.059 -g ctsm_sci-ctsm5.3.062)
+     derecho ---- FAIL and I will open an issue and mark EXPECTED FAILURE as the problem originates in ctsm5.3.060
+
+  mosart tests: (-c mosart1.1.08-ctsm5.3.061 -g mosart1.1.09-ctsm5.3.062)
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm tests: (-c rtm1_0_86-ctsm5.3.061 -g rtm1_0_87-ctsm5.3.062)
+    derecho ----- OK
+    izumi ------- OK
+
+  crop_calendars tests: (tested while in ctsm5.3.058, before updating to ctsm5.3.061)
+    derecho ----- OK
+    izumi ------- OK
+
+  ssp tests: (tested while in ctsm5.3.058, before updating to ctsm5.3.061)
+    derecho ----- OK
+
+  hillslope tests: (tested while in ctsm5.3.058, before updating to ctsm5.3.061)
+    derecho ----- OK
+
+  fire tests: (tested while in ctsm5.3.058, before updating to ctsm5.3.061)
+    derecho ----- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No, but read caveat
+
+ Caveat: h0 files become h0a (containing non-instantaneous fields) and h0i (containing instantaneous fields). I spot-checked clm, mosart, and rtm files and confirmed no bitwise change in answers.
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ mosart1.1.08 --> mosart1.1.09
+ rtm1_0_86 --> rtm1_0_87
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2445
+ https://github.com/ESCOMP/MOSART/pull/117
+ https://github.com/ESCOMP/RTM/pull/61
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.061
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu 26 Jun 2025 11:28:43 AM MDT

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.062   slevis 07/03/2025 Put inst. and non-inst. fields on separate hist files
        ctsm5.3.061   slevis 06/26/2025 Merge b4b-dev to master
        ctsm5.3.060   slevis 06/24/2025 Preliminary update of ctsm54 defaults (answer changing)
        ctsm5.3.059     erik 06/23/2025 Bring in various cleanup efforts found in previous testing after the chill changes came in

diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py
@@ -78,7 +78,7 @@ def main(argv):
 
     any_bad = False
 
-    annual_outfiles = glob.glob(os.path.join(args.directory, "*.clm2.h1.*.nc"))
+    annual_outfiles = glob.glob(os.path.join(args.directory, "*.clm2.h1a.*.nc"))
 
     # These should be constant in a Prescribed Calendars (rxboth) run, as long as the inputs were
     # static.

diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -280,13 +280,13 @@ def import_and_process_1yr(
         chunks = None
 
     # Get h1 file (list)
-    h1_pattern = os.path.join(indir, "*h1.*.nc")
+    h1_pattern = os.path.join(indir, "*h1a.*.nc")
     h1_filelist = glob.glob(h1_pattern)
     if not h1_filelist:
-        h1_pattern = os.path.join(indir, "*h1.*.nc.base")
+        h1_pattern = os.path.join(indir, "*h1a.*.nc.base")
         h1_filelist = glob.glob(h1_pattern)
         if not h1_filelist:
-            error(logger, "No files found matching pattern '*h1.*.nc(.base)'")
+            error(logger, "No files found matching pattern '*h1a.*.nc(.base)'")
 
     # Get list of crops to include
     if skip_crops is not None:
@@ -566,7 +566,7 @@ def import_and_process_1yr(
     log(logger, "   Importing accumulated GDDs...")
     clm_gdd_var = "GDDACCUM"
     my_vars = [clm_gdd_var, "GDDHARV"]
-    patterns = [f"*h2.{this_year-1}-01*.nc", f"*h2.{this_year-1}-01*.nc.base"]
+    patterns = [f"*h2a.{this_year-1}-01*.nc", f"*h2a.{this_year-1}-01*.nc.base"]
     for pat in patterns:
         pattern = os.path.join(indir, pat)
         h2_files = glob.glob(pattern)