Merge branch 'hist_time_mid_of_time_bounds' into zerothtstep

.git-blame-ignore-revs

@@ -27,6 +27,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
+a51816e0de380300b69db9fc3e2c7fa83b267b64
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.3_api.36.1.0
+fxtag = sci.1.79.3_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
@@ -44,15 +44,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_80
+fxtag = rtm1_0_82
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.02
+fxtag = mosart1.1.04
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

cime_config/testdefs/ExpectedTestFails.xml

@@ -180,6 +180,10 @@
       <status>FAIL</status>
       <issue>#2454</issue>
     </phase>
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
   </test>
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
@@ -188,6 +192,13 @@
       <issue>#2454</issue>
     </phase>
   </test>
+
+  <test name="ERS_Ld60.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdST3">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2867</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
@@ -270,21 +281,22 @@
     </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_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#2325</issue>
     </phase>
   </test>
+
+  <!-- izumi nag failures -->
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
-    <phase name="COMPARE_base_rest">
+  <test name="SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only">
+    <phase name="RUN">
       <status>FAIL</status>
-      <issue>#2325</issue>
+      <issue>#2861</issue>
     </phase>
   </test>
 
-  <!-- izumi nag failures -->
   <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
     <phase name="RUN">
       <status>FAIL</status>
@@ -334,13 +346,6 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2861</issue>
-    </phase>
-  </test>
-
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
     <phase name="RUN">
       <status>FAIL</status>
@@ -361,6 +366,22 @@
       <issue>#2810</issue>
     </phase>
   </test>
+
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELLO">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
 
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
     <phase name="SHAREDLIB_BUILD">

cime_config/testdefs/testlist_clm.xml

@@ -2679,7 +2679,7 @@
       <option name="comment"  >5x5_amazon grid with FATES and latest CLM</option>
     </options>
   </test>
-  <test name="ERS_D_Ld15" grid="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="ERS_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
@@ -2688,7 +2688,7 @@
       <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="f10_f10_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
+  <test name="PEM_D_Ld15" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesColdSeedDisp">
     <machines>
       <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>

cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm

@@ -1 +1,2 @@
 use_fates_ed_st3= .true.
+hist_fexcl1 = 'FATES_ERROR_EL'

doc/ChangeLog

@@ -1,4 +1,166 @@
 ===============================================================
+Tag name: ctsm5.3.014
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 15 Nov 2024 01:24:45 PM MST
+One-line Summary: Change history time to be the middle of the time bounds
+
+Purpose and description of changes
+----------------------------------
+
+ Making the change in order to be consistent with CAM and to make history output more intuitive.
+
+
+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
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Partly addresses issue #1059
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ The history time variable now equals the middle of the time bounds.
+ Instantaneous history tapes now do not include time bounds.
+ Mixed history tapes do not change the treatment of instantaneous fields or move them to separate tapes, yet.
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing:
+ This tag introduces changes to the mosart/rtm testlists.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho -
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+  any other testing (give details below):
+
+  ctsm_sci
+     derecho ----
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only time variable
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all
+    - what platforms/compilers: all
+    - nature of change: only the time variable
+
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm, mosart
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2838
+ https://github.com/ESCOMP/MOSART/pull/70
+ https://github.com/ESCOMP/RTM/issues/54
+ https://github.com/ESCOMP/MOSART/pull/106
+ https://github.com/ESCOMP/RTM/pull/39
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.012
+Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
+Date: Wed 13 Nov 2024 09:53:51 AM MST
+One-line Summary: update fates tag
+
+Purpose and description of changes
+----------------------------------
+
+Updates FATES tag to latest fates main (sci.1.79.3_api.37.0.0), and updates API to go
+along with latest FATES update to refactor it's fire equations
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+
+
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests:
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+Round-off differences for FATES compsets where fire is active.
+NLCOMP differences for some FATES compsets
+
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2782: Fates fuel refactor (https://github.com/ESCOMP/CTSM/pull/2782)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.011
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, [email protected])
 Date: Mon Nov 11 17:55:57 MST 2024

doc/ChangeSum

@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.014   slevis 11/18/2024 Change history time to be the middle of the time bounds
+       ctsm5.3.012  afoster 11/13/2024 update fates tag
        ctsm5.3.011 samrabin 11/11/2024 Improve handling of cold-start finidat
        ctsm5.3.010  afoster 11/09/2024 Merge b4b-dev
        ctsm5.3.009 samrabin 10/15/2024 Reduce outputs from matrixcnOn tests

python/ctsm/crop_calendars/cropcal_module.py

@@ -443,10 +443,7 @@ def import_output(
         )
 
     # Convert time axis to integer year, saving original as 'cftime'
-    this_ds_gs = this_ds_gs.assign_coords(
-        {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
-    )
-    this_ds_gs = this_ds_gs.assign_coords({"time": [t.year for t in this_ds_gs["cftime"].values]})
+    this_ds_gs = convert_time_to_int_year(filename, this_ds, this_ds_gs)
 
     # Get number of harvests
     this_ds_gs["NHARVESTS"] = (this_ds_gs["GDDHARV_PERHARV"] > 0).sum(dim="mxharvests")
@@ -458,6 +455,35 @@ def import_output(
     return this_ds_gs, any_bad
 
 
+def convert_time_to_int_year(filename, this_ds, this_ds_gs):
+    """
+    Convert time axis to integer year, saving original as 'cftime'
+    """
+    if "time_bounds" in this_ds:
+        # Always true before PR #2838, when even files with all instantaneous variables got
+        # time_bounds saved. After that PR (and before the segregation of instantaneous and other
+        # variables onto separate files), files with an instantaneous variable first in their list
+        # do not get time_bounds saved.
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
+        )
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year for t in this_ds_gs["cftime"].values]}
+        )
+    elif this_ds["time"].attrs["long_name"] == "time at end of time step":
+        # This is an "instantaneous file."
+        this_ds_gs = this_ds_gs.assign_coords({"cftime": this_ds["time"]})
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year - 1 for t in this_ds_gs["cftime"].values]}
+        )
+    else:
+        raise RuntimeError(
+            f"{filename} is neither an instantaneous nor a combined/non-instantaneous file."
+        )
+
+    return this_ds_gs
+
+
 def handle_zombie_crops(this_ds):
     """
     When doing transient runs, it's somehow possible for crops in newly-active patches to be