[BROKEN] Merge tag 'ctsm5.3.019' into merge-b4bdev-20250116

Includes merge conflicts in src/cpl/lilac/lnd_comp_esmf.F90 due to PR #2912.

.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

@@ -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_84
 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 = mosart1.1.06
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

doc/ChangeLog

@@ -1,4 +1,214 @@
 ===============================================================
+Tag name: ctsm5.3.019
+Originator(s): olyson (Keith Oleson, UCAR/TSS)
+Date: Tue 14 Jan 2025 02:46:11 PM MST
+One-line Summary: Stop running 0th time step
+
+Purpose and description of changes
+----------------------------------
+ As with the last tag, this is also for consistency with CAM.
+
+Contributors
+------------
+ Bill Sacks. In the final steps, also slevis.
+
+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]:
+ Fixes #925
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ Same or similar changes needed separately in clm, in mosart, and in rtm.
+
+Changes to tests or testing:
+ FAIL RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput RUN
+ I did not label this failure EXPECTED because the fix is planned for the next tag, ctsm5.3.020.
+
+ I resolved the izumi nag tests that failed to build (due to a bug in rtm and mosart) by introducing the bug-fix manually, as explained here:
+https://github.com/ESCOMP/CTSM/pull/2084#issuecomment-2584164690
+ In ctsm5.3.020 we plan to update to the rtm/mosart tags that include the fix.
+
+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
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+ I repeated the rtm & mosart test-suites with mosart1.1.04 instead of 06 and rtm1_0_82 instead of 84 (all else the same) and compared against the new baselines mosart1.1.06-ctsm5.3.019 and rtm1_0_84-ctsm5.3.019. These gave b4b identical answers.
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: larger than roundoff/same climate
+
+ Caveat: We see diffs in mosart and cpl output that will be eliminated in ctsm5.3.020. They are discussed here:
+https://github.com/ESCOMP/CTSM/pull/2838#issuecomment-2477608383
+https://github.com/ESCOMP/MOSART/issues/103#issuecomment-2479679014
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm and mosart were already updated in the previous tag (ctsm5.3.018) to include the corresponding rtm and mosart tags
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2084
+ https://github.com/ESCOMP/MOSART/pull/67
+ https://github.com/ESCOMP/RTM/pull/37
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.018
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 10 Jan 2025 05:37:08 PM MST
+One-line Summary: Change history time to be the middle of the time bounds
+
+Purpose and description of changes
+----------------------------------
+ Making the change 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):
+ Same changes are needed separately in clm, in mosart, and in rtm.
+
+Changes to tests or testing:
+ This tag introduces changes to the mosart/rtm testlists.
+
+ FAIL RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput RUN
+ I did not label this failure EXPECTED because the fix comes in later in this series of "history" tags, in particular ctsm5.3.020.
+
+ I resolved the izumi nag tests that failed to build (due to a bug in rtm and mosart) by introducing the bug-fix manually, as explained here:
+https://github.com/ESCOMP/CTSM/pull/2084#issuecomment-2584164690
+ In the next tag we expect to update to the rtm/mosart tags that include the fix.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests
+
+    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
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only time variable, plus read caveat
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all
+    - what platforms/compilers: all
+    - nature of change: only the time variable
+
+ Caveat: We see diffs in mosart and cpl output that will be eliminated later in this series of "history" tags, in particular ctsm5.3.020. They are discussed here:
+https://github.com/ESCOMP/CTSM/pull/2838#issuecomment-2477608383
+https://github.com/ESCOMP/MOSART/issues/103#issuecomment-2479679014
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm, mosart (see related note in ctsm5.3.019)
+
+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: ctsm5.3.017
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu 09 Jan 2025 11:56:43 AM MST

doc/ChangeSum

@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.019   olyson 01/14/2025 Stop running 0th time step
+       ctsm5.3.018   slevis 01/10/2025 Change history time to be the middle of the time bounds
        ctsm5.3.017   slevis 01/09/2025 Merge tmp-241219 branch to master
 tmp-241219.n03.ctsm5.3.016  01/09/2025 Bug fix for izumi nag tests to pass (slevis)
 tmp-241219.n02.ctsm5.3.016  01/08/2025 FATES hydro test update (glemieux)

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

python/ctsm/crop_calendars/generate_gdds_functions.py

@@ -60,6 +60,7 @@ def error(logger, string):
     """
     Simultaneously print ERROR messages to console and to log file
     """
+    print(string)
     logger.error(string)
     raise RuntimeError(string)
 
@@ -271,7 +272,7 @@ def import_and_process_1yr(
     else:
         chunks = None
 
-    # Get h2 file (list)
+    # Get h1 file (list)
     h1_pattern = os.path.join(indir, "*h1.*.nc")
     h1_filelist = glob.glob(h1_pattern)
     if not h1_filelist:
@@ -551,13 +552,14 @@ def import_and_process_1yr(
     log(logger, "   Importing accumulated GDDs...")
     clm_gdd_var = "GDDACCUM"
     my_vars = [clm_gdd_var, "GDDHARV"]
-    pattern = os.path.join(indir, f"*h2.{this_year-1}-01-01*.nc")
-    h2_files = glob.glob(pattern)
-    if not h2_files:
-        pattern = os.path.join(indir, f"*h2.{this_year-1}-01-01*.nc.base")
+    patterns = [f"*h2.{this_year-1}-01*.nc", f"*h2.{this_year-1}-01*.nc.base"]
+    for p in patterns:
+        pattern = os.path.join(indir, p)
         h2_files = glob.glob(pattern)
-        if not h2_files:
-            error(logger, f"No files found matching pattern '*h2.{this_year-1}-01-01*.nc(.base)'")
+        if h2_files:
+            break
+    if not h2_files:
+        error(logger, f"No files found matching patterns: {patterns}")
     h2_ds = import_ds(
         h2_files,
         my_vars=my_vars,

src/biogeochem/CNPhenologyMod.F90

@@ -392,19 +392,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, &
             soilstate_inst, temperature_inst, atm2lnd_inst, wateratm2lndbulk_inst, cnveg_state_inst, &
             cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst)
 
-       ! BACKWARDS_COMPATIBILITY(wjs, 2022-02-03) Old restart files generated at the end
-       ! of the year can indicate that a crop was panted on Jan 1, because that used to be
-       ! the time given to the last time step of the year. This would cause problems if we
-       ! ran CropPhenology in time step 0, because now time step 0 is labeled as Dec 31,
-       ! so CropPhenology would see the crop as having been planted 364 days ago, and so
-       ! would want to harvest this newly-planted crop. To avoid this situation, we avoid
-       ! calling CropPhenology on time step 0.
-       !
-       ! This .not. is_first_step() condition can be removed either when we can rely on
-       ! all restart files having been generated with
-       ! https://github.com/ESCOMP/CTSM/issues/1623 resolved, or we stop having a time
-       ! step 0 (https://github.com/ESCOMP/CTSM/issues/925).
-       if (num_pcropp > 0 .and. .not. is_first_step()) then
+       if (num_pcropp > 0) then
           call CropPhenology(num_pcropp, filter_pcropp, &
                waterdiagnosticbulk_inst, temperature_inst, crop_inst, canopystate_inst, cnveg_state_inst, &
                cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, &

src/biogeochem/CNVegetationFacade.F90

@@ -1285,7 +1285,7 @@ subroutine EndOfTimeStepVegDynamics(this, bounds, num_natvegp, filter_natvegp, &
        ! Call dv (dynamic vegetation) at last time step of year
 
        call t_startf('d2dgvm')
-       if (is_end_curr_year() .and. .not. is_first_step())  then
+       if (is_end_curr_year())  then
 
           ! Get date info.  kyr is used in lpj().  At end of first year, kyr = 2.
           call get_curr_date(yr, mon, day, sec)
@@ -1337,7 +1337,7 @@ subroutine WriteHistory(this, bounds)
 
     ! Write to CNDV history buffer if appropriate
     if (use_cndv) then
-       if (is_end_curr_year() .and. .not. is_first_step())  then
+       if (is_end_curr_year())  then
           call t_startf('clm_drv_io_hdgvm')
           call CNDVHist( bounds, this%dgvs_inst )
           if (masterproc) write(iulog,*) 'Annual CNDV calculations are complete'

src/biogeochem/CropType.F90

@@ -930,7 +930,7 @@ subroutine CropIncrementYear (this, num_pcropp, filter_pcropp)
     ! Update nyrs when it's the end of the year (unless it's the very start of the
     ! run). This assumes that, if this patch is active at the end of the year, then it was
     ! active for the whole year.
-    if ((kmo == 1 .and. kda == 1 .and. mcsec == 0) .and. .not. is_first_step()) then
+    if ((kmo == 1 .and. kda == 1 .and. mcsec == 0)) then
        do fp = 1, num_pcropp
           p = filter_pcropp(fp)
 

src/biogeochem/dynCNDVMod.F90

@@ -99,7 +99,7 @@ subroutine dynCNDV_interp( bounds, dgvs_inst)
           patch%wtcol(p)   = dgvs_inst%fpcgrid_patch(p) + &
                     wt1 * (dgvs_inst%fpcgridold_patch(p) - dgvs_inst%fpcgrid_patch(p))
 
-          if (mon==1 .and. day==1 .and. sec==dtime .and. nstep>0) then
+          if (mon==1 .and. day==1 .and. sec==dtime) then
              dgvs_inst%fpcgridold_patch(p) = dgvs_inst%fpcgrid_patch(p)
           end if
        end if