diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index c02e20b678..eb3e286e9e 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+d89c86e7776bbf7451860b60038b4725fe7a0560
 b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
diff --git a/.gitmodules b/.gitmodules
index 9aeb7d4de0..3b7de3fd60 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -52,7 +52,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.07
+fxtag = mosart1.1.08
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
@@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.16
+fxtag = ccs_config_cesm1.0.20
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
diff --git a/WhatsNewInCTSM5.3.md b/WhatsNewInCTSM5.3.md
index 1fabfd1192..4717deac30 100644
--- a/WhatsNewInCTSM5.3.md
+++ b/WhatsNewInCTSM5.3.md
@@ -1,48 +1,108 @@
-# What's new in CTSM 5.3 (tag `ctsm5.3.0`)
+# What's new in CTSM 5.3 (tag `ctsm5.3.021`)
 
 ## Purpose and description of changes since CTSM 5.2 (tag `ctsm5.2.005`)
-- Adds CN Matrix method to speed up spinup for the BGC model.
-- Updates surface datasets.
-- Brings in new Leung 2023 dust emissions.
-- Adds explicit air conditioning for the urban model.
-- Updates crop calendars.
-- Updates fire model with various improvements, including default parameterization against climate reanalysis from CRU-JRA instead of GSWP.
-- FATES compsets can now be run with transient land use.
-
-These changes were needed ahead of the CESM3 capability/functionality "chill". For `clm6_0` physics these options are now turned on by default, in addition to Sturm snow and excess ice.
-
-## Changes to CTSM infrastructure
- - `manage_externals` removed and replaced by `git-fleximod`
- - Ability to handle CAM7 in `LND_TUNING_MODE`
-
-## Changes to CTSM answers
-
- Changes to defaults for `clm6_0` physics:
-  - Urban explicit A/C turned on
-  - Snow thermal conductivity method is now `Sturm_1997`
-  - New initial conditions file for f09 ("1-degree") 1850, with more in progress
-  - New crop calendars
-  - Dust emissions method is now `Leung_2023`
-  - Excess ice is turned on
-  - Updates to MEGAN for BVOCs
-  - Updates to BGC fire method
-
- Changes for all physics versions:
-  - Parameter files updated
-  - FATES parameter file updated
-  - Glacier region 1 is now undefined
-  - Update in FATES transient land use
-  - Pass active glacier (CISM) runoff directly to river model (MOSART)
-  - Add the option for using Matrix CN method for Carbon/Nitrogen BGC spinup
-
-## New surface datasets
-
-- With new surface datasets the following GLC fields have region "1" set to UNSET: glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
-- Updates to allow creating transient landuse timeseries files going back to 1700.
-- Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should.
-- Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid.
-- Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version.
-- Remove the `--hires_pft` option from `mksurfdata_esmf` as we don't have the datasets for it.
-- Remove `VIC` fields from surface datasets.
-- Updates to input datasets in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (crop fire peak month, peatland fraction), and the glacier behavior dataset.
 
+### New features
+
+* `manage_externals` replaced by [`git-fleximod`](https://github.com/ESMCI/git-fleximod/blob/main/README.md). ([PR \#2559](https://github.com/ESCOMP/CTSM/pull/2559))
+* No longer runs the 0th time step in first segment of startup and hybrid runs; branch and continue runs never had this 0th time step. ([PR \#2084](https://github.com/ESCOMP/CTSM/pull/2084))
+* New CN Matrix method speeds up spinup for the BGC model. ([PR \#640](https://github.com/ESCOMP/CTSM/pull/640); [Liao et al. 2023](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023MS003625)).
+* New `Leung_2023` dust emissions. ([PR \#1897](https://github.com/ESCOMP/CTSM/pull/1897); [Leung et al 2023](https://doi.org/10.5194/acp-23-6487-2023), [Leung et al. 2024](https://doi.org/10.5194/acp-24-2287-2024))
+* Explicit air conditioning for the urban model. ([PR \#2275](https://github.com/ESCOMP/CTSM/pull/2275); [Li et al. 2024](https://agupubs.onlinelibrary.wiley.com/share/NY4AYPREB8Y8BUDP7DXD?target=10.1029/2023MS004107))
+* FATES compsets can now be run with transient land use; off by default. ([PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507))
+* Ability to handle CAM7 in `LND_TUNING_MODE`. ([PR \#2632](https://github.com/ESCOMP/CTSM/pull/2632))
+
+### Answer changes
+
+Changes to defaults for `clm6_0` physics:
+
+* Urban explicit A/C turned on (links above).
+* Snow thermal conductivity method is now `Sturm1997`. ([PR \#2348](https://github.com/ESCOMP/CTSM/pull/2348); see also [discussion \#1960](https://github.com/ESCOMP/CTSM/discussions/1960))
+* New initial conditions files for f09 ("1-degree" 1850, 2000), f19 (“2-degree” 1850), and ne30 (1850, 1979, 2000) resolutions.
+* New crop calendars. ([PR \#2664](https://github.com/ESCOMP/CTSM/pull/2664); informed by [Rabin et al., 2023](https://gmd.copernicus.org/articles/16/7253/2023/gmd-16-7253-2023.html))
+* Dust emissions method is now `Leung_2023` (links above).
+* Excess ice is turned on. ([PR \#1787](https://github.com/ESCOMP/CTSM/pull/1787))
+* Updates to MEGAN for BVOCs. ([PR \#2588](https://github.com/ESCOMP/CTSM/pull/2588))
+* New BGC fire method `li2024crujra`: Avoid crop fires during growing season; allow lightning ignitions in tropical closed forests; add effect of landscape fragmentation on ignitions and duration; recalibrate against GFED5 burned area and with CRU-JRA climate. ([PR \#2684](https://github.com/ESCOMP/CTSM/pull/2684), [PR \#2711](https://github.com/ESCOMP/CTSM/pull/2711), [PR \#2715](https://github.com/ESCOMP/CTSM/issues/2715))
+
+Changes for all physics versions:
+
+* Parameters updated for CRU-JRA forcing: PPE-based modifications were made to the parameters `leafcn`, `slatop`, `froot_leaf`, `medlynslope`, and `kmax`. Lowers LAI and biomass in boreal and tropical forests, without reducing latent heat in the tropics. Affected PFTs: NET temperate, NET boreal, BET tropical, BDS boreal, C3 arctic grass. ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+* FATES parameter file updated (see section below).
+* Pass active glacier (CISM) runoff directly to river model (MOSART) ([MOSART PR \#94](https://github.com/ESCOMP/MOSART/pull/94))
+* New surface datasets and landuse timeseries files (see section below).
+* CNMatrix is new default spinup method (links above).
+
+### Heads up
+
+* Small glacier changes mean that you can’t use a 5.3 surface dataset with pre-5.3 code and vice versa anymore. (Merged with [PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+* Updates the definition of history variable “time” from *end* of `time_bounds` to *middle* of `time_bounds`. ([PR \#2838](https://github.com/ESCOMP/CTSM/pull/2838); see section below)
+* Standardizes history variable attributes and a history dimension name. ([PR \#2052](https://github.com/ESCOMP/CTSM/pull/2052); see section below)
+
+##
+
+## Additional detail
+
+### Changes related to time and history files
+
+(Note that the same information in this section applies to MOSART and RTM.)
+
+Startup and hybrid runs no longer run the 0th time step, consistent with the same change in CAM. (Branch and continue runs never had this 0th time step.) This means you will not get an extraneous initial history file anymore. In some circumstances this may also affect the names of history files.
+
+In most cases, the history `time` variable is now defined as the middle of a history file’s `time_bounds` instead of the end, for consistency with the same change in CAM. The exception is if you specify `hist_avgflag_pertape = 'I'` for that file, in which case it will be treated as an “instantaneous” file. Instantaneous history files (a) have their `time` coordinate set to the end of the last timestep (as did all history files before this tag) and (b) do not include `time_bounds`.
+
+The history dimension name `hist_interval` (of output variable `time_bounds`) is standardized to be `nbnd`. History variables `time_bounds`, `mcdate`, `mcsec`, `mdcur`, and `mscur` are standardized to include the calendar attribute.
+
+### New surface datasets and landuse timeseries files ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
+
+* Transient landuse timeseries files going back to 1700 now possible (and made for f09).
+* Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should. ([Issue \#2744](https://github.com/ESCOMP/CTSM/issues/2744))
+* Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid. ([PR \#2716](https://github.com/ESCOMP/CTSM/pull/2716), [issue \#2720](https://github.com/ESCOMP/CTSM/issues/2720))
+* Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version. ([Issue \#2723](https://github.com/ESCOMP/CTSM/issues/2723))
+* Remove outdated hydrology `VIC` (Variable Infiltration Capacity Hydrology model) fields from surface datasets.
+* Updates to input datasets:
+  * PFT/LAI/soil-color raw datasets; now from the TRENDY2024 timeseries that ends in 2023. (Issues [\#2570](https://github.com/ESCOMP/CTSM/issues/2570) and [\#2452](https://github.com/ESCOMP/CTSM/issues/2452))
+  * Two fire datasets: crop fire peak month and peatland fraction. (Issue [\#2618](https://github.com/ESCOMP/CTSM/issues/2618))
+  * Glacier behavior dataset (related to how non-Greenland glaciers are handled). (Issue [\#423](https://github.com/ESCOMP/CTSM/issues/423))
+
+### Changes to FATES parameter file
+
+* [PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507) ([ctsm5.2.013](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.2.013)) / [FATES PR \#1116](https://github.com/NGEET/fates/pull/1116) ([sci.1.77.1\_api.36.0.0](https://github.com/NGEET/fates/releases/tag/sci.1.77.0_api.36.0.0))
+  * Adds new parameters for new land use harvest mode and land use by PFT capabilities
+* [PR \#2700](https://github.com/ESCOMP/CTSM/pull/2700) ([ctsm5.3.003](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.3.003)) / [FATES PR \#1255](https://github.com/NGEET/fates/pull/1255) ([sci.1.78.3\_api.36.1.0](https://github.com/NGEET/fates/releases/tag/sci.1.78.3_api.36.1.0))
+  * Adds two arctic shrub PFTs, increasing the number of default PFTs to 14 and update arctic grass parameters ([FATES PR\#1236](https://github.com/NGEET/fates/pull/1236))
+  * Splits `fates_turnover_leaf` parameter into canopy and understory specific turnover rates and provides new values for both ([FATES PR\#1136](https://github.com/NGEET/fates/pull/1136))
+  * Updates grass allometry parameters ([FATES PR\#1206](https://github.com/NGEET/fates/pull/1206))
+  * Changes the prescribe nutrient uptake defaults from 1 to 0 for all PFTs (only relevant to ELM-FATES)
+
+### Changes to rpointer files
+
+The rpointer files are simple text files that CESM uses to keep track of how far simulations have progressed, pointing to the filename of the latest restart file for that component. There is one such file for each component, so for CTSM `I` cases that's `lnd`, `cpl`, and `atm` (and `rof` if it's active). Normally, when the user is just extending the length  of simulations, there’s no need to worry about these files.
+
+However, if there was a problem when a simulation shut down, it's possible that different components will have mismatched restarts and rpointer files. In the past, this meant figuring out what restart file should be pointed to in each component rpointer file and correcting it by hand in an editor. There was only the final set of rpointer files that was kept for a case.
+
+Now, with this update, the `lnd`, `cpl`, and `atm` rpointer files have the simulation date in the filenames, so it's easy to spot if the restarts are mismatched for one of the components. Also, since there are matching rpointer files for each time restarts are created, it's now easier to (a) make sure restarts and rpointer files are all correctly matched and (b) for a user to take a set of restarts and matching rpointer files to start up from for any part of an existing simulation. This means you don't have to hand-edit the rpointer files, making sure you don't make a mistake when you do.
+
+Old rpointer filenames:
+
+* `rpointer.atm`
+* `rpointer.cpl`
+* `rpointer.lnd`
+
+New names:
+
+* `rpointer.atm.YYYY-MM-DD-SSSSS`
+* `rpointer.cpl.YYYY-MM-DD-SSSSS`
+* `rpointer.lnd.YYYY-MM-DD-SSSSS`
+
+Where `YYYY-MM-DD-SSSSS` is the year, month, day, and seconds into the day for the simulation timestamp. For example, `rpointer.lnd.2000-01-01-00000` for a rpointer file for starting at midnight (beginning of the day) on January 1st, 2000\.
+
+Note that this is backwards-compatible, so for all the components you can use either the new or old format for the rpointer filenames. Thus, if you are restarting from an existing case before `ctsm5.3.016`, you CAN use the rpointer filenames that don't have the timestamps in the name.
+
+## Simulations supporting this release
+
+- f19 `Clm60Bgc` 16pft: [https://github.com/NCAR/LMWG\_dev/issues/70](https://github.com/NCAR/LMWG_dev/issues/70)
+- f09 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/69](https://github.com/NCAR/LMWG_dev/issues/69)
+- ne30 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/68](https://github.com/NCAR/LMWG_dev/issues/68)
+
+Note: Dust emissions in CTSM 5.3 will be different from the above simulations because of a tuning update that came in after those.
\ No newline at end of file
diff --git a/ccs_config b/ccs_config
index a712a92045..77fd32c6c4 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit a712a920453dc0cb2831dce576e78c389b567f7e
+Subproject commit 77fd32c6c4b57bb195239753f4c7838f05c1dfe8
diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py
index fb254c408f..a0eced83c5 100644
--- a/cime_config/SystemTests/rxcropmaturity.py
+++ b/cime_config/SystemTests/rxcropmaturity.py
@@ -106,7 +106,7 @@ def __init__(self, case):
         # Which conda environment should we use?
         self._get_conda_env()
 
-    def _run_phase(self, skip_gen=False):
+    def _run_phase(self, skip_gen=False, h1_inst=False):
         # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't
         # want to be saved as baseline.
 
@@ -129,7 +129,7 @@ def _run_phase(self, skip_gen=False):
         self._set_active_case(case_gddgen)
 
         # Set up stuff that applies to both tests
-        self._setup_all()
+        self._setup_all(h1_inst)
 
         # Add stuff specific to GDD-Generating run
         logger.info("RXCROPMATURITY log:  modify user_nl files: generate GDDs")
@@ -196,7 +196,7 @@ def _run_phase(self, skip_gen=False):
         self._set_active_case(case_rxboth)
 
         # Set up stuff that applies to both tests
-        self._setup_all()
+        self._setup_all(h1_inst)
 
         # Add stuff specific to Prescribed Calendars run
         logger.info("RXCROPMATURITY log:  modify user_nl files: Prescribed Calendars")
@@ -264,7 +264,7 @@ def _get_rx_dates(self):
             logger.error(error_message)
             raise RuntimeError(error_message)
 
-    def _setup_all(self):
+    def _setup_all(self, h1_inst):
         logger.info("RXCROPMATURITY log:  _setup_all start")
 
         # Get some info
@@ -274,7 +274,7 @@ def _setup_all(self):
 
         # Set sowing dates file (and other crop calendar settings) for all runs
         logger.info("RXCROPMATURITY log:  modify user_nl files: all tests")
-        self._modify_user_nl_allruns()
+        self._modify_user_nl_allruns(h1_inst)
         logger.info("RXCROPMATURITY log:  _setup_all done")
 
     # Make a surface dataset that has every crop in every gridcell
@@ -399,7 +399,7 @@ def _run_check_rxboth_run(self, skip_gen):
             tool_path,
         )
 
-    def _modify_user_nl_allruns(self):
+    def _modify_user_nl_allruns(self, h1_inst):
         nl_additions = [
             "cropcals_rx = .true.",
             "cropcals_rx_adapt = .false.",
@@ -417,6 +417,8 @@ def _modify_user_nl_allruns(self):
             "hist_type1d_pertape(2) = 'PFTS'",
             "hist_dov2xy(2) = .false.",
         ]
+        if h1_inst:
+            nl_additions.append("hist_avgflag_pertape(2) = 'I'")
         self._append_to_user_nl_clm(nl_additions)
 
     def _run_generate_gdds(self, case_gddgen):
diff --git a/cime_config/SystemTests/rxcropmaturityinst.py b/cime_config/SystemTests/rxcropmaturityinst.py
new file mode 100644
index 0000000000..bf8bf7750b
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityinst.py
@@ -0,0 +1,6 @@
+from rxcropmaturity import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYINST(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase(h1_inst=True)
diff --git a/cime_config/SystemTests/rxcropmaturityskipgeninst.py b/cime_config/SystemTests/rxcropmaturityskipgeninst.py
new file mode 100644
index 0000000000..4cab9bd7c0
--- /dev/null
+++ b/cime_config/SystemTests/rxcropmaturityskipgeninst.py
@@ -0,0 +1,6 @@
+from rxcropmaturity import RXCROPMATURITYSHARED
+
+
+class RXCROPMATURITYSKIPGENINST(RXCROPMATURITYSHARED):
+    def run_phase(self):
+        self._run_phase(skip_gen=True, h1_inst=True)
diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml
index 12859b9131..ee80087a08 100644
--- a/cime_config/config_tests.xml
+++ b/cime_config/config_tests.xml
@@ -145,6 +145,16 @@ 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>
@@ -155,6 +165,16 @@ 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
index 1986098533..2845bf8d7c 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -3649,6 +3649,17 @@
     </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"/>
@@ -3661,6 +3672,17 @@
     </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"/>
diff --git a/components/mosart b/components/mosart
index 330574fbd8..00a87c9084 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit 330574fbd8a4810b7a168175690cbf7e1a7f6dab
+Subproject commit 00a87c9084af1af0d2b14d14e3d432f6808681f9
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 2c08950b2d..0dc446448b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,106 @@
 ===============================================================
+Tag name: ctsm5.3.021
+Originator(s): samrabin (Sam Rabin, UCAR/TSS)
+Date: Wed 29 Jan 2025 04:21:40 PM MST
+One-line Summary: Standardize time metadata (release tag for ctsm5.3)
+
+Purpose and description of changes
+----------------------------------
+ Standardizes a dimension name of output variable time_bounds from hist_interval to nbnd.
+ Standardizes attributes for time_bounds, mcdate, mcsec, mdcur, and mscur.
+
+Contributors
+------------
+ Also Bill Sacks and Erik Kluzek.
+
+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 #1693
+ Fixes #2923
+ Resolves https://github.com/ESCOMP/MOSART/pull/66
+ Resolves https://github.com/ESCOMP/RTM/pull/35
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to documentation:
+ This is the release tag for ctsm5.3, so it includes the file WhatsNewInCTSM5.3.md.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ Same or similar changes needed in all three: clm, rtm, mosart.
+
+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
+    derecho ----- OK against baseline fates-sci.1.80.4_api.37.0.0-tmp-241219.n02.ctsm5.3.016
+    izumi ------- OK against baseline fates-sci.1.80.4_api.37.0.0-ctsm5.3.014
+
+  ctsm_sci against baseline ctsm_sci-ctsm5.3.016
+    derecho ---- OK
+
+  rtm tests against baseline rtm1_0_86-ctsm5.3.019
+    derecho ----- PASS
+
+  mosart tests against baseline mosart1.1.08-ctsm5.3.019
+    derecho ----- OK
+    izumi ------- PASS
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No
+ Just new metadata in history.
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ mosart1.1.07 to mosart1.1.08
+ ccs_config_cesm1.0.16 to ccs_config_cesm1.0.20 to gain access to f09_t232 grid
+ rtm was already updated to rtm1_0_86 in an earlier tag
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2052
+ https://github.com/ESCOMP/MOSART/pull/66
+ https://github.com/ESCOMP/RTM/pull/35
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.020
 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
 Date: Fri Jan 17 12:21:24 MST 2025
@@ -45,8 +147,6 @@ Testing summary:
 
 Other details
 -------------
-[Remove any lines that don't apply. Remove entire section if nothing applies.]
-
 List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
 
 Pull Requests that document the changes (include PR ids):
@@ -65,7 +165,7 @@ Purpose and description of changes
 
 Contributors
 ------------
- Bill Sacks. In the final steps, also slevis.
+ Also Bill Sacks and, in the final steps, slevis.
 
 Significant changes to scientifically-supported configurations
 --------------------------------------------------------------
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 98739639a4..e411947225 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.021 samrabin 01/29/2025 Standardize time metadata (release tag for ctsm5.3)
        ctsm5.3.020 samrabin 01/17/2025 Merge b4b-dev
        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
diff --git a/python/ctsm/crop_calendars/convert_axis_time2gs.py b/python/ctsm/crop_calendars/convert_axis_time2gs.py
index d48514370d..004dca5518 100644
--- a/python/ctsm/crop_calendars/convert_axis_time2gs.py
+++ b/python/ctsm/crop_calendars/convert_axis_time2gs.py
@@ -5,6 +5,7 @@
 import sys
 import numpy as np
 import xarray as xr
+from ctsm.crop_calendars.cropcal_utils import get_integer_years
 
 try:
     import pandas as pd
@@ -85,7 +86,7 @@ def set_up_ds_with_gs_axis(ds_in):
         if not any(x in ["mxsowings", "mxharvests"] for x in ds_in[var].dims):
             data_vars[var] = ds_in[var]
     # Set up the new dataset
-    gs_years = [t.year - 1 for t in ds_in.time.values[:-1]]
+    gs_years = get_integer_years(ds_in)[:-1]
     coords = ds_in.coords
     coords["gs"] = gs_years
     ds_out = xr.Dataset(data_vars=data_vars, coords=coords, attrs=ds_in.attrs)
diff --git a/python/ctsm/crop_calendars/cropcal_figs_module.py b/python/ctsm/crop_calendars/cropcal_figs_module.py
index f26b5975d4..519f28d98a 100644
--- a/python/ctsm/crop_calendars/cropcal_figs_module.py
+++ b/python/ctsm/crop_calendars/cropcal_figs_module.py
@@ -13,6 +13,7 @@
 from matplotlib import cm
 import matplotlib.collections as mplcol
 
+# pylint: disable=abstract-class-instantiated
 
 # Colormaps (maps)
 cropcal_colors = {
diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index 3ea084e1d2..5118186cca 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -12,6 +12,7 @@
 from ctsm.crop_calendars.check_rx_obeyed import check_rx_obeyed
 from ctsm.crop_calendars.cropcal_constants import DEFAULT_GDD_MIN
 from ctsm.crop_calendars.import_ds import import_ds
+from ctsm.utils import is_instantaneous
 
 MISSING_RX_GDD_VAL = -1
 
@@ -20,28 +21,23 @@ def check_and_trim_years(year_1, year_n, ds_in):
     """
     After importing a file, restrict it to years of interest.
     """
-    ### In annual outputs, file with name Y is actually results from year Y-1.
-    ### Note that time values refer to when it was SAVED. So 1981-01-01 is for year 1980.
-
-    def get_year_from_cftime(cftime_date):
-        # Subtract 1 because the date for annual files is when it was SAVED
-        return cftime_date.year - 1
 
     # Check that all desired years are included
-    if get_year_from_cftime(ds_in.time.values[0]) > year_1:
-        raise RuntimeError(
-            f"Requested year_1 is {year_1} but first year in outputs is "
-            + f"{get_year_from_cftime(ds_in.time.values[0])}"
-        )
-    if get_year_from_cftime(ds_in.time.values[-1]) < year_1:
-        raise RuntimeError(
-            f"Requested year_n is {year_n} but last year in outputs is "
-            + f"{get_year_from_cftime(ds_in.time.values[-1])}"
-        )
+    year = utils.get_timestep_year(ds_in, ds_in.time.values[0])
+    if year > year_1:
+        raise RuntimeError(f"Requested year_1 is {year_1} but first year in outputs is {year}")
+    year = utils.get_timestep_year(ds_in, ds_in.time.values[-1])
+    if year < year_1:
+        raise RuntimeError(f"Requested year_n is {year_n} but last year in outputs is {year}")
 
     # Remove years outside range of interest
     ### Include an extra year at the end to finish out final seasons.
-    ds_in = utils.safer_timeslice(ds_in, slice(f"{year_1+1}-01-01", f"{year_n+2}-01-01"))
+    slice_yr_1 = year_1
+    slice_yr_n = year_n + 1
+    if is_instantaneous(ds_in["time"]):
+        slice_yr_1 += 1
+        slice_yr_n += 1
+    ds_in = utils.safer_timeslice(ds_in, slice(f"{slice_yr_1}-01-01", f"{slice_yr_n}-12-31"))
 
     # Make sure you have the expected number of timesteps (including extra year)
     n_years_expected = year_n - year_1 + 2
@@ -464,9 +460,7 @@ def convert_time_to_int_year(filename, this_ds, this_ds_gs):
         # 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({"cftime": this_ds["time_bounds"].isel({"nbnd": 0})})
         this_ds_gs = this_ds_gs.assign_coords(
             {"time": [t.year for t in this_ds_gs["cftime"].values]}
         )
diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py
index 584046edee..4eaff2c94f 100644
--- a/python/ctsm/crop_calendars/cropcal_utils.py
+++ b/python/ctsm/crop_calendars/cropcal_utils.py
@@ -5,6 +5,8 @@
 import numpy as np
 import xarray as xr
 
+from ctsm.utils import is_instantaneous
+
 
 def define_pftlist():
     """
@@ -317,11 +319,12 @@ def safer_timeslice(ds_in, time_slice, time_var="time"):
     """
     ctsm_pylib can't handle time slicing like Dataset.sel(time=slice("1998-01-01", "2005-12-31"))
     for some reason. This function tries to fall back to slicing by integers. It should work with
-    both Datasets and DataArrays.
+    both Datasets and DataArrays. NOTE: This isn't a problem for more modern Python environments.
+    Even npl-2022b can use the straightforward slicing in the "try" block.
     """
     try:
         ds_in = ds_in.sel({time_var: time_slice})
-    except:  # pylint: disable=bare-except
+    except Exception as this_exception:  # pylint: disable=broad-except
         # If the issue might have been slicing using strings, try to fall back to integer slicing
         can_try_integer_slicing = (
             isinstance(time_slice.start, str)
@@ -337,15 +340,15 @@ def safer_timeslice(ds_in, time_slice, time_var="time"):
         if can_try_integer_slicing:
             fileyears = np.array([x.year for x in ds_in.time.values])
             if len(np.unique(fileyears)) != len(fileyears):
-                print("Could not fall back to integer slicing of years: Time axis not annual")
-                raise
+                msg = "Could not fall back to integer slicing of years: Time axis not annual"
+                raise RuntimeError(msg) from this_exception
             y_start = int(time_slice.start.split("-")[0])
             y_stop = int(time_slice.stop.split("-")[0])
             where_in_timeslice = np.where((fileyears >= y_start) & (fileyears <= y_stop))[0]
             ds_in = ds_in.isel({time_var: where_in_timeslice})
         else:
-            print(f"Could not fall back to integer slicing for time_slice {time_slice}")
-            raise
+            msg = f"Could not fall back to integer slicing for time_slice {time_slice}"
+            raise RuntimeError(msg) from this_exception
 
     return ds_in
 
@@ -430,3 +433,38 @@ def make_lon_increasing(xr_obj):
         raise RuntimeError("Unable to rearrange longitude axis so it's monotonically increasing")
 
     return xr_obj.roll(lon=shift, roll_coords=True)
+
+
+def get_beg_inst_timestep_year(timestep):
+    """
+    Get year associated with the BEGINNING of a timestep in an
+    instantaneous file
+    """
+    year = timestep.year
+
+    is_jan1 = timestep.dayofyr == 1
+    is_midnight = timestep.hour == timestep.minute == timestep.second == 0
+    if is_jan1 and is_midnight:
+        year -= 1
+
+    return year
+
+
+def get_timestep_year(dsa, timestep):
+    """
+    Get the year associated with a timestep, with different handling
+    depending on whether the file is instantaneous
+    """
+    if is_instantaneous(dsa["time"]):
+        year = get_beg_inst_timestep_year(timestep)
+    else:
+        year = timestep.year
+    return year
+
+
+def get_integer_years(dsa):
+    """
+    Convert time axis to numpy array of integer years
+    """
+    out_array = [get_timestep_year(dsa, t) for t in dsa["time"].values]
+    return out_array
diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py
index 49226e6f75..4c08f6a614 100644
--- a/python/ctsm/crop_calendars/generate_gdds.py
+++ b/python/ctsm/crop_calendars/generate_gdds.py
@@ -43,6 +43,7 @@ def main(
     unlimited_season_length=False,
     skip_crops=None,
     logger=None,
+    no_pickle=None,
 ):
     # pylint: disable=missing-function-docstring,too-many-statements
     # Directories to save output files and figures
@@ -109,7 +110,7 @@ def main(
 
         pickle_file = os.path.join(output_dir, f"{first_season}-{last_season}.pickle")
         h2_ds_file = os.path.join(output_dir, f"{first_season}-{last_season}.h2_ds.nc")
-        if os.path.exists(pickle_file):
+        if os.path.exists(pickle_file) and not no_pickle:
             with open(pickle_file, "rb") as file:
                 (
                     first_season,
@@ -144,6 +145,7 @@ def main(
         else:
             mxmats = None
 
+        h1_instantaneous = None
         for yr_index, this_yr in enumerate(np.arange(first_season + 1, last_season + 3)):
             if this_yr <= pickle_year:
                 continue
@@ -160,6 +162,7 @@ def main(
                 incl_vegtypes_str,
                 incl_patches1d_itype_veg,
                 mxsowings,
+                h1_instantaneous,
             ) = gddfn.import_and_process_1yr(
                 first_season,
                 last_season,
@@ -180,6 +183,7 @@ def main(
                 skip_crops,
                 outdir_figs,
                 logger,
+                h1_instantaneous,
             )
 
             gddfn.log(logger, f"   Saving pickle file ({pickle_file})...")
@@ -470,6 +474,12 @@ def add_attrs_to_map_ds(
         type=str,
         default="",
     )
+    parser.add_argument(
+        "--no-pickle",
+        help="Don't read from existing pickle file; instead, overwrite. For troubleshooting.",
+        action="store_true",
+        default=False,
+    )
 
     # Get arguments
     args = parser.parse_args(sys.argv[1:])
@@ -493,4 +503,5 @@ def add_attrs_to_map_ds(
         last_land_use_year=args.last_land_use_year,
         unlimited_season_length=args.unlimited_season_length,
         skip_crops=args.skip_crops,
+        no_pickle=args.no_pickle,
     )
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index e83eb7bb50..41b1627ed7 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -10,6 +10,7 @@
 import numpy as np
 import xarray as xr
 
+from ctsm.utils import is_instantaneous
 import ctsm.crop_calendars.cropcal_utils as utils
 import ctsm.crop_calendars.cropcal_module as cc
 from ctsm.crop_calendars.xr_flexsel import xr_flexsel
@@ -258,6 +259,7 @@ def import_and_process_1yr(
     skip_crops,
     outdir_figs,
     logger,
+    h1_instantaneous,
 ):
     """
     Import one year of CLM output data for GDD generation
@@ -287,12 +289,19 @@ def import_and_process_1yr(
     else:
         crops_to_read = utils.define_mgdcrop_list_withgrasses()
 
-    print(h1_filelist)
+    # Are h1 files instantaneous?
+    if h1_instantaneous is None:
+        h1_instantaneous = is_instantaneous(xr.open_dataset(h1_filelist[0])["time"])
+
+    if h1_instantaneous:
+        slice_year = this_year
+    else:
+        slice_year = this_year - 1
     dates_ds = import_ds(
         h1_filelist,
         my_vars=["SDATES", "HDATES"],
         my_vegtypes=crops_to_read,
-        time_slice=slice(f"{this_year}-01-01", f"{this_year}-12-31"),
+        time_slice=slice(f"{slice_year}-01-01", f"{slice_year}-12-31"),
         chunks=chunks,
     )
     for timestep in dates_ds["time"].values:
@@ -553,8 +562,8 @@ def import_and_process_1yr(
     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"]
-    for p in patterns:
-        pattern = os.path.join(indir, p)
+    for pat in patterns:
+        pattern = os.path.join(indir, pat)
         h2_files = glob.glob(pattern)
         if h2_files:
             break
@@ -810,6 +819,7 @@ def import_and_process_1yr(
         incl_vegtypes_str,
         incl_patches1d_itype_veg,
         mxsowings,
+        h1_instantaneous,
     )
 
 
diff --git a/python/ctsm/crop_calendars/import_ds.py b/python/ctsm/crop_calendars/import_ds.py
index 486757492f..181d34a9cf 100644
--- a/python/ctsm/crop_calendars/import_ds.py
+++ b/python/ctsm/crop_calendars/import_ds.py
@@ -10,6 +10,7 @@
 from importlib.util import find_spec
 import numpy as np
 import xarray as xr
+from ctsm.utils import is_instantaneous
 import ctsm.crop_calendars.cropcal_utils as utils
 from ctsm.crop_calendars.xr_flexsel import xr_flexsel
 
@@ -23,7 +24,8 @@ def compute_derived_vars(ds_in, var):
         and "HDATES" in ds_in
         and ds_in.HDATES.dims == ("time", "mxharvests", "patch")
     ):
-        year_list = np.array([np.float32(x.year - 1) for x in ds_in.time.values])
+        year_adj = 1 if is_instantaneous(ds_in["time"]) else 0
+        year_list = np.array([np.float32(x.year - year_adj) for x in ds_in.time.values])
         hyears = ds_in["HDATES"].copy()
         hyears.values = np.tile(
             np.expand_dims(year_list, (1, 2)),
diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py
index a5a02a5c9d..e224c5e06e 100644
--- a/python/ctsm/utils.py
+++ b/python/ctsm/utils.py
@@ -237,3 +237,15 @@ def parse_isoduration(iso_string):
     # Convert all to timedelta
     delta_t = timedelta(days=int(days) + 365 * int(years) + 30 * int(months))
     return int(delta_t.total_seconds() / 86400)
+
+
+def is_instantaneous(time_var):
+    """
+    Check whether a time variable came from an instantaneous file
+    """
+    long_name = time_var.attrs["long_name"]
+    if "time at end of" in long_name:
+        return True
+    if "time at exact middle" in long_name:
+        return False
+    raise RuntimeError(f"Does this long_name mean instantaneous or not? {long_name}")
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index cbb6e268f7..f5147559d9 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -340,7 +340,7 @@ end subroutine copy_entry_interface
   type(file_desc_t), target :: nfid(max_tapes)       ! file ids
   type(file_desc_t), target :: ncid_hist(max_tapes)  ! file ids for history restart files
   integer :: time_dimid                      ! time dimension id
-  integer :: hist_interval_dimid             ! time bounds dimension id
+  integer :: nbnd_dimid                      ! time bounds dimension id
   integer :: strlen_dimid                    ! string dimension id
   !
   ! Time Constant variable names and filename
@@ -2538,7 +2538,7 @@ subroutine htape_create (t, histrest)
     end if
 
     if ( .not. lhistrest )then
-       call ncd_defdim(lnfid, 'hist_interval', 2, hist_interval_dimid)
+       call ncd_defdim(lnfid, 'nbnd', 2, nbnd_dimid)
        call ncd_defdim(lnfid, 'time', ncd_unlimited, time_dimid)
        if (masterproc)then
           write(iulog,*) trim(subname), &
@@ -3392,6 +3392,7 @@ subroutine htape_timeconst(t, mode)
        long_name = 'current date (YYYYMMDD) at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mcdate', ncd_int, 1, dim1id , varid, &
           long_name = long_name)
+       call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
        !
        ! add global attribute time_period_freq
        !
@@ -3421,19 +3422,24 @@ subroutine htape_timeconst(t, mode)
        long_name = 'current seconds of current date at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mcsec' , ncd_int, 1, dim1id , varid, &
           long_name = long_name, units='s')
+       call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
        long_name = 'current day (from base day) at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mdcur' , ncd_int, 1, dim1id , varid, &
           long_name = long_name)
+       call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
        long_name = 'current seconds of current day at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mscur' , ncd_int, 1, dim1id , varid, &
           long_name = long_name)
+       call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
        call ncd_defvar(nfid(t) , 'nstep' , ncd_int, 1, dim1id , varid, &
           long_name = 'time step')
 
-       dim2id(1) = hist_interval_dimid;  dim2id(2) = time_dimid
+       dim2id(1) = nbnd_dimid;  dim2id(2) = time_dimid
        if (hist_avgflag_pertape(t) /= 'I') then  ! NOT instantaneous fields tape
           call ncd_defvar(nfid(t), 'time_bounds', ncd_double, 2, dim2id, varid, &
-             long_name = 'history time interval endpoints')
+             long_name = 'time interval endpoints', &
+             units = str)
+          call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
        end if
 
        dim2id(1) = strlen_dimid;  dim2id(2) = time_dimid
diff --git a/tools/contrib/test_rxcropmaturity_python.sh b/tools/contrib/test_rxcropmaturity_python.sh
new file mode 100755
index 0000000000..69e9b00a04
--- /dev/null
+++ b/tools/contrib/test_rxcropmaturity_python.sh
@@ -0,0 +1,107 @@
+#!/usr/bin/env bash
+set -e
+
+# This script is designed to easily test updated versions of the code in python/ctsm/crop_calendars/
+# on outputs of the rxcropmaturity test suite. For RXCROPMATURITYSKIPGEN tests (i.e., skipping the
+# GDD-generating step, it will rerun check_rxboth_run.py. It will also do this for RXCROPMATURITY
+# tests whose call of generate_gdds.py completed successfully. For RXCROPMATURITY tests where that
+# failed, it will retry the generate_gdds.py call. Tests are performed with both the ctsm_pylib
+# and npl conda environments.
+#
+# Note that the python/ctsm/crop_calendars/ this test uses will be in the same CTSM directory as
+# you used to start the tests.
+#
+# The script takes one positional input:
+#     suite_dir: The directory where your test suite was performed. E.g., $SCRATCH/tests_0123-142858de.
+#
+# Output will look something like this (✅ for success, 🔴 for failure):
+#     ctsm_pylib
+#        RXCROPMATURITYINST_Lm61.f10_f10_mg37.IHist check_rxboth_run ✅
+#        RXCROPMATURITY_Lm61.f10_f10_mg37.IHist generate_gdds 🔴
+#        RXCROPMATURITYSKIPGENINST_Ld1097.f10_f10_mg37.IHist check_rxboth_run ✅
+#        RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHist check_rxboth_run 🔴
+#     npl
+#        RXCROPMATURITYINST_Lm61.f10_f10_mg37.IHist check_rxboth_run ✅
+#        RXCROPMATURITY_Lm61.f10_f10_mg37.IHist generate_gdds ✅
+#        RXCROPMATURITYSKIPGENINST_Ld1097.f10_f10_mg37.IHist check_rxboth_run ✅
+#        RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHist check_rxboth_run ✅
+#
+# Log files for each will be saved as TEST_SHORTNAME.CONDA_ENV.log.
+
+# Process input arguments
+suite_dir="$1"
+if [[ ! -d "${suite_dir}" ]]; then
+    echo "You must provide suite_dir" >&2
+    exit 1
+fi
+
+# Where do we save log files?
+log_dir="$PWD"
+
+cd "${suite_dir}"
+test_dir_list="$(ls -d RXCROPMATURITY*/ | grep -v gddgen)"
+
+for conda_env in ctsm_pylib npl; do
+    echo "${conda_env}"
+    for d in ${test_dir_list}; do
+
+        # Get test shortname
+        t="$(echo $d | grep -oE ".*IHist")"
+        echo -n "   $t "
+
+        # Set up
+        pushd $d 1>/dev/null 2>&1
+        logfile="${log_dir}/${t}.${conda_env}.log"
+
+        # Get python command to test
+        script="check_rxboth_run"
+        set +e
+        cmd="$(grep -h "${script}.py" *int.o* | grep -oE "python3.*" | tail -n 1)"
+        set -e
+        if [[ "${cmd}" == "" ]]; then
+            # check_rxboth_run.py wasn't run. Look for generate_gdds.py command.
+            script="generate_gdds"
+            set +e
+            cmd="$(grep -h "${script}.py" *int.o* | grep -oE "python3.*" | tail -n 1)"
+            set -e
+
+            # Neither were found
+            if [[ "${cmd}" == "" ]]; then
+                echo -e "\n      Command not found" >&2
+                popd 1>/dev/null 2>&1
+                continue
+            fi
+
+            cd ../$t*gddgen
+        fi
+
+        # Strip extraneous text off command
+        cmd="$(echo ${cmd} | sed "s/ returned non-zero exit status 1.//")"
+        cmd="$(echo ${cmd} | sed -E "s/ '$//")"
+        cmd="$(echo ${cmd} | sed -E "s/'$//")"
+        
+        # generate_gdds.py should be run with --no-pickle for troubleshooting
+        if [[ "${cmd}" == *"generate_gdds.py "* ]]; then
+            cmd="${cmd} --no-pickle"
+        fi
+
+        # Run the command
+        echo -n "${script} "
+        set +e
+        conda run -n ${conda_env} ${cmd} 1>"${logfile}" 2>&1
+        result=$?
+        set -e
+
+        # Print emoji to indicate result
+        if [[ ${result} -eq 0 ]]; then
+            echo ✅
+        else
+            echo 🔴
+        fi
+
+        # Return to test suite directory
+        popd 1>/dev/null 2>&1
+    done
+done
+
+exit 0