Merge tag 'ctsm5.1.dev014' into cn-matrix_v3

Grass/crop snow burial fraction fix, and some other fixes

(1) Crop/grass snow burial changed based on height and lodging (Danica
    Lombardozzi) - resolves ESCOMP#516. Updates grass and crop snow
    burial ('fb' in SatellitePhenologyMod.F90) from being 0.2m to change
    with PFT height and accounts for 20% lodging (falling over).

(2) In BGC code, make elai and esai depend on frac_sno (Danica
    Lombardozzi, Keith Oleson & Bill Sacks) - resolves ESCOMP#1116

(3) Fix to quadratic solution error bug caused by negative shaded
    photosynthesis (Danica Lombardozzi & Keith Oleson) - resolves
    ESCOMP#756

(4) Point to cime branch tag that avoids building CDEPS with LILAC, to
    avoid dependence on unreleased ESMF code (Bill Sacks) - resolves
    ESCOMP#1203

(5) Some tweaks to documentation and how the documentation is built
    (Bill Sacks)

Externals.cfg

@@ -37,15 +37,15 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime5.8.32
+tag = branch_tags/cime5.8.32_a01
 externals = ../Externals_cime.cfg
 required = True
 
 [doc-builder]
 local_path = doc/doc-builder
 protocol = git
 repo_url = https://github.com/ESMCI/doc-builder
-tag = v1.0.2
+tag = v1.0.4
 required = False
 
 [externals_description]

cime_config/config_pes.xml

@@ -757,14 +757,14 @@
 	  <ntasks_cpl>-48</ntasks_cpl>
 	</ntasks>
 	<nthrds>
-	  <nthrds_atm>2</nthrds_atm>
-	  <nthrds_lnd>2</nthrds_lnd>
-	  <nthrds_rof>2</nthrds_rof>
-	  <nthrds_ice>2</nthrds_ice>
-	  <nthrds_ocn>2</nthrds_ocn>
-	  <nthrds_glc>2</nthrds_glc>
-	  <nthrds_wav>2</nthrds_wav>
-	  <nthrds_cpl>2</nthrds_cpl>
+	  <nthrds_atm>1</nthrds_atm>
+	  <nthrds_lnd>1</nthrds_lnd>
+	  <nthrds_rof>1</nthrds_rof>
+	  <nthrds_ice>1</nthrds_ice>
+	  <nthrds_ocn>1</nthrds_ocn>
+	  <nthrds_glc>1</nthrds_glc>
+	  <nthrds_wav>1</nthrds_wav>
+	  <nthrds_cpl>1</nthrds_cpl>
 	</nthrds>
 	<rootpe>
 	  <rootpe_atm>0</rootpe_atm>
@@ -831,14 +831,14 @@
 	  <ntasks_cpl>-48</ntasks_cpl>
 	</ntasks>
 	<nthrds>
-	  <nthrds_atm>2</nthrds_atm>
-	  <nthrds_lnd>2</nthrds_lnd>
-	  <nthrds_rof>2</nthrds_rof>
-	  <nthrds_ice>2</nthrds_ice>
-	  <nthrds_ocn>2</nthrds_ocn>
-	  <nthrds_glc>2</nthrds_glc>
-	  <nthrds_wav>2</nthrds_wav>
-	  <nthrds_cpl>2</nthrds_cpl>
+	  <nthrds_atm>1</nthrds_atm>
+	  <nthrds_lnd>1</nthrds_lnd>
+	  <nthrds_rof>1</nthrds_rof>
+	  <nthrds_ice>1</nthrds_ice>
+	  <nthrds_ocn>1</nthrds_ocn>
+	  <nthrds_glc>1</nthrds_glc>
+	  <nthrds_wav>1</nthrds_wav>
+	  <nthrds_cpl>1</nthrds_cpl>
 	</nthrds>
 	<rootpe>
 	  <rootpe_atm>0</rootpe_atm>

cime_config/testdefs/testlist_clm.xml

@@ -302,13 +302,13 @@
       <option name="wallclock">00:60:00</option>
     </options>
   </test>
-  <test name="SMS_Ln9" grid="C96_C96_mg17" compset="IHistClm50BgcCrop" testmods="clm/default">
+  <test name="SMS_Ln9_P360x2" grid="C96_C96_mg17" compset="IHistClm50BgcCrop" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment">Want one C96 test in the aux_clm test suite; just a short smoke test to make sure it can get off the ground</option>
+      <option name="wallclock">00:10:00</option>
+      <option name="comment">Want one C96 test in the aux_clm test suite; just a short smoke test to make sure it can get off the ground. Use a PE layout that (1) has threading, because CAM uses threading at this resolution; and (2) has a smaller-than-standard task count in order to get through the queue faster.</option>
     </options>
   </test>
   <test name="SMS_Ld5" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/default">
@@ -1052,7 +1052,7 @@
       <machine name="cheyenne" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
-      <option name="wallclock">00:20:00</option>
+      <option name="wallclock">00:10:00</option>
       <option name="comment">We have one C96 test in aux_clm; this is another that uses a different compset. No need to run this additional C96 test with every tag, but include it in the less frequent ctsm_sci testing. decStart doesn't accomplish a lot in this very short test, but we're using it anyway to be consistent with other Hist tests.</option>
     </options>
   </test>

doc/ChangeLog

@@ -1,4 +1,278 @@
 ===============================================================
+Tag name:  ctsm5.1.dev014
+Originator(s): dll (Danica Lombardozzi) / oleson (Keith Oleson) / sacks (Bill Sacks)
+Date:  Sat Nov  7 12:19:14 MST 2020
+One-line Summary: Grass/crop snow burial fraction fix, and some other fixes
+
+Purpose of changes
+------------------
+
+(1) Crop/grass snow burial changed based on height and lodging (Danica
+    Lombardozzi) - resolves ESCOMP/CTSM#516. Updates grass and crop snow
+    burial ('fb' in SatellitePhenologyMod.F90) from being 0.2m to change
+    with PFT height and accounts for 20% lodging (falling over).
+
+(2) In BGC code, make elai and esai depend on frac_sno (Danica
+    Lombardozzi, Keith Oleson & Bill Sacks) - resolves ESCOMP/CTSM#1116
+
+(3) Fix to quadratic solution error bug caused by negative shaded
+    photosynthesis (Danica Lombardozzi & Keith Oleson) - resolves
+    ESCOMP/CTSM#756
+
+(4) Point to cime branch tag that avoids building CDEPS with LILAC, to
+    avoid dependence on unreleased ESMF code (Bill Sacks) - resolves
+    ESCOMP/CTSM#1203
+
+(5) Some tweaks to documentation and how the documentation is built
+    (Bill Sacks)
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/CTSM#516 (crop and grass snow burial)
+- Resolves ESCOMP/CTSM#1116 (elai and esai for non-SP runs should use
+  frac_sno)
+- Resolves ESCOMP/CTSM#756 (Quadratic solution error)
+- Resolves ESCOMP/CTSM#1203 (Rework LILAC build to avoid dependence on
+  unreleased ESMF code)
+
+CIME Issues fixed (include issue #):
+- https://github.com/ESMCI/cime/issues/3769 (Avoid building CDEPS with
+  CTSM's LILAC)
+
+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.]
+
+[X] clm5_1
+
+[X] clm5_0
+
+[X] ctsm5_0-nwp
+
+[X] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none
+
+Changes made to namelist defaults (e.g., changed parameter values): none
+
+Changes to the datasets (e.g., parameter, surface or initial files): none
+
+Substantial timing or memory changes: none
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): none
+
+Changes to tests or testing: none
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- ok
+    izumi ------- ok
+
+    ok: tests pass, baselines fail as expected
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all (or at least most)
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): 
+      new climate, at least to some extent
+
+      Changes arise from (1) & (2) (large changes) and from (3) (small
+      changes). The change in snow burial parameterizations results in
+      changes to albedo and water & energy fluxes.
+
+   If bitwise differences were observed, how did you show they were no worse
+   than roundoff? N/A
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       - casename: N/A
+
+   URL for LMWG diagnostics output used to validate new climate:
+       For analysis of diffs, see
+       https://github.com/danicalombardozzi/ctsm_py/blob/7543b0f3b413bae9974c11b467fdbc0413c3b7fa/notebooks/SnowBurial.ipynb
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+- cime: cime5.8.32 -> branch_tags/cime5.8.32_a01
+- doc-builder: v1.0.2 -> v1.0.4
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/1112
+
+===============================================================
+===============================================================
+Tag name:  ctsm5.1.dev013
+Originator(s): jedwards (Jim Edwards) / sacks (Bill Sacks)
+Date:  Wed Nov  4 14:24:55 MST 2020
+One-line Summary: Allow pnetcdf for vector history files
+
+Purpose of changes
+------------------
+
+Ever since clm4_5_1_r091, we had been avoiding the use of pnetcdf for
+vector history files (i.e., history files with dov2xy = .false.). This
+was to workaround an issue that was found on the old yellowstone
+supercomputer (bugzilla 1730). However, I cannot reproduce this issue on
+cheyenne, either with PIO1 or with PIO2. Moreover, the workaround was
+leading to very slow performance with PIO2, at least for some
+tests. This tag removes that old workaround.
+
+See https://github.com/ESCOMP/CTSM/issues/33 for details.
+
+Also change PE layouts for C96 and C192. The main motivation for this is
+to get the aux_clm C96 test through the queue faster (the current test
+sometimes waits for multiple hours in the queue):
+
+(1) Make the out-of-the-box PE counts unthreaded, as is standard for I
+    compsets
+
+(2) In the aux_clm test for C92, use a 360x2 PE layout: Use a PE layout
+    that (a) has threading, because CAM uses threading at this
+    resolution; and (b) has a smaller-than-standard task count in order
+    to get through the queue faster.
+
+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.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none
+
+Changes made to namelist defaults (e.g., changed parameter values): none
+
+Changes to the datasets (e.g., parameter, surface or initial files): none
+
+Substantial timing or memory changes:
+
+   Timing changes seem small, though not investigated carefully. No
+   timing changes are expected to show up in the PFS test (because it
+   doesn't do history output), but I looked at a few other non-debug f09
+   cases: ERP_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay,
+   ERP_Ld3.f09_g17.I1850Clm50BgcCropCru.cheyenne_intel.clm-ciso,
+   ERS_Ld3.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-rad_hrly_light_res_half,
+   ERS_Ld3.f09_g17.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef. Total
+   runtime of these increased in some tests and decreased in others
+   relative to the baseline, but on average, there was little change
+   relative to the baseline. I have more carefully investigated this
+   change in the context of pio2, which will soon become the default:
+   with pio2, this change is important to get good performance.
+
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): none
+
+Changes to tests or testing: Changed PE layout for C96 test
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- pass
+    izumi ------- pass
+
+    Note: testing was done on 13c693d88, which was before the PE layout
+    change for C96 and C192. I then ran the new C96 test manually.
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/1190
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev012
 Originator(s): oleson (Keith Oleson) / sacks (Bill Sacks)
 Date:  Tue Nov  3 09:31:41 MST 2020

doc/ChangeSum

@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm5.1.dev014 dll/oles 11/07/2020 Grass/crop snow burial fraction fix, and some other fixes
+  ctsm5.1.dev013 jedwards 11/04/2020 Allow pnetcdf for vector history files
   ctsm5.1.dev012 oleson/s 11/03/2020 Allow nlevgrnd < nlevurb
   ctsm5.1.dev011    sacks 11/02/2020 Change CISM2%NOEVOLVE compsets to use SGLC; documentation updates
   ctsm5.1.dev010 sacks/je 10/23/2020 Fix reading netcdf variable into a different data type

doc/Makefile

@@ -12,12 +12,12 @@ BUILDDIR      = build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-# Before building html or pdf, obtain all of the images. This is needed
-# because we have configured this repository (via an .lfsconfig file at
-# the top level) to NOT automatically fetch any of the large files when
-# cloning / fetching.
-html: fetch-images
-latexpdf: fetch-images
+# 'make fetch-images' should be run before building the
+# documentation. (If building via https://github.com/ESMCI/doc-builder,
+# this is run automatically for you.) This is needed because we have
+# configured this repository (via an .lfsconfig file at the top level)
+# to NOT automatically fetch any of the large files when cloning /
+# fetching.
 fetch-images:
 	git lfs pull --exclude=""