Merge tag 'ctsm1.0.dev089' into fv3port

Bring documentation source to master

1. Bring documentation source to master: Pulls in the source from
   https://github.com/escomp/ctsm-docs. This is important so that
   documentation can remain in sync with changes in the model
   code. Images are stored here using git-lfs (Git Large File
   Storage). I also made some minor fixes to get the pdf build of the
   tech note working.

2. Use a different documentation theme that supports a version dropdown
   menu, and add the code needed to support this versioning on the
   documentation web pages. At a high level, the way the versioned
   documentation works is to have separate subdirectories in the
   gh-pages branch of the ctsm-docs repository for each version of the
   documentation we want to support. There is then a bit of JavaScript
   code which uses a json file in the gh-pages branch to determine which
   versions exist and how these should be named in the dropdown
   menu. Most of these changes were borrowed from ESMCI/cime#3439, which
   in turn borrowed from ESCOMP/CISM-wrapper#23, which in turn was a
   slight modification of an implementation provided by @mnlevy1981 for
   the MARBL documentation, which in turn borrowed from an
   implementation put together by Unidata (credit where credit is due).

   I am not aware of out-of-the-box support for a version pull-down in
   out-of-the-box sphinx themes (though the last time I looked was in
   Fall, 2018, so there may be something available now). However,
   support for a version dropdown exists in an open PR in the sphinx
   readthedocs theme repository: readthedocs/sphinx_rtd_theme#438. I
   have pushed this branch to a new repository in ESMCI
   (https://github.com/ESMCI/sphinx_rtd_theme) to facilitate long-term
   maintenance of this branch in case it disappears from the official
   sphinx_rtd_theme repository. I have also cherry-picked a commit onto
   that branch, which is needed to fix search functionality in sphinx1.8
   (from readthedocs/sphinx_rtd_theme#672) (which is another reason for
   maintaining our own copy of this branch). The branch in this
   repository is now named version-dropdown-with-fixes (branching off of
   the version-dropdown branch in the sphinx_rtd_theme repository). In
   the long-term, I am a little concerned about using this theme that
   isn't showing any signs of being merged to the main branch of the
   readthedocs theme, but this has been working for us in other projects
   for the last 2 years, so I feel this is a reasonable approach in the
   short-medium term.

The new process for building the documentation is given here:
https://github.com/ESCOMP/CTSM/wiki/Directions-for-editing-CLM-documentation-on-github-and-sphinx

Resolves ESCOMP#239

.gitattributes

@@ -0,0 +1,6 @@
+*.svg filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: CESM forums
+    url: https://xenforo.cgd.ucar.edu/cesm/
+    about: For support with model use, troubleshooting, etc., please use the CTSM forum

.lfsconfig

@@ -0,0 +1,2 @@
+[lfs]
+        fetchexclude = *

Externals.cfg

@@ -16,21 +16,21 @@ required = True
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/rtm
-tag = rtm1_0_70
+tag = rtm1_0_71
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/mosart
-tag = mosart1_0_35
+tag = mosart1_0_36
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime5.8.15
+tag = cime5.8.17
 externals = ../Externals_cime.cfg
 required = True
 

Externals_cime.cfg

@@ -1,5 +1,5 @@
 [cmeps]
-hash = 181ff1ed9dfb279e619e8a2173f43baf7bf1dce3
+hash = 253f612acae07b2b1dc73c84f1bb30b8e1b86ddd
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = src/drivers/nuopc/

README.rst

@@ -23,6 +23,11 @@ and
 
 https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup
 
+For support with model use, troubleshooting, etc., please use the CTSM forum (or other
+appropriate forum) here:
+
+https://xenforo.cgd.ucar.edu/cesm/
+
 To get updates on CTSM tags and important notes on CTSM developments
 join our low traffic email list:
 

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -372,8 +372,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c190829.nc</paramfile>
-<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c190829.nc</paramfile>
+<paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c200402.nc</paramfile>
+<paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c200402.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -984,7 +984,7 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <use_fun phys="clm5_0" use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
 <use_fun                                                           >.false.</use_fun>
 
-<br_root phys="clm5_0" use_cn=".true." use_fun=".true.">0.83d-06</br_root>
+<br_root>0.83d-06</br_root>
 
 <!-- Scalar of leaf respiration to vcmax (used for SP mode and with luna)-->
 <leaf_mr_vcm phys="clm5_0" >0.015d00</leaf_mr_vcm>

cime_config/config_compsets.xml

@@ -37,13 +37,13 @@
 <!-- I single point forcing -->
 
   <compset>
-    <alias>I1PtClm50SpGs</alias>
-    <lname>2000_DATM%1PT_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+    <alias>I1PtClm50SpRsGs</alias>
+    <lname>2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
 
   <compset>
-    <alias>I1PtClm45SpGs</alias>
-    <lname>2000_DATM%1PT_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV</lname>
+    <alias>I1PtClm45SpRsGs</alias>
+    <lname>2000_DATM%1PT_CLM45%SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
 
 <!-- I CLM50 Compsets -->
@@ -76,6 +76,12 @@
     <lname>2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV</lname>
   </compset>
 
+  <!-- Primarily for testing; used in the RTM test suite -->
+  <compset>
+    <alias>I2000Clm50BgcCropRtmGs</alias>
+    <lname>2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>I2000Clm50BgcCrop</alias>
     <lname>2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>
@@ -187,6 +193,11 @@
     <lname>2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
 
+  <compset>
+    <alias>I2000Clm50FatesRsGs</alias>
+    <lname>2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
      <alias>I1850Clm50Bgc</alias>
      <lname>1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV</lname>
@@ -326,7 +337,12 @@
     <lname>2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV</lname>
   </compset>
 
-  <!-- Stub glacier needed for regional / single-point -->
+  <!-- Stub glacier / stub rof needed for regional / single-point -->
+  <compset>
+    <alias>I2000Clm45FatesRsGs</alias>
+    <lname>2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>I2000Clm45FatesGs</alias>
     <lname>2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_SGLC_SWAV</lname>

cime_config/testdefs/testlist_clm.xml

@@ -264,7 +264,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_P720x1_Ln3" grid="hcru_hcru" compset="I2000Clm50BgcCruGs" testmods="clm/coldStart">
+  <test name="SMS_P720x1_Ln6" grid="hcru_hcru" compset="I2000Clm50BgcCruGs" testmods="clm/coldStart">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -440,7 +440,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">0:20:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment"  >Do a test with RTM and flooding on as that also impacts CLM code</option>
     </options>
   </test>
@@ -748,7 +748,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Want an ERP test covering some non-default irrigation options. Long enough so that we're likely to exercise the various groundwater irrigation code.</option>
         </options>
       </machine>
@@ -850,7 +850,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="ERS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
@@ -884,23 +884,23 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpGs" testmods="clm/default">
+  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRsGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="ERS_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1133,23 +1133,23 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpGs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm45SpRsGs" testmods="clm/default">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
@@ -1242,7 +1242,7 @@
       <option name="comment"  >include a nag debug test of Clm45BgcCrop</option>
     </options>
   </test>
-  <test name="SMS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="SMS_D_Ld5_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1251,7 +1251,7 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="SMS_D_Lm1_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm50SpGs" testmods="clm/USUMB">
+  <test name="SMS_D_Lm1_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm50SpRsGs" testmods="clm/USUMB">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="prebeta"/>
@@ -1313,7 +1313,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpGs" testmods="clm/default">
+  <test name="SMS_Ld1_Mmpi-serial" grid="1x1_mexicocityMEX" compset="I1PtClm50SpRsGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1654,7 +1654,7 @@
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm">
         <options>
-          <option name="wallclock">0:20:00</option>
+          <option name="wallclock">00:20:00</option>
           <option name="comment">Debug test covering some non-default irrigation options.</option>
         </options>
       </machine>
@@ -1665,7 +1665,7 @@
 
       <machine name="izumi" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a tracer consistency check in debug mode.</option>
         </options>
       </machine>
@@ -1677,7 +1677,7 @@
 
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">A debug ERP test of the NWP configuration with active BGC and CROP.</option>
         </options>
       </machine>
@@ -1688,7 +1688,7 @@
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Ensure that turning on water tracers doesn't change answers. Cold start for now, until we can use initial conditions from a non-isotope case in an isotope case; once we can do that, this should be changed to not be cold start (e.g., 5-day decStart transient test: see also https://github.com/ESCOMP/ctsm/issues/495#issuecomment-516619853).</option>
         </options>
       </machine>
@@ -1699,7 +1699,7 @@
 
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a debug ERP test of the NWP configuration.</option>
         </options>
       </machine>
@@ -1711,7 +1711,7 @@
 
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a short smoke test covering the nldas2 grid and the I2000Ctsm50NwpSpNldasGs compset, which uses NLDAS datm forcing.</option>
         </options>
       </machine>
@@ -1723,7 +1723,7 @@
 
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a short smoke test covering the nldas2 grid and the I2000Ctsm50NwpSpNldasRsGs compset, which uses NLDAS datm forcing.</option>
         </options>
       </machine>
@@ -1894,7 +1894,7 @@
       </machine>
     </machines>
   </test>
-  <test name="SMS_Ly1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpGs" testmods="clm/output_sp_highfreq">
+  <test name="SMS_Ly1_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRsGs" testmods="clm/output_sp_highfreq">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
@@ -1904,11 +1904,11 @@
       </machine>
     </machines>
   </test>
-  <test name="SMS_D_Vnuopc" grid="f10_f10_musgs" compset="I2000Clm50SpRsGs" testmods="clm/default">
+  <test name="SMS_D_Ld5_Vnuopc" grid="f10_f10_musgs" compset="I2000Clm50BgcCropGs" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a test of the NUOPC cap</option>
         </options>
       </machine>
@@ -1918,7 +1918,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Can use this test to determine if there are significant throughput changes, at least for this common and important configuration. Note that this deliberately doesn't have any testmods in order to (1) avoid doing history output (because the timing of output can be very variable, and mixing output timing with other aspects of model time can be confusing), and (2) generally keep the test replicating a production configuration as closely as possible (so, for example, we do NOT set BFBFLAG=TRUE for this test).</option>
         </options>
       </machine>
@@ -1928,7 +1928,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">This test runs CTSM's Fortran unit tests. We're abusing the system test infrastructure to run these, so that a run of the test suite results in the unit tests being run as well. Grid and compset are irrelevant here, except that compset must be one that includes CTSM in order for CIME to find the test definition.</option>
         </options>
       </machine>