Merge branch 'simple_bfb_v2'

Minor bug fixes, cleanup, documentation and enhancements A collection of minor bug fixes, code cleanup, documentation and enhancements, all bit-for-bit. See list of issues fixed below for details. Issues fixed (include CTSM Issue #): - Fixes #24 (ncd_io_1d_log_glob is broken) - Fixes #120 (Incorrect comments in Biogeophysics1Mod.F90 - Fixes #217 (Change some cheyenne_gnu tests to cheyenne_intel) - Fixes #245 (Put all .gitignore entries in top-level file) - Fixes #272 (Code should error on missing mxsoil_color when SOIL_COLOR is used) - Fixes #283 (Add more helpful message about need to do init_interp with wrong number of vertical layers) - Fixes #367 (For cmip6 runs: Turn on cpl hist output needed to drive a TG compset) - Fixes #412 (Fix documentation of init_interp_method) - Fixes #419 (Do not allow SOYFIXN diagnostic field with FUN) - Fixes #464 (Some lines longer than 132 characters) - Fixes #465 (Remove backwards compatibility check for snw_rds) - Fixes #467 (Increase wallclock limit for test)
ESCOMP · Aug 4, 2018 · 8ad23e5 · 8ad23e5
2 parents b043949 + 8998341
commit 8ad23e5
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diff --git a/.gitignore b/.gitignore
@@ -1,10 +1,10 @@
 # directories checked out by manage_externals, and other files created
 # by manage_externals
 manage_externals.log
-src/fates/
-tools/PTCLM/
-cime/
-components/
+/src/fates/
+/tools/PTCLM/
+/cime/
+/components/
 
 # ignore svn directories
 **/.svn/**
@@ -26,28 +26,35 @@ CMakeFiles/
 
 
 # unit testing directories
-src/unit_tests.*
+/src/unit_tests.*
+
+# files generated by the unit test build
+/src/dyn_subgrid/dynVarMod.F90
+/src/dyn_subgrid/dynVarTimeInterpMod.F90
+/src/dyn_subgrid/dynVarTimeUninterpMod.F90
+/src/utils/array_utils.F90
+/src/unit_test_stubs/utils/restUtilMod_stub.F90
+/src/unit_test_stubs/main/ncdio_pio_fake.F90
+/src/unit_test_stubs/main/ncdio_var.F90
+/src/unit_test_shr/unittestArrayMod.F90
 
 # cime_config
 buildnmlc
 buildcppc
 
-# don't ignore cism build utilities directory
-!components/cism/**/build
-
 # configure / build files
-bld/**/CESM_cppdefs
-bld/**/Filepath
-bld/**/config_cache.xml
-bld/**/lnd_in
-bld/**/drv_flds_in
+/bld/**/CESM_cppdefs
+/bld/**/Filepath
+/bld/**/config_cache.xml
+/bld/**/lnd_in
+/bld/**/drv_flds_in
 
 # build-naemlist testing
-bld/unit_testers/lnd_in*
-bld/unit_testers/drv_flds_in*
-bld/unit_testers/temp_file.txt*
-bld/unit_testers/user_nl_clm_real_parameters*
-bld/unit_testers/env_run.xml
+/bld/unit_testers/lnd_in*
+/bld/unit_testers/drv_flds_in*
+/bld/unit_testers/temp_file.txt*
+/bld/unit_testers/user_nl_clm_real_parameters*
+/bld/unit_testers/env_run.xml
 
 # tools testing output
 td.*.status
@@ -66,19 +73,19 @@ clm.input_data_list.previous
 *.stdout.txt.o*
 
 # Tools executables
-tools/mksurfdata_map/mksurfdata_map
-tools/mkprocdata_map/mkprocdata_map
+/tools/mksurfdata_map/mksurfdata_map
+/tools/mkprocdata_map/mkprocdata_map
 
 # mksurfdata output files
-tools/mksurfdata_map/surfdata_*.nc
-tools/mksurfdata_map/landuse.timeseries_*.nc
+/tools/mksurfdata_map/surfdata_*.nc
+/tools/mksurfdata_map/landuse.timeseries_*.nc
 
 # mkmapdata output files
-tools/mkmapdata/PET*.RegridWeightGen.Log
-tools/mkmapdata/regrid.*.out
-tools/mkmapdata/regrid.*.err
-tools/mkmapdata/regrid.o*
-tools/mkmapdata/map*.nc
+/tools/mkmapdata/PET*.RegridWeightGen.Log
+/tools/mkmapdata/regrid.*.out
+/tools/mkmapdata/regrid.*.err
+/tools/mkmapdata/regrid.o*
+/tools/mkmapdata/map*.nc
 
 # build output
 *.o

diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -2432,20 +2432,24 @@ to the atmosphere) (but using the 'general' method will typically have
 only a very minor impact on results in this case). For this method to
 work, the input finidat file needs to be at the same resolution as the
 current configuration. So this is a less general form of
-init_interp. However, it can be used when transitioning from a spinup
-run to a transient run, or in other cases where the only difference is
-in internal memory allocation. In order to catch possible problems, this
-uses a different algorithm for finding the input point for each output
-point, which ensures that each active output point is associated with
-exactly one input point with the same latitude, longitude and type. This
-method requires (a) the same grid for input and output, within roundoff;
-(b) any non-zero-weight point in the input must have memory allocated
-for it in this grid cell in the output (this will be satisfied if the
-point is non-zero-weight on the surface dataset or if it's a point for
-which we allocate memory even for zero-weight points); (c) any active
-point in the output (based on the surface dataset and rules for
-determining active points) must have a matching point in this grid cell
-in the input.
+init_interp. However, it can be used in cases where the only difference
+is in internal memory allocation. In order to catch possible problems,
+this uses a different algorithm for finding the input point for each
+output point, which ensures that each active output point is associated
+with exactly one input point with the same latitude, longitude and
+type. This method requires (a) the same grid for input and output,
+within roundoff; (b) any non-zero-weight point in the input must have
+memory allocated for it in this grid cell in the output (this will be
+satisfied if the point is non-zero-weight on the surface dataset or if
+it's a point for which we allocate memory even for zero-weight points);
+(c) any active point in the output (based on the surface dataset and
+rules for determining active points) must have a matching point in this
+grid cell in the input. (Note that this generally can NOT be used when
+transitioning from a spinup run to a transient run, because spinup runs
+typically have irrigation off and transient runs have irrigation on, and
+the presence/absence of irrigation affects the subgrid structure; if it
+weren't for that difference, then this option would be useful for this
+use case.)
 
 </entry>
 

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -4,7 +4,6 @@
   <category name="aux_clm">
     <entry issue="#404"     >FAIL ERP_D_Ld10_P36x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_decStart RUN</entry>
     <entry issue="#158"     >FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropGs.cheyenne_gnu.clm-monthly RUN</entry>
-    <entry issue="#158"     >FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-monthly RUN</entry>
     <entry issue="#384"     >FAIL ERP_D_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay RUN</entry>
     <entry issue="#442"     >FAIL SMS.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>
     <entry issue="#442"     >FAIL SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -657,14 +657,6 @@
       <option name="tput_tolerance">0.5</option>
     </options>
   </test>
-  <test name="ERP_P36x2_Lm36" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/irrigOn_reduceOutput">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="prebeta"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:60:00</option>
-    </options>
-  </test>
   <test name="ERP_P180x2_D" grid="f19_g17" compset="I2000Clm50SpRtmFl" testmods="clm/default">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
@@ -753,6 +745,7 @@
   <test name="ERP_P72x2_Lm36" grid="f10_f10_musgs" compset="I2000Clm50BgcCrop" testmods="clm/clm50cropIrrigMonth_interp">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
+      <machine name="cheyenne" compiler="intel" category="prebeta"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -945,7 +938,6 @@
   </test>
   <test name="ERS_Lm20_Mmpi-serial" grid="1x1_smallvilleIA" compset="I2000Clm50BgcCropGs" testmods="clm/monthly">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -955,7 +947,6 @@
   </test>
   <test name="ERS_Lm40_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropGs" testmods="clm/monthly">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
@@ -966,7 +957,6 @@
   <test name="ERS_Lm54_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropGs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
@@ -976,7 +966,6 @@
   <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcDvCropQianGs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1003,7 +992,6 @@
   <test name="ERS_Ly3_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropGs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1047,7 +1035,6 @@
   </test>
   <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropGs" testmods="clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
@@ -1350,10 +1337,10 @@
   </test>
   <test name="SMS_D_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm45BgcCropQianGs" testmods="clm/cropMonthOutput">
     <machines>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
+      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">02:00:00</option>
       <option name="comment"  >Want a debug test that tests a number of aspects of transient crops, including a new crop landunit and shifting PCT_CFT; move to CLM50 once we can get it fast enough (see bug 2391)</option>
     </options>
   </test>

diff --git a/cime_config/usermods_dirs/cmip6_output/user_nl_cpl b/cime_config/usermods_dirs/cmip6_output/user_nl_cpl
@@ -0,0 +1 @@
+histaux_l2x1yrg = .true.
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,140 @@
 ===============================================================
+Tag name:  ctsm1.0.dev006
+Originator(s):  sacks (Bill Sacks)
+Date: Sat Aug  4 07:48:09 MDT 2018
+One-line Summary: Minor bug fixes, cleanup, documentation and enhancements
+
+Purpose of changes
+------------------
+
+A collection of minor bug fixes, code cleanup, documentation and
+enhancements, all bit-for-bit. See list of issues fixed below for
+details.
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Fixes #24 (ncd_io_1d_log_glob is broken)
+- Fixes #120 (Incorrect comments in Biogeophysics1Mod.F90
+- Fixes #217 (Change some cheyenne_gnu tests to cheyenne_intel)
+- Fixes #245 (Put all .gitignore entries in top-level file)
+- Fixes #272 (Code should error on missing mxsoil_color when SOIL_COLOR
+  is used)
+- Fixes #283 (Add more helpful message about need to do init_interp with
+  wrong number of vertical layers)
+- Fixes #367 (For cmip6 runs: Turn on cpl hist output needed to drive a
+  TG compset)
+- Fixes #412 (Fix documentation of init_interp_method)
+- Fixes #419 (Do not allow SOYFIXN diagnostic field with FUN)
+- Fixes #464 (Some lines longer than 132 characters)
+- Fixes #465 (Remove backwards compatibility check for snw_rds)
+- Fixes #467 (Increase wallclock limit for test)
+
+
+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_0
+
+[ ] clm4_5
+
+[ ] clm4_0
+
+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 .CTSMTrunkChecklist 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 a single-point test from gnu to intel to get better debugging
+   information
+   (SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianGs.cheyenne_intel.clm-cropMonthOutput)
+- For some single-point tests on both gnu and intel: removed one
+  compiler, keeping the tests on just one
+
+Code reviewed by: self
+
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  unit-tests (components/clm/src):
+
+    cheyenne - pass
+
+  tools-tests (components/clm/test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     cheyenne - not run
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- pass
+    cheyenne_gnu ------ pass
+    hobart_nag -------- pass
+    hobart_pgi -------- pass
+    hobart_intel ------ pass
+
+    NLCOMP failures as expected for tests with the cmip6 test mod
+
+    Some long single-point gnu tests failed due to running out of
+    wallclock time; I have removed these, just keeping them on intel
+    (along with removing a few other tests after I ran the testing - see
+    commit 5c226bdf):
+
+       FAIL ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=4803
+       FAIL ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=6024
+
+
+CTSM tag used for the baseline comparisons: ctsm1.0.dev005
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO - bit-for-bit
+
+
+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):
+- #392 (Remove old code for snw_rds restart that looks no longer needed)
+- (Other changes not documented in PRs)
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev005
 Originator(s):  sacks (Bill Sacks), mvr (Mathew Rothstein)
 Date: Fri Aug  3 07:54:59 MDT 2018

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev006    sacks 08/04/2018 Minor bug fixes, cleanup, documentation and enhancements
   ctsm1.0.dev005    sacks 08/03/2018 Rework water data types to accommodate isotopes and other tracers
   ctsm1.0.dev004     erik 07/18/2018 Add some new diagnostic fields, fix a few issues, update cmip6 output
   ctsm1.0.dev003     erik 07/15/2018 Update cime/cism to work on upgraded hobart and with glade changes on cheyenne

diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90
@@ -756,7 +756,7 @@ subroutine CNDriverNoLeaching(bounds,
          dgvs_inst, cnveg_state_inst,                                                                                              &
          cnveg_carbonstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst,                         &
          leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full),                                  &
-         froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full),                                & 
+         froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full),                                &
          croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full),                                &
          stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full),                                  &
          totsomc_col=soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc),                                                       &

diff --git a/src/biogeochem/CNFUNMod.F90 b/src/biogeochem/CNFUNMod.F90
@@ -1236,7 +1236,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
                      frac_ideal_C_use = max(0.0_r8,1.0_r8 - (total_N_resistance-fun_cn_flex_a(ivt(p)))/fun_cn_flex_b(ivt(p)) )
                      ! then, if the plant is very much in need of N, the C used for uptake is increased accordingly.                  
                      if(delta_CN .gt.0.and. frac_ideal_C_use.lt.1.0)then           
-                       frac_ideal_C_use = frac_ideal_C_use + (1.0_r8-frac_ideal_C_use)*min(1.0_r8, delta_CN/fun_cn_flex_c(ivt(p)));                       
+                       frac_ideal_C_use = frac_ideal_C_use + (1.0_r8-frac_ideal_C_use)*min(1.0_r8, delta_CN/fun_cn_flex_c(ivt(p)))
                      end if    
                      ! If we have too much N (e.g. from free N retranslocation) then make frac_ideal_c_use even lower.    
                      ! For a CN delta of fun_cn_flex_c, then we reduce C expendiure to the minimum of 0.5.