Merge remote-tracking branch 'escomp/master' into no_dynlu_first_step

.github/ISSUE_TEMPLATE/01_bug_report.md

@@ -4,6 +4,10 @@ about: Report a problem with the code
 
 ---
 
+### Brief summary of bug
+
+[Give a one or two sentence summary. This could be the same as the issue title if you feel that is a sufficient summary.]
+
 ### General bug information
 
 **CTSM version you are using:** [output of `git describe`]

.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

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>
 

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>

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>

cime_config/usermods_dirs/cmip6_output/user_nl_cpl

@@ -0,0 +1 @@
+histaux_l2x1yrg = .true.