Merge pull request #698 from ekluzek/relcisofix

Bring the carbon isotope fix to the release branch

cime_config/testdefs/ExpectedTestFails.xml

@@ -2,13 +2,11 @@
 
 <expectedFails>
   <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>
-    <entry issue="#675"            >FAIL LCISO_Lm13.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly COMPARE_base_cisoallon</entry>
   </category>
   <category name="fates">
     <entry issue="667"              >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro COMPARE_base_rest</entry>

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+release-clm5.0.22     erik 05/08/2019 Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change
 release-clm5.0.21     erik 05/03/2019 New ndep files, update fates, fix some issues
 release-clm5.0.20     erik 03/12/2019 Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes
 release-clm5.0.19     erik 03/08/2019 Update cime version to one with updates for cheyenne after the Mar/5th/2019 downtime that resulting in mpt2.16 not being able to be used

doc/release-clm5.0.ChangeLog

@@ -1,4 +1,105 @@
 ===============================================================
+Tag name:  release-clm5.0.22
+Originator(s):  erik (Erik Kluzek)
+Date: Wed May  8 13:32:51 MDT 2019
+One-line Summary: Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change
+
+Purpose of this version:
+------------------------
+
+We currently have a bug so that for transient land-use change cases answers are different starting in soil
+carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no
+land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same.
+There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic
+pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't 
+cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool
+does have a meaningful impact on the simulation of the Carbon isotopic fields.
+
+
+CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many other changes)
+
+Summary of changes:
+-------------------
+
+Issues fixed (include CTSM Issue #): #262 #675
+   Fixes #675 -- Carbon isotopes under transient land-use change
+   Fixes #262 -- hirespft option to mksurfdata.pl
+
+Issues found: #707
+   #707 -- missing hirespft mapping files
+
+Science changes since: release-clm5.0.21
+    Fix Carbon isotope issue under transient land-use change
+
+Software changes since: release-clm5.0.21
+    Bring in mapping files for 3x3min MODISv2 grid for most resolutions
+
+Changes to User Interface since: release-clm5.0.21
+    None
+
+Testing:
+--------
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - PASS
+
+  unit-tests (components/clm/src):
+
+    cheyenne - PASS
+    hobart ---PASS
+
+  regular tests (aux_clm):
+
+    cheyenne_intel ---- OK
+    cheyenne_gnu ------ OK
+    hobart_nag -------- OK
+    hobart_pgi -------- OK
+    hobart_intel ------ OK
+
+Summary of Answer changes:
+-------------------------
+
+Baseline version for comparison: release-clm5.0.21
+
+Changes answers relative to baseline: Yes, but only when Carbon isotopes on under transient land-use change!
+
+  Summarize any changes to answers:
+    - what code configurations: Bgc with use_c13 or use_c14 T and with a transient land-use change after each year boundary
+    - what platforms/compilers: All
+    - nature of change: same climate for bulk Carbon, isotopic Carbon is quite different for regions with land-use change
+
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+      /oleson/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist
+
+  URL for LMWG diagnostics output for new climate:
+http://webext.cgd.ucar.edu/I20TR/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist/lnd/clm50_release-clm5.0.20_1deg_GSWP3V1_isofix2_hist.1995_2014-clm50_release-clm5.0.20_1deg_GSWP3V1_isofix_hist.1995_2014/setsIndex.html  
+
+Detailed list of changes:
+------------------------
+
+Externals being used:
+
+   cism:   release-cesm2.0.04
+   rtm:    release-cesm2.0.02
+   mosart: release-cesm2.0.03
+   cime:   cime5.6.14
+   FATES:  fates_s1.21.0_a7.0.0_br_rev2
+   PTCLM:  PTCLM2_180611
+
+CTSM Tag versions pulled over from master development branch: ctsm1.0.dev036
+
+Pull Requests that document the changes (include PR ids): #698
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #698 -- Bring the carbon isotope fix to the release branch
+
+===============================================================
+===============================================================
 Tag name:  release-clm5.0.21
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Fri May  3 16:10:35 MDT 2019

src/biogeochem/CNVegetationFacade.F90

@@ -709,12 +709,12 @@ subroutine DynamicAreaConservation(this, bounds, clump_index, &
     if (use_c13) then
        call CStateUpdateDynPatch(bounds, num_soilc_with_inactive, filter_soilc_with_inactive, &
             this%c13_cnveg_carbonflux_inst, this%c13_cnveg_carbonstate_inst, &
-            soilbiogeochem_carbonstate_inst)
+            c13_soilbiogeochem_carbonstate_inst)
     end if
     if (use_c14) then
        call CStateUpdateDynPatch(bounds, num_soilc_with_inactive, filter_soilc_with_inactive, &
             this%c14_cnveg_carbonflux_inst, this%c14_cnveg_carbonstate_inst, &
-            soilbiogeochem_carbonstate_inst)
+            c14_soilbiogeochem_carbonstate_inst)
     end if
     call NStateUpdateDynPatch(bounds, num_soilc_with_inactive, filter_soilc_with_inactive, &
          this%cnveg_nitrogenflux_inst, this%cnveg_nitrogenstate_inst, &

tools/mkmapdata/README

@@ -76,7 +76,7 @@ That will enable the --netcdf4 and --64bit_offset options to be used.
 Important files:
 
   regridbatch.sh ------- Script to run mkmapdata.sh for many resolutions on cheyenne
-  regridgeyser.sh ------ Script to run mkmapdata.sh for many resolutions on geyser
+  regriddav.sh --------- Script to run mkmapdata.sh for many resolutions on the DAV cluster (Casper)
   mvNimport.sh --------- Script to copy and import mapping files in for many resolutions
   mkmapdata.sh --------- Script to create mapping datasets for a given resolution
 

tools/mkmapdata/mkmapdata.sh

@@ -90,7 +90,7 @@ usage() {
   echo "  REGRID_PROC -- Number of MPI processors to use"
   echo "                 (default is $REGRID_PROC)"
   echo ""
-  echo "**defaults can be determined on the machines: cheyenne or geyser"
+  echo "**defaults can be determined on the machines: cheyenne or casper"
   echo ""
   echo "**pass environment variables by preceding above commands "
   echo "  with 'env var1=setting var2=setting '"
@@ -350,12 +350,10 @@ case $hostname in
   module load ncl
   module load nco
 
-  if [ "$interactive" = "NO" ]; then
+  if [[ $REGRID_PROC > 1 ]]; then
      mpi=mpi
-     mpitype="mpich2"
   else
      mpi=uni
-     mpitype="mpiuni"
   fi
   module load esmf-${esmfvers}-ncdfio-${mpi}-O
   if [ -z "$ESMFBIN_PATH" ]; then
@@ -367,35 +365,43 @@ case $hostname in
   ;;
 
   ## DAV
-  pronghorn* | caldera* | geyser* )
+  pronghorn* | casper* )
   . /glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/bash
   if [ -z "$REGRID_PROC" ]; then
      REGRID_PROC=8
   fi
+  echo "REGRID_PROC=$REGRID_PROC"
   esmfvers=7.1.0r
-  intelvers=15.0.0
-  #intelvers=12.1.5
+  intelvers=17.0.1
   module purge
   module load intel/$intelvers
+  if [ $? != 0 ]; then
+    echo "Error doing module load: intel/$intelvers"
+    exit 1
+  fi
   module load ncl
   module load nco
-  #module load impi
-  module load mpich-slurm
-  module load netcdf/4.3.3.1
-  #module load netcdf/4.3.0
+  module load netcdf
   module load ncarcompilers
 
-  module load esmf
+  module load esmflibs/$esmfvers
+  if [ $? != 0 ]; then
+    echo "Error doing module load: esmflibs/$esmfvers"
+    exit 1
+  fi
 
-  if [ "$interactive" = "NO" ]; then
+  if [[ $REGRID_PROC > 1 ]]; then
      mpi=mpi
-     mpitype="mpich2"
+     echo "MPI option is NOT currently available"
+     exit 1
   else
      mpi=uni
-     mpitype="mpiuni"
   fi
-  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/lib/gcc/x86_64-redhat-linux/4.4.7:/usr/lib64:/glade/apps/opt/usr/lib:/usr/lib:/glade/u/ssg/ys/opt/intel/12.1.0.233/composer_xe_2011_sp1.11.339/compiler/lib/intel64:/lib:/lib64"
   module load esmf-${esmfvers}-ncdfio-${mpi}-O
+  if [ $? != 0 ]; then
+    echo "Error doing module load: esmf-${esmfvers}-ncdfio-${mpi}-O"
+    exit 1
+  fi
   if [ -z "$ESMFBIN_PATH" ]; then
      ESMFBIN_PATH=`grep ESMF_APPSDIR $ESMFMKFILE | awk -F= '{print $2}'`
   fi
@@ -405,8 +411,6 @@ case $hostname in
   if [ -z "$MPIEXEC" ]; then
      MPIEXEC="mpiexec -n $REGRID_PROC"
   fi
-  echo "ERROR: Currently can NOT run on the DAV cluster, because ESMF is not configured correctly"
-  exit 1
   ;;
 
   ##no other machine currently supported