Merge branch 'misc_bugfixes'

Miscellaneous minor, bit-for-bit bug fixes Four miscellaneous minor, bit-for-bit bug fixes: (1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim Edwards: ESCOMP#526) (2) Change uppercase DEBUG variables to lowercase debug (requested by Jim Edwards to avoid conflicting with the DEBUG CPP token) (Fixes ESCOMP#534) (3) Remove unnecessary line of code in LunaMod.F90 that was causing problems with some compilers due to an uninitialized variable (Fixes ESCOMP#322) (4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim Edwards: ESCOMP#531)
billsacks · Oct 26, 2018 · 40e4d42 · 40e4d42
2 parents 8901c9e + c54566e
commit 40e4d42
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diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -3,7 +3,7 @@
 """
 build clm library
 """
-import sys, os, time, filecmp, shutil, imp
+import sys, os, shutil, imp
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -3,7 +3,7 @@
 """
 CLM namelist creator
 """
-import sys, os, time, shutil, re, imp, filecmp
+import sys, os, shutil, imp, filecmp
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
@@ -46,7 +46,6 @@ def buildnml(case, caseroot, compname):
     clm_force_coldstart = case.get_value("CLM_FORCE_COLDSTART")
     lnd_tuning_mode = case.get_value("LND_TUNING_MODE")
     clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP")
-    comp_glc = case.get_value("COMP_GLC")
     comp_atm = case.get_value("COMP_ATM")
     lnd_grid = case.get_value("LND_GRID")
     lnd_ncpl = case.get_value("LND_NCPL")
@@ -62,14 +61,6 @@ def buildnml(case, caseroot, compname):
     glc_nec = case.get_value("GLC_NEC")
     mask = case.get_value("MASK_GRID")
 
-    # -----------------------------------------------------
-    # Clear out old data
-    # -----------------------------------------------------
-
-    input_data_list = os.path.join(caseroot,"Buildconf","clm.input_data_list")
-    if os.path.exists(input_data_list):
-        os.remove(input_data_list)
-
     # -----------------------------------------------------
     # Set clmconf
     # -----------------------------------------------------
@@ -133,10 +124,10 @@ def buildnml(case, caseroot, compname):
     if run_type == "branch":
         startfile_type = "nrevsn"
         if clm_force_coldstart == "on":
-           clm_force_coldstart = "off"
-           logger.warning( "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n" +
-                           "  turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning"
-                         )
+            clm_force_coldstart = "off"
+            logger.warning( "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n" +
+                            "  turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning")
+
 
     if (clm_force_coldstart == "on"):
         logger.warning( "WARNING: CLM is starting up from a cold state" )
@@ -168,9 +159,9 @@ def buildnml(case, caseroot, compname):
         usecase = ""
 
     if ( (mask != "null") and (mask != "UNSET") ):
-       gridmask = "-mask %s" %mask
+        gridmask = "-mask %s" %mask
     else:
-       gridmask = ""
+        gridmask = ""
 
     start_ymd = run_startdate.replace('-','')
 
@@ -191,6 +182,13 @@ def buildnml(case, caseroot, compname):
 
     config_cache_file = os.path.join(caseroot,"Buildconf","clmconf","config_cache.xml")
 
+    # -----------------------------------------------------
+    # Clear out old data
+    # -----------------------------------------------------
+
+    if os.path.exists(inputdata_file):
+        os.remove(inputdata_file)
+
     # -----------------------------------------------------
     # loop over instances
     # -----------------------------------------------------

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,144 @@
 ===============================================================
+Tag name:  ctsm1.0.dev014
+Originator(s):  sacks (Bill Sacks)
+Date: Fri Oct 26 06:20:34 MDT 2018
+One-line Summary: Miscellaneous minor, bit-for-bit bug fixes
+
+Purpose of changes
+------------------
+
+Four miscellaneous minor, bit-for-bit bug fixes:
+
+(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim
+    Edwards: ESCOMP/ctsm#526)
+
+(2) Change uppercase DEBUG variables to lowercase debug (requested by
+    Jim Edwards to avoid conflicting with the DEBUG CPP token)
+    (Fixes ESCOMP/ctsm#534)
+
+(3) Remove unnecessary line of code in LunaMod.F90 that was causing
+    problems with some compilers due to an uninitialized variable
+    (Fixes ESCOMP/ctsm#322)
+
+(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim
+    Edwards: ESCOMP/ctsm#531)
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+- Fixes ESCOMP/ctsm#322 (ERS_D_Ld5.f19_g16.I2000Clm50BgcCruGs run FAIL (intel))
+- Fixes ESCOMP/ctsm#534 (Rename DEBUG to debug in a few places)
+
+
+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 ../CTSMMasterChecklist as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing: none
+
+Code reviewed by: different pieces reviewed by different people
+
+
+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 ---- ok
+    cheyenne_gnu ------ ok
+    hobart_nag -------- ok
+    hobart_pgi -------- ok
+    hobart_intel ------ ok
+
+    ok means tests and baseline comparisons pass. There were unexpected
+    NLCOMP diffs. From spot-checking a few tests, I see the following:
+
+
+    (1) On both cheyenne and hobart: Diffs in logfile. This looks like a
+        problem in cime: it says:
+
+        BASE: logfile = 'rof.log.136342.hobart.cgd.ucar.edu
+        COMP: logfile = 'rof.log
+
+    (2) On hobart: Diffs in pio_typename: netcdf vs. pnetcdf (says that
+        new uses pnetcdf): but when I compare files by hand, they look
+        the same in this respect (both baseline and new use netcdf), so
+        maybe this is due to a problem in the timing of when nlcomp is
+        run?
+
+    Since these both look like problems in the comparison script rather
+    than in the tag, I'm letting these go, but will open a cime issue if
+    we see this again.
+
+
+CTSM tag used for the baseline comparisons: ctsm1.0.dev013
+
+
+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/531 (fix build issue with xlf compiler)
+- https://github.com/ESCOMP/ctsm/pull/526 (fix cime issue 2822 and pylint chk)
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev013
 Originator(s):  erik (Erik Kluzek)/slevisconsulting
 Date: Thu Oct 25 18:09:47 MDT 2018

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev014    sacks 10/26/2018 Miscellaneous minor, bit-for-bit bug fixes
   ctsm1.0.dev013     erik 10/25/2018 Fix the fact that transient Bgc and SP cases had constant crop area in time
   ctsm1.0.dev012     erik 09/29/2018 Add snow-free fields for snowmip, fix several issues
   ctsm1.0.dev011    sacks 09/12/2018 Add water tracer consistency checks, and other water tracer work

diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
@@ -574,7 +574,7 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col)
 
     call extract_accum_field ('GDDPLANT', rbufslp, nstep)
     do p = begp,endp
-      rbufslp(p) = max(0.,this%gddplant_patch(p)-rbufslp(p))
+      rbufslp(p) = max(0.0_r8,this%gddplant_patch(p)-rbufslp(p))
     end do
     call update_accum_field  ('GDDPLANT', rbufslp, nstep)
     do p = begp,endp

diff --git a/src/biogeophys/LunaMod.F90 b/src/biogeophys/LunaMod.F90
@@ -36,10 +36,10 @@ module LunaMod
   ! PRIVATE MEMBER FUNCTIONS:
   public  :: LunaReadNML                                   !subroutine to read in the Luna namelist
   public  :: Update_Photosynthesis_Capacity                !subroutine to update the canopy nitrogen profile
-  public  :: NitrogenAllocation                            !subroutine to update the Vcmax25 and Jmax25 at the leaf level
   public  :: Acc24_Climate_LUNA                            !subroutine to accumulate 24 hr climates
   public  :: Acc240_Climate_LUNA                           !subroutine to accumulate 10 day climates
   public  :: Clear24_Climate_LUNA                          !subroutine to clear 24 hr climates
+  private :: NitrogenAllocation                            !subroutine to update the Vcmax25 and Jmax25 at the leaf level
   private :: NUEref                                        !Calculate the Nitrogen use effieciency based on reference CO2 and leaf temperature
   private :: NUE                                           !Calculate the Nitrogen use effieciency based on current CO2 and leaf temperature
   private :: JmxTLeuning                                   !Calculate the temperature response for Jmax, based on Leunning 2002 Plant, Cell & Environment
@@ -367,7 +367,7 @@ subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
                          PNcbold   = 0.0_r8                                     
                          call NitrogenAllocation(FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, hourpd, &
                               tair10, tleafd10, tleafn10, &
-                              Jmaxb0, Jmaxb1, Wc2Wjb0, relhExp,  PNstoreold, PNlcold, PNetold, PNrespold, &
+                              Jmaxb0, Jmaxb1, Wc2Wjb0, relhExp, PNlcold, PNetold, PNrespold, &
                               PNcbold, PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
                          vcmx25_opt= PNcbopt * FNCa * Fc25
                          jmx25_opt= PNetopt * FNCa * Fj25
@@ -756,7 +756,7 @@ end subroutine Clear24_Climate_LUNA
 !Use the LUNA model to calculate the Nitrogen partioning 
 subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PARimx10,rb10, hourpd, tair10, tleafd10, tleafn10, &
      Jmaxb0, Jmaxb1, Wc2Wjb0, relhExp,&
-     PNstoreold, PNlcold, PNetold, PNrespold, PNcbold, &
+     PNlcold, PNetold, PNrespold, PNcbold, &
      PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
   implicit none
   real(r8), intent (in) :: FNCa                       !Area based functional nitrogen content (g N/m2 leaf)
@@ -775,7 +775,6 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
   real(r8), intent (in) :: Jmaxb1                     !coefficient determining the response of electron transport rate to light availability (unitless) 
   real(r8), intent (in) :: Wc2Wjb0                    !the baseline ratio of rubisco-limited rate vs light-limited photosynthetic rate (Wc:Wj)
   real(r8), intent (in) :: relhExp                    !specifies the impact of relative humidity on electron transport rate (unitless)
-  real(r8), intent (in) :: PNstoreold                 !old value of the proportion of nitrogen allocated to storage (unitless)
   real(r8), intent (in) :: PNlcold                    !old value of the proportion of nitrogen allocated to light capture (unitless)
   real(r8), intent (in) :: PNetold                    !old value of the proportion of nitrogen allocated to electron transport (unitless)
   real(r8), intent (in) :: PNrespold                  !old value of the proportion of nitrogen allocated to respiration (unitless)
@@ -848,7 +847,6 @@ subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PAR
 
   call NUEref(NUEjref, NUEcref, Kj2Kcref)
   theta_cj = 0.95_r8
-  Nstore = PNstoreold * FNCa                          !proportion of storage nitrogen in functional nitrogen
   Nlc = PNlcold * FNCa                                !proportion of light capturing nitrogen in functional nitrogen
   Net = PNetold * FNCa                                !proportion of light harvesting (electron transport) nitrogen in functional nitrogen
   Nresp = PNrespold * FNCa                            !proportion of respirational nitrogen in functional nitrogen

diff --git a/src/biogeophys/SurfaceRadiationMod.F90 b/src/biogeophys/SurfaceRadiationMod.F90
@@ -25,7 +25,7 @@ module SurfaceRadiationMod
   implicit none
   private
 
-  logical :: DEBUG = .false.  ! for debugging this module
+  logical, parameter :: debug = .false.  ! for debugging this module
 
   !
   ! !PUBLIC MEMBER FUNCTIONS:
@@ -977,7 +977,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, &
           g = patch%gridcell(p)
 
           if(elai(p)==0.0_r8.and.fabd(p,1)>0._r8)then
-             if ( DEBUG ) write(iulog,*) 'absorption without LAI',elai(p),tlai(p),fabd(p,1),p
+             if ( debug ) write(iulog,*) 'absorption without LAI',elai(p),tlai(p),fabd(p,1),p
           endif
           ! Solar incident 
 

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
@@ -198,7 +198,7 @@ module CLMFatesInterfaceMod
    ! developer will at least question its usage (RGK)
    private :: hlm_bounds_to_fates_bounds
 
-   logical :: DEBUG  = .false.
+   logical :: debug  = .false.
 
    character(len=*), parameter, private :: sourcefile = &
         __FILE__
@@ -367,7 +367,7 @@ subroutine init(this, bounds_proc )
       ! Check through FATES parameters to see if all have been set
       call set_fates_ctrlparms('check_allset')
 
-      if(DEBUG)then
+      if(debug)then
          write(iulog,*) 'clm_fates%init():  allocating for ',nclumps,' threads'
       end if
 
@@ -402,15 +402,15 @@ subroutine init(this, bounds_proc )
                s = s + 1
                collist(s) = c
                this%f2hmap(nc)%hsites(c) = s
-               if(DEBUG)then
+               if(debug)then
                   write(iulog,*) 'clm_fates%init(): thread',nc,': found column',c,'with lu',l
                   write(iulog,*) 'LU type:', lun%itype(l)
                end if
             endif
 
          enddo
 
-         if(DEBUG)then
+         if(debug)then
             write(iulog,*) 'clm_fates%init(): thread',nc,': allocated ',s,' sites'
          end if
 

diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90
@@ -15,7 +15,7 @@ module CLMFatesParamInterfaceMod
   private :: SetParameterDimensions
   private :: GetUsedDimensionSizes
 
-  logical :: DEBUG  = .false.
+  logical :: debug  = .false.
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__