Merge pull request #2000 from adrifoster/fates_refactor

FATES API Updates to facilitate refactor
ESCOMP · Aug 10, 2023 · 942de5c · 942de5c
2 parents 0f7e5d4 + 3897807
commit 942de5c
Show file tree

Hide file tree

Showing 8 changed files with 159 additions and 58 deletions.
diff --git a/Externals.cfg b/Externals.cfg
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.64
+tag = ccs_config_cesm0.0.65
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.66.1_api.25.5.0
+tag = sci.1.67.1_api.26.0.0
 required = True
 
 [externals_description]

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -43,6 +43,20 @@
     </phase>
   </test>
 
+  <test name="SMS.f45_f45_mg37.I2000Clm51FatesSpRsGs.cheyenne_nvhpc.clm-FatesColdSatPhen">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1733</issue>
+    </phase>
+  </test>
+
+  <test name="SMS.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_nvhpc.clm-crop">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1733</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,100 @@
 ===============================================================
+Tag name: ctsm5.1.dev133
+Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET)
+Date: Wed Aug  9 22:44:46 MDT 2023
+One-line Summary: FATES API update to facilitate fates refactor
+
+Purpose and description of changes
+----------------------------------
+
+This updates a number of FATES type names and module use statements
+which correspond with a refactoring effort that moves FATES
+patches and cohorts into their own respective modules.
+
+With the FATES update is a minor science update, so there are
+changes to answers for FATES.
+
+This also incorporates a minor update to a more recent version
+of the ccs config external.
+
+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_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+Issues updated:
+
+    Updated #1733 -- nvhpc compiler tests failing on cheyenne
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+    - Note that the fates patch and cohort types now use the `fates_` prefix instead
+      of the `ed_` prefix.
+    - The expected failures list of tests has been expanded to include the remaining
+      nvhpc compiler tests on cheyenne with this update
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+      cheyenne - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    cheyenne ---- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+    Note that the previous ctsm5.1.dev132 tag was generated using FATES tagname
+    sci.1.66.1_api.25.5.0.  This api update includes intermediate FATES science
+    tags that are non-b4b, so aux_clm FATES tests result in DIFFs as expected.
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, but only for aux_clm fates tests.
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+
+    sci.1.66.1_api.25.5.0 -> sci.1.67.1_api.26.0.0
+    ccs_config_cesm0.0.64 -> ccs_config_cesm0.0.65
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+    https://github.com/ESCOMP/CTSM/pull/2000 -- refactor
+    https://github.com/ESCOMP/CTSM/pull/2089 -- Change template update
+    https://github.com/NGEET/fates/pull/1024 -- FATES refactor
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev132
 Originator(s): mvdebolskiy (NORCE, Bergen, Norway), slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Fri Aug  4 17:52:45 MDT 2023
@@ -91,13 +187,9 @@ Testing summary:
 
     cheyenne - PASS
 
-  tools-tests (test/tools) (if tools have been changed):
-
-    cheyenne -
-
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    cheyenne ---- OK
+    heyenne ---- OK
     izumi ------- OK
 
   any other testing (give details below):

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev133 glemieux 08/09/2023 FATES API update to facilitate fates refactor
     ctsm5.1.dev132   slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence
     ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars
     ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update

diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
@@ -22,12 +22,12 @@ module histFileMod
   use LandunitType   , only : lun
   use ColumnType     , only : col
   use PatchType      , only : patch
-  use EDTypesMod     , only : nclmax
-  use EDTypesMod     , only : nlevleaf
+  use EDParamsMod    , only : nclmax
+  use EDParamsMod    , only : nlevleaf
   use FatesInterfaceTypesMod , only : nlevsclass, nlevage, nlevcoage
   use FatesInterfaceTypesMod , only : nlevheight
   use FatesInterfaceTypesMod , only : nlevdamage
-  use EDTypesMod        , only : nfsc
+  use FatesLitterMod        , only : nfsc
   use FatesLitterMod    , only : ncwd
   use PRTGenericMod     , only : num_elements_fates  => num_elements
   use FatesInterfaceTypesMod , only : numpft_fates => numpft

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
@@ -126,7 +126,7 @@ module CLMFatesInterfaceMod
    use FatesHistoryInterfaceMod, only : fates_hist
    use FatesRestartInterfaceMod, only : fates_restart_interface_type
 
-   use EDTypesMod            , only : ed_patch_type
+   use FatesPatchMod         , only : fates_patch_type
    use PRTGenericMod         , only : num_elements
    use FatesInterfaceTypesMod, only : hlm_stepsize
    use FatesInterfaceTypesMod, only : fates_maxPatchesPerSite
@@ -1053,7 +1053,6 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
             call ed_update_site(this%fates(nc)%sites(s), &
                   this%fates(nc)%bc_in(s), &
                   this%fates(nc)%bc_out(s))
-
       enddo
 
       ! ---------------------------------------------------------------------------------
@@ -1144,11 +1143,11 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump,      &
      type(waterdiagnosticbulk_type)   , intent(inout)        :: waterdiagnosticbulk_inst
      type(canopystate_type)  , intent(inout)        :: canopystate_inst
      type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst
+
 
      ! is this being called during a read from restart sequence (if so then use the restarted fates
      ! snow depth variable rather than the CLM variable).
      logical                 , intent(in)           :: is_initing_from_restart
-
      integer :: npatch  ! number of patches in each site
      integer :: ifp     ! index FATES patch
      integer :: p       ! HLM patch index
@@ -1190,7 +1189,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump,      &
        ! Canopy diagnostics for FATES
        call canopy_summarization(this%fates(nc)%nsites, &
             this%fates(nc)%sites,  &
-            this%fates(nc)%bc_in)
+            this%fates(nc)%bc_in)            
 
        ! Canopy diagnostic outputs for HLM
        call update_hlm_dynamics(this%fates(nc)%nsites, &
@@ -1413,7 +1412,6 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, &
       integer                 :: nvar
       integer                 :: ivar
       logical                 :: readvar
-
       logical, save           :: initialized = .false.
 
      call t_startf('fates_restart')
@@ -1908,7 +1906,7 @@ subroutine wrap_sunfrac(this,nc,atm2lnd_inst,canopystate_inst)
                                               ! this is the order increment of patch
                                               ! on the site
 
-      type(ed_patch_type), pointer :: cpatch  ! c"urrent" patch  INTERF-TODO: SHOULD
+      type(fates_patch_type), pointer :: cpatch  ! c"urrent" patch  INTERF-TODO: SHOULD
                                               ! BE HIDDEN AS A FATES PRIVATE
 
      call t_startf('fates_wrapsunfrac')
@@ -2187,12 +2185,13 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
     use shr_log_mod       , only : errMsg => shr_log_errMsg
     use abortutils        , only : endrun
     use decompMod         , only : bounds_type
-    use clm_varcon        , only : rgas, tfrz, namep
+    use clm_varcon        , only : tfrz, namep
     use clm_varctl        , only : iulog
-    use pftconMod         , only : pftcon
     use PatchType         , only : patch
     use quadraticMod      , only : quadratic
-    use EDtypesMod        , only : ed_patch_type, ed_cohort_type, ed_site_type
+    use EDtypesMod        , only : ed_site_type
+    use FatesPatchMod,      only : fates_patch_type
+    use FatesCohortMod    , only : fates_cohort_type
 
     !
     ! !ARGUMENTS:
@@ -3158,13 +3157,13 @@ end subroutine wrap_hydraulics_drive
 
  subroutine hlm_bounds_to_fates_bounds(hlm, fates)
 
-   use FatesIODimensionsMod, only : fates_bounds_type
+   use FatesIODimensionsMod,   only : fates_bounds_type
    use FatesInterfaceTypesMod, only : nlevsclass, nlevage, nlevcoage
    use FatesInterfaceTypesMod, only : nlevheight
    use FatesInterfaceTypesMod, only : nlevdamage
-   use EDtypesMod,        only : nfsc
-   use FatesLitterMod,    only : ncwd
-   use EDtypesMod,        only : nlevleaf, nclmax
+   use FatesLitterMod,         only : nfsc
+   use FatesLitterMod,         only : ncwd
+   use EDParamsMod,            only : nlevleaf, nclmax
    use FatesInterfaceTypesMod, only : numpft_fates => numpft
 
 

diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90
@@ -2,8 +2,13 @@ module CLMFatesParamInterfaceMod
   ! NOTE(bja, 2017-01) this code can not go into the main clm-fates
   ! interface module because of circular dependancies with pftvarcon.
 
-  use shr_kind_mod, only : r8 => shr_kind_r8
-  use FatesGlobals, only : fates_log
+  use shr_kind_mod,             only : r8 => shr_kind_r8, SHR_KIND_CL
+  use FatesGlobals,             only : fates_log
+  use FatesParametersInterface, only : fates_parameters_type
+  use EDParamsMod,              only : FatesRegisterParams, FatesReceiveParams
+  use SFParamsMod,              only : SpitFireRegisterParams, SpitFireReceiveParams
+  use PRTInitParamsFATESMod,    only : PRTRegisterParams, PRTReceiveParams
+  use FatesSynchronizedParamsMod, only : FatesSynchronizedParamsInst
 
   implicit none
 
@@ -25,49 +30,39 @@ module CLMFatesParamInterfaceMod
 
  !-----------------------------------------------------------------------
  subroutine FatesReadParameters()
-
-   use clm_varctl, only : use_fates, paramfile, fates_paramfile
-   use spmdMod, only : masterproc
-
-   use FatesParametersInterface, only : fates_parameters_type
-
-   use EDParamsMod, only : FatesRegisterParams, FatesReceiveParams
-   use SFParamsMod, only : SpitFireRegisterParams, SpitFireReceiveParams
-   use PRTInitParamsFATESMod, only : PRTRegisterParams, PRTReceiveParams
-   use FatesSynchronizedParamsMod, only : FatesSynchronizedParamsInst
+  use clm_varctl, only : use_fates, paramfile, fates_paramfile
+  use spmdMod, only : masterproc
 
    implicit none
-
+   
    character(len=32)  :: subname = 'FatesReadParameters'
    class(fates_parameters_type), allocatable :: fates_params
    logical :: is_host_file
 
-   if (use_fates) then
-      if (masterproc) then
-         write(fates_log(), *) 'clmfates_interfaceMod.F90::'//trim(subname)//' :: CLM reading ED/FATES '//' parameters '
-      end if
+    if (masterproc) then
+      write(fates_log(), *) 'clmfates_interfaceMod.F90::'//trim(subname)//' :: CLM reading ED/FATES '//' parameters '
+    end if
 
-      allocate(fates_params)
-      call fates_params%Init()
-      call FatesRegisterParams(fates_params)
-      call SpitFireRegisterParams(fates_params)
-      call PRTRegisterParams(fates_params)
-      call FatesSynchronizedParamsInst%RegisterParams(fates_params)
+    allocate(fates_params)
+    call fates_params%Init()   ! fates_params class, in FatesParameterInterfaceMod
+    call FatesRegisterParams(fates_params)  !EDParamsMod, only operates on fates_params class
+    call SpitFireRegisterParams(fates_params) !SpitFire Mod, only operates of fates_params class
+    call PRTRegisterParams(fates_params)     ! PRT mod, only operates on fates_params class
+    call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params class in Synchronized params mod, only operates on fates_params class
 
-      is_host_file = .false.
-      call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params)
+    is_host_file = .false.
+    call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params)
 
-      is_host_file = .true.
-      call ParametersFromNetCDF(paramfile, is_host_file, fates_params)
+    is_host_file = .true.
+    call ParametersFromNetCDF(paramfile, is_host_file, fates_params)
 
-      call FatesReceiveParams(fates_params)
-      call SpitFireReceiveParams(fates_params)
-      call PRTReceiveParams(fates_params)
-      call FatesSynchronizedParamsInst%ReceiveParams(fates_params)
+    call FatesReceiveParams(fates_params)
+    call SpitFireReceiveParams(fates_params)
+    call PRTReceiveParams(fates_params)
+    call FatesSynchronizedParamsInst%ReceiveParams(fates_params)
 
-      call fates_params%Destroy()
-      deallocate(fates_params)
-   end if
+    call fates_params%Destroy()
+    deallocate(fates_params)
 
  end subroutine FatesReadParameters
 
@@ -211,7 +206,7 @@ subroutine ParametersFromNetCDF(filename, is_host_file, fates_params)
    call SetParameterDimensions(ncid, is_host_file, fates_params)
    max_dim_size = fates_params%GetMaxDimensionSize()
    allocate(data(max_dim_size, max_dim_size))
-
+   
    num_params = fates_params%num_params()
    do i = 1, num_params
       call fates_params%GetMetaData(i, name, dimension_shape, dimension_sizes, dimension_names, is_host_param)