New test

.github/workflows/bumpversion.yml

@@ -8,13 +8,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-        with:
-          fetch-depth: '0'
       - name: Bump version and push tag
-        uses: anothrNick/github-tag-action@1.26.0
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          WITH_V: true
-          DEFAULT_BUMP: minor
-          RELEASE_BRANCHES: master
-          DRY_RUN: False
+        id: tag_version
+        uses: mathieudutour/github-tag-action@v5.5
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          create_annotated_tag: true
+          default_bump: patch
+          dry_run: false

.github/workflows/extbuild.yml

@@ -18,10 +18,12 @@ jobs:
       CXX: mpicxx
       CPPFLAGS: "-I/usr/include -I/usr/local/include"
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: ESMF_8_1_0_beta_snapshot_25
-      PNETCDF_VERSION: pnetcdf-1.12.1
+      ESMF_VERSION: ESMF_8_1_1
+      PNETCDF_VERSION: pnetcdf-1.12.2
       NETCDF_FORTRAN_VERSION: v4.5.2
-      PIO_VERSION: pio-2.5.1
+      # These should match in number
+      PIO_VERSION: pio-2.5.4
+      PIO_VERSION_DUMB: pio2_5_4
     steps:
       - uses: actions/checkout@v2
         # Build the ESMF library, if the cache contains a previous build
@@ -32,7 +34,7 @@ jobs:
           path: ~/ESMF
           key: ${{ runner.os }}-${{ env.ESMF_VERSION }}-ESMF
       - id: load-env
-        run: sudo apt-get install gfortran wget openmpi-bin netcdf-bin libopenmpi-dev
+        run: sudo apt-get install gfortran wget openmpi-bin netcdf-bin libopenmpi-dev libnetcdf-dev
       - id: build-ESMF
         if: steps.cache-esmf.outputs.cache-hit != 'true'
         run: |
@@ -93,11 +95,11 @@ jobs:
       - name: Build PIO
         if: steps.cache-PIO.outputs.cache-hit != 'true'
         run: |
-          wget https://github.com/NCAR/ParallelIO/releases/download/pio_2_5_1/${{ env.PIO_VERSION }}.tar.gz
+          wget https://github.com/NCAR/ParallelIO/releases/download/${{ env.PIO_VERSION_DUMB }}/${{ env.PIO_VERSION }}.tar.gz
           tar -xzvf ${{ env.PIO_VERSION }}.tar.gz
           mkdir build-pio
           pushd build-pio
-          cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -DCMAKE_INSTALL_PREFIX=$HOME/pio -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_PATH=$HOME/netcdf-fortran -DPnetCDF_PATH=$HOME/pnetcdf ../${{ env.PIO_VERSION }}
+          cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -DCMAKE_INSTALL_PREFIX=$HOME/pio -DPIO_HDF5_LOGGING=Off -DPIO_ENABLE_EXAMPLES=Off -DPIO_ENABLE_LOGGING=Off -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_PATH=$HOME/netcdf-fortran -DPnetCDF_PATH=$HOME/pnetcdf ../${{ env.PIO_VERSION }}
           make VERBOSE=1
           make install
           popd

CMakeLists.txt

@@ -1,5 +1,6 @@
 cmake_minimum_required(VERSION 3.10)
 include(ExternalProject)
+include(FetchContent)
 
 if (DEFINED CIMEROOT)
   message("Using CIME in ${CIMEROOT} with compiler ${COMPILER}")
@@ -55,11 +56,29 @@ if(BLD_STANDALONE)
 endif()
 if("${COMPILER}" STREQUAL "nag")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -D__NAG__")
-endif()
-add_subdirectory(fox)
+endif()     
 add_subdirectory(streams)
 add_subdirectory(dshr)
 
+if(IS_DIRECTORY "${PROJECT_SOURCE_DIR}/fox")
+  message(STATUS "FoX library is already checked out!")
+  message(STATUS "FoX source dir: ${PROJECT_SOURCE_DIR}/fox")
+else()
+  FetchContent_Declare(fox
+    GIT_REPOSITORY https://github.com/ESMCI/fox.git
+    GIT_TAG 4.1.2.1
+    SOURCE_DIR ${PROJECT_SOURCE_DIR}/fox
+    BINARY_DIR ${PROJECT_SOURCE_DIR}
+  )
+  FetchContent_GetProperties(fox)
+  if(NOT fox_POPULATED)
+    FetchContent_Populate(fox)
+    message(STATUS "FoX source dir: ${fox_SOURCE_DIR}")
+    message(STATUS "FoX binary dir: ${fox_BINARY_DIR}")
+  endif()
+endif()
+add_subdirectory(fox)
+
 foreach(COMP datm dice dlnd docn drof dwav)
   add_subdirectory("${COMP}")
 endforeach(COMP)

Externals_CDEPS.cfg

@@ -0,0 +1,16 @@
+[fox]
+tag = 4.1.2.1
+protocol = git
+repo_url = https://github.com/ESMCI/fox.git
+local_path = fox
+required = True
+
+[genf90]
+tag = 4816965
+protocol = git
+repo_url = https://github.com/PARALLELIO/genf90
+local_path = share/genf90
+required = True
+
+[externals_description]
+schema_version = 1.0.0

datm/CMakeLists.txt

@@ -8,6 +8,7 @@ set(SRCFILES atm_comp_nuopc.F90
              datm_datamode_cfsr_mod.F90
              datm_datamode_era5_mod.F90)
 
+
 foreach(FILE ${SRCFILES})
   if(EXISTS "${CASEROOT}/SourceMods/src.datm/${FILE}")
     list(REMOVE_ITEM SRCFILES ${FILE})

datm/cime_config/config_component.xml

@@ -206,7 +206,7 @@
     <valid_values></valid_values>
     <default_value>2004</default_value>
     <values match="last">
-      <value compset="2000.*_DATM%1PT">1972</value>
+      <value compset="2000.*_DATM%1PT">2018</value>
       <value compset="1850.*_DATM%QIA">1948</value>
       <value compset="1850.*_DATM%CRU">1901</value>
       <value compset="1850.*_DATM%GSW">1901</value>
@@ -248,7 +248,7 @@
     <valid_values></valid_values>
     <default_value>2004</default_value>
     <values match="last">
-      <value   compset="2000.*_DATM%1PT">2004</value>
+      <value   compset="2000.*_DATM%1PT">2019</value>
       <value   compset="1850.*_DATM%QIA">1972</value>
       <value   compset="1850.*_DATM%CRU">1920</value>
       <value   compset="1850.*_DATM%GSW">1920</value>

datm/cime_config/stream_definition_datm.xml

@@ -203,7 +203,7 @@
       <meshfile>none</meshfile>
     </stream_meshfile>
     <stream_datafiles>
-      <file first_year="2018" last_year="2019">$DIN_LOC_ROOT/atm/cdeps/v1/$NEONSITE/%ym.nc</file>
+      <file first_year="$DATM_YR_START" last_year="$DATM_YR_END">$DIN_LOC_ROOT/atm/cdeps/v1/$NEONSITE/%ym.nc</file>
     </stream_datafiles>
     <stream_datavars>
       <var>PRECTmms Faxa_precn</var>
@@ -220,9 +220,9 @@
       <mapalgo>none</mapalgo>
     </stream_mapalgo>
     <stream_vectors>null</stream_vectors>
-    <stream_year_align>2018</stream_year_align>
-    <stream_year_first>2018</stream_year_first>
-    <stream_year_last>2019</stream_year_last>
+    <stream_year_align>$DATM_YR_ALIGN</stream_year_align>
+    <stream_year_first>$DATM_YR_START</stream_year_first>
+    <stream_year_last>$DATM_YR_END</stream_year_last>
     <stream_offset>0</stream_offset>
     <stream_tintalgo>
       <tintalgo>linear</tintalgo>

datm/datm_datamode_cfsr_mod.F90

@@ -1,6 +1,6 @@
 module datm_datamode_cfsr_mod
 
-  use ESMF
+  use ESMF             , only : ESMF_State, ESMF_SUCCESS, ESMF_LogWrite, ESMF_LOGMSG_INFO
   use NUOPC            , only : NUOPC_Advertise
   use shr_kind_mod     , only : r8=>shr_kind_r8, i8=>shr_kind_i8, cl=>shr_kind_cl, cs=>shr_kind_cs
   use shr_sys_mod      , only : shr_sys_abort
@@ -21,7 +21,6 @@ module datm_datamode_cfsr_mod
   public  :: datm_datamode_cfsr_advance
   public  :: datm_datamode_cfsr_restart_write
   public  :: datm_datamode_cfsr_restart_read
-!  private :: datm_eSat  ! determine saturation vapor pressure
 
   ! export state data
   real(r8), pointer :: Sa_z(:)              => null()
@@ -32,19 +31,19 @@ module datm_datamode_cfsr_mod
   real(r8), pointer :: Sa_pbot(:)           => null()
   real(r8), pointer :: Sa_u10m(:)           => null()
   real(r8), pointer :: Sa_v10m(:)           => null()
-  real(r8), pointer :: Sa_t2m(:)           => null()
-  real(r8), pointer :: Sa_q2m(:)           => null()
+  real(r8), pointer :: Sa_t2m(:)            => null()
+  real(r8), pointer :: Sa_q2m(:)            => null()
   real(r8), pointer :: Sa_pslv(:)           => null()
   real(r8), pointer :: Faxa_lwdn(:)         => null()
   real(r8), pointer :: Faxa_rain(:)         => null()
-  real(r8), pointer :: Faxa_snow(:)        => null()
+  real(r8), pointer :: Faxa_snow(:)         => null()
   real(r8), pointer :: Faxa_swndr(:)        => null()
   real(r8), pointer :: Faxa_swndf(:)        => null()
   real(r8), pointer :: Faxa_swvdr(:)        => null()
   real(r8), pointer :: Faxa_swvdf(:)        => null()
 
   ! stream data
-  real(r8), pointer :: strm_mask(:)      => null()
+  real(r8), pointer :: strm_mask(:)         => null()
 
   real(r8) :: tbotmax ! units detector
   real(r8) :: maskmax ! units detector
@@ -86,11 +85,11 @@ subroutine datm_datamode_cfsr_advertise(exportState, fldsexport, &
     call dshr_fldList_add(fldsExport, 'Sa_shum'    )
     call dshr_fldList_add(fldsExport, 'Sa_u10m'    )
     call dshr_fldList_add(fldsExport, 'Sa_v10m'    )
-    call dshr_fldList_add(fldsExport, 'Sa_t2m'    )
-    call dshr_fldList_add(fldsExport, 'Sa_q2m'    )
+    call dshr_fldList_add(fldsExport, 'Sa_t2m'     )
+    call dshr_fldList_add(fldsExport, 'Sa_q2m'     )
     call dshr_fldList_add(fldsExport, 'Sa_pslv'    )
     call dshr_fldList_add(fldsExport, 'Faxa_rain'  )
-    call dshr_fldList_add(fldsExport, 'Faxa_snow' )
+    call dshr_fldList_add(fldsExport, 'Faxa_snow'  )
     call dshr_fldList_add(fldsExport, 'Faxa_swndr' )
     call dshr_fldList_add(fldsExport, 'Faxa_swvdr' )
     call dshr_fldList_add(fldsExport, 'Faxa_swndf' )
@@ -184,8 +183,6 @@ subroutine datm_datamode_cfsr_advance(exportstate, masterproc, logunit, mpicom,
     integer  :: lsize               ! size of attr vect
     real(r8) :: rtmp
     real(r8) :: tbot, pbot
-!    real(r8) :: vp
-    real(r8) :: e, qsat
     character(len=*), parameter :: subname='(datm_datamode_cfsr_advance): '
     !-------------------------------------------------------------------------------
 
@@ -209,9 +206,6 @@ subroutine datm_datamode_cfsr_advance(exportstate, masterproc, logunit, mpicom,
     end if
 
     do n = 1, lsize
-       !--- bottom layer height ---
-!       Sa_z(n) = 10.0_r8
-
        !--- temperature ---
        if (tbotmax < 50.0_r8) Sa_tbot(n) = Sa_tbot(n) + tkFrz
        ! Limit very cold forcing to 180K

datm/datm_datamode_gefs_mod.F90

@@ -1,6 +1,6 @@
 module datm_datamode_gefs_mod
 
-  use ESMF
+  use ESMF             , only : ESMF_State, ESMF_SUCCESS, ESMF_LogWrite, ESMF_LOGMSG_INFO
   use NUOPC            , only : NUOPC_Advertise
   use shr_kind_mod     , only : r8=>shr_kind_r8, i8=>shr_kind_i8, cl=>shr_kind_cl, cs=>shr_kind_cs
   use shr_sys_mod      , only : shr_sys_abort
@@ -21,7 +21,6 @@ module datm_datamode_gefs_mod
   public  :: datm_datamode_gefs_advance
   public  :: datm_datamode_gefs_restart_write
   public  :: datm_datamode_gefs_restart_read
-!  private :: datm_eSat  ! determine saturation vapor pressure
 
   ! export state data
   real(r8), pointer :: Sa_z(:)              => null()
@@ -32,19 +31,19 @@ module datm_datamode_gefs_mod
   real(r8), pointer :: Sa_pbot(:)           => null()
   real(r8), pointer :: Sa_u10m(:)           => null()
   real(r8), pointer :: Sa_v10m(:)           => null()
-  real(r8), pointer :: Sa_t2m(:)           => null()
-  real(r8), pointer :: Sa_q2m(:)           => null()
+  real(r8), pointer :: Sa_t2m(:)            => null()
+  real(r8), pointer :: Sa_q2m(:)            => null()
   real(r8), pointer :: Sa_pslv(:)           => null()
   real(r8), pointer :: Faxa_lwdn(:)         => null()
   real(r8), pointer :: Faxa_rain(:)         => null()
-  real(r8), pointer :: Faxa_snow(:)        => null()
+  real(r8), pointer :: Faxa_snow(:)         => null()
   real(r8), pointer :: Faxa_swndr(:)        => null()
   real(r8), pointer :: Faxa_swndf(:)        => null()
   real(r8), pointer :: Faxa_swvdr(:)        => null()
   real(r8), pointer :: Faxa_swvdf(:)        => null()
 
   ! stream data
-  real(r8), pointer :: strm_mask(:)      => null()
+  real(r8), pointer :: strm_mask(:)         => null()
 
   real(r8) :: tbotmax ! units detector
   real(r8) :: maskmax ! units detector
@@ -86,11 +85,11 @@ subroutine datm_datamode_gefs_advertise(exportState, fldsexport, &
     call dshr_fldList_add(fldsExport, 'Sa_shum'    )
     call dshr_fldList_add(fldsExport, 'Sa_u10m'    )
     call dshr_fldList_add(fldsExport, 'Sa_v10m'    )
-    call dshr_fldList_add(fldsExport, 'Sa_t2m'    )
-    call dshr_fldList_add(fldsExport, 'Sa_q2m'    )
+    call dshr_fldList_add(fldsExport, 'Sa_t2m'     )
+    call dshr_fldList_add(fldsExport, 'Sa_q2m'     )
     call dshr_fldList_add(fldsExport, 'Sa_pslv'    )
     call dshr_fldList_add(fldsExport, 'Faxa_rain'  )
-    call dshr_fldList_add(fldsExport, 'Faxa_snow' )
+    call dshr_fldList_add(fldsExport, 'Faxa_snow'  )
     call dshr_fldList_add(fldsExport, 'Faxa_swndr' )
     call dshr_fldList_add(fldsExport, 'Faxa_swvdr' )
     call dshr_fldList_add(fldsExport, 'Faxa_swndf' )
@@ -184,8 +183,6 @@ subroutine datm_datamode_gefs_advance(exportstate, masterproc, logunit, mpicom,
     integer  :: lsize               ! size of attr vect
     real(r8) :: rtmp
     real(r8) :: tbot, pbot
-!    real(r8) :: vp
-    real(r8) :: e, qsat
     character(len=*), parameter :: subname='(datm_datamode_gefs_advance): '
     !-------------------------------------------------------------------------------
 
@@ -209,9 +206,6 @@ subroutine datm_datamode_gefs_advance(exportstate, masterproc, logunit, mpicom,
     end if
 
     do n = 1, lsize
-       !--- bottom layer height ---
-!       Sa_z(n) = 10.0_r8
-
        !--- temperature ---
        if (tbotmax < 50.0_r8) Sa_tbot(n) = Sa_tbot(n) + tkFrz
        ! Limit very cold forcing to 180K

dice/CMakeLists.txt

@@ -17,9 +17,9 @@ add_library(dice ${SRCFILES})
 
 add_dependencies(dice dshr streams)
 target_include_directories (dice PRIVATE ${ESMF_F90COMPILEPATHS})
-target_include_directories (dice PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/../fox/include")
 target_include_directories (dice PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/../dshr")
 target_include_directories (dice PRIVATE "${CMAKE_SOURCE_DIR}")
 target_include_directories (dice PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/../share")
 target_include_directories (dice PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/../streams")
 target_include_directories (dice PRIVATE "${PIO_Fortran_INCLUDE_DIR}")
+target_include_directories (dice PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/../fox/include)

docn/cime_config/buildnml

@@ -71,7 +71,7 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
 
     if case.get_value('PTS_LON'):
         scol_lon = float(case.get_value('PTS_LON'))
-    else: 
+    else:
         scol_lon = -999.
     if case.get_value('PTS_LAT'):
         scol_lat = float(case.get_value('PTS_LAT'))
@@ -90,6 +90,7 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
     nmlgen.write_output_file(namelist_file, data_list_path, groups=['docn_nml'])
 
     # Generate docn.streams.xml if needed
+    print("docn_mode is {}".format(docn_mode))
     if (re.search(r'sst_aquap[0-9]+',docn_mode) is not None) or (docn_mode == 'sst_aquap_constant'):
         generate_stream_file = False
     else:

docn/docn_datamode_som_mod.F90

@@ -250,10 +250,14 @@ subroutine docn_datamode_som_advance(importState, exportState, clock, restart_re
        dt = idt * 1.0_r8
 
        do n = 1,lsize
-          if (.not. restart_read) then
-             somtp(n) = So_t(n) + TkFrz
-          endif
-          So_t(n) = somtp(n)
+          if (So_omask(n) /= 0._r8) then
+             if (.not. restart_read) then
+                somtp(n) = So_t(n) + TkFrz
+             endif
+             So_t(n) = somtp(n)
+          else
+             So_t(n) = 0._r8
+          end if
           Fioo_q(n) = 0.0_R8
        enddo
 

share/CMakeLists.txt

@@ -24,8 +24,27 @@ target_include_directories (cdeps_share PRIVATE ${CMAKE_CURRENT_SOURCE_DIR} ${ES
 install(TARGETS cdeps_share
         LIBRARY DESTINATION lib)
 #===== genf90 =====
-set(GENF90_PATH ${CMAKE_CURRENT_SOURCE_DIR}/genf90)
-add_custom_target(genf90 DEPENDS ${GENF90_PATH}/genf90.pl)
+if(IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/genf90")
+  message(STATUS "genf90 library is already checked out!")
+  message(STATUS "genf90 source dir: ${CMAKE_CURRENT_SOURCE_DIR}/genf90")
+  set(GENF90_PATH ${CMAKE_CURRENT_SOURCE_DIR}/genf90)
+endif()
+if (DEFINED GENF90_PATH)
+  add_custom_target(genf90
+    DEPENDS ${GENF90_PATH}/genf90.pl)
+else ()
+  ExternalProject_Add (genf90
+    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/genf90
+    GIT_REPOSITORY https://github.com/PARALLELIO/genf90
+    GIT_TAG genf90_200608
+    UPDATE_COMMAND ""
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND "")
+  ExternalProject_Get_Property (genf90 SOURCE_DIR)
+  set (GENF90_PATH ${SOURCE_DIR})
+  unset (SOURCE_DIR)
+endif ()
 add_dependencies (cdeps_share genf90)
 
 #===== Fortran Source Generation with GenF90 =====

streams/CMakeLists.txt

@@ -23,6 +23,7 @@ if(BLD_STANDALONE)
   add_dependencies(streams cdeps_share)
 endif()
 
+
 target_include_directories (streams PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/../fox/include)
 target_include_directories (streams PRIVATE ${ESMF_F90COMPILEPATHS})
 target_include_directories (streams PRIVATE ${PIO_Fortran_INCLUDE_DIR})