Merged changes from master (2023.11.24-2024.03.22)

.github/workflows/CI.yml

@@ -0,0 +1,136 @@
+name: CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches:  [ main, master, ubuntu2204] 
+  pull_request:
+    branches: [ main, master, ubuntu2204]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    env:
+      CC: mpicc
+      FC: mpifort
+      CXX: mpicxx
+      CPPFLAGS: "-I/usr/include -I/usr/local/include"
+      CIME_TEST_PLATFORM: ubuntu-latest
+      # Versions of all dependencies can be updated here
+      PNETCDF_VERSION: pnetcdf-1.12.3
+      NETCDF_FORTRAN_VERSION: v4.6.0
+      MCT_VERSION: MCT_2.11.0
+      PARALLELIO_VERSION: pio2_5_10
+      NETCDF_C_PATH: /usr
+      NETCDF_FORTRAN_PATH: ${HOME}/netcdf-fortran
+      PNETCDF_PATH: ${HOME}/pnetcdf
+      CIME_MODEL: cesm
+      CIME_DRIVER: mct
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+
+      - id: load-env
+        run: |
+          sudo apt-get update
+          sudo apt-get install libxml2-utils pylint wget gfortran openmpi-bin netcdf-bin libopenmpi-dev cmake libnetcdf-dev
+
+      # - name: Set up Python ${{ matrix.python-version }}
+      #   uses: actions/setup-python@v4
+      #   with:
+      #     python-version: ${{ matrix.python-version }}
+      #     cache: 'pip'
+
+      # - name: pip install
+      #   run: pip install PyYAML
+
+      - name: cache pnetcdf
+        id: cache-pnetcdf
+        uses: actions/cache@v3
+        with:
+          path: ~/pnetcdf
+          key: ${{ runner.os }}-${{ env.PNETCDF_VERSION}}-pnetcdf-redo
+
+      - name: pnetcdf build
+        if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+        run: |
+          wget https://parallel-netcdf.github.io/Release/${{ env.PNETCDF_VERSION }}.tar.gz
+          tar -xzvf ${{ env.PNETCDF_VERSION }}.tar.gz
+          ls -l
+          pushd ${{ env.PNETCDF_VERSION }}
+          ./configure --prefix=$HOME/pnetcdf --enable-shared --disable-cxx
+          make
+          make install
+          popd
+
+      - name: Cache netcdf-fortran
+        id: cache-netcdf-fortran
+        uses: actions/cache@v3
+        with:
+          path: ~/netcdf-fortran
+          key: ${{ runner.os }}-${{ env.NETCDF_FORTRAN_VERSION }}-netcdf-fortran-redo
+
+      - name: netcdf fortran build
+        if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+        run: |
+          wget https://github.com/Unidata/netcdf-fortran/archive/${{ env.NETCDF_FORTRAN_VERSION }}.tar.gz
+          tar -xzvf ${{ env.NETCDF_FORTRAN_VERSION }}.tar.gz
+          ls -l
+          pushd netcdf-fortran-*
+          ./configure --prefix=$HOME/netcdf-fortran
+          make
+          make install
+
+      - name: link netcdf-c to netcdf-fortran path
+        # link netcdf c library here to simplify build
+        run: |
+          pushd ${{ env.NETCDF_FORTRAN_PATH }}/include
+          ln -fs /usr/include/*netcdf* .
+          pushd ${{ env.NETCDF_FORTRAN_PATH }}/lib
+          clibdir=`nc-config --libdir`
+          ln -fs $clibdir/lib* .
+
+          sudo ln -s $HOME/pnetcdf/lib/pkgconfig/pnetcdf.pc /usr/lib/pkgconfig
+          sudo ln -s $HOME/netcdf-fortran/lib/pkgconfig/netcdf-fortran.pc /usr/lib/pkgconfig
+
+#      The following can be used to ssh to the testnode for debugging
+#      see https://github.com/mxschmitt/action-tmate for details
+#      - name: Setup tmate session
+#        uses: mxschmitt/action-tmate@v3
+      - uses: actions/checkout@v4
+      - name: build eCLM
+        run: |
+          # User-specific variables
+          ls -al
+          BUILD_DIR="bld"
+          INSTALL_DIR="eclm"
+
+          # Run cmake
+          cmake -S src -B "$BUILD_DIR" \
+                -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \
+                -DCMAKE_C_COMPILER=mpicc \
+                -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch -fallow-invalid-boz" \
+                -DCMAKE_Fortran_COMPILER=mpifort
+
+          cd bld
+          make -j${nproc}
+
+          ls -al
+          ls -al eclm
+      # - name: Cache inputdata
+      #   if: ${{ ! env.ACT }}
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: $HOME/cesm/inputdata
+      #     key: inputdata
+
+#     the following can be used by developers to login to the github server in case of errors
+#     see https://github.com/marketplace/actions/debugging-with-tmate for further details
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.gitignore

@@ -8,4 +8,6 @@ src/externals/mct/config.log
 src/externals/mct/config.status
 
 # Python byte-compiled / optimized / DLL files
-*.py[cod]
+*.py[cod]
+build
+bld

README.md

@@ -1,4 +1,6 @@
 # eCLM
+
+[![CI](https://github.com/HPSCTerrSys/eCLM/actions/workflows/CI.yml/badge.svg)](https://github.com/HPSCTerrSys/eCLM/actions/workflows/CI.yml)
 [![status: alpha](https://img.shields.io/badge/status-alpha-yellow)](https://github.com/HPSCTerrSys/eCLM)
 
 eCLM is based from [Community Land Model 5.0 (CLM5.0)]. It has the same modelling capabilities as CLM5 but with a more simplified infrastructure for build and namelist generation. The build system is handled entirely by CMake and namelists are generated through a small set of Python scripts. Only Fortran source codes necessary for a functional land model simulation were imported from CLM5. 

cmake/SetBuildOptions.cmake

@@ -22,6 +22,7 @@ endif()
 
 # Set compiler specific flags.
 if(COMPILER STREQUAL "GNU")
+    add_compile_options(-fallow-argument-mismatch)
     add_compile_definitions(CPRGNU)
     set(CMAKE_C_FLAGS "-std=gnu99 -fopenmp")
     set(CMAKE_C_FLAGS_DEBUG "-fcheck=bounds")
@@ -44,4 +45,4 @@ endif()
 message(STATUS " ******* ${CMAKE_PROJECT_NAME} build options ******* ")
 message(STATUS " Build type = '${CMAKE_BUILD_TYPE}'")
 message(STATUS " Compiler = '${COMPILER}'")
-message(STATUS " ********************************** ")
+message(STATUS " ********************************** ")

src/CMakeLists.txt

@@ -1,11 +1,19 @@
 cmake_minimum_required (VERSION 3.16.3)
 project (eCLM LANGUAGES C Fortran)
 
+
 get_filename_component(ECLM_ROOT ${CMAKE_SOURCE_DIR} DIRECTORY)
 list(APPEND CMAKE_MODULE_PATH "${ECLM_ROOT}/cmake")
 set(GENF90 ${CMAKE_MODULE_PATH}/genf90.pl)
+
 include(SetBuildOptions)
 
+if (USE_PDAF)
+  set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/eCLM)
+  set(CMAKE_Fortran_MODULE_DIRECTORY_MCT ${CMAKE_BINARY_DIR}/externals/mct/include)
+  set(CMAKE_Fortran_MODULE_DIRECTORY_GPTL ${CMAKE_BINARY_DIR}/externals/gptl/include)
+endif()
+
 add_subdirectory(externals)
 add_subdirectory(csm_share)
 add_subdirectory(clm5)
@@ -24,4 +32,13 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
 if("${isSystemDir}" STREQUAL "-1")
     set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-endif("${isSystemDir}" STREQUAL "-1")
+endif("${isSystemDir}" STREQUAL "-1")
+
+if (USE_PDAF)
+  install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
+  install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY_MCT}
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/include/eCLM/externals/mct)
+  install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY_GPTL}
+          DESTINATION ${CMAKE_INSTALL_PREFIX}/include/eCLM/externals/gptl)
+endif()

src/clm5/biogeochem/FireEmisFactorsMod.F90

@@ -227,7 +227,7 @@ integer function gen_hashkey(string)
     integer :: i
     integer :: strlen
     integer, parameter :: tbl_max_idx = 15  ! 2**N - 1
-    integer, parameter :: gen_hash_key_offset = z'000053db'
+    integer, parameter :: gen_hash_key_offset = INT(z'000053db', KIND=4)
     integer, dimension(0:tbl_max_idx) :: tbl_gen_hash_key =  (/61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1/)
 
     hash = gen_hash_key_offset

src/clm5/biogeochem/MEGANFactorsMod.F90

@@ -274,7 +274,7 @@ integer function gen_hashkey(string)
     integer :: i
 
     integer, parameter :: tbl_max_idx = 15  ! 2**N - 1
-    integer, parameter :: gen_hash_key_offset = z'000053db'
+    integer, parameter :: gen_hash_key_offset = INT(z'000053db', KIND=4)
     integer, dimension(0:tbl_max_idx) :: tbl_gen_hash_key =  (/61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1/)
 
     hash = gen_hash_key_offset

src/clm5/oasis3/oas_defineMod.F90

@@ -10,6 +10,7 @@ module oas_defineMod
 
   subroutine oas_definitions_init(bounds)
     use spmdMod      , only : masterproc
+    use domainMod    , only : ldomain
     use clm_varpar   , only : nlevsoi, nlevgrnd
     use decompMod    , only : ldecomp, bounds_type
     use oas_vardefMod
@@ -30,15 +31,17 @@ subroutine oas_definitions_init(bounds)
     integer              :: var_nodims(2)     ! var dimension parameters
 
 
-    if (masterproc) then
-      call define_grid()
-    end if
-
+    ! TODO: Fix grids.nc and masks.nc generation for 1D grid representation
+    !if (masterproc) then
+    ! call define_grid()
+    !end if
 
     ! -----------------------------------------------------------------
     ! ... Define partition
     ! -----------------------------------------------------------------
-    allocate(partition(200))
+    ! partition length = (# elements for partition info) + (max segments ORANGE partition) x (# elements per segment info)
+    !                  = 2 + 200*2 = 402
+    allocate(partition(402))
     partition(:) = 0; k = 0
 
     ! Use ORANGE partitioning scheme. This scheme defines an ensemble
@@ -58,18 +61,18 @@ subroutine oas_definitions_init(bounds)
         partition(3+k) = gcell_start - 1                  ! segment global offset (0-based)
         partition(4+k) = gcell_previous - gcell_start + 1 ! segment length
         k = k + 2
-
         gcell_start  = ldecomp%gdc2glo(g) ! current gridcell marks the start of a new segment 
-        partition(2) = partition(2) + 1   ! increment number of segments
+        partition(2) = partition(2) + 1   ! increment number of segments (limited to 200 based from OASIS3-MCT User's guide)
       end if
       gcell_previous = ldecomp%gdc2glo(g)
     enddo
 
     ! Define partition params for last segment
     partition(3+k) = gcell_start - 1
     partition(4+k) = gcell_previous - gcell_start + 1
+    partition(2) = partition(2) + 1
 
-    call oasis_def_partition(grid_id, partition, ierror)
+    call oasis_def_partition(grid_id, partition, ierror, ldomain%ns)
     deallocate(partition)
 
     ! -----------------------------------------------------------------
@@ -143,6 +146,7 @@ end subroutine oas_definitions_init
   subroutine define_grid()
     use shr_kind_mod , only : r8 => shr_kind_r8
     use domainMod    , only : ldomain
+
     character(len=4), parameter   :: grid_name='gclm'
     integer,          parameter   :: SOUTH = 1
     integer,          parameter   :: NORTH = 2
@@ -244,5 +248,6 @@ subroutine define_grid()
       call oasis_terminate_grids_writing()
       deallocate(oas_lon, oas_lat, oas_corner_lon, oas_corner_lat, oas_mask, corner_lon, corner_lat)
     end if
+
   end subroutine define_grid
 end module oas_defineMod

src/csm_share/CMakeLists.txt

@@ -127,4 +127,9 @@ if (USE_OASIS)
         endif()
     endif()
 endif()
+
+if (USE_PDAF)
+  target_compile_definitions(${PROJECT_NAME} PUBLIC USE_PDAF)
+endif()
+
 install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})