Merge branch 'develop' into HR4_roughness

.github/workflows/GCC.yml

@@ -0,0 +1,89 @@
+# This is a CI workflow for the fv3atm project.
+#
+# This workflow builds and tests the fv3atm library using GCC, and it tests
+# different CMake build options.
+#
+# Alex Richert, 6 Dec 2023
+
+name: GCC
+on:
+  push:
+    branches:
+    - develop
+  pull_request:
+    branches:
+    - develop
+
+jobs:
+  GCC:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        cmake_opts: ["-D32BIT=ON", "-D32BIT=OFF"]
+        gcc_ver: ["11"]
+        mpi: ["mpich"]
+
+    steps:
+
+    - name: install-doxygen
+      run: |
+        sudo apt-get install doxygen graphviz
+        
+    - name: checkout-fv3atm
+      uses: actions/checkout@v3
+      with:
+        path: ${{ github.workspace }}/fv3atm
+        submodules: recursive
+
+    - name: cache-spack
+      id: cache-spack
+      uses: actions/cache@v3
+      with:
+        path: ${{ github.workspace }}/spack-develop
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2-${{ matrix.cmake_opts }}-${{ matrix.mpich }}
+
+    # Building dependencies takes 40+ min
+    - name: spack-install
+      if: steps.cache-spack.outputs.cache-hit != 'true'
+      run: |
+        wget --no-verbose https://github.com/spack/spack/archive/refs/heads/develop.zip
+        unzip develop.zip -d ${GITHUB_WORKSPACE}/ &> unzip.out
+        . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
+        spack env create gcc${{ matrix.gcc_ver }} ${GITHUB_WORKSPACE}/fv3atm/ci/spack.yaml
+        spack env activate gcc${{ matrix.gcc_ver }}
+        spack compiler find | grep gcc@${{ matrix.gcc_ver }}
+        spack external find gmake cmake git git-lfs perl python ${{ matrix.mpi }}
+        spack config add "packages:all:require:['%gcc@${{ matrix.gcc_ver }}']"
+        spack config add "packages:mpi:require:'${{ matrix.mpi }}'"
+        spack concretize |& tee ${SPACK_ENV}/log.concretize
+        spack install -j2 --fail-fast
+
+    - name: build-fv3atm
+      run: |
+        . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
+        spack env activate gcc${{ matrix.gcc_ver }}
+        spack load $(spack find --format "{name}")
+        cd ${GITHUB_WORKSPACE}/fv3atm
+        git clone https://github.com/NOAA-EMC/CMakeModules
+        git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics stochastic_physics_repo
+        mkdir ${GITHUB_WORKSPACE}/build
+        sed -i 's/doc /upp_doc /' upp/docs/CMakeLists.txt
+        cd ${GITHUB_WORKSPACE}/build
+        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=ON
+        make -j2
+        ls -l /home/runner/work/fv3atm/fv3atm/fv3atm/io
+
+    - uses: actions/upload-artifact@v3
+      with:
+        name: docs
+        path: |
+          build/docs/html
+          
+    - name: debug-artifacts
+      uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: ccpp_prebuild_logs
+        path: ${{ github.workspace }}/build/ccpp/ccpp_prebuild.*
+

CMakeLists.txt

@@ -1,3 +1,22 @@
+# This is the main CMake file for fv3atm.
+#
+# Dusan Jovic, Alex Richert
+cmake_minimum_required(VERSION 3.19)
+
+# Handle user build options.
+option(ENABLE_DOCS "Enable generation of doxygen-based documentation." OFF)
+
+# Determine whether or not to generate documentation.
+if(ENABLE_DOCS)
+  find_package(Doxygen REQUIRED)
+  add_subdirectory(docs)  
+endif()
+
+# Enable CI build & unit testing:
+if(BUILD_TESTING)
+  project(fv3atm VERSION 1.0 LANGUAGES C CXX Fortran)
+  include(ci/CMakeLists.txt)
+endif()
 
 ###############################################################################
 ### CCPP

ci/CMakeLists.txt

@@ -0,0 +1,70 @@
+# This file is used by fv3atm's root CMakeLists.txt when BUILD_TESTING=ON. It is
+# used for CI runs and is based on the ufs-weather-model root CMakeLists.txt. It
+# cannot be built directly, and should not be used for compiling for general R&D
+# or operations.
+#
+# Alex Richert, 6 Dec 2023
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
+
+if(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 9.0.0)
+    message(FATAL_ERROR "GNU Compiler >= 9 is required")
+  endif()
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ggdb -fbacktrace -cpp -fcray-pointer -ffree-line-length-none -fno-range-check")
+
+  if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+  endif()
+
+  if(NOT 32BIT)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8 -fdefault-double-8")
+  endif()
+elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -nowarn -sox -align array64byte -qno-opt-dynamic-align")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qno-opt-dynamic-align -sox -fp-model source")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -debug minimal -qoverride-limits")
+  set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -fp-model consistent")
+  set(CMAKE_C_FLAGS_RELEASE       "-O2 -debug minimal")
+
+  if(NOT 32BIT)
+      set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -real-size 64")
+  endif()
+endif()
+
+set(32BIT           OFF CACHE BOOL "Enable 32BIT (single precision arithmetic in dycore and fast physics)")
+set(CCPP_32BIT      OFF CACHE BOOL "Enable CCPP_32BIT (single precision arithmetic in slow physics)")
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post")
+set(MULTI_GASES     OFF CACHE BOOL "Enable MULTI_GASES")
+set(MOVING_NEST     OFF CACHE BOOL "Enable moving nest code")
+set(OPENMP          ON  CACHE BOOL "Enable OpenMP threading")
+set(PARALLEL_NETCDF OFF CACHE BOOL "Enable parallel NetCDF")
+
+message("32BIT ............ ${32BIT}")
+message("CCPP_32BIT ....... ${CCPP_32BIT}")
+message("INLINE_POST ...... ${INLINE_POST}")
+message("MULTI_GASES ...... ${MULTI_GASES}")
+message("MOVING_NEST ...... ${MOVING_NEST}")
+message("OPENMP ........... ${OPENMP}")
+message("PARALLEL_NETCDF .. ${PARALLEL_NETCDF}")
+
+find_package(MPI REQUIRED)
+if(OPENMP)
+  find_package(OpenMP REQUIRED)
+endif()
+
+find_package(NetCDF 4.7.4 REQUIRED C Fortran)
+find_package(ESMF 8.3.0 MODULE REQUIRED)
+find_package(FMS 2022.04 REQUIRED COMPONENTS R4 R8)
+if(32BIT)
+  add_library(fms ALIAS FMS::fms_r4)
+else()
+  add_library(fms ALIAS FMS::fms_r8)
+endif()
+find_package(bacio 2.4.0 REQUIRED)
+find_package(sp 2.3.3 REQUIRED)
+find_package(w3emc 2.9.2 REQUIRED)
+
+find_package(Python 3.6 REQUIRED COMPONENTS Interpreter)
+
+add_subdirectory(stochastic_physics_repo)

ci/spack.yaml

@@ -0,0 +1,29 @@
+# This file is used in the CI to define the libraries needed to build fv3atm. It
+# is used by the 'spack env create' command to generate a Spack environment. It
+# is generally preferred to avoid defining settings here that are not shared
+# across CI workflows, such as requiring the use of a specific compiler. Any
+# such modifications should be done in the appropriate CI workflow using the
+# 'spack config add' command, or with search-and-replace.
+# WARNING: Changing this file will automatically cause the cached Spack builds
+# in GitHub Actions to be regenerated, which takes a considerable amount of
+# time.
+#
+# Alex Richert, 6 Dec 2023
+spack:
+  specs:
+  - [email protected] precision=4,d,8
+  - ip@develop precision=4,d,8
+  - [email protected] precision=4,d,8
+  - [email protected]
+  - upp@develop
+  - [email protected]
+  - [email protected] +gfs_phys +openmp +pic +quad_precision +deprecated_io constants=GFS precision=32,64
+  - [email protected] ~blosc
+  view: false
+  concretizer:
+    unify: true
+  packages:
+    mpich:
+      require: ['~libxml2 ~hwloc ~pci'] # minimize unneeded dependencies
+    yaksa:
+      buildable: false # minimize unneeded dependencies

docs/CMakeLists.txt

@@ -0,0 +1,17 @@
+# This is the CMake file for building the docs directory of fv3atm.
+#
+# Ed Hartnett 12/28/23
+
+IF(ENABLE_DOCS)
+
+  # Create doxyfile.
+  SET(abs_top_srcdir "${CMAKE_SOURCE_DIR}")
+  SET(abs_top_builddir "${CMAKE_BINARY_DIR}")
+  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+  ADD_CUSTOM_TARGET(doxygen_doc ALL
+    ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    COMMENT "Generating API Documentation with Doxygen" VERBATIM)
+
+ENDIF(ENABLE_DOCS)
+