Sync develop branch 20241220 to dev/ufs-weather-model

.github/workflows/intel.yml

@@ -13,7 +13,7 @@ concurrency:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel12
+  cache_key: intel10-3
   CC: icc
   FC: ifort
   CXX: icpc

.github/workflows/io_gnu_yml.old

@@ -0,0 +1,122 @@
+name: io_gnu
+on: [push, pull_request, workflow_dispatch]
+
+# Cancel in-progress workflows when pushing to a branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  cache_key: gnu11-1
+  CC: gcc-10
+  FC: gfortran-10
+  CXX: g++-10
+
+
+# Split into a steup step, and a WW3 build step which
+# builds multiple switches in a matrix. The setup is run once and
+# the environment is cached so each build of WW3 can share the dependencies.
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout-ww3
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+            path: ww3
+      # Cache spack, OASIS, and compiler
+      # No way to flush Action cache, so key may have # appended
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      # Build WW3 spack environment
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          # Install NetCDF, ESMF, g2, etc using Spack
+          sudo apt install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
+          spack env activate ww3-gnu
+          spack compiler find
+          spack external find cmake
+          spack add mpich@3.4.2
+          spack concretize
+          spack install --dirty -v
+
+      - name: build-oasis
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          export WWATCH3_DIR=${GITHUB_WORKSPACE}/ww3/model
+          export OASIS_INPUT_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/oasis3-mct
+          export OASIS_WORK_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct
+          cd ww3/regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir
+          cmake .
+          make VERBOSE=1
+          cp -r ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct ${GITHUB_WORKSPACE}
+
+  io_gnu:
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: install-dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install doxygen gcovr valgrind
+
+      - name: checkout-ww3
+        uses: actions/checkout@v3
+        with:
+            path: ww3
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      - name: build-ww3
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          set -x
+          cd ww3
+          export CC=mpicc
+          export FC=mpif90
+          export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
+          mkdir build && cd build
+          export LD_LIBRARY_PATH="/home/runner/work/WW3/WW3/spack/var/spack/environments/ww3-gnu/.spack-env/view/:$LD_LIBRARY_PATH"
+          cmake -DSWITCH=${GITHUB_WORKSPACE}/ww3/regtests/unittests/data/switch.io -DCMAKE_BUILD_TYPE=Debug -DCMAKE_Fortran_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" -DCMAKE_C_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" ..
+          make -j2 VERBOSE=1
+          ./bin/ww3_grid
+          mv mod_def.ww3 regtests/unittests
+          ctest --verbose --output-on-failure --rerun-failed
+          gcovr --root .. -v  --html-details --exclude ../regtests/unittests --exclude CMakeFiles --print-summary -o test-coverage.html &> /dev/null
+
+      - name: upload-test-coverage
+        uses: actions/upload-artifact@v3
+        with:
+          name: ww3-test-coverage
+          path: |
+            ww3/build/*.html
+            ww3/build/*.css
+
+

.github/workflows/regtest_gnu.yml

@@ -0,0 +1,130 @@
+name: regtest_gnu
+on: [push, pull_request, workflow_dispatch]
+
+# Cancel in-progress workflows when pushing to a branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  cache_key: gnu11-1
+  CC: gcc-10
+  FC: gfortran-10
+  CXX: g++-10
+
+
+# Split into a steup step, and a WW3 build step which
+# builds multiple switches in a matrix. The setup is run once and
+# the environment is cached so each build of WW3 can share the dependencies.
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout-ww3
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+            path: ww3
+      # Cache spack, OASIS, and compiler
+      # No way to flush Action cache, so key may have # appended
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      # Build WW3 spack environment
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          # Install NetCDF, ESMF, g2, etc using Spack
+          sudo apt install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
+          spack env activate ww3-gnu
+          spack compiler find
+          spack external find cmake
+          spack add mpich@3.4.2
+          spack concretize
+          spack install --dirty -v
+
+      - name: build-oasis
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          export WWATCH3_DIR=${GITHUB_WORKSPACE}/ww3/model
+          export OASIS_INPUT_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/oasis3-mct
+          export OASIS_WORK_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct
+          cd ww3/regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir
+          cmake .
+          make VERBOSE=1
+          cp -r ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct ${GITHUB_WORKSPACE}
+
+  regtest_gnu:
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: install-dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install doxygen gcovr valgrind
+
+      - name: checkout-ww3
+        uses: actions/checkout@v3
+        with:
+            path: ww3
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      - name: build-ww3
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          set -x
+          cd ww3
+          export CC=mpicc
+          export FC=mpif90
+          export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
+          # mkdir build && cd build
+          export LD_LIBRARY_PATH="/home/runner/work/WW3/WW3/spack/var/spack/environments/ww3-gnu/.spack-env/view/:$LD_LIBRARY_PATH"
+          # cmake -DSWITCH=${GITHUB_WORKSPACE}/ww3/regtests/unittests/data/switch.io -DCMAKE_BUILD_TYPE=Debug ..
+          # make -j2 VERBOSE=1
+          cd ${GITHUB_WORKSPACE}/ww3
+          ls -l
+          ${GITHUB_WORKSPACE}/ww3/model/bin/ww3_from_ftp.sh -k
+          cd regtests
+          ./bin/run_cmake_test -o all -S -T -s PR1_MPI -w work_PR1_MPI -f -p mpirun -n 24 ../model ww3_tp2.5
+          cd ww3_tp2.5
+          ls -l
+          cd work_PR1_MPI
+          pwd
+          ls -l
+          # ncdump -h out_pnt.ww3.nc > ncdump_out.txt
+          # cat ncdump_out.txt
+          # pwd
+          # cat ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.5/out_pnt_ncdump.txt
+          # cmp ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.5/out_pnt_ncdump.txt ncdump_out.txt
+
+      - name: cache-data
+        id: cache-data
+        uses: actions/cache@v3
+        with:
+          path: ww3/ww3_from_ftp.v7.14.1.tar.gz
+          key: ww3_from_ftp.v7.14.1

CMakeLists.txt

@@ -13,7 +13,7 @@ project(
 
 get_directory_property(hasParent PARENT_DIRECTORY)
 if(hasParent)
-  # Unset flags that come from Parent (ie UFS or other coupled build) 
+  # Unset flags that come from Parent (ie UFS or other coupled build)
   # for potential (-r8/-r4) conflict
   set(CMAKE_Fortran_FLAGS "")
   set(CMAKE_C_FLAGS "")
@@ -24,8 +24,9 @@ set(valid_caps "MULTI_ESMF" "NUOPC_MESH")
 
 set(UFS_CAP "" CACHE STRING "Valid options are ${valid_caps}")
 set(NETCDF ON CACHE BOOL "Build NetCDF programs (requires NetCDF)")
-set(ENDIAN "BIG" CACHE STRING "Endianness of unformatted output files. Valid values are 'BIG', 'LITTLE', 'NATIVE'.") 
+set(ENDIAN "BIG" CACHE STRING "Endianness of unformatted output files. Valid values are 'BIG', 'LITTLE', 'NATIVE'.")
 set(EXCLUDE_FIND "" CACHE STRING "Don't try and search for these libraries (assumd to be handled by the compiler/wrapper)")
+set(ENABLE_DOCS OFF CACHE BOOL "Enable building of doxygen generated documentation")
 
 # make sure all "exclude_find" entries are lower case
 list(TRANSFORM EXCLUDE_FIND TOLOWER)
@@ -66,3 +67,16 @@ if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
 endif()
 
 add_subdirectory(model)
+
+# Turn on doxygen documentation
+if (ENABLE_DOCS)
+  list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/docs/cmake")
+  include(EnableDoxygen)
+  add_subdirectory(docs)
+endif()
+
+# Turn on unit testing.
+#include(CTest)
+#if(BUILD_TESTING)
+#  add_subdirectory(regtests/unittests)
+#endif()

README.md

@@ -1,23 +1,25 @@
 # The WAVEWATCH III Framework
 
-WAVEWATCH III<sup>&reg;</sup>  is a community wave modeling framework that includes the 
+WAVEWATCH III<sup>&reg;</sup>  is a community wave modeling framework that includes the
 latest scientific advancements in the field of wind-wave modeling and dynamics.
 
 ## General Features
 
-WAVEWATCH III<sup>&reg;</sup> solves the random phase spectral action density 
-balance equation for wavenumber-direction spectra. The model includes options 
-for shallow-water (surf zone) applications, as well as wetting and drying of 
-grid points. Propagation of a wave spectrum can be solved using regular 
-(rectilinear or curvilinear) and unstructured (triangular) grids. See 
-[About WW3](https://github.com/NOAA-EMC/WW3/wiki/About-WW3) for a 
-detailed description of WAVEWATCH III<sup>&reg;</sup> .
+WAVEWATCH III<sup>&reg;</sup> solves the random phase spectral action density
+balance equation for wavenumber-direction spectra. The model includes options
+for shallow-water (surf zone) applications, as well as wetting and drying of
+grid points. Propagation of a wave spectrum can be solved using regular
+(rectilinear or curvilinear) and unstructured (triangular) grids. See
+[About WW3](https://github.com/NOAA-EMC/WW3/wiki/About-WW3) for a
+detailed description of WAVEWATCH III<sup>&reg;</sup>. For a web-based
+view of the WAVEWATCH III<sup>&reg;</sup> source code
+refer to the [WW3 doxygen documentation](https://noaa-emc.github.io/WW3).
 
 ## Installation
 
-The WAVEWATCH III<sup>&reg;</sup>  framework package has two parts that need to be combined so 
-all runs smoothly: the GitHub repo itself, and a binary data file bundle that 
-needs to be obtained from our ftp site. Steps to successfully acquire and install 
+The WAVEWATCH III<sup>&reg;</sup>  framework package has two parts that need to be combined so
+all runs smoothly: the GitHub repo itself, and a binary data file bundle that
+needs to be obtained from our ftp site. Steps to successfully acquire and install
 the framework are outlined in our [Quick Start](https://github.com/NOAA-EMC/WW3/wiki/Quick-Start)
 guide.
 
@@ -35,4 +37,3 @@ endorsement, recommendation or favoring by the Department of Commerce. The
 Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
 shall not be used in any manner to imply endorsement of any commercial product
 or activity by DOC or the United States Government.
-

docs/CMakeLists.txt

@@ -0,0 +1 @@
+EnableDoxygen(docs)

docs/Doxyfile.in

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = docs
+OUTPUT_DIRECTORY       = @doc_output@
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -829,7 +829,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = model/src
+INPUT                  = @src_input@
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -2285,7 +2285,7 @@ CLASS_DIAGRAMS         = NO
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.
 # If left empty dia is assumed to be found in the default search path.
 
-DIA_PATH               = 
+DIA_PATH               =
 
 # If set to YES the inheritance and collaboration graphs will hide inheritance
 # and usage relations if the target is undocumented or is not a class.

docs/cmake/EnableDoxygen.cmake

@@ -0,0 +1,27 @@
+# Doxygen documentation- Matt Masarik 24-Jul-2024.
+function(EnableDoxygen outdir)
+  find_package(Doxygen REQUIRED)
+    if (NOT DOXYGEN_FOUND)
+      add_custom_target(enable_docs
+          COMMAND false
+          COMMENT "Doxygen not found")
+      return()
+    endif()
+
+    set(src_input "${CMAKE_SOURCE_DIR}/model/src")
+    set(doc_output "${CMAKE_BINARY_DIR}/${outdir}")
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/${outdir}/html)
+    CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/docs/Doxyfile.in
+        ${CMAKE_BINARY_DIR}/${outdir}/Doxyfile @ONLY)
+    set(DOXYGEN_GENERATE_HTML YES)
+    set(DOXYGEN_QUIET YES)
+    add_custom_target(enable_docs
+        COMMAND
+          ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/${outdir}/Doxyfile
+        WORKING_DIRECTORY
+          ${CMAKE_BINARY_DIR}/${outdir}
+        COMMENT
+          "Generate Doxygen HTML documentation")
+    message("-- Doxygen HTML index page: "
+        ${CMAKE_BINARY_DIR}/${outdir}/html/index.html)
+endfunction()