Merge pull request #12 from NOAA-EMC/develop

merge changes from NOAA develop

.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 }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      # Build WW3 spack environment
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          # Install NetCDF, ESMF, g2, etc using Spack
+          sudo apt install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
+          spack env activate ww3-gnu
+          spack compiler find
+          spack external find cmake
+          spack add [email protected]
+          spack concretize
+          spack install --dirty -v
+
+      - name: build-oasis
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          export WWATCH3_DIR=${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 "")
@@ -22,8 +22,9 @@ endif()
 
 set(MULTI_ESMF OFF CACHE BOOL "Build ww3_multi_esmf library")
 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)
@@ -59,8 +60,15 @@ endif()
 
 add_subdirectory(model)
 
-# Turn on unit testing.
-include(CTest)
-if(BUILD_TESTING)
-  add_subdirectory(regtests/unittests)
+# 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()

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()

model/bin/ww3_from_ftp.sh

@@ -61,11 +61,14 @@ fi
 #Move to top level directory of ww3:
 cd $ww3dir
 
-#Download from ftp and uptar:
-echo -e "Downloading and untaring file from ftp:"
-wget --no-check-certificate https://ftp.emc.ncep.noaa.gov/static_files/public/WW3/ww3_from_ftp.${ww3ver}.tar.gz
+#Download from ftp (if not already present) and uptar:
+echo -e "Downloading (or finding) and untaring file from ftp:"
+if ! test -f ww3_from_ftp.${ww3ver}.tar.gz; then
+  wget --no-check-certificate https://ftp.emc.ncep.noaa.gov/static_files/public/WW3/ww3_from_ftp.${ww3ver}.tar.gz
+fi
 tar -xvzf ww3_from_ftp.${ww3ver}.tar.gz
 
+
 #Move regtest info from data_regtests to regtests:
 echo -e "Moving data from data_regtests to regtests"
 cp -r data_regtests/ww3_tp2.18/input/*.nc  regtests/ww3_tp2.18/input/

model/src/CMakeLists.txt

@@ -174,10 +174,9 @@ if("SCRIP" IN_LIST switches)
   target_sources(ww3_lib PRIVATE ${scrip_src})
 endif()
 
-
-if("SCRIPNC" IN_LIST switches OR "OASIS" IN_LIST switches OR "TRKNC" IN_LIST switches)
+if("SCRIPNC" IN_LIST switches OR "OASIS" IN_LIST switches OR "TRKNC" IN_LIST switches OR "BIN2NC" IN_LIST switches)
   if(NOT NetCDF_Fortran_FOUND)
-    message(FATAL_ERROR "Cannot build SCRIPNC, OASIS, or TRKNC without NetCDF")
+	  message(FATAL_ERROR "Cannot build SCRIPNC, OASIS, TRKNC, or BIN2NC without NetCDF")
   endif()
 endif()
 

model/src/cmake/switches.json

@@ -814,6 +814,16 @@
             }
         ]
     },
+    {
+        "name": "bin2nc",
+        "num_switches": "upto1",
+        "description": "use netcdf instead of binary model output",
+        "valid-options": [
+            {
+                "name": "BIN2NC"
+            }
+        ]
+    },
     {
         "name": "ascii",
         "num_switches": "upto1",

model/src/gx_outp.F90

@@ -165,7 +165,11 @@ PROGRAM GXOUTP
 #endif
   USE W3ODATMD, ONLY: W3SETO, W3NOUT
   USE W3IOGRMD, ONLY: W3IOGR
+#ifdef W3_BIN2NC
+  USE W3IOPOMD, ONLY: W3IOPON
+#else 
   USE W3IOPOMD, ONLY: W3IOPO
+#endif
   USE W3SERVMD, ONLY : ITRACE, NEXTLN, EXTCDE
 #ifdef W3_S
   USE W3SERVMD, ONLY : STRACE
@@ -277,7 +281,11 @@ PROGRAM GXOUTP
   !--- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   ! 3.  Read general data and first fields from file
   !
+#ifdef W3_BIN2NC
+  CALL W3IOPON ( 'READ', NDSOP, IOTEST )
+#else
   CALL W3IOPO ( 'READ', NDSOP, IOTEST )
+#endif
   ALLOCATE ( FLREQ(NOPTS) )
   !
   WRITE (NDSO,930)
@@ -369,7 +377,11 @@ PROGRAM GXOUTP
   DO
     DTEST  = DSEC21 ( TIME , TOUT )
     IF ( DTEST .GT. 0. ) THEN
+#ifdef W3_BIN2NC
+      CALL W3IOPON ( 'READ', NDSOP, IOTEST )
+#else 
       CALL W3IOPO ( 'READ', NDSOP, IOTEST )
+#endif
       IF ( IOTEST .EQ. -1 ) THEN
         WRITE (NDSO,998)
         EXIT

model/src/w3bullmd.F90

@@ -268,8 +268,8 @@ SUBROUTINE W3BULL                                                &
     !
     CSVBLINE      = BLANK2
     !
+    IPG1 = 0
     IF (IOUT .EQ. 1) THEN
-      IPG1 = 0
       DO IP=1, NPTAB
         HST(IP,1) = -99.9
         TPT(IP,1) = -99.9
@@ -286,10 +286,12 @@ SUBROUTINE W3BULL                                                &
     !
     HSTOT  = XPART(1,0)
     TP     = XPART(2,0)
-    HSP = XPART(1,1:NPART)
-    TPP = XPART(2,1:NPART)
-    WNP = TPI / XPART(3,1:NPART)
-    DMP = MOD( XPART(4,1:NPART) + 180., 360.)
+    DO IP=1, NPART
+      HSP(IP) = XPART(1,IP)
+      TPP(IP) = XPART(2,IP)
+      WNP(IP) = TPI / XPART(3,IP)
+      DMP(IP) = MOD( XPART(4,IP) + 180., 360.)
+    ENDDO
 
     NZERO = 0
     NZERO = COUNT( HSP <= BHSMIN .AND. HSP /= 0.  )