Merge remote-tracking branch 'origin/develop' into fb_reg_gpuport

* origin/develop:
  Enable doxygen documentation in the cmake build system (NOAA-EMC#1281)
  Simplify MPI ifdefs in subroutine W3MPIO (NOAA-EMC#1266)
  Add depth scaling value to SMC regression tests. (NOAA-EMC#1264)
  Updates to NCEP regtests for Orion Rocky9 OS(NOAA-EMC#1263)
  Fix code stability issue in ww3_outp (NOAA-EMC#1258)
  Fix GNU regtest CI failure (NOAA-EMC#1253)

Author: ukmo-ccbunney

.github/workflows/regtest_gnu.yml

@@ -91,7 +91,7 @@ jobs:
             spack
             ~/.spack
             work_oasis3-mct
-          key: spack2-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
 
       - name: build-ww3
         run: |
@@ -102,10 +102,10 @@ jobs:
           export CC=mpicc
           export FC=mpif90
           export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
-#          mkdir build && cd build
+          # mkdir build && cd build
           export LD_LIBRARY_PATH="/home/runner/work/WW3/WW3/spack/var/spack/environments/ww3-gnu/.spack-env/view/:$LD_LIBRARY_PATH"
-#          cmake -DSWITCH=${GITHUB_WORKSPACE}/ww3/regtests/unittests/data/switch.io -DCMAKE_BUILD_TYPE=Debug ..
-#          make -j2 VERBOSE=1
+          # cmake -DSWITCH=${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
@@ -116,18 +116,15 @@ jobs:
           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          
-        
+          # 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)
@@ -59,6 +60,13 @@ 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)

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/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.  )