wrf-model · islas · Dec 16, 2024 · Dec 17, 2024 · Dec 17, 2024 · Dec 17, 2024
@@ -155,18 +155,19 @@ set( USE_HDF5    OFF CACHE BOOL "USE_HDF5"    )
 set( USE_JASPER  OFF CACHE BOOL "USE_JASPER"  )
 set( USE_PIO     OFF CACHE BOOL "USE_PIO"     )
 set( USE_IPO     OFF CACHE BOOL "USE_IPO"     )
-
-
-set( ENABLE_CHEM       OFF CACHE BOOL "ENABLE_CHEM"      )
-set( ENABLE_CMAQ       OFF CACHE BOOL "ENABLE_CMAQ"      )
-set( ENABLE_CTSM       OFF CACHE BOOL "ENABLE_CTSM"      )
-set( ENABLE_DFI_RADAR  OFF CACHE BOOL "ENABLE_DFI_RADAR" )
-set( ENABLE_HYDRO      OFF CACHE BOOL "ENABLE_HYDRO"     )
-set( ENABLE_KPP        OFF CACHE BOOL "ENABLE_KPP"       )
-set( ENABLE_MARS       OFF CACHE BOOL "ENABLE_MARS"      )
-set( ENABLE_TERRAIN    OFF CACHE BOOL "ENABLE_TERRAIN"   )
-set( ENABLE_TITAN      OFF CACHE BOOL "ENABLE_TITAN"     )
-set( ENABLE_VENUS      OFF CACHE BOOL "ENABLE_VENUS"     )
+set( USE_PNETCDF OFF CACHE BOOL "USE_PNETCDF" )
+
+set( ENABLE_PNETCDF_QUILT OFF CACHE BOOL "ENABLE_PNETCDF_QUILT" )
+set( ENABLE_CHEM          OFF CACHE BOOL "ENABLE_CHEM"          )
+set( ENABLE_CMAQ          OFF CACHE BOOL "ENABLE_CMAQ"          )
+set( ENABLE_CTSM          OFF CACHE BOOL "ENABLE_CTSM"          )
+set( ENABLE_DFI_RADAR     OFF CACHE BOOL "ENABLE_DFI_RADAR"     )
+set( ENABLE_HYDRO         OFF CACHE BOOL "ENABLE_HYDRO"         )
+set( ENABLE_KPP           OFF CACHE BOOL "ENABLE_KPP"           )
+set( ENABLE_MARS          OFF CACHE BOOL "ENABLE_MARS"          )
+set( ENABLE_TERRAIN       OFF CACHE BOOL "ENABLE_TERRAIN"       )
+set( ENABLE_TITAN         OFF CACHE BOOL "ENABLE_TITAN"         )
+set( ENABLE_VENUS         OFF CACHE BOOL "ENABLE_VENUS"         )
 
 # What do these defines even do if they are always on????
 set( USE_ALLOCATABLES     ON CACHE BOOL "USE_ALLOCATABLES"    )
@@ -286,6 +287,16 @@ if ( NOT ${WRFIO_NCD_NO_LARGE_FILE_SUPPORT} )
   message( STATUS "netCDF large file support not suppressed, if available it will be used" )
 endif()
 
+# PnetCDF options require MPI
+if ( ${ENABLE_PNETCDF_QUILT} AND NOT ${USE_PNETCDF} )
+  message( STATUS "PnetCDF Quilt IO requires PnetCDF" )
+  set( USE_PNETCDF ON CACHE BOOL "Required by configuration" FORCE )
+endif()
+if ( ${USE_PNETCDF} AND NOT ${USE_MPI} )
+  message( STATUS "PnetCDF require MPI usage" )
+  set( USE_MPI ON CACHE BOOL "Required by configuration" FORCE )
+endif()
+
 # Hydro option requires MPI
 if ( ${ENABLE_HYDRO} AND NOT ${USE_MPI} )
   message( STATUS "WRF Hydro requires MPI usage" )
@@ -521,6 +532,12 @@ endif()
 # Will need our own finder
 # find_package( GPFS   REQUIRED )
 
+# Find this first in case we need to use pnetcdf's netCDF
+# Priority is given to pnetcdf due to performance
+if ( ${USE_PNETCDF} )
+  find_package( PnetCDF REQUIRED )
+endif()
+
 # Included is a lightweight finder, but we really should switch to using UniData's netCDF cmake config
 # The reason these are two separate and not COMPONENTS of one larger package is because that is the way UniData
 # has laid out the cmake configs for each respective package
@@ -542,12 +559,10 @@ if ( NOT ${FORCE_NETCDF_CLASSIC} )
   endif()
 endif()
 
-find_package( pnetCDF QUIET )
 
 # Attempt to find zlib packaged with netcdf first
 set( ZLIB_ROOT ${netCDF_PREFIX} )
 find_package( ZLIB   REQUIRED )
-find_package( CURL   REQUIRED )
 
 ################################################################################
 ##
@@ -763,6 +778,13 @@ else()
   list( APPEND PROJECT_COMPILE_DEFINITIONS_OPTIONS WRF_USE_CLM )
 endif()
 
+if ( ${PnetCDF_FOUND} )
+  list( APPEND PROJECT_COMPILE_DEFINITIONS_OPTIONS PNETCDF )
+endif()
+if ( ${ENABLE_PNETCDF_QUILT} )
+  list( APPEND PROJECT_COMPILE_DEFINITIONS_OPTIONS PNETCDF_QUILT=1 )
+endif()
+
 # If force classic or no nc-4 support enable classic
 if ( ${FORCE_NETCDF_CLASSIC} OR ( NOT ${netCDF_HAS_NC4} ) )
   list( APPEND PROJECT_COMPILE_DEFINITIONS_OPTIONS NETCDF_classic=1 )
@@ -1075,7 +1097,6 @@ target_include_directories(
                               ${PROJECT_SOURCE_DIR}/external/io_int
 
                               # Found Packages not handled through :: imported target
-                              ${pnetCDF_INCLUDE_DIRS}
                             )
 
 # Configure core
@@ -1093,8 +1114,8 @@ target_link_options( ${PROJECT_NAME}_Core PRIVATE ${WRF_LINK_FLAGS} )
 
 target_link_libraries(  ${PROJECT_NAME}_Core
                           PUBLIC
-                            netCDF::netcdff
-                            ${pnetCDF_LIBRARIES}
+                            $<TARGET_NAME_IF_EXISTS:PnetCDF::pnetcdf>
+                            $<TARGET_NAME_IF_EXISTS:netCDF::netcdff>
                             $<$<BOOL:${USE_MPI}>:$<TARGET_NAME_IF_EXISTS:MPI::MPI_Fortran>>
                             $<$<BOOL:${USE_OPENMP}>:$<TARGET_NAME_IF_EXISTS:OpenMP::OpenMP_Fortran>>
                             # This will add in target dependencies if they exist

@@ -0,0 +1,156 @@
+# Find pnetcdf
+# Eventually replace with PnetCDF's actual config if using that
+# Once found this file will define:
+#  PnetCDF_FOUND - System has pnetcdf
+#  PnetCDF_INCLUDE_DIRS - The pnetcdf include directories
+#  PnetCDF_LIBRARIES - The libraries needed to use pnetcdf
+#  PnetCDF_DEFINITIONS - Compiler switches required for using pnetcdf
+
+# list( REMOVE_ITEM CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR} )
+# find_package( PnetCDF )
+# list( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR} )
+
+
+# exit early if we don't even need to be here
+if ( PnetCDF_FOUND )
+  return()
+endif()
+
+# Use pnetcdf-config
+find_program( 
+                PNETCDF_PROGRAM
+                pnetcdf-config
+                QUIET
+                )
+
+if ( ${PNETCDF_PROGRAM} MATCHES "-NOTFOUND$" )
+  message( STATUS "No pnetcdf-config found" )
+else()
+  message( STATUS "Found PNETCDF_PROGRAM : ${PNETCDF_PROGRAM}" )
+
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --includedir   OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_INCLUDE_DIR )
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --prefix       OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_PREFIX )
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --libdir       OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_LIBDIR   )
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --version      OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_VERSION_RAW )
+
+  # These are what PnetCDF was built with
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --ldflags      OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_LDFLAGS )
+  execute_process( COMMAND ${PNETCDF_PROGRAM} --libs         OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_BUILD_LIBS )
+
+  # Sanitize version
+  string( REPLACE " " ";" PnetCDF_VERSION_LIST ${PnetCDF_VERSION_RAW} )
+  list( GET PnetCDF_VERSION_LIST -1 PnetCDF_VERSION )
+
+  # These do not pull all options available from nc-config out, but rather mirrors what is available from PnetCDFConfig.cmake.in
+  set(
+      PnetCDF_QUERY_YES_OPTIONS
+      has-c++
+      has-fortran
+      netcdf4
+      adios
+      )
+
+  foreach( PN_QUERY ${PnetCDF_QUERY_YES_OPTIONS} )
+    string( REPLACE "has-" "" PN_QUERY_FILTERED ${PN_QUERY} )
+    execute_process( COMMAND ${PNETCDF_PROGRAM} --${PN_QUERY} OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE PnetCDF_${PN_QUERY_FILTERED}_LOWERCASE )
+    if ( "${PnetCDF_${PN_QUERY_FILTERED}_LOWERCASE}" STREQUAL "" )
+      # might be empty
+      set( PnetCDF_${PN_QUERY_FILTERED}_LOWERCASE no )
+    endif()
+
+    string( TOUPPER ${PN_QUERY_FILTERED}                      PN_QUERY_UPPERCASE )
+    string( TOUPPER ${PnetCDF_${PN_QUERY_FILTERED}_LOWERCASE} PN_ANSWER_UPPERCASE )
+
+    set( PN_QUERY_YES_RESPONSE YES ENABLED )
+    list( FIND PN_QUERY_YES_RESPONSE ${PN_ANSWER_UPPERCASE} PN_FIND_ANSWER )
+    if ( ${PN_FIND_ANSWER} EQUAL -1 )
+      set( PN_ANSWER_UPPERCASE NO )
+    else()
+      set( PN_ANSWER_UPPERCASE YES )
+    endif()
+
+    # Convert to PnetCDF_HAS_* = YES/NO - Note this cannot be generator expression if you want to use it during configuration time
+    set( PnetCDF_HAS_${PN_QUERY_UPPERCASE} ${PN_ANSWER_UPPERCASE} )
+  endforeach()
+
+  # Because we may need this for in-situ manual preprocessing do not use genex
+  set( PnetCDF_INCLUDE_DIRS ${PnetCDF_INCLUDE_DIR} )
+
+  # Find the actual name of the library
+  find_library(
+                PnetCDF_LIBRARY
+                pnetcdf
+                PATHS ${PnetCDF_LIBDIR}
+                NO_DEFAULT_PATH
+                )
+
+  set( PnetCDF_DEFINITIONS  )
+  set( PnetCDF_LIBRARIES ${PnetCDF_LIBRARY} )
+endif()
+
+include(FindPackageHandleStandardArgs)
+
+# handle the QUIETLY and REQUIRED arguments and set PnetCDF_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(
+                                  PnetCDF
+                                  FOUND_VAR PnetCDF_FOUND
+                                  REQUIRED_VARS
+                                    PnetCDF_INCLUDE_DIRS
+                                    PnetCDF_LIBRARIES
+                                    PnetCDF_VERSION
+                                  VERSION_VAR PnetCDF_VERSION
+                                  HANDLE_VERSION_RANGE
+                                )
+
+if ( PnetCDF_FOUND AND NOT TARGET PnetCDF::pnetcdf )
+  if ( ${PnetCDF_HAS_NETCDF4} )
+    list( APPEND CMAKE_MESSAGE_INDENT "  " )
+    if ( NOT "${PnetCDF_LDFLAGS}" STREQUAL "" )
+      # Find prefix
+      message( STATUS "Looking for netCDF location provided by ${PNETCDF_PROGRAM}")
+      foreach( PNETCDF_BUILD_LINK_DIR ${PnetCDF_LDFLAGS} )
+        string( REGEX MATCH "^-L([^ ]*)" PN_LIBRARY_LINK_LOCATION_TMP ${PNETCDF_BUILD_LINK_DIR} )
+        if ( NOT "${PN_LIBRARY_LINK_LOCATION_TMP}" STREQUAL "" )
+          message( STATUS "Searching ${PN_LIBRARY_LINK_LOCATION_TMP}..." )
+          set( PN_LIBRARY_LINK_DIR ${CMAKE_MATCH_1} )
+          find_library( 
+                        netCDF_LIBRARY_FOR_PNETCDF
+                        netcdf
+                        PATHS ${PN_LIBRARY_LINK_DIR}
+                        NO_DEFAULT_PATH
+                        )
+          if ( NOT "${netCDF_LIBRARY_FOR_PNETCDF}" MATCHES "-NOTFOUND$" )
+            string( REGEX REPLACE "/(lib|lib64)$" "" netCDF_ROOT ${PN_LIBRARY_LINK_DIR} )
+            message( STATUS "Using ${netCDF_ROOT} as prefix for netCDF requirements of PnetCDF" )
+            break()
+          endif() # found netcdf location
+        endif() # found valid link library location
+      endforeach() # looped over ldflags built with
+    endif() # see if we should use the built-with ldflags
+    list( POP_BACK CMAKE_MESSAGE_INDENT )
+    find_package( netCDF REQUIRED )
+  endif()
+
+  set( PNETCDF_LINK_INTERFACE_LANGUAGES )
+  list( APPEND PNETCDF_LINK_INTERFACE_LANGUAGES C )
+  if ( ${PnetCDF_HAS_CXX} )
+    list( APPEND PNETCDF_LINK_INTERFACE_LANGUAGES CXX )
+  endif()
+  if( ${PnetCDF_HAS_FORTRAN} )
+    list( APPEND PNETCDF_LINK_INTERFACE_LANGUAGES Fortran )
+  endif()
+  add_library( PnetCDF::pnetcdf UNKNOWN IMPORTED )
+  set_target_properties(
+                        PnetCDF::pnetcdf
+                        PROPERTIES
+                          IMPORTED_LOCATION                   "${PnetCDF_LIBRARY}"
+                          IMPORTED_LINK_INTERFACE_LANGUAGES   "${PNETCDF_LINK_INTERFACE_LANGUAGES}"
+                          INTERFACE_INCLUDE_DIRECTORIES       "${PnetCDF_INCLUDE_DIRS}"
+                        )
+  if ( ${PnetCDF_HAS_NETCDF4} )
+    target_link_libraries( PnetCDF::pnetcdf INTERFACE netCDF::netcdf )
+  endif()
+endif()
+
+mark_as_advanced( PnetCDF_FLIBS PnetCDF_PREFIX PnetCDF_LIBRARY_DIR )
@@ -59,7 +59,7 @@ if ( ${netCDF_HAS_PARALLEL} AND ${USE_MPI} )
   add_subdirectory( io_netcdfpar     )
 endif()
 
-if ( ${pnetCDF_FOUND} )
+if ( ${PnetCDF_FOUND} )
   message( STATUS "Adding [io_pnetcdf] to configuration" )
   add_subdirectory( io_pnetcdf       )
 endif()

@@ -18,19 +18,18 @@ set_target_properties(
 
 target_link_libraries(  ${FOLDER_COMPILE_TARGET}
                           PRIVATE
-                            ${netCDF_LIBRARIES}
-                            ${pnetCDF_LIBRARIES}
                             $<$<BOOL:${USE_MPI}>:$<TARGET_NAME_IF_EXISTS:MPI::MPI_Fortran>>
                             $<$<BOOL:${USE_OPENMP}>:$<TARGET_NAME_IF_EXISTS:OpenMP::OpenMP_Fortran>>
+                            PnetCDF::pnetcdf
                         )
 
 target_include_directories( ${FOLDER_COMPILE_TARGET}
+                            PUBLIC
+                              $<TARGET_PROPERTY:${FOLDER_COMPILE_TARGET},Fortran_MODULE_DIRECTORY>
+                              $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/external/ioapi_share>
+                              $<INSTALL_INTERFACE:include/external/ioapi_share>
                             PRIVATE
-                              ${netCDF_INCLUDE_DIRS}
-                              ${pnetCDF_INCLUDE_DIRS}
                               ${CMAKE_CURRENT_SOURCE_DIR}
-                              ${CMAKE_CURRENT_SOURCE_DIR}/../ioapi_share
-                              ${CMAKE_INSTALL_PREFIX}/${FOLDER_COMPILE_TARGET}
                             )
 
 

@@ -38,7 +38,7 @@
   use ext_pnc_support_routines
   implicit none
   include 'wrf_status_codes.h'
-#  include "pnetcdf.inc"
+  include "pnetcdf.inc"
   integer               ,intent(in)     :: DataHandle
   character*(*)         ,intent(in)     :: Element
   TYPE_DATA