Merge pull request #2841 from ZedThree/find_pnetcdf

Pull out `FindPNETCDF` CMake module

.github/workflows/run_tests_ubuntu.yml

@@ -223,7 +223,7 @@ jobs:
 
  strategy:
  matrix:
- hdf5: [ 1.14.0 ]
+ hdf5: [ 1.14.3 ]
  steps:
 
  - uses: actions/checkout@v3

CMakeLists.txt

@@ -893,47 +893,16 @@ if(ENABLE_PARALLEL4 AND ENABLE_HDF5)
 endif()
 
 # Options to enable parallel IO for classic formats with PnetCDF library.
-set(STATUS_PNETCDF "OFF")
+set(STATUS_PNETCDF ${ENABLE_PNETCDF})
+set(USE_PNETCDF ${ENABLE_PNETCDF})
 if(ENABLE_PNETCDF)
- # Check for ncmpi_create in libpnetcdf, define USE_PNETCDF
- # Does the user want to turn on PnetCDF read ability?
- set(USE_PNETCDF ON CACHE BOOL "")
- if(NOT PNETCDF)
- message(STATUS "Cannot find PnetCDF library. Disabling PnetCDF support.")
- set(USE_PNETCDF OFF CACHE BOOL "")
- else(NOT PNETCDF)
- set(USE_PARALLEL ON CACHE BOOL "")
-
- # Check PnetCDF version. Must be >= 1.6.0
- set(pnetcdf_h "${PNETCDF_INCLUDE_DIR}/pnetcdf.h" )
- message(STATUS "PnetCDF include file ${pnetcdf_h} will be searched for version")
- file(STRINGS "${pnetcdf_h}" pnetcdf_major_string REGEX "^#define PNETCDF_VERSION_MAJOR")
- string(REGEX REPLACE "[^0-9]" "" pnetcdf_major "${pnetcdf_major_string}")
- file(STRINGS "${pnetcdf_h}" pnetcdf_minor_string REGEX "^#define PNETCDF_VERSION_MINOR")
- string(REGEX REPLACE "[^0-9]" "" pnetcdf_minor "${pnetcdf_minor_string}")
- file(STRINGS "${pnetcdf_h}" pnetcdf_sub_string REGEX "^#define PNETCDF_VERSION_SUB")
- string(REGEX REPLACE "[^0-9]" "" pnetcdf_sub "${pnetcdf_sub_string}")
- set(pnetcdf_version "${pnetcdf_major}.${pnetcdf_minor}.${pnetcdf_sub}")
- message(STATUS "Found PnetCDF version ${pnetcdf_version}")
-
- if(${pnetcdf_version} VERSION_GREATER "1.6.0")
- set(STATUS_PNETCDF "ON")
- include_directories(${PNETCDF_INCLUDE_DIR})
- set(HAVE_LIBPNETCDF ON)
- # PnetCDF => parallel
- set(STATUS_PARALLEL ON)
- set(USE_PARALLEL ON)
- message(STATUS "Using PnetCDF Library: ${PNETCDF}")
- else()
- message(WARNING "ENABLE_PNETCDF requires version 1.6.1 or later; found version ${pnetcdf_version}. PnetCDF is disabled")
- endif()
-
+ set(STATUS_PARALLEL ON)
+ set(USE_PARALLEL ON CACHE BOOL "")
  ### 
- # Generate pnetcdf test. 
+ # Generate pnetcdf test
  ###
  configure_file("${netCDF_SOURCE_DIR}/nc_test/run_pnetcdf_tests.sh.in"
  "${netCDF_BINARY_DIR}/nc_test/run_pnetcdf_tests.sh")
- endif(NOT PNETCDF)
 endif()
 
 # Options to enable use of fill values for elements causing NC_ERANGE
@@ -956,38 +925,19 @@ endif(ENABLE_ERANGE_FILL)
 set(ENABLE_ZERO_LENGTH_COORD_BOUND ON)
 
 # check and conform with PnetCDF settings on ERANGE_FILL and RELAX_COORD_BOUND
-if(STATUS_PNETCDF)
- file(STRINGS "${pnetcdf_h}" enable_erange_fill_pnetcdf REGEX "^#define PNETCDF_ERANGE_FILL")
- string(REGEX REPLACE "[^0-9]" "" erange_fill_pnetcdf "${enable_erange_fill_pnetcdf}")
- if("x${erange_fill_pnetcdf}" STREQUAL "x1")
- set(erange_fill_pnetcdf "ON")
- else()
- set(erange_fill_pnetcdf "OFF")
- endif()
+if(USE_PNETCDF)
  if(ENABLE_ERANGE_FILL STREQUAL "AUTO") # not set on command line
- set(ENABLE_ERANGE_FILL "${erange_fill_pnetcdf}")
+ set(ENABLE_ERANGE_FILL "${PNETCDF_HAS_ERANGE_FILL}")
  else()
  # user explicitly set this option on command line
- if(NOT ENABLE_ERANGE_FILL STREQUAL "${erange_fill_pnetcdf}")
+ if(NOT ENABLE_ERANGE_FILL STREQUAL "${PNETCDF_HAS_ERANGE_FILL}")
  if(ENABLE_ERANGE_FILL)
  message(FATAL_ERROR "Enabling erange-fill conflicts with PnetCDF setting")
  else()
  message(FATAL_ERROR "Disabling erange-fill conflicts with PnetCDF setting")
  endif()
  endif()
  endif()
-
- file(STRINGS "${pnetcdf_h}" relax_coord_bound_pnetcdf REGEX "^#define PNETCDF_RELAX_COORD_BOUND")
- string(REGEX REPLACE "[^0-9]" "" relax_coord_bound "${relax_coord_bound_pnetcdf}")
- if("x${relax_coord_bound}" STREQUAL "x1")
- set(relax_coord_bound_pnetcdf "ON")
- else()
- set(relax_coord_bound_pnetcdf "OFF")
- endif()
- # pnetcdf must have relaxed coord bounds to build with netCDF-4
- if(NOT ENABLE_ZERO_LENGTH_COORD_BOUND STREQUAL "${relax_coord_bound_pnetcdf}")
- message(FATAL_ERROR "Pnetcdf must be built with relax-coord-bound enabled")
- endif()
 endif()
 
 if(ENABLE_ERANGE_FILL)

cmake/dependencies.cmake

@@ -446,20 +446,18 @@ endif(ENABLE_LIBXML2)
 
 ################################
 # MPI
-################################ 
+################################
 if(ENABLE_PARALLEL4 OR HDF5_PARALLEL)
  find_package(MPI REQUIRED)
 endif()
 
 ################################
-# parallel IO
+# Parallel IO
 ################################ 
 if(ENABLE_PNETCDF)
- find_library(PNETCDF NAMES pnetcdf)
- find_path(PNETCDF_INCLUDE_DIR pnetcdf.h)
- if(NOT PNETCDF)
- message(STATUS "Cannot find PnetCDF library. Disabling PnetCDF support.")
- set(USE_PNETCDF OFF CACHE BOOL "")
+ find_package(PNETCDF 1.6.0 REQUIRED)
+ if(NOT PNETCDF_HAS_RELAXED_COORD_BOUND)
+ message(FATAL_ERROR "Pnetcdf must be built with relax-coord-bound enabled")
  endif()
 endif()
 

cmake/modules/FindPNETCDF.cmake

@@ -0,0 +1,80 @@
+# FindPNETCDF
+# -----------
+#
+# Find parallel IO library for classic netCDF files
+#
+# This module will define the following variables:
+#
+# ::
+#
+# PNETCDF_FOUND
+# PNETCDF_INCLUDE_DIRS
+# PNETCDF_LIBRARIES
+# PNETCDF_VERSION
+# PNETCDF_HAS_ERANGE_FILL - True if PnetCDF was built with ``NC_ERANGE`` support`
+# PNETCDF_HAS_RELAXED_COORD_BOUND - True if PnetCDF was built with relaxed coordinate bounds
+#
+# The ``PNETCDF::pnetcdf`` target will also be exported
+
+include(FindPackageHandleStandardArgs)
+
+find_path(PNETCDF_INCLUDE_DIR NAMES pnetcdf.h)
+find_library(PNETCDF_LIBRARY NAMES pnetcdf)
+
+if (PNETCDF_INCLUDE_DIR)
+ set(pnetcdf_h "${PNETCDF_INCLUDE_DIR}/pnetcdf.h" )
+ message(DEBUG "PnetCDF include file ${pnetcdf_h} will be searched for version")
+ file(STRINGS "${pnetcdf_h}" pnetcdf_major_string REGEX "^#define PNETCDF_VERSION_MAJOR")
+ string(REGEX REPLACE "[^0-9]" "" pnetcdf_major "${pnetcdf_major_string}")
+ file(STRINGS "${pnetcdf_h}" pnetcdf_minor_string REGEX "^#define PNETCDF_VERSION_MINOR")
+ string(REGEX REPLACE "[^0-9]" "" pnetcdf_minor "${pnetcdf_minor_string}")
+ file(STRINGS "${pnetcdf_h}" pnetcdf_sub_string REGEX "^#define PNETCDF_VERSION_SUB")
+ string(REGEX REPLACE "[^0-9]" "" pnetcdf_sub "${pnetcdf_sub_string}")
+ set(pnetcdf_version "${pnetcdf_major}.${pnetcdf_minor}.${pnetcdf_sub}")
+ message(DEBUG "Found PnetCDF version ${pnetcdf_version}")
+endif()
+
+message(DEBUG "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ]"
+ " PNETCDF_ROOT = ${PNETCDF_ROOT}"
+ " PNETCDF_INCLUDE_DIR = ${PNETCDF_INCLUDE_DIR}"
+ " PNETCDF_LIBRARY = ${PNETCDF_LIBRARY}"
+ " PNETCDF_VERSION = ${PNETCDF_VERSION}"
+)
+
+file(STRINGS "${pnetcdf_h}" enable_erange_fill_pnetcdf REGEX "^#define PNETCDF_ERANGE_FILL")
+string(REGEX REPLACE "[^0-9]" "" erange_fill_pnetcdf "${enable_erange_fill_pnetcdf}")
+if("${erange_fill_pnetcdf}" STREQUAL "1")
+ set(PNETCDF_HAS_ERANGE_FILL ON CACHE BOOL "")
+else()
+ set(PNETCDF_HAS_ERANGE_FILL OFF CACHE BOOL "")
+endif()
+
+mark_as_advanced(PNETCDF_INCLUDE_DIR PNETCDF_LIBRARY PNETCDF_ERANGE_FILL)
+
+file(STRINGS "${pnetcdf_h}" relax_coord_bound_pnetcdf REGEX "^#define PNETCDF_RELAX_COORD_BOUND")
+string(REGEX REPLACE "[^0-9]" "" relax_coord_bound "${relax_coord_bound_pnetcdf}")
+if ("${relax_coord_bound}" STREQUAL "1")
+ set(PNETCDF_HAS_RELAXED_COORD_BOUND ON CACHE BOOL "")
+else()
+ set(PNETCDF_HAS_RELAXED_COORD_BOUND OFF CACHE BOOL "")
+endif()
+
+find_package_handle_standard_args(PNETCDF
+ REQUIRED_VARS PNETCDF_LIBRARY PNETCDF_INCLUDE_DIR
+ VERSION_VAR PNETCDF_VERSION
+ )
+
+if (PNETCDF_FOUND AND NOT TARGET PNETCDF::PNETCDF)
+ find_package(MPI REQUIRED)
+ add_library(PNETCDF::PNETCDF UNKNOWN IMPORTED)
+ set_target_properties(PNETCDF::PNETCDF PROPERTIES
+ IMPORTED_LINK_INTERFACE_LIBRARIES MPI::MPI_C
+ IMPORTED_LOCATION "${PNETCDF_LIBRARY}"
+ INTERFACE_INCLUDE_DIRECTORIES "${PNETCDF_INCLUDE_DIR}"
+ )
+ find_library(MATH_LIBRARY m)
+ if (MATH_LIBRARY)
+ set_target_properties(PNETCDF::PNETCDF PROPERTIES
+ IMPORTED_LINK_INTERFACE_LIBRARIES ${MATH_LIBRARY})
+ endif()
+endif()

config.h.cmake.in

@@ -301,9 +301,6 @@ are set when opening a binary file on Windows. */
 /* Define to 1 if you have the `mfhdf' library (-lmfhdf). */
 #cmakedefine HAVE_LIBMFHDF 1
 
-/* Define to 1 if you have the `pnetcdf' library (-lpnetcdf). */
-#cmakedefine HAVE_LIBPNETCDF 1
-
 /* Define to 1 if you have the libxml2 library. */
 #cmakedefine ENABLE_LIBXML2 1
 

libdispatch/CMakeLists.txt

@@ -80,7 +80,11 @@ if(STATUS_PARALLEL)
  target_link_libraries(dispatch PUBLIC MPI::MPI_C)
 endif(STATUS_PARALLEL)
 
-if(ENABLE_NCZARR)
+if (ENABLE_PNETCDF)
+ target_link_libraries(dispatch PUBLIC PNETCDF::PNETCDF)
+endif()
+
+IF(ENABLE_NCZARR)
  target_include_directories(dispatch PUBLIC ../libnczarr)
 endif(ENABLE_NCZARR)
 

liblib/CMakeLists.txt

@@ -151,8 +151,8 @@ if(USE_HDF4)
  set(TLL_LIBS ${HDF4_LIBRARIES} ${TLL_LIBS})
 endif()
 
-if(ENABLE_PNETCDF AND PNETCDF)
- set(TLL_LIBS ${TLL_LIBS} ${PNETCDF})
+if(ENABLE_PNETCDF)
+ SET(TLL_LIBS ${TLL_LIBS} PNETCDF::PNETCDF)
 endif()
 
 
@@ -188,6 +188,7 @@ target_link_libraries(netcdf PRIVATE ${TLL_LIBS})
 set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${TLL_LIBS})
 if(MSVC)
  set_target_properties(netcdf PROPERTIES
+
  LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
  )
 endif()

libsrcp/CMakeLists.txt

@@ -6,6 +6,7 @@
 # See netcdf-c/COPYRIGHT file for more info.
 
 add_library(netcdfp OBJECT ${libsrcp_SOURCES})
+target_link_libraries(netcdfp PUBLIC PNETCDF::PNETCDF)
 
 target_sources(netcdfp PRIVATE ncpdispatch.c)
 

nc_test/CMakeLists.txt

@@ -33,6 +33,7 @@ TARGET_INCLUDE_DIRECTORIES(nc_test PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
 TARGET_LINK_LIBRARIES(nc_test
  netcdf
  ${HAVE_LIBM}
+ ${ALL_TLL_LIBS}
  )
 
 ##