harmonize HDF5 build with h5fortran

Author: scivision

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.21...3.30)
+cmake_minimum_required(VERSION 3.21...4.2)
 
 if(CMAKE_SOURCE_DIR STREQUAL CMAKE_BINARY_DIR)
   message(FATAL_ERROR "please use out-of-source build
@@ -28,7 +28,7 @@ endif()
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 # --- avoid Anaconda libraries
-if(DEFINED ENV{CONDA_PREFIX})
+if(DEFINED ENV{CONDA_PREFIX} AND h5fortran_IGNORE_CONDA_LIBRARIES)
   list(APPEND CMAKE_IGNORE_PREFIX_PATH $ENV{CONDA_PREFIX})
   list(APPEND CMAKE_IGNORE_PATH $ENV{CONDA_PREFIX}/bin)
   # need CMAKE_IGNORE_PATH for CMake < 3.23
@@ -44,7 +44,7 @@ if(hdf5_parallel)
   include(cmake/check_mpi.cmake)
   check_mpi_version()
 
-  if(find_hdf5)
+  if(h5fortran_find)
     find_package(HDF5 COMPONENTS Fortran parallel)
   endif()
 
@@ -58,7 +58,7 @@ if(hdf5_parallel)
     include(cmake/hdf5.cmake)
   endif()
 else()
-  if(find_hdf5)
+  if(h5fortran_find)
     find_package(HDF5 COMPONENTS Fortran)
   endif()
   if(NOT HDF5_FOUND)
@@ -67,6 +67,13 @@ else()
   set(hdf5_parallel_compression ".false.")
 endif()
 
+if(WIN32 AND CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
+if(HDF5_VERSION MATCHES "(1\.14\.[2-6]|2\.0\.0)")
+  message(STATUS "HDF5: applying workaround for HDF5 bug #3663 with Intel oneAPI on Windows")
+  target_link_libraries(HDF5::HDF5 INTERFACE shlwapi)
+endif()
+endif()
+
 # --- h5fortran library
 
 configure_file(src/hdf5_config.f90.in hdf5_config.f90 @ONLY)

cmake/ExtProj.cmake

@@ -182,16 +182,19 @@ if(hdf5_have_zlib)
     NAMES szip sz
     NAMES_PER_DIR
     HINTS ${SZIP_ROOT} ${ZLIB_ROOT}
+    PATH_SUFFIXES lib lib64
     DOC "SZIP API"
     )
 
     find_path(SZIP_INCLUDE_DIR
     NAMES szlib.h
     HINTS ${SZIP_ROOT} ${ZLIB_ROOT}
+    PATH_SUFFIXES include
     DOC "SZIP header"
     )
 
-    if(NOT SZIP_LIBRARY AND SZIP_INCLUDE_DIR)
+    if(NOT (SZIP_LIBRARY AND SZIP_INCLUDE_DIR))
+      message(VERBOSE "FindHDF5: SZIP not found, but HDF5 indicates it was built with SZIP. This may cause build errors.")
       return()
     endif()
 
@@ -303,6 +306,14 @@ if(HDF5_ROOT)
   HINTS ${HDF5_C_INCLUDE_DIR} ${HDF5_ROOT}
   DOC "HDF5 Fortran module path"
   )
+
+  find_path(HDF5_Fortran_HL_INCLUDE_DIR
+  NAMES h5lt.mod
+  NO_DEFAULT_PATH
+  HINTS ${HDF5_Fortran_INCLUDE_DIR}
+  DOC "HDF5 Fortran HL module path"
+  PATH_SUFFIXES ${hdf5_msuf_hl}
+  )
 else()
   if(HDF5_parallel_FOUND)
     # HDF5-MPI system library presents a unique challenge, as when non-MPI HDF5 is
@@ -312,19 +323,29 @@ else()
     # search in a for loop and do a link check.
     if(NOT HDF5_Fortran_INCLUDE_DIR)
       foreach(i IN LISTS HDF5_C_INCLUDE_DIR hdf5_inc_dirs)
+
         find_path(HDF5_Fortran_INCLUDE_DIR
         NAMES hdf5.mod
         NO_DEFAULT_PATH
         HINTS ${i}
         DOC "HDF5 Fortran module path"
         )
-        message(VERBOSE "FindHDF5: trying hdf5.mod in ${i} - got: ${HDF5_Fortran_INCLUDE_DIR}")
-        if(HDF5_Fortran_INCLUDE_DIR)
+
+        find_path(HDF5_Fortran_HL_INCLUDE_DIR
+        NAMES h5lt.mod
+        NO_DEFAULT_PATH
+        HINTS ${HDF5_Fortran_INCLUDE_DIR}
+        DOC "HDF5 Fortran HL module path"
+        PATH_SUFFIXES ${hdf5_msuf_hl}
+        )
+        message(VERBOSE "FindHDF5: trying hdf5.mod in ${i} - got: ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_Fortran_HL_INCLUDE_DIR}")
+        if(HDF5_Fortran_INCLUDE_DIR AND HDF5_Fortran_HL_INCLUDE_DIR)
           check_fortran_links()
           if(HDF5_Fortran_links)
             break()
           else()
             unset(HDF5_Fortran_INCLUDE_DIR CACHE)
+            unset(HDF5_Fortran_HL_INCLUDE_DIR CACHE)
             unset(HDF5_Fortran_links CACHE)
           endif()
         endif()
@@ -340,6 +361,14 @@ else()
       PATH_SUFFIXES ${hdf5_msuf}
       DOC "HDF5 Fortran module path"
       )
+
+      find_path(HDF5_Fortran_HL_INCLUDE_DIR
+      NAMES h5lt.mod
+      NO_DEFAULT_PATH
+      HINTS ${HDF5_Fortran_INCLUDE_DIR}
+      DOC "HDF5 Fortran HL module path"
+      PATH_SUFFIXES ${hdf5_msuf_hl}
+      )
     endif()
   else()
     find_path(HDF5_Fortran_INCLUDE_DIR
@@ -349,6 +378,14 @@ else()
     PATH_SUFFIXES ${hdf5_msuf}
     DOC "HDF5 Fortran module path"
     )
+
+    find_path(HDF5_Fortran_HL_INCLUDE_DIR
+    NAMES h5lt.mod
+    NO_DEFAULT_PATH
+    HINTS ${HDF5_Fortran_INCLUDE_DIR}
+    DOC "HDF5 Fortran HL module path"
+    PATH_SUFFIXES ${hdf5_msuf_hl}
+    )
   endif()
 endif()
 
@@ -715,7 +752,7 @@ endfunction(check_c_links)
 function(check_fortran_links)
 
 list(PREPEND CMAKE_REQUIRED_LIBRARIES ${HDF5_Fortran_LIBRARIES} ${HDF5_C_LIBRARIES})
-set(CMAKE_REQUIRED_INCLUDES ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR})
+set(CMAKE_REQUIRED_INCLUDES ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_Fortran_HL_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR})
 
 if(HDF5_parallel_FOUND)
   find_mpi()
@@ -823,9 +860,11 @@ endif()
 if(BUILD_SHARED_LIBS)
   set(hdf5_isuf shared include)
   set(hdf5_msuf shared include)
+  set(hdf5_msuf_hl mod/shared)
 else()
   set(hdf5_isuf static include)
   set(hdf5_msuf static include)
+  set(hdf5_msuf_hl mod/static)
 endif()
 
 # Ubuntu
@@ -901,29 +940,41 @@ HANDLE_COMPONENTS
 )
 
 if(HDF5_FOUND)
-  set(HDF5_INCLUDE_DIRS ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_CXX_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR})
+  set(HDF5_INCLUDE_DIRS ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_Fortran_HL_INCLUDE_DIR} ${HDF5_CXX_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR})
   set(HDF5_LIBRARIES ${HDF5_Fortran_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${HDF5_C_LIBRARIES})
 
   if(NOT TARGET HDF5::HDF5)
     add_library(HDF5::HDF5 INTERFACE IMPORTED)
     set_property(TARGET HDF5::HDF5 PROPERTY INTERFACE_LINK_LIBRARIES "${HDF5_LIBRARIES}")
     set_property(TARGET HDF5::HDF5 PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${HDF5_INCLUDE_DIRS}")
 
-    target_include_directories(HDF5::HDF5 INTERFACE
-    $<$<BOOL:${hdf5_have_szip}>:${SZIP_INCLUDE_DIR}>
-    )
+    if(hdf5_have_szip)
+      if(IS_DIRECTORY "${SZIP_INCLUDE_DIR}")
+        target_include_directories(HDF5::HDF5 INTERFACE ${SZIP_INCLUDE_DIR})
+      else()
+        message(STATUS "FindHDF5: SZIP_INCLUDE_DIR ${SZIP_INCLUDE_DIR} is not a directory.")
+      endif()
+    endif()
+
+    target_link_libraries(HDF5::HDF5 INTERFACE $<$<BOOL:${hdf5_have_zlib}>:ZLIB::ZLIB>)
+
+    if(hdf5_have_szip)
+      if(EXISTS "${SZIP_LIBRARY}")
+        target_link_libraries(HDF5::HDF5 INTERFACE ${SZIP_LIBRARY})
+      else()
+        message(STATUS "FindHDF5: SZIP_LIBRARY ${SZIP_LIBRARY} is not a file.")
+      endif()
+    endif()
+
     target_link_libraries(HDF5::HDF5 INTERFACE
-    $<$<BOOL:${hdf5_have_zlib}>:ZLIB::ZLIB>
-    $<$<BOOL:${hdf5_have_szip}>:${SZIP_LIBRARY}>
     ${CMAKE_THREAD_LIBS_INIT}
     ${CMAKE_DL_LIBS}
     $<$<BOOL:${UNIX}>:m>
     )
-
   endif()
 endif(HDF5_FOUND)
 
 mark_as_advanced(HDF5_Fortran_LIBRARY HDF5_Fortran_HL_LIBRARY
 HDF5_C_LIBRARY HDF5_C_HL_LIBRARY
 HDF5_CXX_LIBRARY HDF5_CXX_HL_LIBRARY
-HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR HDF5_Fortran_INCLUDE_DIR)
+HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR HDF5_Fortran_INCLUDE_DIR HDF5_Fortran_HL_INCLUDE_DIR)

cmake/FindHDF5.cmake

@@ -30,12 +30,12 @@ try_run(mpi_run_code mpi_build_code
 ${CMAKE_CURRENT_BINARY_DIR}/find_mpi/build
 ${CMAKE_CURRENT_BINARY_DIR}/find_mpi/get_mpi_version.c
 CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:PATH=${MPI_C_INCLUDE_DIRS}"
-# must have quotes as include_dirs is a list
 # LINK_OPTIONS ${MPI_C_LINK_FLAGS}  # breaks CentOS GCC with -Wl,-rpath
 LINK_LIBRARIES ${MPI_C_LIBRARIES}
 RUN_OUTPUT_VARIABLE MPI_VERSION_STRING
 COMPILE_OUTPUT_VARIABLE mpi_vers_build_out
 )
+# CMAKE_FLAGS must have quotes to handles CMake list
 
 if(NOT mpi_build_code)
   message(CHECK_FAIL "MPI_VERSION test failed to build:

cmake/check_mpi.cmake

@@ -1,8 +1,21 @@
+include(CheckSourceCompiles)
+
+# --- not all platforms have ieee_arithmetic e.g. aarch64 GCC
+check_source_compiles(Fortran
+"program a
+use, intrinsic :: ieee_arithmetic, only : ieee_quiet_nan, ieee_value
+real :: NaN
+NaN = ieee_value(0., ieee_quiet_nan)
+end program"
+HAVE_IEEE_ARITH
+)
+
 # --- C compile flags
 if(CMAKE_C_COMPILER_ID MATCHES "Clang|GNU|^Intel")
   add_compile_options(
   "$<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:Debug>>:-Wextra>"
-  "$<$<COMPILE_LANGUAGE:C>:-Wall;-Werror=implicit-function-declaration>"
+  "$<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:Debug,RelWithDebInfo>>:-Wall>"
+  "$<$<COMPILE_LANGUAGE:C>:-Werror=implicit-function-declaration>"
   )
 elseif(CMAKE_C_COMPILER_ID MATCHES "MSVC")
   add_compile_options("$<$<COMPILE_LANGUAGE:C>:/W3>")
@@ -20,7 +33,7 @@ endif()
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
 
 add_compile_options(
-"$<$<COMPILE_LANGUAGE:Fortran>:-warn>"
+"$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug,RelWithDebInfo>>:-warn>"
 "$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:-traceback;-check;-debug>"
 )
 
@@ -33,22 +46,23 @@ endif()
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
 
 add_compile_options(
-"$<$<COMPILE_LANGUAGE:Fortran>:-Wall;-fimplicit-none;-Wno-maybe-uninitialized>"
+"$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug,RelWithDebInfo>>:-Wall>"
+"$<$<COMPILE_LANGUAGE:Fortran>:-fimplicit-none;-Wno-maybe-uninitialized>"
 "$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:-Wextra;-fcheck=all;-Werror=array-bounds>"
 "$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Release>>:-fno-backtrace>"
 )
 
 endif()
 
 # --- code coverage
-if(coverage)
+if(h5fortran_coverage)
   include(${CMAKE_CURRENT_LIST_DIR}/Modules/CodeCoverage.cmake)
   append_coverage_compiler_flags()
   set(COVERAGE_EXCLUDES ${PROJECT_SOURCE_DIR}/test)
 endif()
 
 # --- clang-tidy
-if(tidy)
+if(h5fortran_tidy AND h5fortran_IS_TOP_LEVEL)
   find_program(CLANG_TIDY_EXE NAMES "clang-tidy" REQUIRED)
   set(CMAKE_C_CLANG_TIDY ${CLANG_TIDY_EXE})
   set(CMAKE_CXX_CLANG_TIDY ${CLANG_TIDY_EXE})