Merge branch 'develop' of https://github.com/HDFGroup/hdf5 into nvidi…

…a_compiler_config Adjust nvhpc compiler flags.
HDFGroup · Oct 12, 2023 · 2f5d6cf · 2f5d6cf
2 parents 82f4c88 + 85c1762
commit 2f5d6cf
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Showing 115 changed files with 8,177 additions and 5,398 deletions.
diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -58,9 +58,7 @@ jobs:
           -DCMAKE_TOOLCHAIN_FILE=config/toolchain/intel.cmake \
           -DMKL_ROOT="/opt/intel/oneapi/mkl/latest" \
           -DTBB_ROOT="/opt/intel/oneapi/tbb/latest" \
-          -DBUILD_SZIP_WITH_FETCHCONTENT=ON \
           -DLIBAEC_USE_LOCALCONTENT=OFF \
-          -DBUILD_ZLIB_WITH_FETCHCONTENT=ON \
           -DZLIB_USE_LOCALCONTENT=OFF \
           -DHDF5_BUILD_FORTRAN=OFF \
           $GITHUB_WORKSPACE

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -184,9 +184,7 @@ jobs:
             -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} \
             -DHDF5_BUILD_JAVA=${{ matrix.java }} \
             -DHDF5_BUILD_DOC=${{ matrix.docs }} \
-            -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} \
             -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} \
-            -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} \
             -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} \
             -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} \
             -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} \
@@ -213,9 +211,7 @@ jobs:
             -DHDF5_BUILD_JAVA:BOOL=OFF \
             -DHDF5_BUILD_HL_LIB:BOOL=OFF \
             -DHDF5_BUILD_DOC=OFF \
-            -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} \
             -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} \
-            -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} \
             -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} \
             -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} \
             -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} \

diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
@@ -13,30 +13,24 @@ option (USE_LIBAEC_STATIC "Use static AEC library " OFF)
 option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0)
 option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0)
 
-option (BUILD_ZLIB_WITH_FETCHCONTENT "Use FetchContent to use original source files" OFF)
-if (BUILD_ZLIB_WITH_FETCHCONTENT)
-  set (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 1)
-  if (NOT ZLIB_USE_LOCALCONTENT)
-    set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_ORIGNAME})
-  else ()
-    set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_ORIGNAME})
-  endif ()
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "Filter ZLIB file is ${ZLIB_URL}")
-  endif ()
+set (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 1)
+if (NOT ZLIB_USE_LOCALCONTENT)
+  set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_NAME})
+else ()
+  set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
+endif ()
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
+  message (VERBOSE "Filter ZLIB file is ${ZLIB_URL}")
 endif ()
 
-option (BUILD_SZIP_WITH_FETCHCONTENT "Use FetchContent to use original source files" OFF)
-if (BUILD_SZIP_WITH_FETCHCONTENT)
-  set (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 1)
-  if (NOT LIBAEC_USE_LOCALCONTENT)
-    set (SZIP_URL ${LIBAEC_TGZ_ORIGPATH}/${LIBAEC_TGZ_ORIGNAME})
-  else ()
-    set (SZIP_URL ${TGZPATH}/${LIBAEC_TGZ_ORIGNAME})
-  endif ()
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "Filter SZIP file is ${SZIP_URL}")
-  endif ()
+set (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 1)
+if (NOT LIBAEC_USE_LOCALCONTENT)
+  set (SZIP_URL ${LIBAEC_TGZ_ORIGPATH}/${LIBAEC_TGZ_NAME})
+else ()
+  set (SZIP_URL ${TGZPATH}/${LIBAEC_TGZ_NAME})
+endif ()
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
+  message (VERBOSE "Filter SZIP file is ${SZIP_URL}")
 endif ()
 
 include (ExternalProject)
@@ -55,18 +49,12 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
     if (NOT TGZPATH)
       set (TGZPATH ${HDF5_SOURCE_DIR})
     endif ()
-    if (NOT BUILD_ZLIB_WITH_FETCHCONTENT)
-      set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
-    endif ()
     if (ZLIB_USE_LOCALCONTENT)
       if (NOT EXISTS "${ZLIB_URL}")
         set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
         message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
       endif ()
     endif ()
-    if (NOT BUILD_SZIP_WITH_FETCHCONTENT)
-      set (SZIP_URL ${TGZPATH}/${SZAEC_TGZ_NAME})
-    endif ()
     if (LIBAEC_USE_LOCALCONTENT)
       if (NOT EXISTS "${SZIP_URL}")
         set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
@@ -97,12 +85,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
         set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_LIBRARIES})
       endif ()
     else ()
-      if (BUILD_ZLIB_WITH_FETCHCONTENT)
-        # Only tgz files available
-        ORIGINAL_ZLIB_LIBRARY ("TGZ")
-        message (VERBOSE "HDF5_ZLIB is built from fetch content")
-        set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
-      elseif (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+      if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
         EXTERNAL_ZLIB_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
         message (VERBOSE "Filter HDF5_ZLIB is built")
         set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
@@ -153,13 +136,7 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
       set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
     endif ()
   else ()
-    if (BUILD_SZIP_WITH_FETCHCONTENT)
-      # Only tgz files available
-      ORIGINAL_SZIP_LIBRARY ("TGZ" ${HDF5_ENABLE_SZIP_ENCODING})
-      message (VERBOSE "SZIP is built from fetch content")
-      message (VERBOSE "... with library AEC")
-      set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
-    elseif (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+    if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
       EXTERNAL_SZIP_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT} ${HDF5_ENABLE_SZIP_ENCODING})
       message (VERBOSE "Filter SZIP is built")
       message (VERBOSE "... with library AEC")

diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -335,7 +335,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
       set (CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
       set (CPACK_PACKAGE_INSTALL_REGISTRY_KEY "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
     endif ()
-    # set the install/unistall icon used for the installer itself
+    # set the install/uninstall icon used for the installer itself
     # There is a bug in NSI that does not handle full unix paths properly.
     set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
     set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -450,6 +450,12 @@ include (${HDF_RESOURCES_DIR}/ConfigureChecks.cmake)
 
 set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
 
+#-----------------------------------------------------------------------------
+# Include directories in the source or build tree should come before other
+# directories to prioritize headers in the sources over installed ones.
+#-----------------------------------------------------------------------------
+set(CMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE ON)
+
 #-----------------------------------------------------------------------------
 # Mac OS X Options
 #-----------------------------------------------------------------------------
@@ -671,6 +677,12 @@ if (HDF5_ENABLE_PARALLEL)
   find_package(MPI REQUIRED)
   if (MPI_C_FOUND)
     set (H5_HAVE_PARALLEL 1)
+
+    # Require MPI standard 3.0 and greater
+    if (MPI_VERSION LESS 3)
+      message (FATAL_ERROR "HDF5 requires MPI standard 3.0 or greater")
+    endif ()
+
     # MPI checks, only do these if MPI_C_FOUND is true, otherwise they always fail
     # and once set, they are cached as false and not regenerated
     set (CMAKE_REQUIRED_LIBRARIES "${MPI_C_LIBRARIES}")
@@ -723,6 +735,9 @@ set (HDF5_SRC_INCLUDE_DIRS
 )
 option (HDF5_ENABLE_SUBFILING_VFD "Build Parallel HDF5 Subfiling VFD" OFF)
 if (HDF5_ENABLE_SUBFILING_VFD)
+  if (WIN32)
+    message (FATAL_ERROR " **** Subfiling is not supported on Windows **** ")
+  endif ()
   if (NOT HDF5_ENABLE_PARALLEL)
     message (FATAL_ERROR "Subfiling VFD requires a parallel HDF5 build")
   else ()
@@ -731,7 +746,7 @@ if (HDF5_ENABLE_SUBFILING_VFD)
     if (NOT H5_HAVE_MPI_Comm_split_type)
       message (FATAL_ERROR "Subfiling VFD requires MPI-3 support for MPI_Comm_split_type")
     endif ()
-  endif()
+  endif ()
 
   if (NOT DEFINED Threads_FOUND)
     set (THREADS_PREFER_PTHREAD_FLAG ON)
@@ -855,13 +870,6 @@ option (HDF5_PACKAGE_EXTLIBS "CPACK - include external libraries" OFF)
 if (NOT HDF5_EXTERNALLY_CONFIGURED)
   if (HDF5_PACKAGE_EXTLIBS)
     set (HDF5_NO_PACKAGES OFF CACHE BOOL "CPACK - Disable packaging" FORCE)
-    if (HDF5_ENABLE_Z_LIB_SUPPORT AND ZLIB_FOUND AND NOT BUILD_ZLIB_WITH_FETCHCONTENT)
-      PACKAGE_ZLIB_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
-    endif ()
-
-    if (HDF5_ENABLE_SZIP_SUPPORT AND SZIP_FOUND AND NOT BUILD_SZIP_WITH_FETCHCONTENT)
-      PACKAGE_SZIP_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
-    endif ()
   endif ()
 endif ()
 
@@ -872,8 +880,9 @@ option (HDF5_ENABLE_THREADSAFE "Enable thread-safety" OFF)
 if (HDF5_ENABLE_THREADSAFE)
   # check for unsupported options
   if (WIN32)
-    message (VERBOSE " **** thread-safety option not supported with static library **** ")
-    message (VERBOSE " **** thread-safety option will not be used building static library **** ")
+    if (BUILD_STATIC_LIBS)
+      message (FATAL_ERROR " **** thread-safety option not supported with static library **** ")
+    endif ()
   endif ()
   if (HDF5_BUILD_FORTRAN)
     if (NOT ALLOW_UNSUPPORTED)
@@ -955,100 +964,7 @@ endif ()
 #-----------------------------------------------------------------------------
 option (BUILD_TESTING "Build HDF5 Unit Testing" ON)
 if (BUILD_TESTING)
-  set (DART_TESTING_TIMEOUT 1200
-      CACHE STRING
-      "Timeout in seconds for each test (default 1200=20minutes)"
-  )
-
-  # Generate a list of timeouts based on DART_TESTING_TIMEOUT
-  math (EXPR CTEST_SHORT_TIMEOUT "${DART_TESTING_TIMEOUT} / 2")
-  math (EXPR CTEST_LONG_TIMEOUT "${DART_TESTING_TIMEOUT} * 2")
-  math (EXPR CTEST_VERY_LONG_TIMEOUT "${DART_TESTING_TIMEOUT} * 3")
-
-  option (HDF5_TEST_API "Execute HDF5 API tests" OFF)
-  mark_as_advanced (HDF5_TEST_API)
-  if (HDF5_TEST_API)
-    option (HDF5_TEST_API_INSTALL "Install HDF5 API tests" OFF)
-    mark_as_advanced (HDF5_TEST_API_INSTALL)
-
-    # Enable HDF5 Async API tests
-    option (HDF5_TEST_API_ENABLE_ASYNC "Enable HDF5 Async API tests" OFF)
-    mark_as_advanced (HDF5_TEST_API_ENABLE_ASYNC)
-
-    # Build and use HDF5 test driver program for API tests
-    option (HDF5_TEST_API_ENABLE_DRIVER "Enable HDF5 API test driver program" OFF)
-    mark_as_advanced (HDF5_TEST_API_ENABLE_DRIVER)
-    if (HDF5_TEST_API_ENABLE_DRIVER)
-      set (HDF5_TEST_API_SERVER "" CACHE STRING "Server executable for running API tests")
-      mark_as_advanced (HDF5_TEST_API_SERVER)
-    endif ()
-  endif ()
-
-  option (HDF5_TEST_VFD "Execute tests with different VFDs" OFF)
-  mark_as_advanced (HDF5_TEST_VFD)
-  if (HDF5_TEST_VFD)
-    option (HDF5_TEST_FHEAP_VFD "Execute tests with different VFDs" ON)
-    mark_as_advanced (HDF5_TEST_FHEAP_VFD)
-
-    # Initialize the list of VFDs to be used for testing and create a test folder for each VFD
-    H5_SET_VFD_LIST()
-  endif ()
-
-  option (HDF5_TEST_PASSTHROUGH_VOL "Execute tests with different passthrough VOL connectors" OFF)
-  mark_as_advanced (HDF5_TEST_PASSTHROUGH_VOL)
-  if (HDF5_TEST_PASSTHROUGH_VOL)
-    option (HDF5_TEST_FHEAP_PASSTHROUGH_VOL "Execute fheap test with different passthrough VOL connectors" ON)
-    mark_as_advanced (HDF5_TEST_FHEAP_PASSTHROUGH VOL)
-  endif ()
-
-  set (H5_TEST_EXPRESS_LEVEL_DEFAULT "3")
-  set (HDF_TEST_EXPRESS "${H5_TEST_EXPRESS_LEVEL_DEFAULT}"
-      CACHE STRING "Control testing framework (0-3) (0 = exhaustive testing; 3 = quicker testing)")
-  mark_as_advanced (HDF_TEST_EXPRESS)
-  if (NOT "${HDF_TEST_EXPRESS}" STREQUAL "")
-    set (H5_TEST_EXPRESS_LEVEL_DEFAULT "${HDF_TEST_EXPRESS}")
-  endif ()
-
-  enable_testing ()
-  include (CTest)
-
-  include (${HDF5_SOURCE_DIR}/CTestConfig.cmake)
-  configure_file (${HDF_RESOURCES_DIR}/CTestCustom.cmake ${HDF5_BINARY_DIR}/CTestCustom.ctest @ONLY)
-
-  option (HDF5_TEST_SERIAL "Execute non-parallel tests" ON)
-  mark_as_advanced (HDF5_TEST_SERIAL)
-
-  option (HDF5_TEST_TOOLS "Execute tools tests" ON)
-  mark_as_advanced (HDF5_TEST_TOOLS)
-
-  option (HDF5_TEST_EXAMPLES "Execute tests on examples" ON)
-  mark_as_advanced (HDF5_TEST_EXAMPLES)
-
-  option (HDF5_TEST_SWMR "Execute SWMR tests" ON)
-  mark_as_advanced (HDF5_TEST_SWMR)
-
-  option (HDF5_TEST_PARALLEL "Execute parallel tests" ON)
-  mark_as_advanced (HDF5_TEST_PARALLEL)
-
-  option (HDF5_TEST_FORTRAN "Execute fortran tests" ON)
-  mark_as_advanced (HDF5_TEST_FORTRAN)
-
-  option (HDF5_TEST_CPP "Execute cpp tests" ON)
-  mark_as_advanced (HDF5_TEST_CPP)
-
-  option (HDF5_TEST_JAVA "Execute java tests" ON)
-  mark_as_advanced (HDF5_TEST_JAVA)
-
-  if (NOT HDF5_EXTERNALLY_CONFIGURED)
-    if (EXISTS "${HDF5_TEST_SRC_DIR}" AND IS_DIRECTORY "${HDF5_TEST_SRC_DIR}")
-      add_subdirectory (test)
-    endif ()
-    if (H5_HAVE_PARALLEL)
-      if (EXISTS "${HDF5_TEST_PAR_DIR}" AND IS_DIRECTORY "${HDF5_TEST_PAR_DIR}")
-        add_subdirectory (testpar)
-      endif ()
-    endif ()
-  endif ()
+  include (CMakeTests.cmake)
 endif ()
 
 #-----------------------------------------------------------------------------

diff --git a/CMakePlugins.cmake b/CMakePlugins.cmake
@@ -9,27 +9,41 @@
 # If you do not have access to either file, you may request a copy from
 # [email protected].
 #
+option (PLUGIN_USE_EXTERNAL "Use External Library Building for filter PLUGIN" 0)
+
+set (PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGIN" 1)
+if (NOT PLUGIN_USE_LOCALCONTENT)
+  set (PLUGIN_URL ${PLUGIN_TGZ_ORIGPATH}/${PLUGIN_TGZ_NAME})
+else ()
+  if (NOT H5PL_TGZPATH)
+    set (H5PL_TGZPATH ${TGZPATH})
+  endif ()
+  set (PLUGIN_URL ${H5PL_TGZPATH}/${PLUGIN_TGZ_NAME})
+endif ()
+message (STATUS "Filter PLUGIN file is ${PLUGIN_URL}")
 
 include (ExternalProject)
 #option (HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO")
 set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)")
 set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
 if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
-  option (PLUGIN_USE_EXTERNAL "Use External Library Building for filter PLUGIN" 1)
+  set (PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGIN" 1)
   if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT")
     set (PLUGIN_URL ${PLUGIN_GIT_URL} CACHE STRING "Path to PLUGIN git repository")
     set (PLUGIN_BRANCH ${PLUGIN_GIT_BRANCH})
   elseif (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
-    if (NOT TGZPATH)
-      set (TGZPATH ${HDF5_SOURCE_DIR})
+    if (NOT H5PL_TGZPATH)
+      set (H5PL_TGZPATH ${TGZPATH})
     endif ()
-    set (PLUGIN_URL ${TGZPATH}/${PLUGIN_TGZ_NAME})
-    if (NOT EXISTS "${PLUGIN_URL}")
-      set (HDF5_ENABLE_PLUGIN_SUPPORT OFF CACHE BOOL "" FORCE)
-      message (STATUS "Filter PLUGIN file ${PLUGIN_URL} not found")
+    if (PLUGIN_USE_LOCALCONTENT)
+      if (NOT EXISTS "${PLUGIN_URL}")
+        set (HDF5_ENABLE_PLUGIN_SUPPORT OFF CACHE BOOL "" FORCE)
+        message (VERBOSE "Filter PLUGIN file ${PLUGIN_URL} not found")
+      endif ()
     endif ()
   else ()
     set (PLUGIN_USE_EXTERNAL 0)
+    message (VERBOSE "Filter PLUGIN not built")
   endif ()
 endif ()