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

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This commit is contained in:
Quincey Koziol 2019-04-03 17:27:10 -05:00
commit fc945999d0
170 changed files with 1455 additions and 1019 deletions
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4
CMakeInstallation.cmake
View File

@ -33,7 +33,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
EXPORT ${HDF5_EXPORTED_TARGETS}
DESTINATION ${HDF5_INSTALL_CMAKE_DIR}/hdf5
FILE ${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-targets.cmake
NAMESPACE ${HDF5_PACKAGE}::
NAMESPACE ${HDF_PACKAGE_NAMESPACE}
COMPONENT configinstall
)
endif ()
@ -45,7 +45,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
export (
TARGETS ${HDF5_LIBRARIES_TO_EXPORT} ${HDF5_LIB_DEPENDENCIES} ${HDF5_UTILS_TO_EXPORT}
FILE ${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-targets.cmake
NAMESPACE ${HDF5_PACKAGE}::
NAMESPACE ${HDF_PACKAGE_NAMESPACE}
)
endif ()
endif ()

3
CMakeLists.txt
View File

@ -756,7 +756,7 @@ endif ()
option (BUILD_TESTING "Build HDF5 Unit Testing" ON)
if (BUILD_TESTING)
set (DART_TESTING_TIMEOUT 1200
CACHE INTEGER
CACHE STRING
"Timeout in seconds for each test (default 1200=20minutes)"
)
@ -806,6 +806,7 @@ endif ()
if (EXISTS "${HDF5_SOURCE_DIR}/tools" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/tools")
option (HDF5_BUILD_TOOLS "Build HDF5 Tools" ON)
if (HDF5_BUILD_TOOLS)
option (SKIP_ERROR_STACK_TESTS "Skip HDF5 Tools Error Stack Tests" OFF)
add_subdirectory (tools)
endif ()
endif ()

2
README.txt
View File

@ -1,4 +1,4 @@
HDF5 version 1.11.4 currently under development
HDF5 version 1.11.5 currently under development
------------------------------------------------------------------------------
Please refer to the release_docs/INSTALL file for installation instructions.

2
c++/src/cpp_doc_config
View File

@ -38,7 +38,7 @@ PROJECT_NAME =
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = "1.11.4"
PROJECT_NUMBER = "1.11.5"
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a

4
c++/test/tobject.cpp
View File

@ -609,10 +609,10 @@ static void test_getobjectinfo_same_file()
catch (Exception& E)
{
cerr << " in Exception " << E.getCFuncName() << "detail: " << E.getCDetailMsg() << endl;
issue_fail_msg("test_file_name()", __LINE__, __FILE__, E.getCDetailMsg());
issue_fail_msg("test_getobjectinfo_same_file()", __LINE__, __FILE__, E.getCDetailMsg());
}
} // test_h5o_getinfo_same_file
} // test_getobjectinfo_same_file
/*-------------------------------------------------------------------------
* Function: test_object

2
config/cmake/HDF5_Examples.cmake.in
View File

@ -103,6 +103,8 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_NAME:STRING=@HDF5_PAC
if(WIN32)
include(${CTEST_SCRIPT_DIRECTORY}\\HDF5_Examples_options.cmake)
include(${CTEST_SCRIPT_DIRECTORY}\\CTestScript.cmake)
else()
include(${CTEST_SCRIPT_DIRECTORY}/HDF5_Examples_options.cmake)
include(${CTEST_SCRIPT_DIRECTORY}/CTestScript.cmake)
endif()

103
config/cmake/HDF5_Examples_options.cmake
View File

@ -57,106 +57,3 @@
#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCOMPARE_TESTING:BOOL=ON")
#############################################################################################
# Do not edit below this line
#############################################################################################
#-----------------------------------------------------------------------------
# MAC machines need special option
#-----------------------------------------------------------------------------
if (APPLE)
# Compiler choice
execute_process (COMMAND xcrun --find cc OUTPUT_VARIABLE XCODE_CC OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process (COMMAND xcrun --find c++ OUTPUT_VARIABLE XCODE_CXX OUTPUT_STRIP_TRAILING_WHITESPACE)
set (ENV{CC} "${XCODE_CC}")
set (ENV{CXX} "${XCODE_CXX}")
if (NOT NO_MAC_FORTRAN)
# Shared fortran is not supported, build static
set (BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_ANSI_CFLAGS:STRING=-fPIC")
else ()
set (BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF_BUILD_FORTRAN:BOOL=OFF")
endif ()
set (BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_USE_LAUNCHERS:BOOL=ON -DCMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF")
else ()
set (BUILD_OPTIONS "${ADD_BUILD_OPTIONS}")
endif ()
#-----------------------------------------------------------------------------
set (CTEST_CMAKE_COMMAND "\"${CMAKE_COMMAND}\"")
## --------------------------
if (CTEST_USE_TAR_SOURCE)
## Uncompress source if tar or zip file provided
## --------------------------
if (WIN32)
message (STATUS "extracting... [${CMAKE_EXECUTABLE_NAME} -E tar -xvf ${CTEST_USE_TAR_SOURCE}.zip]")
execute_process (COMMAND ${CMAKE_EXECUTABLE_NAME} -E tar -xvf ${CTEST_DASHBOARD_ROOT}\\${CTEST_USE_TAR_SOURCE}.zip RESULT_VARIABLE rv)
else ()
message (STATUS "extracting... [${CMAKE_EXECUTABLE_NAME} -E tar -xvf ${CTEST_USE_TAR_SOURCE}.tar]")
execute_process (COMMAND ${CMAKE_EXECUTABLE_NAME} -E tar -xvf ${CTEST_DASHBOARD_ROOT}/${CTEST_USE_TAR_SOURCE}.tar RESULT_VARIABLE rv)
endif ()
if (NOT rv EQUAL 0)
message (STATUS "extracting... [error-(${rv}) clean up]")
file (REMOVE_RECURSE "${CTEST_SOURCE_DIRECTORY}")
message (FATAL_ERROR "error: extract of ${CTEST_SOURCE_NAME} failed")
endif ()
endif()
#-----------------------------------------------------------------------------
## Clear the build directory
## --------------------------
set (CTEST_START_WITH_EMPTY_BINARY_DIRECTORY TRUE)
if (EXISTS "${CTEST_BINARY_DIRECTORY}" AND IS_DIRECTORY "${CTEST_BINARY_DIRECTORY}")
ctest_empty_binary_directory (${CTEST_BINARY_DIRECTORY})
else ()
file (MAKE_DIRECTORY "${CTEST_BINARY_DIRECTORY}")
endif ()
# Use multiple CPU cores to build
include (ProcessorCount)
ProcessorCount (N)
if (NOT N EQUAL 0)
if (NOT WIN32)
set (CTEST_BUILD_FLAGS -j${N})
endif ()
set (ctest_test_args ${ctest_test_args} PARALLEL_LEVEL ${N})
endif ()
set (CTEST_CONFIGURE_COMMAND
"${CTEST_CMAKE_COMMAND} -C \"${CTEST_SOURCE_DIRECTORY}/config/cmake/cacheinit.cmake\" -DCMAKE_BUILD_TYPE:STRING=${CTEST_CONFIGURATION_TYPE} ${BUILD_OPTIONS} \"-G${CTEST_CMAKE_GENERATOR}\" \"${CTEST_SOURCE_DIRECTORY}\""
)
#-----------------------------------------------------------------------------
## -- set output to english
set ($ENV{LC_MESSAGES} "en_EN")
#-----------------------------------------------------------------------------
configure_file (${CTEST_SOURCE_DIRECTORY}/config/cmake/CTestCustom.cmake ${CTEST_BINARY_DIRECTORY}/CTestCustom.cmake)
ctest_read_custom_files ("${CTEST_BINARY_DIRECTORY}")
## NORMAL process
## --------------------------
ctest_start (Experimental)
ctest_configure (BUILD "${CTEST_BINARY_DIRECTORY}" RETURN_VALUE res)
if (${res} LESS 0 OR ${res} GREATER 0)
file (APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Configure: ${res}\n")
endif ()
if (LOCAL_SUBMIT)
ctest_submit (PARTS Configure Notes)
endif ()
ctest_build (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND APPEND RETURN_VALUE res NUMBER_ERRORS errval)
if (${res} LESS 0 OR ${res} GREATER 0 OR ${errval} GREATER 0)
file(APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed ${errval} Build: ${res}\n")
endif ()
if (LOCAL_SUBMIT)
ctest_submit (PARTS Build)
endif ()
ctest_test (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND ${ctest_test_args} RETURN_VALUE res)
if (${res} LESS 0 OR ${res} GREATER 0)
file(APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Tests: ${res}\n")
endif ()
if (LOCAL_SUBMIT)
ctest_submit (PARTS Test)
endif ()
if (${res} LESS 0 OR ${res} GREATER 0)
message (FATAL_ERROR "tests FAILED")
endif ()
#-----------------------------------------------------------------------------
##############################################################################################################
message (STATUS "DONE")

2
config/cmake/README.txt.cmake.in
View File

@ -34,9 +34,9 @@ utility should be installed.
To test the installation with the examples;
Create a directory to run the examples.
Copy HDF5Examples folder to this directory.
Copy CTestScript.cmake to this directory.
Copy HDF5_Examples.cmake to this directory.
Copy HDF5_Examples_options.cmake to this directory.
Copy CTestScript.cmake to this directory.
The default source folder is defined as "HDF5Examples". It can be changed
with the CTEST_SOURCE_NAME script option.
The default installation folder is defined as "@CMAKE_INSTALL_PREFIX@".

2
config/cmake/cacheinit.cmake
View File

@ -19,6 +19,8 @@ set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Framework
set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace (can be empty)" FORCE)
set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE)
set (HDF5_BUILD_GENERATORS ON CACHE BOOL "Build Test Generators" FORCE)

4
config/cmake/hdf5-config.cmake.in
View File

@ -108,10 +108,10 @@ set (HDF5_VERSION_MINOR @HDF5_VERSION_MINOR@)
# project which has already built hdf5 as a subproject
#-----------------------------------------------------------------------------
if (NOT TARGET "@HDF5_PACKAGE@")
if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS AND NOT TARGET "zlib")
if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
endif ()
if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS AND NOT TARGET "szip")
if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
endif ()
include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake)

2
config/cmake/mccacheinit.cmake
View File

@ -23,6 +23,8 @@ set (BUILD_TESTING ON CACHE BOOL "Build HDF5 Unit Testing" FORCE)
set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace" FORCE)
set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build HDF5 C++ Library" FORCE)
set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE)

2
config/cmake/scripts/HDF5config.cmake
View File

@ -34,7 +34,7 @@ cmake_minimum_required (VERSION 3.10)
# CTEST_SOURCE_NAME - source folder
##############################################################################
set (CTEST_SOURCE_VERSION "1.11.4")
set (CTEST_SOURCE_VERSION "1.11.5")
set (CTEST_SOURCE_VERSEXT "")
##############################################################################

122
config/cmake_ext_mod/HDFLibMacros.cmake
View File

@ -14,25 +14,7 @@ macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic)
# May need to build JPEG with PIC on x64 machines with gcc
# Need to use CMAKE_ANSI_CFLAGS define so that compiler test works
if (${compress_type} MATCHES "SVN")
EXTERNALPROJECT_ADD (JPEG
SVN_REPOSITORY ${JPEG_URL}
# [SVN_REVISION rev]
INSTALL_COMMAND ""
CMAKE_ARGS
-DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
-DJPEG_PACKAGE_EXT:STRING=${HDF_PACKAGE_EXT}
-DJPEG_EXTERNALLY_CONFIGURED:BOOL=OFF
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
-DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${jpeg_pic}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
)
elseif (${compress_type} MATCHES "GIT")
if (${compress_type} MATCHES "GIT")
EXTERNALPROJECT_ADD (JPEG
GIT_REPOSITORY ${JPEG_URL}
GIT_TAG ${JPEG_BRANCH}
@ -49,6 +31,7 @@ macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic)
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${jpeg_pic}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
elseif (${compress_type} MATCHES "TGZ")
EXTERNALPROJECT_ADD (JPEG
@ -67,23 +50,24 @@ macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic)
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${jpeg_pic}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
endif ()
externalproject_get_property (JPEG BINARY_DIR SOURCE_DIR)
##include (${BINARY_DIR}/${JPEG_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake)
# Create imported target jpeg-static
add_library(jpeg-static STATIC IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (jpeg-static "jpeg" STATIC "")
add_dependencies (jpeg-static JPEG)
set (JPEG_STATIC_LIBRARY "jpeg-static")
add_library(${HDF_PACKAGE_NAMESPACE}jpeg-static STATIC IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}jpeg-static "jpeg" STATIC "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}jpeg-static JPEG)
set (JPEG_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}jpeg-static")
set (JPEG_LIBRARIES ${JPEG_STATIC_LIBRARY})
if (BUILD_SHARED_LIBS)
# Create imported target jpeg-shared
add_library(jpeg-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (jpeg-shared "jpeg" SHARED "")
add_dependencies (jpeg-shared JPEG)
set (JPEG_SHARED_LIBRARY "jpeg-shared")
add_library(${HDF_PACKAGE_NAMESPACE}jpeg-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}jpeg-shared "jpeg" SHARED "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}jpeg-shared JPEG)
set (JPEG_SHARED_LIBRARY "${HDF_PACKAGE_NAMESPACE}jpeg-shared")
set (JPEG_LIBRARIES ${JPEG_LIBRARIES} ${JPEG_SHARED_LIBRARY})
endif ()
@ -100,33 +84,14 @@ macro (PACKAGE_JPEG_LIBRARY compress_type)
COMMENT "Copying ${JPEG_INCLUDE_DIR_GEN}/jconfig.h to ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/"
)
set (EXTERNAL_HEADER_LIST ${EXTERNAL_HEADER_LIST} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/jconfig.h)
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "SVN" OR ${compress_type} MATCHES "TGZ")
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "TGZ")
add_dependencies (JPEG-GenHeader-Copy JPEG)
endif ()
endmacro ()
#-------------------------------------------------------------------------------
macro (EXTERNAL_SZIP_LIBRARY compress_type encoding)
if (${compress_type} MATCHES "SVN")
EXTERNALPROJECT_ADD (SZIP
SVN_REPOSITORY ${SZIP_URL}
# [SVN_REVISION rev]
INSTALL_COMMAND ""
CMAKE_ARGS
-DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
-DSZIP_PACKAGE_EXT:STRING=${HDF_PACKAGE_EXT}
-DSZIP_EXTERNALLY_CONFIGURED:BOOL=OFF
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
-DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DSZIP_ENABLE_ENCODING:BOOL=${encoding}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
)
elseif (${compress_type} MATCHES "GIT")
if (${compress_type} MATCHES "GIT")
EXTERNALPROJECT_ADD (SZIP
GIT_REPOSITORY ${SZIP_URL}
GIT_TAG ${SZIP_BRANCH}
@ -144,6 +109,7 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding)
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DSZIP_ENABLE_ENCODING:BOOL=${encoding}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
elseif (${compress_type} MATCHES "TGZ")
EXTERNALPROJECT_ADD (SZIP
@ -163,23 +129,24 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding)
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DSZIP_ENABLE_ENCODING:BOOL=${encoding}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
endif ()
externalproject_get_property (SZIP BINARY_DIR SOURCE_DIR)
##include (${BINARY_DIR}/${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake)
# Create imported target szip-static
add_library(szip-static STATIC IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (szip-static "szip" STATIC "")
add_dependencies (szip-static SZIP)
set (SZIP_STATIC_LIBRARY "szip-static")
add_library(${HDF_PACKAGE_NAMESPACE}szip-static STATIC IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}szip-static "szip" STATIC "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}szip-static SZIP)
set (SZIP_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}szip-static")
set (SZIP_LIBRARIES ${SZIP_STATIC_LIBRARY})
if (BUILD_SHARED_LIBS)
# Create imported target szip-shared
add_library(szip-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (szip-shared "szip" SHARED "")
add_dependencies (szip-shared SZIP)
set (SZIP_SHARED_LIBRARY "szip-shared")
add_library(${HDF_PACKAGE_NAMESPACE}szip-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}szip-shared "szip" SHARED "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}szip-shared SZIP)
set (SZIP_SHARED_LIBRARY "${HDF_PACKAGE_NAMESPACE}szip-shared")
set (SZIP_LIBRARIES ${SZIP_LIBRARIES} ${SZIP_SHARED_LIBRARY})
endif ()
@ -196,32 +163,14 @@ macro (PACKAGE_SZIP_LIBRARY compress_type)
COMMENT "Copying ${SZIP_INCLUDE_DIR_GEN}/SZconfig.h to ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/"
)
set (EXTERNAL_HEADER_LIST ${EXTERNAL_HEADER_LIST} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/SZconfig.h)
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "SVN" OR ${compress_type} MATCHES "TGZ")
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "TGZ")
add_dependencies (SZIP-GenHeader-Copy SZIP)
endif ()
endmacro ()
#-------------------------------------------------------------------------------
macro (EXTERNAL_ZLIB_LIBRARY compress_type)
if (${compress_type} MATCHES "SVN")
EXTERNALPROJECT_ADD (ZLIB
SVN_REPOSITORY ${ZLIB_URL}
# [SVN_REVISION rev]
INSTALL_COMMAND ""
CMAKE_ARGS
-DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
-DZLIB_PACKAGE_EXT:STRING=${HDF_PACKAGE_EXT}
-DZLIB_EXTERNALLY_CONFIGURED:BOOL=OFF
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
-DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
)
elseif (${compress_type} MATCHES "GIT")
if (${compress_type} MATCHES "GIT")
EXTERNALPROJECT_ADD (ZLIB
GIT_REPOSITORY ${ZLIB_URL}
GIT_TAG ${ZLIB_BRANCH}
@ -238,6 +187,7 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type)
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
elseif (${compress_type} MATCHES "TGZ")
EXTERNALPROJECT_ADD (ZLIB
@ -256,6 +206,7 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type)
-DCMAKE_PDB_OUTPUT_DIRECTORY:PATH=${CMAKE_PDB_OUTPUT_DIRECTORY}
-DCMAKE_ANSI_CFLAGS:STRING=${CMAKE_ANSI_CFLAGS}
-DCMAKE_TOOLCHAIN_FILE:STRING=${CMAKE_TOOLCHAIN_FILE}
-DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE}
)
endif ()
externalproject_get_property (ZLIB BINARY_DIR SOURCE_DIR)
@ -267,17 +218,18 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type)
endif ()
##include (${BINARY_DIR}/${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake)
# Create imported target zlib-static
add_library(zlib-static STATIC IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (zlib-static ${ZLIB_LIB_NAME} STATIC "")
add_dependencies (zlib-static ZLIB)
set (ZLIB_STATIC_LIBRARY "zlib-static")
add_library(${HDF_PACKAGE_NAMESPACE}zlib-static STATIC IMPORTED)
# add_library(${HDF_PACKAGE_NAMESPACE}zlib-static ALIAS zlib-static)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}zlib-static ${ZLIB_LIB_NAME} STATIC "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-static ZLIB)
set (ZLIB_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-static")
set (ZLIB_LIBRARIES ${ZLIB_STATIC_LIBRARY})
if (BUILD_SHARED_LIBS)
# Create imported target zlib-shared
add_library(zlib-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (zlib-shared ${ZLIB_LIB_NAME} SHARED "")
add_dependencies (zlib-shared ZLIB)
set (ZLIB_SHARED_LIBRARY "zlib-shared")
add_library(${HDF_PACKAGE_NAMESPACE}zlib-shared SHARED IMPORTED)
HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}zlib-shared ${ZLIB_LIB_NAME} SHARED "")
add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-shared ZLIB)
set (ZLIB_SHARED_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-shared")
set (ZLIB_LIBRARIES ${ZLIB_LIBRARIES} ${ZLIB_SHARED_LIBRARY})
endif ()
@ -294,7 +246,7 @@ macro (PACKAGE_ZLIB_LIBRARY compress_type)
COMMENT "Copying ${ZLIB_INCLUDE_DIR_GEN}/zconf.h to ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/"
)
set (EXTERNAL_HEADER_LIST ${EXTERNAL_HEADER_LIST} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/zconf.h)
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "SVN" OR ${compress_type} MATCHES "TGZ")
if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "TGZ")
add_dependencies (ZLIB-GenHeader-Copy ZLIB)
endif ()
endmacro ()

4
configure.ac
View File

@ -24,7 +24,7 @@ AC_PREREQ([2.69])
## NOTE: Do not forget to change the version number here when we do a
## release!!!
##
AC_INIT([HDF5], [1.11.4], [help@hdfgroup.org])
AC_INIT([HDF5], [1.11.5], [help@hdfgroup.org])
AC_CONFIG_SRCDIR([src/H5.c])
AC_CONFIG_HEADERS([src/H5config.h])
@ -48,7 +48,7 @@ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])]) # use silent rules where a
##
## By default, it is enabled. Users can configure with
## --disable-maintainer-mode to prevent running the autotools.
AM_MAINTAINER_MODE([enable])
AM_MAINTAINER_MODE([disable])
## ----------------------------------------------------------------------
## Set prefix default (install directory) to a directory in the build area.

34
hl/fortran/src/H5DSff.F90
View File

@ -304,7 +304,7 @@ CONTAINS
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! The dataset
INTEGER , INTENT(in) :: idx ! The dimension
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: label ! The label
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: label ! The label
INTEGER(SIZE_T), INTENT(in) :: label_len ! Length of label
END FUNCTION H5DSset_label_c
END INTERFACE
@ -337,11 +337,11 @@ CONTAINS
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! The dataget
INTEGER , INTENT(in) :: idx ! The dimension
CHARACTER(LEN=*), INTENT(in) :: label ! The label
INTEGER(size_t) , INTENT(inout) :: size ! The length of the label buffer
INTEGER :: errcode ! Error code
INTEGER(hid_t), INTENT(in) :: did ! The dataget
INTEGER , INTENT(in) :: idx ! The dimension
CHARACTER(LEN=*), INTENT(INOUT) :: label ! The label
INTEGER(size_t) , INTENT(INOUT) :: size ! The length of the label buffer
INTEGER :: errcode ! Error code
INTEGER :: c_idx
INTERFACE
@ -352,7 +352,7 @@ CONTAINS
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! The dataget
INTEGER , INTENT(in) :: idx ! The dimension
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: label ! The label
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(INOUT) :: label ! The label
INTEGER(SIZE_T), INTENT(inout) :: size ! Length of label
END FUNCTION H5DSget_label_c
END INTERFACE
@ -386,8 +386,8 @@ CONTAINS
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! The dataget
CHARACTER(LEN=*), INTENT(out) :: name ! The name
INTEGER(size_t) , INTENT(inout) :: size ! The length of the name buffer
CHARACTER(LEN=*), INTENT(INOUT) :: name ! The name
INTEGER(size_t) , INTENT(INOUT) :: size ! The length of the name buffer
INTEGER :: errcode ! Error code
INTERFACE
@ -397,7 +397,7 @@ CONTAINS
IMPORT :: HID_T, SIZE_T
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! The dataget
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(out) :: name ! The name
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(INOUT) :: name ! The name
INTEGER(SIZE_T), INTENT(inout) :: size ! Length of name
END FUNCTION H5DSget_scale_name_c
END INTERFACE
@ -426,10 +426,10 @@ CONTAINS
SUBROUTINE H5DSget_num_scales_f( did, idx, num_scales, errcode)
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! the dataset
INTEGER , INTENT(in) :: idx ! the dimension of did to query
INTEGER , INTENT(out) :: num_scales ! the number of Dimension Scales associated with did
INTEGER :: errcode ! error code
INTEGER(hid_t), INTENT(in) :: did ! the dataset
INTEGER , INTENT(in) :: idx ! the dimension of did to query
INTEGER , INTENT(INOUT) :: num_scales ! the number of Dimension Scales associated with did
INTEGER :: errcode ! error code
INTEGER :: c_idx
INTERFACE
@ -437,9 +437,9 @@ CONTAINS
BIND(C,NAME='h5dsget_num_scales_c')
IMPORT :: HID_T
IMPLICIT NONE
INTEGER(hid_t), INTENT(in) :: did ! the dataset
INTEGER , INTENT(in) :: idx ! the dimension of did to query
INTEGER , INTENT(out) :: num_scales ! the number of Dimension Scales associated with did
INTEGER(hid_t), INTENT(in) :: did ! the dataset
INTEGER , INTENT(in) :: idx ! the dimension of did to query
INTEGER , INTENT(INOUT) :: num_scales ! the number of Dimension Scales associated with did
END FUNCTION H5DSget_num_scales_c
END INTERFACE

16
hl/fortran/src/H5HL_buildiface.F90
View File

@ -293,7 +293,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(IN) :: dset_name'
WRITE(11,'(A)') ' INTEGER(hid_t), INTENT(in) :: type_id'
WRITE(11,'(A)') ' INTEGER(hsize_t), DIMENSION(*), INTENT(in) :: dims'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
@ -354,7 +354,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' INTEGER(hid_t) , INTENT(IN) :: loc_id'
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(IN) :: dset_name'
WRITE(11,'(A)') ' INTEGER(hsize_t), DIMENSION(*), INTENT(in) :: dims'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
@ -414,7 +414,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' INTEGER(hid_t) , INTENT(IN) :: loc_id'
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(IN) :: dset_name'
WRITE(11,'(A)') ' INTEGER(hsize_t), DIMENSION(*), INTENT(in) :: dims'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
@ -510,7 +510,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(IN) :: dset_name'
WRITE(11,'(A)') ' INTEGER(hsize_t), DIMENSION(*), INTENT(in) :: dims'
WRITE(11,'(A)') ' INTEGER(hid_t), INTENT(in) :: type_id'
WRITE(11,'(A)') ' INTEGER(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
@ -540,7 +540,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' INTEGER(hid_t) , INTENT(IN) :: loc_id'
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(IN) :: dset_name'
WRITE(11,'(A)') ' INTEGER(hsize_t), DIMENSION(*), INTENT(in) :: dims'
WRITE(11,'(A)') ' INTEGER(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT)'//TRIM(rank_dim_line(j))//', TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
@ -712,7 +712,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' INTEGER(hsize_t), INTENT(in) :: start'
WRITE(11,'(A)') ' INTEGER(hsize_t), INTENT(in) :: nrecords'
WRITE(11,'(A)') ' INTEGER(size_t), INTENT(in) :: type_size'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen1'
@ -778,7 +778,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' INTEGER(hsize_t), INTENT(in) :: start'
WRITE(11,'(A)') ' INTEGER(hsize_t), INTENT(in) :: nrecords'
WRITE(11,'(A)') ' INTEGER(size_t), INTENT(in) :: type_size'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(IN), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'),INTENT(INOUT), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' INTEGER :: errcode '
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
WRITE(11,'(A)') ' TYPE(C_PTR) :: f_ptr'
@ -809,7 +809,7 @@ PROGRAM H5HL_buildiface
WRITE(11,'(A)') ' CHARACTER(LEN=*), INTENT(in) :: field_name'
WRITE(11,'(A)') ' INTEGER(hid_t), INTENT(in) :: field_type'
WRITE(11,'(A)') ' INTEGER, INTENT(in) :: field_index'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'), INTENT(in), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' REAL(KIND='//TRIM(ADJUSTL(chr2))//'), INTENT(IN), DIMENSION(*), TARGET :: buf'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen'
WRITE(11,'(A)') ' INTEGER(size_t) :: namelen1'
WRITE(11,'(A)') ' INTEGER :: errcode'

4
hl/fortran/src/H5IMff.F90
View File

@ -539,7 +539,7 @@ CONTAINS
INTEGER, INTENT(in) :: pal_number ! palette number
INTEGER(hsize_t), DIMENSION(*), INTENT(inout) :: dims ! dimensions
INTEGER :: errcode ! error code
INTEGER(size_t) :: namelen ! name length
INTEGER(size_t) :: namelen ! name length
INTERFACE
INTEGER FUNCTION h5imget_palette_info_c(loc_id,namelen,dset_name,pal_number,dims) &
@ -551,7 +551,7 @@ CONTAINS
CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: dset_name ! name of the dataset
INTEGER, INTENT(in) :: pal_number ! palette number
INTEGER(hsize_t), DIMENSION(*), INTENT(inout) :: dims ! dimensions
INTEGER(size_t) :: namelen ! name length
INTEGER(size_t) :: namelen ! name length
END FUNCTION h5imget_palette_info_c
END INTERFACE

8
hl/fortran/src/H5TBff.F90
View File

@ -532,7 +532,7 @@ CONTAINS
INTEGER(hsize_t), INTENT(in) :: start ! start record
INTEGER(hsize_t), INTENT(in) :: nrecords ! records
INTEGER(size_t), INTENT(in) :: type_size ! type size
INTEGER, INTENT(in), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER, INTENT(INOUT), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER :: errcode ! error code
INTEGER(size_t) :: namelen ! name length
INTEGER(size_t) :: namelen1
@ -564,7 +564,7 @@ CONTAINS
INTEGER(hsize_t), INTENT(in) :: start ! start record
INTEGER(hsize_t), INTENT(in) :: nrecords ! records
INTEGER(size_t), INTENT(in) :: type_size ! type size
CHARACTER(LEN=*), INTENT(in), DIMENSION(*), TARGET :: buf ! data buffer
CHARACTER(LEN=*), INTENT(INOUT), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER :: errcode ! error code
INTEGER(size_t) :: namelen ! name length
INTEGER(size_t) :: namelen1 ! name length
@ -687,7 +687,7 @@ CONTAINS
INTEGER(hsize_t), INTENT(in) :: start ! start record
INTEGER(hsize_t), INTENT(in) :: nrecords ! records
INTEGER(size_t), INTENT(in) :: type_size ! type size
INTEGER, INTENT(in), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER, INTENT(INOUT), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER :: errcode ! error code
INTEGER(size_t) :: namelen ! name length
TYPE(C_PTR) :: f_ptr
@ -716,7 +716,7 @@ CONTAINS
INTEGER(hsize_t), INTENT(in) :: start ! start record
INTEGER(hsize_t), INTENT(in) :: nrecords ! records
INTEGER(size_t), INTENT(in) :: type_size ! type size
CHARACTER(LEN=*), INTENT(in), DIMENSION(*), TARGET :: buf ! data buffer
CHARACTER(LEN=*), INTENT(INOUT), DIMENSION(*), TARGET :: buf ! data buffer
INTEGER :: errcode ! error code
INTEGER(size_t) :: namelen ! name length
TYPE(C_PTR) :: f_ptr

32
hl/tools/h5watch/CMakeTests.cmake
View File

@ -88,18 +88,26 @@ add_custom_target(H5WATCH_files ALL COMMENT "Copying files needed by H5WATCH tes
macro (ADD_H5_ERR_TEST resultfile resultcode)
if (NOT HDF5_ENABLE_USING_MEMCHECKER)
add_test (
NAME H5WATCH_ARGS-h5watch-${resultfile}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5watch>"
-D "TEST_ARGS:STRING=${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}.out"
-D "TEST_EXPECT=${resultcode}"
-D "TEST_REFERENCE=${resultfile}.mty"
-D "TEST_ERRREF=${resultfile}.err"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
if (SKIP_ERROR_STACK_TESTS)
add_test (
NAME H5WATCH_ARGS-h5watch-${resultfile}
COMMAND ${CMAKE_COMMAND} -E echo "SKIP Error Stack Test"
)
set_property(TEST H5WATCH_ARGS-h5watch-${resultfile} PROPERTY DISABLED)
else ()
add_test (
NAME H5WATCH_ARGS-h5watch-${resultfile}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5watch>"
-D "TEST_ARGS:STRING=${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}.out"
-D "TEST_EXPECT=${resultcode}"
-D "TEST_REFERENCE=${resultfile}.mty"
-D "TEST_ERRREF=${resultfile}.err"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
set_tests_properties (H5WATCH_ARGS-h5watch-${resultfile} PROPERTIES DEPENDS ${last_test})
set (last_test "H5WATCH_ARGS-h5watch-${resultfile}")
endif ()

4
java/src/hdf/hdf5lib/H5.java
View File

@ -212,7 +212,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* exception handlers to print out the HDF-5 error stack.
* <hr>
*
* @version HDF5 1.11.4 <BR>
* @version HDF5 1.11.5 <BR>
* <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR>
* <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR>
* <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR>
@ -235,7 +235,7 @@ public class H5 implements java.io.Serializable {
*
* Make sure to update the versions number when a different library is used.
*/
public final static int LIB_VERSION[] = { 1, 11, 4 };
public final static int LIB_VERSION[] = { 1, 11, 5 };
public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";

4
java/test/TestH5.java
View File

@ -162,7 +162,7 @@ public class TestH5 {
*/
@Test
public void testH5get_libversion() {
int libversion[] = { 1, 11, 4 };
int libversion[] = { 1, 11, 5 };
try {
H5.H5get_libversion(libversion);
@ -201,7 +201,7 @@ public class TestH5 {
*/
@Test
public void testH5check_version() {
int majnum = 1, minnum = 11, relnum = 4;
int majnum = 1, minnum = 11, relnum = 5;
try {
H5.H5check_version(majnum, minnum, relnum);

1
release_docs/INSTALL_CMake.txt
View File

@ -652,6 +652,7 @@ HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks"
HDF_TEST_EXPRESS "Control testing framework (0-3)" "0"
HDF5_TEST_VFD "Execute tests with different VFDs" OFF
HDF5_TEST_VOL "Execute tests with different VOL connectors" OFF
SKIP_ERROR_STACK_TESTS "Skip tests that check the error stack" OFF
HDF5_USE_16_API_DEFAULT "Use the HDF5 1.6.x API by default" OFF
HDF5_USE_18_API_DEFAULT "Use the HDF5 1.8.x API by default" OFF
HDF5_USE_110_API_DEFAULT "Use the HDF5 1.10.x API by default" OFF

64
release_docs/RELEASE.txt
View File

@ -1,4 +1,4 @@
version 1.11.4 currently under development
HDF5 version 1.11.5 currently under development
================================================================================
@ -48,6 +48,14 @@ New Features
Configuration:
-------------
- Skip tools test that test the error stack
There are some use cases which can cause the error stack of tools to be
different then the expected. An option, SKIP_ERROR_STACK_TESTS, was added
that will skip over tests that test the error stack.
(ADB - 2019/03/26, HDFFV-10741)
- Keep stderr and stdout separate in tests
Changed test handling of output capture. Tests now keep the stderr
@ -135,14 +143,22 @@ New Features
(DER - 2018/12/08, HDFFV-10252)
- Added the ability to open files with UTF-8 file names on Windows.
The POSIX open(2) API call on Windows is limited to ASCII
file names. The library has been updated to convert incoming file
names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use
_wopen() instead.
(DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691)
Parallel Library:
-----------------
- Changed the default behavior in parallel when reading the same dataset in its entirely
(i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
The dataset mush be contiguous, less than 2GB, and of an atomic datatype.
The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
the disk by the root process to the remain processes in the MPI communicator associated
The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
the disk by the root process to the remain processes in the MPI communicator associated
with the HDF5 file.
(MSB - 2019/01/02, HDFFV-10652)
@ -157,10 +173,10 @@ New Features
- Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
to Fortran DATE AND TIME storage format.
(MSB, 2019/01/08, HDFFV-10443)
- Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
- Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
(MSB, 2019/01/08, HDFFV-10443)
@ -224,15 +240,27 @@ Bug Fixes since HDF5-1.10.3 release
Library
-------
- Fixed a bug that would cause an error or cause fill values to be
incorrectly read from a chunked dataset using the "single chunk" index if
the data was held in cache and there was no data on disk.
(NAF - 2019/03/06)
- Fixed a bug that could cause an error or cause fill values to be
incorrectly read from a dataset that was written to using H5Dwrite_chunk
if the dataset was not closed after writing.
(NAF - 2019/03/06, HDFFV-10716)
- Fixed memory leak in scale offset filter
In a special case where the MinBits is the same as the number of bits in
the datatype's precision, the filter's data buffer was not freed, causing
the datatype's precision, the filter's data buffer was not freed, causing
the memory usage to grow. In general the buffer was freed correctly. The
Minbits are the minimal number of bits to store the data values. Please
Minbits are the minimal number of bits to store the data values. Please
see the reference manual for H5Pset_scaleoffset for the detail.
(RL - 2019/3/4, HDFFV-10705)
(RL - 2019/3/4, HDFFV-10705)
- Fix hangs with collective metadata reads during chunked dataset I/O
@ -273,8 +301,8 @@ Bug Fixes since HDF5-1.10.3 release
When deleting the attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes,
which may be merged/redistributed in the process, we need to
free the dynamically allocated spaces for the intermediate
which may be merged/redistributed in the process, we need to
free the dynamically allocated spaces for the intermediate
decoded attribute.
(VC - 2018/12/26, HDFFV-10659)
@ -351,10 +379,10 @@ Bug Fixes since HDF5-1.10.3 release
Fortran
--------
- Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
autotools installs. These were added to match the name of the files
installed by cmake and the general pattern of hl lib files. We will
change the names of the installed lib files to the matching name in
libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
autotools installs. These were added to match the name of the files
installed by cmake and the general pattern of hl lib files. We will
change the names of the installed lib files to the matching name in
the next major release.
(LRK - 2019/01/04, HDFFV-10596)
@ -365,7 +393,7 @@ Bug Fixes since HDF5-1.10.3 release
(MSB, 2018/12/04, HDFFV-10511)
- Fixed issue with Fortran not returning h5o_info_t field values
- Fixed issue with Fortran not returning h5o_info_t field values
meta_size%attr%index_size and meta_size%attr%heap_size.
(MSB, 2018/1/8, HDFFV-10443)
@ -648,10 +676,10 @@ Bug Fixes since HDF5-1.10.2 release
conversions from or to long double types, especially when special values
such as infinity or NAN were involved. In some cases the results differed
by extremely small amounts from those on other machines, while some other
tests resulted in segmentation faults. These conversion tests with long
double types have been disabled for ppc64 machines until the problems are
tests resulted in segmentation faults. These conversion tests with long
double types have been disabled for ppc64 machines until the problems are
better understood and can be properly addressed.
(SRL - 2019/01/07, TRILAB-98)
Supported Platforms

2
release_docs/USING_CMake_Examples.txt
View File

@ -38,12 +38,14 @@ II. Building HDF5 Examples with CMake
Files in the HDF5 install directory:
HDF5Examples folder
CTestScript.cmake
HDF5_Examples.cmake
HDF5_Examples_options.cmake
Default installation process:
Create a directory to run the examples, i.e. \test_hdf5.
Copy HDF5Examples folder to this directory.
Copy CTestScript.cmake to this directory.
Copy HDF5_Examples.cmake to this directory.
Copy HDF5_Examples_options.cmake to this directory.
The default source folder is defined as "HDF5Examples". It can be changed

6
src/CMakeLists.txt
View File

@ -1120,7 +1120,7 @@ target_link_libraries (${HDF5_LIB_TARGET}
)
if (NOT WIN32)
target_link_libraries (${HDF5_LIB_TARGET}
PUBLIC $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
PRIVATE $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
)
endif ()
set_global_variable (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET})
@ -1152,8 +1152,8 @@ if (BUILD_SHARED_LIBS)
)
TARGET_C_PROPERTIES (${HDF5_LIBSH_TARGET} SHARED)
target_link_libraries (${HDF5_LIBSH_TARGET}
PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>"
PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}> $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>" $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads>
PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}>
)
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_LIBSH_TARGET}")
H5_SET_LIB_OPTIONS (${HDF5_LIBSH_TARGET} ${HDF5_LIB_NAME} SHARED "LIB")

9
src/H5Abtree2.c
View File

@ -35,6 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Apkg.h" /* Attributes */
#include "H5Eprivate.h" /* Error handling */
#include "H5MMprivate.h" /* Memory management */
#include "H5SMprivate.h" /* Shared object header messages */
@ -318,7 +319,7 @@ H5A__dense_btree2_name_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_U
FUNC_ENTER_STATIC_NOERR
/* Encode the record's fields */
HDmemcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN);
H5MM_memcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN);
raw += H5O_FHEAP_ID_LEN;
*raw++ = nrecord->flags;
UINT32ENCODE(raw, nrecord->corder)
@ -349,7 +350,7 @@ H5A__dense_btree2_name_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_U
FUNC_ENTER_STATIC_NOERR
/* Decode the record's fields */
HDmemcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN);
raw += H5O_FHEAP_ID_LEN;
nrecord->flags = *raw++;
UINT32DECODE(raw, nrecord->corder)
@ -477,7 +478,7 @@ H5A__dense_btree2_corder_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR
FUNC_ENTER_STATIC_NOERR
/* Encode the record's fields */
HDmemcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN);
H5MM_memcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN);
raw += H5O_FHEAP_ID_LEN;
*raw++ = nrecord->flags;
UINT32ENCODE(raw, nrecord->corder)
@ -507,7 +508,7 @@ H5A__dense_btree2_corder_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR
FUNC_ENTER_STATIC_NOERR
/* Decode the record's fields */
HDmemcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN);
raw += H5O_FHEAP_ID_LEN;
nrecord->flags = *raw++;
UINT32DECODE(raw, nrecord->corder)

20
src/H5Aint.c
View File

@ -646,21 +646,21 @@ H5A__read(const H5A_t *attr, const H5T_t *mem_type, void *buf)
HGOTO_ERROR(H5E_ATTR, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Copy the attribute data into the buffer for conversion */
HDmemcpy(tconv_buf, attr->shared->data, (src_type_size * nelmts));
H5MM_memcpy(tconv_buf, attr->shared->data, (src_type_size * nelmts));
/* Perform datatype conversion. */
if(H5T_convert(tpath, src_id, dst_id, nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf) < 0)
HGOTO_ERROR(H5E_ATTR, H5E_CANTENCODE, FAIL, "datatype conversion failed")
/* Copy the converted data into the user's buffer */
HDmemcpy(buf, tconv_buf, (dst_type_size * nelmts));
H5MM_memcpy(buf, tconv_buf, (dst_type_size * nelmts));
} /* end if */
/* No type conversion necessary */
else {
HDassert(dst_type_size == src_type_size);
/* Copy the attribute data into the user's buffer */
HDmemcpy(buf, attr->shared->data, (dst_type_size * nelmts));
H5MM_memcpy(buf, attr->shared->data, (dst_type_size * nelmts));
} /* end else */
} /* end else */
} /* end if */
@ -747,7 +747,7 @@ H5A__write(H5A_t *attr, const H5T_t *mem_type, const void *buf)
HGOTO_ERROR(H5E_ATTR, H5E_CANTALLOC, FAIL, "memory allocation failed")
/* Copy the user's data into the buffer for conversion */
HDmemcpy(tconv_buf, buf, (src_type_size * nelmts));
H5MM_memcpy(tconv_buf, buf, (src_type_size * nelmts));
/* Perform datatype conversion */
if(H5T_convert(tpath, src_id, dst_id, nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf) < 0)
@ -771,7 +771,7 @@ H5A__write(H5A_t *attr, const H5T_t *mem_type, const void *buf)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Copy the attribute data into the user's buffer */
HDmemcpy(attr->shared->data, buf, (dst_type_size * nelmts));
H5MM_memcpy(attr->shared->data, buf, (dst_type_size * nelmts));
} /* end else */
/* Modify the attribute in the object header */
@ -827,7 +827,7 @@ H5A__get_name(H5A_t *attr, size_t buf_size, char *buf)
/* Copy all/some of the name */
if(buf && copy_len > 0) {
HDmemcpy(buf, attr->shared->name, copy_len);
H5MM_memcpy(buf, attr->shared->name, copy_len);
/* Terminate the string */
buf[copy_len]='\0';
@ -2240,7 +2240,7 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s
if(NULL == (buf = H5FL_BLK_MALLOC(attr_buf, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk")
HDmemcpy(buf, attr_src->shared->data, attr_src->shared->data_size);
H5MM_memcpy(buf, attr_src->shared->data, attr_src->shared->data_size);
/* Allocate background memory */
if(H5T_path_bkg(tpath_src_mem) || H5T_path_bkg(tpath_mem_dst))
@ -2251,7 +2251,7 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s
if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg_buf) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed")
HDmemcpy(reclaim_buf, buf, buf_size);
H5MM_memcpy(reclaim_buf, buf, buf_size);
/* Set background buffer to all zeros */
if(bkg_buf)
@ -2261,14 +2261,14 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg_buf) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed")
HDmemcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size);
H5MM_memcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size);
if(H5D_vlen_reclaim(tid_mem, buf_space, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, NULL, "unable to reclaim variable-length data")
} /* end if */
else {
HDassert(attr_dst->shared->data_size == attr_src->shared->data_size);
HDmemcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size);
H5MM_memcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size);
} /* end else */
} /* end if(attr_src->shared->data) */

53
src/H5B.c
View File

@ -107,6 +107,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */
@ -484,10 +485,10 @@ H5B__split(H5F_t *f, H5B_ins_ud_t *bt_ud, unsigned idx,
*/
split_bt_ud->cache_flags = H5AC__DIRTIED_FLAG;
HDmemcpy(split_bt_ud->bt->native,
H5MM_memcpy(split_bt_ud->bt->native,
bt_ud->bt->native + nleft * shared->type->sizeof_nkey,
(nright + 1) * shared->type->sizeof_nkey);
HDmemcpy(split_bt_ud->bt->child,
H5MM_memcpy(split_bt_ud->bt->child,
&bt_ud->bt->child[nleft],
nright * sizeof(haddr_t));
@ -612,9 +613,9 @@ H5B_insert(H5F_t *f, const H5B_class_t *type, haddr_t addr, void *udata)
/* update left and right keys */
if(!lt_key_changed)
HDmemcpy(lt_key, H5B_NKEY(bt_ud.bt,shared,0), type->sizeof_nkey);
H5MM_memcpy(lt_key, H5B_NKEY(bt_ud.bt,shared,0), type->sizeof_nkey);
if(!rt_key_changed)
HDmemcpy(rt_key, H5B_NKEY(split_bt_ud.bt,shared,split_bt_ud.bt->nchildren), type->sizeof_nkey);
H5MM_memcpy(rt_key, H5B_NKEY(split_bt_ud.bt,shared,split_bt_ud.bt->nchildren), type->sizeof_nkey);
/*
* Copy the old root node to some other file location and make the new root
@ -657,11 +658,11 @@ H5B_insert(H5F_t *f, const H5B_class_t *type, haddr_t addr, void *udata)
new_root_bt->nchildren = 2;
new_root_bt->child[0] = bt_ud.addr;
HDmemcpy(H5B_NKEY(new_root_bt, shared, 0), lt_key, shared->type->sizeof_nkey);
H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 0), lt_key, shared->type->sizeof_nkey);
new_root_bt->child[1] = split_bt_ud.addr;
HDmemcpy(H5B_NKEY(new_root_bt, shared, 1), md_key, shared->type->sizeof_nkey);
HDmemcpy(H5B_NKEY(new_root_bt, shared, 2), rt_key, shared->type->sizeof_nkey);
H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 1), md_key, shared->type->sizeof_nkey);
H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 2), rt_key, shared->type->sizeof_nkey);
/* Insert the modified copy of the old root into the file again */
if(H5AC_insert_entry(f, H5AC_BT, addr, new_root_bt, H5AC__NO_FLAGS_SET) < 0)
@ -726,9 +727,9 @@ H5B__insert_child(H5B_t *bt, unsigned *bt_flags, unsigned idx,
base = H5B_NKEY(bt, shared, (idx + 1));
if((idx + 1) == bt->nchildren) {
/* Make room for the new key */
HDmemcpy(base + shared->type->sizeof_nkey, base,
H5MM_memcpy(base + shared->type->sizeof_nkey, base,
shared->type->sizeof_nkey); /* No overlap possible - memcpy() OK */
HDmemcpy(base, md_key, shared->type->sizeof_nkey);
H5MM_memcpy(base, md_key, shared->type->sizeof_nkey);
/* The MD_KEY is the left key of the new node */
if(H5B_INS_RIGHT == anchor)
@ -741,7 +742,7 @@ H5B__insert_child(H5B_t *bt, unsigned *bt_flags, unsigned idx,
/* Make room for the new key */
HDmemmove(base + shared->type->sizeof_nkey, base,
(bt->nchildren - idx) * shared->type->sizeof_nkey);
HDmemcpy(base, md_key, shared->type->sizeof_nkey);
H5MM_memcpy(base, md_key, shared->type->sizeof_nkey);
/* The MD_KEY is the left key of the new node */
if(H5B_INS_RIGHT == anchor)
@ -915,7 +916,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type,
* node. This node is not empty (handled above).
*/
my_ins = H5B_INS_LEFT;
HDmemcpy(md_key, H5B_NKEY(bt,shared,idx), type->sizeof_nkey);
H5MM_memcpy(md_key, H5B_NKEY(bt,shared,idx), type->sizeof_nkey);
if((type->new_node)(f, H5B_INS_LEFT, H5B_NKEY(bt, shared, idx), udata,
md_key, &new_child_bt_ud.addr/*out*/) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR, "can't insert minimum leaf node")
@ -963,7 +964,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type,
*/
idx = bt->nchildren - 1;
my_ins = H5B_INS_RIGHT;
HDmemcpy(md_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
H5MM_memcpy(md_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
if((type->new_node)(f, H5B_INS_RIGHT, md_key, udata,
H5B_NKEY(bt, shared, idx + 1), &new_child_bt_ud.addr/*out*/) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR, "can't insert maximum leaf node")
@ -1021,7 +1022,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type,
*lt_key_changed = FALSE;
} /* end if */
else
HDmemcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey);
H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey);
} /* end if */
if(*rt_key_changed) {
bt_ud->cache_flags |= H5AC__DIRTIED_FLAG;
@ -1031,7 +1032,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type,
*rt_key_changed = FALSE;
} /* end if */
else
HDmemcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
} /* end if */
/*
@ -1080,7 +1081,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type,
* by the left and right node).
*/
if(split_bt_ud->bt) {
HDmemcpy(md_key, H5B_NKEY(split_bt_ud->bt, shared, 0), type->sizeof_nkey);
H5MM_memcpy(md_key, H5B_NKEY(split_bt_ud->bt, shared, 0), type->sizeof_nkey);
ret_value = H5B_INS_RIGHT;
#ifdef H5B_DEBUG
/*
@ -1339,7 +1340,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
/* Don't propagate change out of this B-tree node */
*lt_key_changed = FALSE;
else
HDmemcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey);
H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey);
} /* end if */
if(*rt_key_changed) {
HDassert(type->critical_key == H5B_RIGHT);
@ -1348,7 +1349,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
/* Don't propagate change out of this B-tree node */
*rt_key_changed = FALSE;
else
HDmemcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey);
} /* end if */
/*
@ -1383,7 +1384,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
* in its left neighbor, but only if it is not the critical
* key for the right-most child of the left neighbor */
if(type->critical_key == H5B_LEFT)
HDmemcpy(H5B_NKEY(sibling, shared, sibling->nchildren),
H5MM_memcpy(H5B_NKEY(sibling, shared, sibling->nchildren),
H5B_NKEY(bt, shared, 1), type->sizeof_nkey);
sibling->right = bt->right;
@ -1400,7 +1401,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
* its right neighbor, but only if it is not the critical
* key for the left-most child of the right neighbor */
if(type->critical_key == H5B_RIGHT)
HDmemcpy(H5B_NKEY(sibling, shared, 0),
H5MM_memcpy(H5B_NKEY(sibling, shared, 0),
H5B_NKEY(bt, shared, 0), type->sizeof_nkey);
sibling->left = bt->left;
@ -1442,7 +1443,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
/* Slide all keys down 1, update lt_key */
HDmemmove(H5B_NKEY(bt, shared, 0), H5B_NKEY(bt, shared, 1),
bt->nchildren * type->sizeof_nkey);
HDmemcpy(lt_key, H5B_NKEY(bt, shared, 0), type->sizeof_nkey);
H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, 0), type->sizeof_nkey);
*lt_key_changed = TRUE;
} else
/* Slide all but the leftmost 2 keys down, leaving the leftmost
@ -1471,7 +1472,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
H5B_NKEY(bt, shared, bt->nchildren), type->sizeof_nkey);
else {
/* Just update rt_key */
HDmemcpy(rt_key, H5B_NKEY(bt, shared, bt->nchildren - 1),
H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, bt->nchildren - 1),
type->sizeof_nkey);
*rt_key_changed = TRUE;
} /* end else */
@ -1516,7 +1517,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
if(NULL == (sibling = (H5B_t *)H5AC_protect(f, H5AC_BT, bt->left, &cache_udata, H5AC__NO_FLAGS_SET)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, H5B_INS_ERROR, "unable to protect node")
HDmemcpy(H5B_NKEY(sibling, shared, sibling->nchildren),
H5MM_memcpy(H5B_NKEY(sibling, shared, sibling->nchildren),
H5B_NKEY(bt, shared, 0), type->sizeof_nkey);
if(H5AC_unprotect(f, H5AC_BT, bt->left, sibling, H5AC__DIRTIED_FLAG) < 0)
@ -1531,7 +1532,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level,
if(NULL == (sibling = (H5B_t *)H5AC_protect(f, H5AC_BT, bt->right, &cache_udata, H5AC__NO_FLAGS_SET)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, H5B_INS_ERROR, "unable to protect node")
HDmemcpy(H5B_NKEY(sibling, shared, 0),
H5MM_memcpy(H5B_NKEY(sibling, shared, 0),
H5B_NKEY(bt, shared, bt->nchildren), type->sizeof_nkey);
if(H5AC_unprotect(f, H5AC_BT, bt->right, sibling, H5AC__DIRTIED_FLAG) < 0)
@ -1811,7 +1812,7 @@ H5B__copy(const H5B_t *old_bt)
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree root node")
/* Copy the main structure */
HDmemcpy(new_node, old_bt, sizeof(H5B_t));
H5MM_memcpy(new_node, old_bt, sizeof(H5B_t));
/* Reset cache info */
HDmemset(&new_node->cache_info, 0, sizeof(H5AC_info_t));
@ -1821,8 +1822,8 @@ H5B__copy(const H5B_t *old_bt)
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree root node")
/* Copy the other structures */
HDmemcpy(new_node->native, old_bt->native, shared->sizeof_keys);
HDmemcpy(new_node->child, old_bt->child, (sizeof(haddr_t) * shared->two_k));
H5MM_memcpy(new_node->native, old_bt->native, shared->sizeof_keys);
H5MM_memcpy(new_node->child, old_bt->child, (sizeof(haddr_t) * shared->two_k));
/* Increment the ref-count on the raw page */
H5UC_INC(new_node->rc_shared);

8
src/H5B2.c
View File

@ -662,7 +662,7 @@ H5B2_find(H5B2_t *bt2, void *udata, H5B2_found_t op, void *op_data)
if(hdr->min_native_rec == NULL)
if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info")
HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
if(idx == (unsigned)(leaf->nrec - 1)) {
@ -670,7 +670,7 @@ H5B2_find(H5B2_t *bt2, void *udata, H5B2_found_t op, void *op_data)
if(hdr->max_native_rec == NULL)
if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info")
HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
} /* end if */
@ -1343,7 +1343,7 @@ H5B2_modify(H5B2_t *bt2, void *udata, H5B2_modify_t op, void *op_data)
if(hdr->min_native_rec == NULL)
if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info")
HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
if(idx == (unsigned)(leaf->nrec - 1)) {
@ -1351,7 +1351,7 @@ H5B2_modify(H5B2_t *bt2, void *udata, H5B2_modify_t op, void *op_data)
if(hdr->max_native_rec == NULL)
if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info")
HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
} /* end if */

6
src/H5B2cache.c
View File

@ -391,7 +391,7 @@ H5B2__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le
HDassert(hdr);
/* Magic number */
HDmemcpy(image, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -811,7 +811,7 @@ H5B2__cache_int_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le
HDassert(internal->hdr);
/* Magic number */
HDmemcpy(image, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1212,7 +1212,7 @@ H5B2__cache_leaf_serialize(const H5F_t H5_ATTR_UNUSED *f, void *_image, size_t H
HDassert(leaf->hdr);
/* magic number */
HDmemcpy(image, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* version # */

75
src/H5B2int.c
View File

@ -35,6 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5B2pkg.h" /* v2 B-trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
@ -241,17 +242,17 @@ H5B2__split1(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr,
mid_record = old_node_nrec / 2;
/* Copy "upper half" of records to new child */
HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0),
H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0),
H5B2_NAT_NREC(left_native, hdr, mid_record + (unsigned)1),
hdr->cls->nrec_size * (old_node_nrec - (mid_record + (unsigned)1)));
/* Copy "upper half" of node pointers, if the node is an internal node */
if(depth > 1)
HDmemcpy(&(right_node_ptrs[0]), &(left_node_ptrs[mid_record + (unsigned)1]),
H5MM_memcpy(&(right_node_ptrs[0]), &(left_node_ptrs[mid_record + (unsigned)1]),
sizeof(H5B2_node_ptr_t) * (size_t)(old_node_nrec - mid_record));
/* Copy "middle" record to internal node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, mid_record), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, mid_record), hdr->cls->nrec_size);
/* Mark nodes as dirty */
left_child_flags |= H5AC__DIRTIED_FLAG;
@ -510,14 +511,14 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
uint16_t move_nrec = (uint16_t)(*right_nrec - new_right_nrec); /* Number of records to move from right node to left */
/* Copy record from parent node down into left child */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* See if we need to move records from right node */
if(move_nrec > 1)
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, (*left_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (size_t)(move_nrec - 1));
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, (*left_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (size_t)(move_nrec - 1));
/* Move record from right node into parent node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), hdr->cls->nrec_size);
/* Slide records in right node down */
HDmemmove(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(right_native, hdr, move_nrec), hdr->cls->nrec_size * new_right_nrec);
@ -534,7 +535,7 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
right_moved_nrec -= (hssize_t)moved_nrec;
/* Copy node pointers from right node to left */
HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * move_nrec);
H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * move_nrec);
/* Slide node pointers in right node down */
HDmemmove(&(right_node_ptrs[0]), &(right_node_ptrs[move_nrec]), sizeof(H5B2_node_ptr_t) * (new_right_nrec + (unsigned)1));
@ -569,14 +570,14 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
hdr->cls->nrec_size * (*right_nrec));
/* Copy record from parent node down into right child */
HDmemcpy(H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* See if we need to move records from left node */
if(move_nrec > 1)
HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, ((*left_nrec - move_nrec) + 1)), hdr->cls->nrec_size * (size_t)(move_nrec - 1));
H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, ((*left_nrec - move_nrec) + 1)), hdr->cls->nrec_size * (size_t)(move_nrec - 1));
/* Move record from left node into parent node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, (*left_nrec - move_nrec)), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, (*left_nrec - move_nrec)), hdr->cls->nrec_size);
/* Handle node pointers, if we have an internal node */
if(depth > 1) {
@ -587,7 +588,7 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
HDmemmove(&(right_node_ptrs[move_nrec]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
/* Copy node pointers from left node to right */
HDmemcpy(&(right_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * move_nrec);
H5MM_memcpy(&(right_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * move_nrec);
/* Count the number of records being moved */
for(u = 0; u < move_nrec; u++)
@ -775,16 +776,16 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
uint16_t moved_middle_nrec = 0; /* Number of records moved into left node */
/* Move left parent record down to left node */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
/* Move records from middle node into left node */
if((new_left_nrec - 1) > *left_nrec) {
moved_middle_nrec = (uint16_t)(new_left_nrec - (*left_nrec + 1));
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * moved_middle_nrec);
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * moved_middle_nrec);
} /* end if */
/* Move record from middle node up to parent node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, moved_middle_nrec), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, moved_middle_nrec), hdr->cls->nrec_size);
moved_middle_nrec++;
/* Slide records in middle node down */
@ -798,7 +799,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
/* Move middle node pointers into left node */
move_nptrs = (unsigned)(new_left_nrec - *left_nrec);
HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t)*move_nptrs);
H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t)*move_nptrs);
/* Count the number of records being moved into the left node */
for(u = 0, moved_nrec = 0; u < move_nptrs; u++)
@ -832,14 +833,14 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
HDmemmove(H5B2_NAT_NREC(right_native, hdr, right_nrec_move), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec));
/* Move right parent record down to right node */
HDmemcpy(H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* Move records from middle node into right node */
if(right_nrec_move > 1)
HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, ((curr_middle_nrec - right_nrec_move) + 1)), hdr->cls->nrec_size * (right_nrec_move - 1));
H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, ((curr_middle_nrec - right_nrec_move) + 1)), hdr->cls->nrec_size * (right_nrec_move - 1));
/* Move record from middle node up to parent node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec - right_nrec_move)), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec - right_nrec_move)), hdr->cls->nrec_size);
/* Move node pointers also if this is an internal node */
if(depth > 1) {
@ -850,7 +851,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
HDmemmove(&(right_node_ptrs[right_nrec_move]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
/* Move middle node pointers into right node */
HDmemcpy(&(right_node_ptrs[0]), &(middle_node_ptrs[(curr_middle_nrec - right_nrec_move) + 1]), sizeof(H5B2_node_ptr_t) * right_nrec_move);
H5MM_memcpy(&(right_node_ptrs[0]), &(middle_node_ptrs[(curr_middle_nrec - right_nrec_move) + 1]), sizeof(H5B2_node_ptr_t) * right_nrec_move);
/* Count the number of records being moved into the right node */
for(u = 0, moved_nrec = 0; u < right_nrec_move; u++)
@ -881,14 +882,14 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
HDmemmove(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * curr_middle_nrec);
/* Move left parent record down to middle node */
HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
/* Move left records to middle node */
if(left_nrec_move > 1)
HDmemmove(H5B2_NAT_NREC(middle_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, new_left_nrec + 1), hdr->cls->nrec_size * (left_nrec_move - 1));
/* Move left parent record up from left node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(left_native, hdr, new_left_nrec), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(left_native, hdr, new_left_nrec), hdr->cls->nrec_size);
/* Move node pointers also if this is an internal node */
if(depth > 1) {
@ -899,7 +900,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
HDmemmove(&(middle_node_ptrs[left_nrec_move]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(curr_middle_nrec + 1));
/* Move left node pointers into middle node */
HDmemcpy(&(middle_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * left_nrec_move);
H5MM_memcpy(&(middle_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * left_nrec_move);
/* Count the number of records being moved into the left node */
for(u = 0, moved_nrec = 0; u < left_nrec_move; u++)
@ -927,13 +928,13 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
unsigned right_nrec_move = (unsigned)(*right_nrec - new_right_nrec); /* Number of records to move out of right node */
/* Move right parent record down to middle node */
HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, curr_middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, curr_middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* Move right records to middle node */
HDmemmove(H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (right_nrec_move - 1));
/* Move right parent record up from right node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), hdr->cls->nrec_size);
/* Slide right records down */
HDmemmove(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(right_native, hdr, right_nrec_move), hdr->cls->nrec_size * new_right_nrec);
@ -944,7 +945,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
unsigned u; /* Local index variable */
/* Move right node pointers into middle node */
HDmemcpy(&(middle_node_ptrs[curr_middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * right_nrec_move);
H5MM_memcpy(&(middle_node_ptrs[curr_middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * right_nrec_move);
/* Count the number of records being moved into the right node */
for(u = 0, moved_nrec = 0; u < right_nrec_move; u++)
@ -1113,14 +1114,14 @@ H5B2__merge2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr,
/* Redistribute records into left node */
{
/* Copy record from parent node to proper location */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* Copy records from right node to left node */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec));
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec));
/* Copy node pointers from right node into left node */
if(depth > 1)
HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
/* Update flush dependencies for grandchildren, if using SWMR */
if(hdr->swmr_write && depth > 1)
@ -1304,13 +1305,13 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr,
middle_moved_nrec = middle_nrec_move;
/* Copy record from parent node to proper location in left node */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size);
/* Copy records from middle node to left node */
HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * (middle_nrec_move - 1));
H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * (middle_nrec_move - 1));
/* Copy record from middle node to proper location in parent node */
HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, (middle_nrec_move - 1)), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, (middle_nrec_move - 1)), hdr->cls->nrec_size);
/* Slide records in middle node down */
HDmemmove(H5B2_NAT_NREC(middle_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, middle_nrec_move), hdr->cls->nrec_size * (*middle_nrec - middle_nrec_move));
@ -1320,7 +1321,7 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr,
unsigned u; /* Local index variable */
/* Copy node pointers from middle node into left node */
HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * middle_nrec_move);
H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * middle_nrec_move);
/* Count the number of records being moved into the left node */
for(u = 0; u < middle_nrec_move; u++)
@ -1348,15 +1349,15 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr,
/* Redistribute records into middle node */
{
/* Copy record from parent node to proper location in middle node */
HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size);
/* Copy records from right node to middle node */
HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec));
H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec));
/* Move node pointers also if this is an internal node */
if(depth > 1)
/* Copy node pointers from right node into middle node */
HDmemcpy(&(middle_node_ptrs[*middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
H5MM_memcpy(&(middle_node_ptrs[*middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1));
/* Update flush dependencies for grandchildren, if using SWMR */
if(hdr->swmr_write && depth > 1)
@ -1539,7 +1540,7 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal node pointers")
/* Copy the node pointers */
HDmemcpy(node_ptrs, internal->node_ptrs, (sizeof(H5B2_node_ptr_t) * (size_t)(curr_node->node_nrec + 1)));
H5MM_memcpy(node_ptrs, internal->node_ptrs, (sizeof(H5B2_node_ptr_t) * (size_t)(curr_node->node_nrec + 1)));
} /* end if */
else {
H5B2_leaf_t *leaf; /* Pointer to leaf node */
@ -1559,7 +1560,7 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal native keys")
/* Copy the native keys */
HDmemcpy(native, node_native, (hdr->cls->nrec_size * curr_node->node_nrec));
H5MM_memcpy(native, node_native, (hdr->cls->nrec_size * curr_node->node_nrec));
/* Unlock the node */
if(H5AC_unprotect(hdr->f, curr_node_class, curr_node->addr, node, (unsigned)(hdr->swmr_write ? H5AC__PIN_ENTRY_FLAG : H5AC__NO_FLAGS_SET)) < 0)

14
src/H5B2leaf.c
View File

@ -412,7 +412,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr,
if(hdr->min_native_rec == NULL)
if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info")
HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
if(idx == (unsigned)(leaf->nrec - 1)) {
@ -420,7 +420,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr,
if(hdr->max_native_rec == NULL)
if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info")
HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
} /* end if */
@ -561,7 +561,7 @@ H5B2__update_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr,
if(hdr->min_native_rec == NULL)
if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info")
HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
if(idx == (unsigned)(leaf->nrec - 1)) {
@ -569,7 +569,7 @@ H5B2__update_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr,
if(hdr->max_native_rec == NULL)
if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info")
HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size);
} /* end if */
} /* end if */
} /* end if */
@ -664,9 +664,9 @@ H5B2__swap_leaf(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal,
} /* end else */
/* Swap records (use disk page as temporary buffer) */
HDmemcpy(hdr->page, H5B2_NAT_NREC(child_native, hdr, 0), hdr->cls->nrec_size);
HDmemcpy(H5B2_NAT_NREC(child_native, hdr, 0), swap_loc, hdr->cls->nrec_size);
HDmemcpy(swap_loc, hdr->page, hdr->cls->nrec_size);
H5MM_memcpy(hdr->page, H5B2_NAT_NREC(child_native, hdr, 0), hdr->cls->nrec_size);
H5MM_memcpy(H5B2_NAT_NREC(child_native, hdr, 0), swap_loc, hdr->cls->nrec_size);
H5MM_memcpy(swap_loc, hdr->page, hdr->cls->nrec_size);
/* Mark parent as dirty */
*internal_flags_ptr |= H5AC__DIRTIED_FLAG;

3
src/H5Bcache.c
View File

@ -35,6 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Bpkg.h" /* B-link trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -304,7 +305,7 @@ H5B__cache_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED len,
HDassert(shared->type->encode);
/* magic number */
HDmemcpy(image, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += 4;
/* node type and level */

14
src/H5C.c
View File

@ -2285,7 +2285,7 @@ H5C_protect(H5F_t * f,
if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE)))
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
if(0 == mpi_rank)
if(H5C__generate_image(f, cache_ptr, entry_ptr) < 0)
@ -6042,7 +6042,7 @@ H5C__flush_single_entry(H5F_t *f, H5C_cache_entry_t *entry_ptr, unsigned flags)
if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE)))
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
} /* end if */
@ -6542,7 +6542,7 @@ H5C_load_entry(H5F_t * f,
if(NULL == (image = (uint8_t *)H5MM_malloc(len + H5C_IMAGE_EXTRA_SPACE)))
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
#ifdef H5_HAVE_PARALLEL
@ -6580,7 +6580,7 @@ H5C_load_entry(H5F_t * f,
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "image null after H5MM_realloc()")
image = (uint8_t *)new_image;
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
} /* end if */
@ -6624,7 +6624,7 @@ H5C_load_entry(H5F_t * f,
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "image null after H5MM_realloc()")
image = (uint8_t *)new_image;
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(image + actual_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(image + actual_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
if(actual_len > len) {
@ -8456,7 +8456,7 @@ H5C__serialize_single_entry(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t *entry
if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE)) )
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + image_size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + image_size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
} /* end if */
@ -8573,7 +8573,7 @@ H5C__generate_image(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t *entry_ptr)
if(NULL == (entry_ptr->image_ptr = H5MM_realloc(entry_ptr->image_ptr, new_len + H5C_IMAGE_EXTRA_SPACE)))
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + new_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + new_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
/* Update statistics for resizing the entry */

12
src/H5CX.c
View File

@ -76,7 +76,7 @@
#define H5CX_RETRIEVE_PROP_COMMON(PL, DEF_PL, PROP_NAME, PROP_FIELD) \
/* Check for default property list */ \
if((*head)->ctx.H5_GLUE(PL,_id) == (DEF_PL)) \
HDmemcpy(&(*head)->ctx.PROP_FIELD, &H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD, sizeof(H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD)); \
H5MM_memcpy(&(*head)->ctx.PROP_FIELD, &H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD, sizeof(H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD)); \
else { \
/* Retrieve the property list */ \
H5CX_RETRIEVE_PLIST(PL, FAIL) \
@ -776,7 +776,7 @@ H5CX_retrieve_state(H5CX_state_t **api_state)
/* Keep a copy of the VOL connector property, if there is one */
if((*head)->ctx.vol_connector_prop_valid && (*head)->ctx.vol_connector_prop.connector_id > 0) {
/* Get the connector property */
HDmemcpy(&(*api_state)->vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t));
H5MM_memcpy(&(*api_state)->vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t));
/* Check for actual VOL connector property */
if((*api_state)->vol_connector_prop.connector_id) {
@ -852,7 +852,7 @@ H5CX_restore_state(const H5CX_state_t *api_state)
/* Restore the VOL connector info */
if(api_state->vol_connector_prop.connector_id) {
HDmemcpy(&(*head)->ctx.vol_connector_prop, &api_state->vol_connector_prop, sizeof(H5VL_connector_prop_t));
H5MM_memcpy(&(*head)->ctx.vol_connector_prop, &api_state->vol_connector_prop, sizeof(H5VL_connector_prop_t));
(*head)->ctx.vol_connector_prop_valid = TRUE;
} /* end if */
@ -1271,7 +1271,7 @@ H5CX_set_vol_connector_prop(const H5VL_connector_prop_t *vol_connector_prop)
HDassert(head && *head);
/* Set the API context value */
HDmemcpy(&(*head)->ctx.vol_connector_prop, vol_connector_prop, sizeof(H5VL_connector_prop_t));
H5MM_memcpy(&(*head)->ctx.vol_connector_prop, vol_connector_prop, sizeof(H5VL_connector_prop_t));
/* Mark the value as valid */
(*head)->ctx.vol_connector_prop_valid = TRUE;
@ -1396,7 +1396,7 @@ H5CX_get_vol_connector_prop(H5VL_connector_prop_t *vol_connector_prop)
/* Check for value that was set */
if((*head)->ctx.vol_connector_prop_valid)
/* Get the value */
HDmemcpy(vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t));
H5MM_memcpy(vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t));
else
HDmemset(vol_connector_prop, 0, sizeof(H5VL_connector_prop_t));
@ -1601,7 +1601,7 @@ H5CX_get_btree_split_ratios(double split_ratio[3])
H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_BTREE_SPLIT_RATIO_NAME, btree_split_ratio)
/* Get the B-tree split ratio values */
HDmemcpy(split_ratio, &(*head)->ctx.btree_split_ratio, sizeof((*head)->ctx.btree_split_ratio));
H5MM_memcpy(split_ratio, &(*head)->ctx.btree_split_ratio, sizeof((*head)->ctx.btree_split_ratio));
done:
FUNC_LEAVE_NOAPI(ret_value)

12
src/H5Cimage.c
View File

@ -2020,11 +2020,11 @@ H5C__decode_cache_image_entry(const H5F_t *f, const H5C_t *cache_ptr,
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
/* Copy the entry image from the cache image block */
HDmemcpy(image_ptr, p, size);
H5MM_memcpy(image_ptr, p, size);
p += size;
/* Copy data into target */
@ -2219,7 +2219,7 @@ H5C__encode_cache_image_header(const H5F_t *f, const H5C_t *cache_ptr,
p = *buf;
/* write signature */
HDmemcpy(p, H5C__MDCI_BLOCK_SIGNATURE, (size_t)H5C__MDCI_BLOCK_SIGNATURE_LEN);
H5MM_memcpy(p, H5C__MDCI_BLOCK_SIGNATURE, (size_t)H5C__MDCI_BLOCK_SIGNATURE_LEN);
p += H5C__MDCI_BLOCK_SIGNATURE_LEN;
/* write version */
@ -2355,7 +2355,7 @@ H5C__encode_cache_image_entry(H5F_t *f, H5C_t *cache_ptr, uint8_t **buf,
H5F_addr_encode(f, &p, ie_ptr->fd_parent_addrs[u]);
/* Copy entry image */
HDmemcpy(p, ie_ptr->image_ptr, ie_ptr->size);
H5MM_memcpy(p, ie_ptr->image_ptr, ie_ptr->size);
p += ie_ptr->size;
/* Update buffer pointer */
@ -3422,11 +3422,11 @@ H5C__reconstruct_cache_entry(const H5F_t *f, H5C_t *cache_ptr,
if(NULL == (pf_entry_ptr->image_ptr = H5MM_malloc(pf_entry_ptr->size + H5C_IMAGE_EXTRA_SPACE)))
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer")
#if H5C_DO_MEMORY_SANITY_CHECKS
HDmemcpy(((uint8_t *)pf_entry_ptr->image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
H5MM_memcpy(((uint8_t *)pf_entry_ptr->image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE);
#endif /* H5C_DO_MEMORY_SANITY_CHECKS */
/* Copy the entry image from the cache image block */
HDmemcpy(pf_entry_ptr->image_ptr, p, pf_entry_ptr->size);
H5MM_memcpy(pf_entry_ptr->image_ptr, p, pf_entry_ptr->size);
p += pf_entry_ptr->size;
/* Initialize the rest of the fields in the prefetched entry */

5
src/H5Dbtree.c
View File

@ -39,6 +39,7 @@
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Sprivate.h" /* Dataspaces */
#include "H5VMprivate.h" /* Vector and array functions */
@ -847,7 +848,7 @@ H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store,
/* Set up the "local" information for this dataset's chunks */
if(NULL == (my_layout = H5FL_MALLOC(H5O_layout_chunk_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk layout")
HDmemcpy(my_layout, layout, sizeof(H5O_layout_chunk_t));
H5MM_memcpy(my_layout, layout, sizeof(H5O_layout_chunk_t));
shared->udata = my_layout;
/* Make shared B-tree info reference counted */
@ -1087,7 +1088,7 @@ H5D__btree_idx_iterate_cb(H5F_t H5_ATTR_UNUSED *f, const void *_lt_key,
HDcompile_assert(sizeof(chunk_rec.filter_mask) == sizeof(lt_key->filter_mask));
/* Compose generic chunk record for callback */
HDmemcpy(&chunk_rec, lt_key, sizeof(*lt_key));
H5MM_memcpy(&chunk_rec, lt_key, sizeof(*lt_key));
chunk_rec.chunk_addr = addr;
/* Make "generic chunk" callback */

3
src/H5Dbtree2.c
View File

@ -32,6 +32,7 @@
#include "H5Dpkg.h" /* Datasets */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector and array functions */
@ -248,7 +249,7 @@ H5D__bt2_crt_context(void *_udata)
/* Set up the "local" information for this dataset's chunk dimension sizes */
if(NULL == (my_dim = (uint32_t *)H5FL_BLK_MALLOC(chunk_dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate chunk dims")
HDmemcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t));
H5MM_memcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t));
ctx->dim = my_dim;
/*

82
src/H5Dchunk.c
View File

@ -313,6 +313,7 @@ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{
H5D__chunk_construct,
H5D__chunk_init,
H5D__chunk_is_space_alloc,
H5D__chunk_is_data_cached,
H5D__chunk_io_init,
H5D__chunk_read,
H5D__chunk_write,
@ -340,6 +341,7 @@ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{
NULL,
NULL,
NULL,
NULL,
#ifdef H5_HAVE_PARALLEL
NULL,
NULL,
@ -394,10 +396,13 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset,
FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
/* Sanity checks */
HDassert(layout->type == H5D_CHUNKED);
io_info.dset = dset;
/* Allocate dataspace and initialize it if it hasn't been. */
if(!(*layout->ops->is_space_alloc)(&layout->storage))
if(!H5D__chunk_is_space_alloc(&layout->storage))
/* Allocate storage */
if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
@ -435,13 +440,17 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset,
if(0 == idx_info.pline->nused && H5F_addr_defined(old_chunk.offset))
/* If there are no filters and we are overwriting the chunk we can just set values */
need_insert = FALSE;
else
else {
/* Otherwise, create the chunk it if it doesn't exist, or reallocate the chunk
* if its size has changed.
*/
if(H5D__chunk_file_alloc(&idx_info, &old_chunk, &udata.chunk_block, &need_insert, scaled) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk")
/* Cache the new chunk information */
H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata);
} /* end else */
/* Make sure the address of the chunk is returned. */
if(!H5F_addr_defined(udata.chunk_block.offset))
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk address isn't defined")
@ -506,7 +515,8 @@ H5D__chunk_direct_read(const H5D_t *dset, hsize_t *offset, uint32_t* filters,
*filters = 0;
/* Allocate dataspace and initialize it if it hasn't been. */
if(!(*layout->ops->is_space_alloc)(&layout->storage))
if(!H5D__chunk_is_space_alloc(&layout->storage)
&& !H5D__chunk_is_data_cached(dset->shared))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized")
/* Calculate the index of this chunk */
@ -1017,6 +1027,30 @@ H5D__chunk_is_space_alloc(const H5O_storage_t *storage)
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_is_space_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D__chunk_is_data_cached
*
* Purpose: Query if raw data is cached for dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Neil Fortner
* Wednessday, March 6, 2016
*
*-------------------------------------------------------------------------
*/
hbool_t
H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset)
{
FUNC_ENTER_PACKAGE_NOERR
/* Sanity checks */
HDassert(shared_dset);
FUNC_LEAVE_NOAPI(shared_dset->cache.chunk.nused > 0)
} /* end H5D__chunk_is_data_cached() */
/*-------------------------------------------------------------------------
* Function: H5D__chunk_io_init
@ -1654,7 +1688,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
new_chunk_info->mspace_shared = FALSE;
/* Copy the chunk's scaled coordinates */
HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
H5MM_memcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
new_chunk_info->scaled[fm->f_ndims] = 0;
/* Insert the new chunk into the skip list */
@ -1914,9 +1948,9 @@ H5D__chunk_file_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type,
chunk_info->chunk_points = 0;
/* Set the chunk's scaled coordinates */
HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
chunk_info->scaled[fm->f_ndims] = 0;
HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims);
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) {
@ -2157,11 +2191,11 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HDassert(fm);
/* Set up "nonexistent" I/O info object */
HDmemcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info));
H5MM_memcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info));
nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT;
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
@ -2169,7 +2203,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
@ -2307,7 +2341,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HDassert(fm);
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
@ -2315,7 +2349,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
@ -2670,7 +2704,7 @@ H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *ud
HDassert(udata->common.scaled);
/* Stored the information to cache */
HDmemcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims);
H5MM_memcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims);
last->addr = udata->chunk_block.offset;
H5_CHECKED_ASSIGN(last->nbytes, uint32_t, udata->chunk_block.length, hsize_t);
last->chunk_idx = udata->chunk_idx;
@ -3039,7 +3073,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset)
*/
if(NULL == (buf = H5MM_malloc(alloc)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline")
HDmemcpy(buf, ent->chunk, alloc);
H5MM_memcpy(buf, ent->chunk, alloc);
} /* end if */
else {
/*
@ -3452,7 +3486,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
*/
if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
HDmemcpy(chunk, ent->chunk, chunk_size);
H5MM_memcpy(chunk, ent->chunk, chunk_size);
ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline);
ent->chunk = (uint8_t *)chunk;
chunk = NULL;
@ -3478,7 +3512,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
*/
if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
HDmemcpy(chunk, ent->chunk, chunk_size);
H5MM_memcpy(chunk, ent->chunk, chunk_size);
ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline);
ent->chunk = (uint8_t *)chunk;
@ -3607,7 +3641,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
(void)H5D__chunk_mem_xfree(tmp_chunk, old_pline);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
} /* end if */
HDmemcpy(chunk, tmp_chunk, chunk_size);
H5MM_memcpy(chunk, tmp_chunk, chunk_size);
(void)H5D__chunk_mem_xfree(tmp_chunk, old_pline);
} /* end if */
} /* end if */
@ -3688,7 +3722,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
ent->chunk_block.offset = chunk_addr;
ent->chunk_block.length = chunk_alloc;
ent->chunk_idx = udata->chunk_idx;
HDmemcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims);
H5MM_memcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims);
H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t);
H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t);
ent->chunk = (uint8_t *)chunk;
@ -3816,7 +3850,7 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata,
fake_ent.edge_chunk_state = H5D_RDCC_DISABLE_FILTERS;
if(udata->new_unfilt_chunk)
fake_ent.edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS;
HDmemcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims);
H5MM_memcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims);
HDassert(layout->u.chunk.size > 0);
fake_ent.chunk_idx = udata->chunk_idx;
fake_ent.chunk_block.offset = udata->chunk_block.offset;
@ -4103,7 +4137,7 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_
if(has_unfilt_edge_chunks) {
if(NULL == (unfilt_fill_buf = H5D__chunk_mem_alloc(orig_chunk_size, &def_pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
HDmemcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size);
H5MM_memcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size);
} /* end if */
/* Retrieve filter settings from API context */
@ -5637,7 +5671,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
if(udata->chunk_in_cache && udata->chunk) {
HDassert(!H5F_addr_defined(chunk_rec->chunk_addr));
HDmemcpy(buf, udata->chunk, nbytes);
H5MM_memcpy(buf, udata->chunk, nbytes);
udata->chunk = NULL;
}
else {
@ -5671,7 +5705,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HDassert(H5F_addr_defined(ent->chunk_block.offset));
H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t);
HDmemcpy(buf, ent->chunk, nbytes);
H5MM_memcpy(buf, ent->chunk, nbytes);
}
else {
/* read chunk data from the source file */
@ -5705,7 +5739,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, reclaim_buf_size);
H5MM_memcpy(reclaim_buf, buf, reclaim_buf_size);
/* Set background buffer to all zeros */
HDmemset(bkg, 0, buf_size);
@ -5736,7 +5770,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
} /* end if */
/* After fix ref, copy the new reference elements to the buffer to write out */
HDmemcpy(buf, bkg, buf_size);
H5MM_memcpy(buf, bkg, buf_size);
} /* end if */
/* Set up destination chunk callback information for insertion */
@ -6036,7 +6070,7 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src,
for(ent = shared_fo->cache.chunk.head; ent; ent = next) {
if(!H5F_addr_defined(ent->chunk_block.offset)) {
HDmemcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled));
H5MM_memcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled));
udata.chunk = ent->chunk;
udata.chunk_in_cache = TRUE;
if(H5D__chunk_copy_cb(&chunk_rec, &udata) < 0)

11
src/H5Dcompact.c
View File

@ -80,6 +80,7 @@ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{
H5D__compact_construct,
NULL,
H5D__compact_is_space_alloc,
NULL,
H5D__compact_io_init,
H5D__contig_read,
H5D__contig_write,
@ -528,7 +529,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds
if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
HDmemcpy(buf, storage_src->buf, storage_src->size);
H5MM_memcpy(buf, storage_src->buf, storage_src->size);
/* allocate temporary bkg buff for data conversion */
if(NULL == (bkg = H5FL_BLK_MALLOC(type_conv, buf_size)))
@ -539,7 +540,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, buf_size);
H5MM_memcpy(reclaim_buf, buf, buf_size);
/* Set background buffer to all zeros */
HDmemset(bkg, 0, buf_size);
@ -548,7 +549,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
HDmemcpy(storage_dst->buf, buf, storage_dst->size);
H5MM_memcpy(storage_dst->buf, buf, storage_dst->size);
if(H5D_vlen_reclaim(tid_mem, buf_space, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data")
@ -573,11 +574,11 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds
} /* end if */
else
/* Type conversion not necessary */
HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size);
H5MM_memcpy(storage_dst->buf, storage_src->buf, storage_src->size);
} /* end if */
else
/* Type conversion not necessary */
HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size);
H5MM_memcpy(storage_dst->buf, storage_src->buf, storage_src->size);
/* Mark destination buffer as dirty */
storage_dst->dirty = TRUE;

48
src/H5Dcontig.c
View File

@ -40,6 +40,7 @@
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5FOprivate.h" /* File objects */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
@ -118,6 +119,7 @@ const H5D_layout_ops_t H5D_LOPS_CONTIG[1] = {{
H5D__contig_construct,
H5D__contig_init,
H5D__contig_is_space_alloc,
H5D__contig_is_data_cached,
H5D__contig_io_init,
H5D__contig_read,
H5D__contig_write,
@ -536,6 +538,30 @@ H5D__contig_is_space_alloc(const H5O_storage_t *storage)
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__contig_is_space_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D__contig_is_data_cached
*
* Purpose: Query if raw data is cached for dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Neil Fortner
* Wednessday, March 6, 2016
*
*-------------------------------------------------------------------------
*/
hbool_t
H5D__contig_is_data_cached(const H5D_shared_t *shared_dset)
{
FUNC_ENTER_PACKAGE_NOERR
/* Sanity checks */
HDassert(shared_dset);
FUNC_LEAVE_NOAPI(shared_dset->cache.contig.sieve_size > 0)
} /* end H5D__contig_is_data_cached() */
/*-------------------------------------------------------------------------
* Function: H5D__contig_io_init
@ -751,7 +777,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed")
/* Grab the data out of the buffer (must be first piece of data in buffer ) */
HDmemcpy(buf, dset_contig->sieve_buf, len);
H5MM_memcpy(buf, dset_contig->sieve_buf, len);
/* Reset sieve buffer dirty flag */
dset_contig->sieve_dirty = FALSE;
@ -766,7 +792,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start);
/* Grab the data out of the buffer */
HDmemcpy(buf, base_sieve_buf, len);
H5MM_memcpy(buf, base_sieve_buf, len);
} /* end if */
/* Entire request is not within this data sieve buffer */
else {
@ -825,7 +851,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed")
/* Grab the data out of the buffer (must be first piece of data in buffer ) */
HDmemcpy(buf, dset_contig->sieve_buf, len);
H5MM_memcpy(buf, dset_contig->sieve_buf, len);
/* Reset sieve buffer dirty flag */
dset_contig->sieve_dirty = FALSE;
@ -1023,7 +1049,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
} /* end if */
/* Grab the data out of the buffer (must be first piece of data in buffer ) */
HDmemcpy(dset_contig->sieve_buf, buf, len);
H5MM_memcpy(dset_contig->sieve_buf, buf, len);
/* Set sieve buffer dirty flag */
dset_contig->sieve_dirty = TRUE;
@ -1043,7 +1069,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start);
/* Put the data into the sieve buffer */
HDmemcpy(base_sieve_buf, buf, len);
H5MM_memcpy(base_sieve_buf, buf, len);
/* Set sieve buffer dirty flag */
dset_contig->sieve_dirty = TRUE;
@ -1086,7 +1112,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
HDmemmove(dset_contig->sieve_buf + len, dset_contig->sieve_buf, dset_contig->sieve_size);
/* Copy in new information (must be first in sieve buffer) */
HDmemcpy(dset_contig->sieve_buf, buf, len);
H5MM_memcpy(dset_contig->sieve_buf, buf, len);
/* Adjust sieve location */
dset_contig->sieve_loc = addr;
@ -1095,7 +1121,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
/* Append to existing sieve buffer */
else {
/* Copy in new information */
HDmemcpy(dset_contig->sieve_buf + sieve_size, buf, len);
H5MM_memcpy(dset_contig->sieve_buf + sieve_size, buf, len);
} /* end else */
/* Adjust sieve size */
@ -1139,7 +1165,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
} /* end if */
/* Grab the data out of the buffer (must be first piece of data in buffer ) */
HDmemcpy(dset_contig->sieve_buf, buf, len);
H5MM_memcpy(dset_contig->sieve_buf, buf, len);
/* Set sieve buffer dirty flag */
dset_contig->sieve_dirty = TRUE;
@ -1494,7 +1520,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src,
if(try_sieve && (addr_src >= sieve_start) && ((addr_src + src_nbytes -1) < sieve_end)) {
unsigned char *base_sieve_buf = shared_fo->cache.contig.sieve_buf + (addr_src - sieve_start);
HDmemcpy(buf, base_sieve_buf, src_nbytes);
H5MM_memcpy(buf, base_sieve_buf, src_nbytes);
} else
/* Read raw data from source file */
if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, src_nbytes, buf) < 0)
@ -1507,7 +1533,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src,
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, mem_nbytes);
H5MM_memcpy(reclaim_buf, buf, mem_nbytes);
/* Set background buffer to all zeros */
HDmemset(bkg, 0, buf_size);
@ -1533,7 +1559,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src,
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
/* After fix ref, copy the new reference elements to the buffer to write out */
HDmemcpy(buf, bkg, buf_size);
H5MM_memcpy(buf, bkg, buf_size);
} /* end if */
else
/* Reset value to zero */

7
src/H5Dearray.c
View File

@ -37,6 +37,7 @@
#include "H5EAprivate.h" /* Extensible arrays */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector functions */
@ -1197,11 +1198,11 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout)
hsize_t swizzled_max_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of max # of chunks in each dimension */
/* Get the swizzled chunk dimensions */
HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0]));
H5MM_memcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0]));
H5VM_swizzle_coords(uint32_t, layout->u.earray.swizzled_dim, layout->u.earray.unlim_dim);
/* Get the swizzled number of chunks in each dimension */
HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0]));
H5MM_memcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0]));
H5VM_swizzle_coords(hsize_t, swizzled_chunks, layout->u.earray.unlim_dim);
/* Get the swizzled "down" sizes for each dimension */
@ -1209,7 +1210,7 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value")
/* Get the swizzled max number of chunks in each dimension */
HDmemcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0]));
H5MM_memcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0]));
H5VM_swizzle_coords(hsize_t, swizzled_max_chunks, layout->u.earray.unlim_dim);
/* Get the swizzled max "down" sizes for each dimension */

3
src/H5Defl.c
View File

@ -91,6 +91,7 @@ const H5D_layout_ops_t H5D_LOPS_EFL[1] = {{
H5D__efl_construct,
NULL,
H5D__efl_is_space_alloc,
NULL,
H5D__efl_io_init,
H5D__contig_read,
H5D__contig_write,
@ -226,7 +227,7 @@ H5D__efl_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNU
{
FUNC_ENTER_STATIC_NOERR
HDmemcpy(&io_info->store->efl, &(io_info->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
H5MM_memcpy(&io_info->store->efl, &(io_info->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5D__efl_io_init() */

7
src/H5Dfill.c
View File

@ -38,6 +38,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector and array functions */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -300,7 +301,7 @@ H5D__fill(const void *fill, const H5T_t *fill_type, void *buf,
HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't get actual buffer")
/* Copy the user's data into the buffer for conversion */
HDmemcpy(elem_ptr, fill, src_type_size);
H5MM_memcpy(elem_ptr, fill, src_type_size);
/* If there's no VL type of data, do conversion first then fill the data into
* the memory buffer. */
@ -577,7 +578,7 @@ H5D__fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts)
HDassert(fb_info->fill_buf);
/* Make a copy of the (disk-based) fill value into the buffer */
HDmemcpy(fb_info->fill_buf, fb_info->fill->buf, fb_info->file_elmt_size);
H5MM_memcpy(fb_info->fill_buf, fb_info->fill->buf, fb_info->file_elmt_size);
/* Reset first element of background buffer, if necessary */
if(H5T_path_bkg(fb_info->fill_to_mem_tpath))
@ -603,7 +604,7 @@ H5D__fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts)
if(!buf)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary fill buffer")
HDmemcpy(buf, fb_info->fill_buf, fb_info->fill_buf_size);
H5MM_memcpy(buf, fb_info->fill_buf, fb_info->fill_buf_size);
/* Type convert the dataset buffer, to copy any VL components */
if(H5T_convert(fb_info->mem_to_dset_tpath, fb_info->mem_tid, fb_info->file_tid, nelmts, (size_t)0, (size_t)0, fb_info->fill_buf, fb_info->bkg_buf) < 0)

17
src/H5Dint.c
View File

@ -470,7 +470,7 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the default dataset information */
HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
H5MM_memcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
/* If we are using the default dataset creation property list, during creation
* don't bother to copy it, just increment the reference count
@ -774,7 +774,7 @@ H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr)
/* Shallow copy the fill value property */
/* guards against shared component modification */
HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
if (H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't reset the copied fill property")
@ -1000,7 +1000,7 @@ H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id)
/* Shallow copy the fill value property */
/* (we only want to make certain that the shared component isn't modified) */
HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
/* Reset shared component info */
H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop);
@ -1642,7 +1642,7 @@ H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id)
dset->shared->append_flush.ndims = info.ndims;
dset->shared->append_flush.func = info.func;
dset->shared->append_flush.udata = info.udata;
HDmemcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary));
H5MM_memcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary));
} /* end if */
} /* end if */
} /* end if */
@ -2778,7 +2778,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
/* Keep the current dataspace dimensions for later */
HDcompile_assert(sizeof(curr_dims) == sizeof(dset->shared->curr_dims));
HDmemcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0]));
H5MM_memcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0]));
/* Modify the size of the dataspace */
if((changed = H5S_set_extent(dset->shared->space, size)) < 0)
@ -2898,7 +2898,8 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
*-------------------------------------------------------------------------
*/
if(H5D_CHUNKED == dset->shared->layout.type) {
if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage))
if(shrink && ((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)
|| (dset->shared->layout.ops->is_data_cached && (*dset->shared->layout.ops->is_data_cached)(dset->shared))))
/* Remove excess chunks */
if(H5D__chunk_prune_by_extent(dset, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks")
@ -3062,7 +3063,7 @@ H5D__format_convert(H5D_t *dataset)
idx_info.storage = &dataset->shared->layout.storage.u.chunk;
/* Copy the current layout info to the new layout */
HDmemcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t));
H5MM_memcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t));
/* Set up info for version 1 B-tree in the new layout */
newlayout->version = H5O_LAYOUT_VERSION_3;
@ -3113,7 +3114,7 @@ H5D__format_convert(H5D_t *dataset)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
/* Copy the new layout to the dataset's layout */
HDmemcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t));
H5MM_memcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t));
break;

4
src/H5Dio.c
View File

@ -518,7 +518,8 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
* has been overwritten. So just proceed in reading.
*/
if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 &&
!(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)) {
!(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) &&
!(dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))) {
H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */
/* Retrieve dataset's fill-value properties */
@ -550,6 +551,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* Sanity check that space is allocated, if there are elements */
if(nelmts > 0)
HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)
|| (dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))
|| dataset->shared->dcpl_cache.efl.nused > 0
|| dataset->shared->layout.type == H5D_COMPACT);

20
src/H5Dmpio.c
View File

@ -1427,7 +1427,7 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in
for (i = 0, offset = 0; i < (size_t) mpi_rank; i++)
offset += num_chunks_selected_array[i];
HDmemcpy(chunk_list, &collective_chunk_list[offset], num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t));
H5MM_memcpy(chunk_list, &collective_chunk_list[offset], num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t));
/* Create single MPI type encompassing each selection in the dataspace */
if (H5D__mpio_filtered_collective_write_type(chunk_list, chunk_list_num_entries,
@ -1553,7 +1553,7 @@ if(H5DEBUG(D))
HGOTO_ERROR(H5E_DATASET, H5E_CANTRECV, FAIL, "unable to obtain MPIO mode")
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
@ -1561,7 +1561,7 @@ if(H5DEBUG(D))
ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size;
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
@ -1788,7 +1788,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list")
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
@ -1893,7 +1893,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i
/* Collect the new chunk info back to the local copy, since only the record in the
* collective array gets updated by the chunk re-allocation */
HDmemcpy(&chunk_list[i].chunk_states.new_chunk, &collective_chunk_list[offset].chunk_states.new_chunk, sizeof(chunk_list[i].chunk_states.new_chunk));
H5MM_memcpy(&chunk_list[i].chunk_states.new_chunk, &collective_chunk_list[offset].chunk_states.new_chunk, sizeof(chunk_list[i].chunk_states.new_chunk));
H5_CHECKED_ASSIGN(mpi_type_count, int, chunk_list[i].chunk_states.new_chunk.length, hsize_t);
@ -2517,8 +2517,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
/* merge buffer io_mode info and chunk addr into one */
HDmemcpy(mergebuf, assign_io_mode, total_chunks);
HDmemcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks);
H5MM_memcpy(mergebuf, assign_io_mode, total_chunks);
H5MM_memcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks);
H5MM_free(nproc_per_chunk);
} /* end if */
@ -2527,8 +2527,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
if(MPI_SUCCESS != (mpi_code = MPI_Bcast(mergebuf, ((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code)
HDmemcpy(assign_io_mode, mergebuf, total_chunks);
HDmemcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks);
H5MM_memcpy(assign_io_mode, mergebuf, total_chunks);
H5MM_memcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks);
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
{
@ -2630,7 +2630,7 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
local_info_array[i].async_info.receive_buffer_array = NULL;
local_info_array[i].async_info.receive_requests_array = NULL;
HDmemcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled));
H5MM_memcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled));
if ((select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")

9
src/H5Dpkg.h
View File

@ -113,12 +113,14 @@ typedef struct H5D_type_info_t {
/* Forward declaration of structs used below */
struct H5D_io_info_t;
struct H5D_chunk_map_t;
typedef struct H5D_shared_t H5D_shared_t;
/* Function pointers for I/O on particular types of dataset layouts */
typedef herr_t (*H5D_layout_construct_func_t)(H5F_t *f, H5D_t *dset);
typedef herr_t (*H5D_layout_init_func_t)(H5F_t *f, const H5D_t *dset,
hid_t dapl_id);
typedef hbool_t (*H5D_layout_is_space_alloc_func_t)(const H5O_storage_t *storage);
typedef hbool_t (*H5D_layout_is_data_cached_func_t)(const H5D_shared_t *shared_dset);
typedef herr_t (*H5D_layout_io_init_func_t)(const struct H5D_io_info_t *io_info,
const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
@ -144,6 +146,7 @@ typedef struct H5D_layout_ops_t {
H5D_layout_construct_func_t construct; /* Layout constructor for new datasets */
H5D_layout_init_func_t init; /* Layout initializer for dataset */
H5D_layout_is_space_alloc_func_t is_space_alloc; /* Query routine to determine if storage is allocated */
H5D_layout_is_data_cached_func_t is_data_cached; /* Query routine to determine if any raw data is cached. If routine is not present then the layout type never caches raw data. */
H5D_layout_io_init_func_t io_init; /* I/O initialization routine */
H5D_layout_read_func_t ser_read; /* High-level I/O routine for reading data in serial */
H5D_layout_write_func_t ser_write; /* High-level I/O routine for writing data in serial */
@ -429,7 +432,7 @@ typedef struct H5D_rdcdc_t {
* created once for a given dataset. Thus, if a dataset is opened twice,
* there will be two IDs and two H5D_t structs, both sharing one H5D_shared_t.
*/
typedef struct H5D_shared_t {
struct H5D_shared_t {
size_t fo_count; /* Reference count */
hbool_t closing; /* Flag to indicate dataset is closing */
hid_t type_id; /* ID for dataset's datatype */
@ -459,7 +462,7 @@ typedef struct H5D_shared_t {
H5D_append_flush_t append_flush; /* Append flush property information */
char *extfile_prefix; /* expanded external file prefix */
char *vds_prefix; /* expanded vds prefix */
} H5D_shared_t;
};
struct H5D_t {
H5O_loc_t oloc; /* Object header location */
@ -618,6 +621,7 @@ H5_DLL herr_t H5D__layout_oh_write(const H5D_t *dataset, H5O_t *oh, unsigned upd
/* Functions that operate on contiguous storage */
H5_DLL herr_t H5D__contig_alloc(H5F_t *f, H5O_storage_contig_t *storage);
H5_DLL hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage);
H5_DLL hbool_t H5D__contig_is_data_cached(const H5D_shared_t *shared_dset);
H5_DLL herr_t H5D__contig_fill(const H5D_io_info_t *io_info);
H5_DLL herr_t H5D__contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
@ -636,6 +640,7 @@ H5_DLL htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr,
H5_DLL herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/);
H5_DLL herr_t H5D__chunk_set_info(const H5D_t *dset);
H5_DLL hbool_t H5D__chunk_is_space_alloc(const H5O_storage_t *storage);
H5_DLL hbool_t H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset);
H5_DLL herr_t H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled,
H5D_chunk_ud_t *udata);
H5_DLL herr_t H5D__chunk_allocated(const H5D_t *dset, hsize_t *nbytes);

9
src/H5Dscatgath.c
View File

@ -27,6 +27,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -117,7 +118,7 @@ H5D__scatter_file(const H5D_io_info_t *_io_info,
HDassert(_buf);
/* Set up temporary I/O info object */
HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
tmp_io_info.op_type = H5D_IO_OP_WRITE;
tmp_io_info.u.wbuf = _buf;
@ -220,7 +221,7 @@ H5D__gather_file(const H5D_io_info_t *_io_info,
HDassert(_buf);
/* Set up temporary I/O info object */
HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
tmp_io_info.op_type = H5D_IO_OP_READ;
tmp_io_info.u.rbuf = _buf;
@ -337,7 +338,7 @@ H5D__scatter_mem (const void *_tscat_buf, const H5S_t *space,
/* Get the number of bytes in sequence */
curr_len = len[curr_seq];
HDmemcpy(buf + off[curr_seq], tscat_buf, curr_len);
H5MM_memcpy(buf + off[curr_seq], tscat_buf, curr_len);
/* Advance offset in destination buffer */
tscat_buf += curr_len;
@ -425,7 +426,7 @@ H5D__gather_mem(const void *_buf, const H5S_t *space,
/* Get the number of bytes in sequence */
curr_len = len[curr_seq];
HDmemcpy(tgath_buf, buf + off[curr_seq], curr_len);
H5MM_memcpy(tgath_buf, buf + off[curr_seq], curr_len);
/* Advance offset in gather buffer */
tgath_buf += curr_len;

2
src/H5Dselect.c
View File

@ -227,6 +227,8 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size,
/* Decrement number of elements left to process */
HDassert(((size_t)tmp_file_len % elmt_size) == 0);
if(elmt_size == 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "Resulted in division by zero")
nelmts -= ((size_t)tmp_file_len / elmt_size);
} /* end while */
} /* end else */

56
src/H5Dvirtual.c
View File

@ -78,6 +78,7 @@
/********************/
/* Layout operation callbacks */
static hbool_t H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset);
static herr_t H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t
*type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
@ -121,6 +122,7 @@ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{
NULL,
H5D__virtual_init,
H5D__virtual_is_space_alloc,
H5D__virtual_is_data_cached,
NULL,
H5D__virtual_read,
H5D__virtual_write,
@ -491,11 +493,11 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
/* Encode each entry */
for(i = 0; i < layout->storage.u.virt.list_nused; i++) {
/* Source file name */
HDmemcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]);
H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]);
heap_block_p += str_size[2 * i];
/* Source dataset name */
HDmemcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]);
H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]);
heap_block_p += str_size[(2 * i) + 1];
/* Source selection */
@ -1107,7 +1109,7 @@ H5D__virtual_str_append(const char *src, size_t src_len, char **p, char **buf,
/* Copy string to *p. Note that since src in not NULL terminated, we must
* use memcpy */
(void)HDmemcpy(*p, src, src_len);
(void)H5MM_memcpy(*p, src, src_len);
/* Advance *p */
*p += src_len;
@ -2206,6 +2208,54 @@ H5D__virtual_is_space_alloc(const H5O_storage_t H5_ATTR_UNUSED *storage)
} /* end H5D__virtual_is_space_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D__virtual_is_data_cached
*
* Purpose: Query if raw data is cached for dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Neil Fortner
* Wednessday, March 6, 2016
*
*-------------------------------------------------------------------------
*/
static hbool_t
H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset)
{
const H5O_storage_virtual_t *storage; /* Convenience pointer */
size_t i, j; /* Local index variables */
hbool_t ret_value = FALSE; /* Return value */
FUNC_ENTER_PACKAGE_NOERR
/* Sanity checks */
HDassert(shared_dset);
storage = &shared_dset->layout.storage.u.virt;
/* Iterate over mappings */
for(i = 0; i < storage->list_nused; i++)
/* Check for "printf" source dataset resolution */
if(storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) {
/* Iterate over sub-source dsets */
for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++)
/* Check for cahced data in source dset */
if(storage->list[i].sub_dset[j].dset
&& storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached
&& storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached(storage->list[i].sub_dset[j].dset->shared))
HGOTO_DONE(TRUE);
} /* end if */
else
if(storage->list[i].source_dset.dset
&& storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached
&& storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached(storage->list[i].source_dset.dset->shared))
HGOTO_DONE(TRUE);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__virtual_is_data_cached() */
/*-------------------------------------------------------------------------
* Function: H5D__virtual_pre_io
*

5
src/H5EA.c
View File

@ -46,6 +46,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector functions */
@ -693,7 +694,7 @@ H5EA_set(const H5EA_t *ea, hsize_t idx, const void *elmt))
HDassert(thing_unprot_func);
/* Set element in thing's element buffer */
HDmemcpy(thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size);
thing_cache_flags |= H5AC__DIRTIED_FLAG;
/* Update max. element set in array, if appropriate */
@ -765,7 +766,7 @@ H5EA_get(const H5EA_t *ea, hsize_t idx, void *elmt))
} /* end if */
else
/* Get element from thing's element buffer */
HDmemcpy(elmt, thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(elmt, thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), hdr->cparam.cls->nat_elmt_size);
} /* end else */
CATCH

13
src/H5EAcache.c
View File

@ -41,6 +41,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -479,7 +480,7 @@ H5EA__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le
HDassert(hdr);
/* Magic number */
HDmemcpy(image, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -867,7 +868,7 @@ H5EA__cache_iblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
/* Get temporary pointer to serialized info */
/* Magic number */
HDmemcpy(image, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1179,7 +1180,7 @@ H5EA__cache_sblock_deserialize(const void *_image, size_t len,
size_t tot_page_init_size = sblock->ndblks * sblock->dblk_page_init_size; /* Compute total size of 'page init' buffer */
/* Retrieve the 'page init' bitmasks */
HDmemcpy(sblock->page_init, image, tot_page_init_size);
H5MM_memcpy(sblock->page_init, image, tot_page_init_size);
image += tot_page_init_size;
} /* end if */
@ -1276,7 +1277,7 @@ H5EA__cache_sblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
HDassert(sblock->hdr);
/* Magic number */
HDmemcpy(image, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1298,7 +1299,7 @@ H5EA__cache_sblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
size_t tot_page_init_size = sblock->ndblks * sblock->dblk_page_init_size; /* Compute total size of 'page init' buffer */
/* Store the 'page init' bitmasks */
HDmemcpy(image, sblock->page_init, tot_page_init_size);
H5MM_memcpy(image, sblock->page_init, tot_page_init_size);
image += tot_page_init_size;
} /* end if */
@ -1690,7 +1691,7 @@ H5EA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
HDassert(dblock->hdr);
/* Magic number */
HDmemcpy(image, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */

3
src/H5EAhdr.c
View File

@ -41,6 +41,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
@ -407,7 +408,7 @@ H5EA__hdr_create(H5F_t *f, const H5EA_create_t *cparam, void *ctx_udata))
hdr->idx_blk_addr = HADDR_UNDEF;
/* Set the creation parameters for the array */
HDmemcpy(&hdr->cparam, cparam, sizeof(hdr->cparam));
H5MM_memcpy(&hdr->cparam, cparam, sizeof(hdr->cparam));
/* Finish initializing extensible array header */
if(H5EA__hdr_init(hdr, ctx_udata) < 0)

3
src/H5EAstat.c
View File

@ -40,6 +40,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -108,7 +109,7 @@ HDfprintf(stderr, "%s: Called\n", FUNC);
HDassert(stats);
/* Copy extensible array statistics */
HDmemcpy(stats, &ea->hdr->stats, sizeof(ea->hdr->stats));
H5MM_memcpy(stats, &ea->hdr->stats, sizeof(ea->hdr->stats));
END_FUNC(PRIV) /* end H5EA_get_stats() */

9
src/H5FA.c
View File

@ -41,6 +41,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector functions */
@ -371,7 +372,7 @@ H5FA_set(const H5FA_t *fa, hsize_t idx, const void *elmt))
/* Check for paging data block */
if(!dblock->npages) {
/* Set element in data block */
HDmemcpy(((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), elmt, hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), elmt, hdr->cparam.cls->nat_elmt_size);
dblock_cache_flags |= H5AC__DIRTIED_FLAG;
} /* end if */
else { /* paging */
@ -410,7 +411,7 @@ H5FA_set(const H5FA_t *fa, hsize_t idx, const void *elmt))
H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array data block page, address = %llu", (unsigned long long)dblk_page_addr)
/* Set the element in the data block page */
HDmemcpy(((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size);
dblk_page_cache_flags |= H5AC__DIRTIED_FLAG;
} /* end else */
@ -474,7 +475,7 @@ H5FA_get(const H5FA_t *fa, hsize_t idx, void *elmt))
/* Check for paged data block */
if(!dblock->npages)
/* Retrieve element from data block */
HDmemcpy(elmt, ((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(elmt, ((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), hdr->cparam.cls->nat_elmt_size);
else { /* paging */
size_t page_idx; /* Index of page within data block */
@ -512,7 +513,7 @@ H5FA_get(const H5FA_t *fa, hsize_t idx, void *elmt))
H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array data block page, address = %llu", (unsigned long long)dblk_page_addr)
/* Retrieve element from data block */
HDmemcpy(elmt, ((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), hdr->cparam.cls->nat_elmt_size);
H5MM_memcpy(elmt, ((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), hdr->cparam.cls->nat_elmt_size);
} /* end else */
} /* end else */
} /* end else */

9
src/H5FAcache.c
View File

@ -41,6 +41,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -409,7 +410,7 @@ H5FA__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le
HDassert(hdr);
/* Magic number */
HDmemcpy(image, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -693,7 +694,7 @@ H5FA__cache_dblock_deserialize(const void *_image, size_t len,
/* Page initialization flags */
if(dblock->npages > 0) {
HDmemcpy(dblock->dblk_page_init, image, dblock->dblk_page_init_size);
H5MM_memcpy(dblock->dblk_page_init, image, dblock->dblk_page_init_size);
image += dblock->dblk_page_init_size;
} /* end if */
@ -797,7 +798,7 @@ H5FA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
HDassert(dblock->hdr);
/* Magic number */
HDmemcpy(image, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -812,7 +813,7 @@ H5FA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED
/* Page init flags */
if(dblock->npages > 0) {
/* Store the 'page init' bitmasks */
HDmemcpy(image, dblock->dblk_page_init, dblock->dblk_page_init_size);
H5MM_memcpy(image, dblock->dblk_page_init, dblock->dblk_page_init_size);
image += dblock->dblk_page_init_size;
} /* end if */

3
src/H5FAhdr.c
View File

@ -39,6 +39,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -207,7 +208,7 @@ H5FA__hdr_create(H5F_t *f, const H5FA_create_t *cparam, void *ctx_udata))
hdr->dblk_addr = HADDR_UNDEF;
/* Set the creation parameters for the array */
HDmemcpy(&hdr->cparam, cparam, sizeof(hdr->cparam));
H5MM_memcpy(&hdr->cparam, cparam, sizeof(hdr->cparam));
/* Finish initializing fixed array header */
if(H5FA__hdr_init(hdr, ctx_udata) < 0)

3
src/H5FAstat.c
View File

@ -38,6 +38,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -105,7 +106,7 @@ HDfprintf(stderr, "%s: Called\n", FUNC);
HDassert(stats);
/* Copy fixed array statistics */
HDmemcpy(stats, &fa->hdr->stats, sizeof(fa->hdr->stats));
H5MM_memcpy(stats, &fa->hdr->stats, sizeof(fa->hdr->stats));
END_FUNC(PRIV) /* end H5FA_get_stats() */

4
src/H5FD.c
View File

@ -293,7 +293,7 @@ H5FD_register(const void *_cls, size_t size, hbool_t app_ref)
/* Copy the class structure so the caller can reuse or free it */
if(NULL == (saved = (H5FD_class_t *)H5MM_malloc(size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5I_INVALID_HID, "memory allocation failed for file driver class struct")
HDmemcpy(saved, cls, size);
H5MM_memcpy(saved, cls, size);
/* Create the new class ID */
if((ret_value = H5I_register(H5I_VFL, saved, app_ref)) < 0)
@ -1367,7 +1367,7 @@ H5FD_get_fs_type_map(const H5FD_t *file, H5FD_mem_t *type_map)
} /* end if */
else
/* Copy class's default free space type mapping */
HDmemcpy(type_map, file->cls->fl_map, sizeof(file->cls->fl_map));
H5MM_memcpy(type_map, file->cls->fl_map, sizeof(file->cls->fl_map));
done:
FUNC_LEAVE_NOAPI(ret_value)

6
src/H5FDcore.c
View File

@ -848,7 +848,7 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
HGOTO_ERROR(H5E_FILE, H5E_CANTCOPY, NULL, "image_memcpy callback failed")
} /* end if */
else
HDmemcpy(file->mem, file_image_info.buffer, size);
H5MM_memcpy(file->mem, file_image_info.buffer, size);
} /* end if */
/* Read in existing data from the file if there is no image */
else {
@ -1300,7 +1300,7 @@ H5FD__core_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
nbytes = MIN(size,(size_t)(file->eof-addr));
#endif /* NDEBUG */
HDmemcpy(buf, file->mem + addr, nbytes);
H5MM_memcpy(buf, file->mem + addr, nbytes);
size -= nbytes;
addr += nbytes;
buf = (char *)buf + nbytes;
@ -1386,7 +1386,7 @@ H5FD__core_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
}
/* Write from BUF to memory */
HDmemcpy(file->mem + addr, buf, size);
H5MM_memcpy(file->mem + addr, buf, size);
/* Mark memory buffer as modified */
file->dirty = TRUE;

10
src/H5FDdirect.c
View File

@ -422,7 +422,7 @@ H5FD_direct_fapl_copy(const void *_old_fa)
HDassert(new_fa);
/* Copy the general information */
HDmemcpy(new_fa, old_fa, sizeof(H5FD_direct_fapl_t));
H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_direct_fapl_t));
FUNC_LEAVE_NOAPI(new_fa)
} /* end H5FD_direct_fapl_copy() */
@ -976,12 +976,12 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
* next section of data. */
p2 = (unsigned char*)copy_buf + copy_offset;
if((copy_size + copy_offset) <= alloc_size) {
HDmemcpy(buf, p2, copy_size);
H5MM_memcpy(buf, p2, copy_size);
buf = (unsigned char *)buf + copy_size;
copy_size = 0;
} /* end if */
else {
HDmemcpy(buf, p2, alloc_size - copy_offset);
H5MM_memcpy(buf, p2, alloc_size - copy_offset);
buf = (unsigned char*)buf + alloc_size - copy_offset;
copy_size -= alloc_size - copy_offset;
copy_offset = 0;
@ -1189,11 +1189,11 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_U
*/
p1 = (unsigned char *)copy_buf + copy_offset;
if((copy_size + copy_offset) <= alloc_size) {
HDmemcpy(p1, p3, copy_size);
H5MM_memcpy(p1, p3, copy_size);
copy_size = 0;
} /* end if */
else {
HDmemcpy(p1, p3, alloc_size - copy_offset);
H5MM_memcpy(p1, p3, alloc_size - copy_offset);
p3 = (const unsigned char *)p3 + (alloc_size - copy_offset);
copy_size -= alloc_size - copy_offset;
copy_offset = 0;

2
src/H5FDfamily.c
View File

@ -411,7 +411,7 @@ H5FD_family_fapl_copy(const void *_old_fa)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the fields of the structure */
HDmemcpy(new_fa, old_fa, sizeof(H5FD_family_fapl_t));
H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_family_fapl_t));
/* Deep copy the property list objects in the structure */
if(old_fa->memb_fapl_id==H5P_FILE_ACCESS_DEFAULT) {

2
src/H5FDlog.c
View File

@ -405,7 +405,7 @@ H5FD_log_fapl_copy(const void *_old_fa)
HGOTO_ERROR(H5E_FILE, H5E_CANTALLOC, NULL, "unable to allocate log file FAPL")
/* Copy the general information */
HDmemcpy(new_fa, old_fa, sizeof(H5FD_log_fapl_t));
H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_log_fapl_t));
/* Deep copy the log file name */
if(old_fa->logfile != NULL)

2
src/H5FDmpio.c
View File

@ -745,7 +745,7 @@ if(H5FD_mpio_Debug[(int)'t'])
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the general information */
HDmemcpy(new_fa, old_fa, sizeof(H5FD_mpio_fapl_t));
H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_mpio_fapl_t));
/* Duplicate communicator and Info object. */
if(H5FD_mpi_comm_info_dup(old_fa->comm, old_fa->info, &new_fa->comm, &new_fa->info) < 0)

4
src/H5FL.c
View File

@ -1142,7 +1142,7 @@ H5FL_blk_realloc(H5FL_blk_head_t *head, void *block, size_t new_size H5FL_TRACK_
if((ret_value=H5FL_blk_malloc(head,new_size H5FL_TRACK_INFO_INT))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for block")
blk_size=MIN(new_size,temp->size);
HDmemcpy(ret_value,block,blk_size);
H5MM_memcpy(ret_value,block,blk_size);
H5FL_blk_free(head,block);
} /* end if */
else {
@ -1630,7 +1630,7 @@ H5FL_arr_realloc(H5FL_arr_head_t *head, void * obj, size_t new_elem)
/* Copy the appropriate amount of elements */
blk_size = head->list_arr[MIN(temp->nelem, new_elem)].size;
HDmemcpy(ret_value, obj, blk_size);
H5MM_memcpy(ret_value, obj, blk_size);
/* Free the old block */
H5FL_arr_free(head, obj);

3
src/H5FS.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FSpkg.h" /* File free space */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -615,7 +616,7 @@ H5FS__new(const H5F_t *f, uint16_t nclasses, const H5FS_section_class_t *classes
HDassert(u == classes[u]->type);
/* Copy the class information into the free space manager */
HDmemcpy(&fspace->sect_cls[u], classes[u], sizeof(H5FS_section_class_t));
H5MM_memcpy(&fspace->sect_cls[u], classes[u], sizeof(H5FS_section_class_t));
/* Call the class initialization routine, if there is one */
if(fspace->sect_cls[u].init_cls)

5
src/H5FScache.c
View File

@ -38,6 +38,7 @@
#include "H5Fprivate.h" /* File */
#include "H5FSpkg.h" /* File free space */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -707,7 +708,7 @@ H5FS__cache_hdr_serialize(const H5F_t *f, void *_image, size_t len,
(fspace->alloc_sect_size == (size_t)fspace->sect_size)));
/* Magic number */
HDmemcpy(image, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1265,7 +1266,7 @@ H5FS__cache_sinfo_serialize(const H5F_t *f, void *_image, size_t len,
HDassert(fspace->sect_cls);
/* Magic number */
HDmemcpy(image, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */

21
src/H5Faccum.c
View File

@ -38,6 +38,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
@ -198,7 +199,7 @@ H5F__accum_read(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
} /* end if */
/* Copy the data out of the buffer */
HDmemcpy(buf, accum->buf + (addr - new_addr), size);
H5MM_memcpy(buf, accum->buf + (addr - new_addr), size);
/* Adjust the accumulator address & size */
accum->loc = new_addr;
@ -250,7 +251,7 @@ H5F__accum_read(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
} /* end else */
/* Copy the dirty region to buffer */
HDmemcpy((unsigned char *)buf + buf_off, (unsigned char *)accum->buf + accum->dirty_off + dirty_off, overlap_size);
H5MM_memcpy((unsigned char *)buf + buf_off, (unsigned char *)accum->buf + accum->dirty_off + dirty_off, overlap_size);
} /* end if */
} /* end else */
} /* end if */
@ -457,7 +458,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
HDmemmove(accum->buf + size, accum->buf, accum->size);
/* Copy the new metadata at the front */
HDmemcpy(accum->buf, buf, size);
H5MM_memcpy(accum->buf, buf, size);
/* Set the new size & location of the metadata accumulator */
accum->loc = addr;
@ -479,7 +480,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator")
/* Copy the new metadata to the end */
HDmemcpy(accum->buf + accum->size, buf, size);
H5MM_memcpy(accum->buf + accum->size, buf, size);
/* Adjust the dirty region and mark accumulator dirty */
if(accum->dirty)
@ -502,7 +503,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
size_t dirty_off = (size_t)(addr - accum->loc);
/* Copy the new metadata to the proper location within the accumulator */
HDmemcpy(accum->buf + dirty_off, buf, size);
H5MM_memcpy(accum->buf + dirty_off, buf, size);
/* Adjust the dirty region and mark accumulator dirty */
if(accum->dirty) {
@ -545,7 +546,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
HDmemmove(accum->buf + size, accum->buf + old_offset, (accum->size - old_offset));
/* Copy the new metadata at the front */
HDmemcpy(accum->buf, buf, size);
H5MM_memcpy(accum->buf, buf, size);
/* Set the new size & location of the metadata accumulator */
accum->loc = addr;
@ -582,7 +583,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
dirty_off = (size_t)(addr - accum->loc);
/* Copy the new metadata to the end */
HDmemcpy(accum->buf + dirty_off, buf, size);
H5MM_memcpy(accum->buf + dirty_off, buf, size);
/* Set the new size of the metadata accumulator */
accum->size += add_size;
@ -625,7 +626,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
} /* end if */
/* Copy the new metadata to the buffer */
HDmemcpy(accum->buf, buf, size);
H5MM_memcpy(accum->buf, buf, size);
/* Set the new size & location of the metadata accumulator */
accum->loc = addr;
@ -688,7 +689,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
accum->size = size;
/* Store the piece of metadata in the accumulator */
HDmemcpy(accum->buf, buf, size);
H5MM_memcpy(accum->buf, buf, size);
/* Adjust the dirty region and mark accumulator dirty */
accum->dirty_off = 0;
@ -721,7 +722,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr,
accum->size = size;
/* Store the piece of metadata in the accumulator */
HDmemcpy(accum->buf, buf, size);
H5MM_memcpy(accum->buf, buf, size);
/* Adjust the dirty region and mark accumulator dirty */
accum->dirty_off = 0;

2
src/H5Fint.c
View File

@ -3245,7 +3245,7 @@ H5F_get_metadata_read_retry_info(H5F_t *file, H5F_retry_info_t *info)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Copy the information */
HDmemcpy(info->retries[j], file->shared->retries[i], tot_size);
H5MM_memcpy(info->retries[j], file->shared->retries[i], tot_size);
}
/* Increment location in info->retries[] array */

5
src/H5Fprivate.h
View File

@ -28,6 +28,7 @@ typedef struct H5F_t H5F_t;
#include "H5FDpublic.h" /* File drivers */
/* Private headers needed by this file */
#include "H5MMprivate.h" /* Memory management */
#ifdef H5_HAVE_PARALLEL
#include "H5Pprivate.h" /* Property lists */
#endif /* H5_HAVE_PARALLEL */
@ -134,7 +135,7 @@ typedef struct H5F_t H5F_t;
\
HDcompile_assert(sizeof(double) == 8); \
HDcompile_assert(sizeof(double) == sizeof(uint64_t)); \
HDmemcpy(&_n, &n, sizeof(double)); \
H5MM_memcpy(&_n, &n, sizeof(double)); \
for(_u = 0; _u < sizeof(uint64_t); _u++, _n >>= 8) \
*_p++ = (uint8_t)(_n & 0xff); \
(p) = (uint8_t *)(p) + 8; \
@ -240,7 +241,7 @@ typedef struct H5F_t H5F_t;
(p) += 8; \
for(_u = 0; _u < sizeof(uint64_t); _u++) \
_n = (_n << 8) | *(--p); \
HDmemcpy(&(n), &_n, sizeof(double)); \
H5MM_memcpy(&(n), &_n, sizeof(double)); \
(p) += 8; \
}

2
src/H5Fsuper.c
View File

@ -555,7 +555,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read)
/* Set the B-tree internal node values, etc */
if(H5P_set(c_plist, H5F_CRT_BTREE_RANK_NAME, udata.btree_k) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "unable to set rank for btree internal nodes")
HDmemcpy(sblock->btree_k, udata.btree_k, sizeof(unsigned) * (size_t)H5B_NUM_BTREE_ID);
H5MM_memcpy(sblock->btree_k, udata.btree_k, sizeof(unsigned) * (size_t)H5B_NUM_BTREE_ID);
} /* end if */
else {
/* Get the (default) B-tree internal node values, etc */

4
src/H5Fsuper_cache.c
View File

@ -269,7 +269,7 @@ H5F__drvrinfo_prefix_decode(H5O_drvinfo_t *drvrinfo, char *drv_name,
/* Driver name and/or version */
if(drv_name) {
HDmemcpy(drv_name, (const char *)image, (size_t)8);
H5MM_memcpy(drv_name, (const char *)image, (size_t)8);
drv_name[8] = '\0';
image += 8; /* advance past name/version */
} /* end if */
@ -682,7 +682,7 @@ H5F__cache_superblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNU
HDassert(sblock->cache_info.flush_me_last);
/* Encode the common portion of the file superblock for all versions */
HDmemcpy(image, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN);
H5MM_memcpy(image, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN);
image += H5F_SIGNATURE_LEN;
*image++ = (uint8_t)sblock->super_vers;

13
src/H5Gbtree2.c
View File

@ -35,6 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Gpkg.h" /* Groups */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -206,7 +207,7 @@ H5G_dense_btree2_name_store(void *_nrecord, const void *_udata)
/* Copy user information info native record */
nrecord->hash = udata->common.name_hash;
HDmemcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_name_store() */
@ -305,7 +306,7 @@ H5G_dense_btree2_name_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_UN
/* Encode the record's fields */
UINT32ENCODE(raw, nrecord->hash)
HDmemcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_name_encode() */
@ -333,7 +334,7 @@ H5G_dense_btree2_name_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_UN
/* Decode the record's fields */
UINT32DECODE(raw, nrecord->hash)
HDmemcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_name_decode() */
@ -393,7 +394,7 @@ H5G_dense_btree2_corder_store(void *_nrecord, const void *_udata)
/* Copy user information info native record */
nrecord->corder = udata->common.corder;
HDmemcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_corder_store() */
@ -469,7 +470,7 @@ H5G_dense_btree2_corder_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_
/* Encode the record's fields */
INT64ENCODE(raw, nrecord->corder)
HDmemcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_corder_encode() */
@ -497,7 +498,7 @@ H5G_dense_btree2_corder_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_
/* Decode the record's fields */
INT64DECODE(raw, nrecord->corder)
HDmemcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN);
H5MM_memcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5G_dense_btree2_corder_decode() */

3
src/H5Gcache.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Gpkg.h" /* Groups */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -287,7 +288,7 @@ H5G__cache_node_serialize(const H5F_t *f, void *_image, size_t len,
HDassert(len == sym->node_size);
/* magic number */
HDmemcpy(image, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* version number */

3
src/H5Gent.c
View File

@ -32,6 +32,7 @@
#include "H5FLprivate.h" /* Free Lists */
#include "H5Gpkg.h" /* Groups */
#include "H5HLprivate.h" /* Local Heaps */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -331,7 +332,7 @@ H5G__ent_copy(H5G_entry_t *dst, const H5G_entry_t *src, H5_copy_depth_t depth)
HDassert(depth == H5_COPY_SHALLOW || depth == H5_COPY_DEEP);
/* Copy the top level information */
HDmemcpy(dst, src, sizeof(H5G_entry_t));
H5MM_memcpy(dst, src, sizeof(H5G_entry_t));
/* Deep copy the names */
if(depth == H5_COPY_DEEP) {

2
src/H5Gname.c
View File

@ -522,7 +522,7 @@ H5G_name_copy(H5G_name_t *dst, const H5G_name_t *src, H5_copy_depth_t depth)
HDassert(depth == H5_COPY_SHALLOW || depth == H5_COPY_DEEP);
/* Copy the top level information */
HDmemcpy(dst, src, sizeof(H5G_name_t));
H5MM_memcpy(dst, src, sizeof(H5G_name_t));
/* Deep copy the names */
if(depth == H5_COPY_DEEP) {

4
src/H5Gnode.c
View File

@ -672,7 +672,7 @@ H5G__node_insert(H5F_t *f, haddr_t addr, void H5_ATTR_UNUSED *_lt_key,
if(NULL == (snrt = (H5G_node_t *)H5AC_protect(f, H5AC_SNODE, *new_node_p, f, H5AC__NO_FLAGS_SET)))
HGOTO_ERROR(H5E_SYM, H5E_CANTLOAD, H5B_INS_ERROR, "unable to split symbol table node")
HDmemcpy(snrt->entry, sn->entry + H5F_SYM_LEAF_K(f),
H5MM_memcpy(snrt->entry, sn->entry + H5F_SYM_LEAF_K(f),
H5F_SYM_LEAF_K(f) * sizeof(H5G_entry_t));
snrt->nsyms = H5F_SYM_LEAF_K(f);
snrt_flags |= H5AC__DIRTIED_FLAG;
@ -1262,7 +1262,7 @@ H5G__node_copy(H5F_t *f, const void H5_ATTR_UNUSED *_lt_key, haddr_t addr,
char *link_name; /* Pointer to value of soft link */
/* Make a temporary copy, so that it will not change the info in the cache */
HDmemcpy(&tmp_src_ent, src_ent, sizeof(H5G_entry_t));
H5MM_memcpy(&tmp_src_ent, src_ent, sizeof(H5G_entry_t));
/* Set up group location for soft link to start in */
H5G_name_reset(&grp_path);

4
src/H5Gtraverse.c
View File

@ -555,7 +555,7 @@ H5G__traverse_real(const H5G_loc_t *_loc, const char *name, unsigned target,
* Copy the component name into a null-terminated buffer so
* we can pass it down to the other symbol table functions.
*/
HDmemcpy(comp, name, nchars);
H5MM_memcpy(comp, name, nchars);
comp[nchars] = '\0';
/*
@ -670,7 +670,7 @@ H5G__traverse_real(const H5G_loc_t *_loc, const char *name, unsigned target,
/* Only keep the creation order information from the parent
* group's link info
*/
HDmemcpy(&tmp_linfo, &def_linfo, sizeof(H5O_linfo_t));
H5MM_memcpy(&tmp_linfo, &def_linfo, sizeof(H5O_linfo_t));
tmp_linfo.track_corder = par_linfo.track_corder;
tmp_linfo.index_corder = par_linfo.index_corder;
linfo = &tmp_linfo;

6
src/H5HF.c
View File

@ -42,6 +42,8 @@
#include "H5FOprivate.h" /* File objects */
#include "H5HFpkg.h" /* Fractal heaps */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
/****************/
/* Local Macros */
@ -104,7 +106,7 @@ H5HF_op_read(const void *obj, size_t obj_len, void *op_data)
FUNC_ENTER_NOAPI_NOINIT_NOERR
/* Perform "read", using memcpy() */
HDmemcpy(op_data, obj, obj_len);
H5MM_memcpy(op_data, obj, obj_len);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5HF_op_read() */
@ -129,7 +131,7 @@ H5HF_op_write(const void *obj, size_t obj_len, void *op_data)
FUNC_ENTER_NOAPI_NOINIT_NOERR
/* Perform "write", using memcpy() */
HDmemcpy((void *)obj, op_data, obj_len); /* Casting away const OK -QAK */
H5MM_memcpy((void *)obj, op_data, obj_len); /* Casting away const OK -QAK */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5HF_op_write() */

20
src/H5HFcache.c
View File

@ -772,7 +772,7 @@ H5HF__cache_hdr_serialize(const H5F_t *f, void *_image, size_t len,
hdr->f = f;
/* Magic number */
HDmemcpy(image, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1362,7 +1362,7 @@ H5HF__cache_iblock_serialize(const H5F_t *f, void *_image, size_t len,
hdr->f = f;
/* Magic number */
HDmemcpy(image, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -1677,7 +1677,7 @@ H5HF__cache_dblock_verify_chksum(const void *_image, size_t len, void *_udata)
/* Set up parameters for filter pipeline */
nbytes = len;
filter_mask = udata->filter_mask;
HDmemcpy(read_buf, image, len);
H5MM_memcpy(read_buf, image, len);
/* Push direct block data through I/O filter pipeline */
if(H5Z_pipeline(&(hdr->pline), H5Z_FLAG_REVERSE, &filter_mask, H5Z_ENABLE_EDC, filter_cb, &nbytes, &len, &read_buf) < 0)
@ -1724,7 +1724,7 @@ H5HF__cache_dblock_verify_chksum(const void *_image, size_t len, void *_udata)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Copy un-filtered data into block's buffer */
HDmemcpy(udata->dblk, read_buf, len);
H5MM_memcpy(udata->dblk, read_buf, len);
} /* end if */
done:
@ -1829,7 +1829,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata,
HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, NULL, "memory allocation failed for pipeline buffer")
/* Copy compressed image into buffer */
HDmemcpy(read_buf, image, len);
H5MM_memcpy(read_buf, image, len);
/* Push direct block data through I/O filter pipeline */
nbytes = len;
@ -1841,7 +1841,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata,
HDassert(nbytes == dblock->size);
/* Copy un-filtered data into block's buffer */
HDmemcpy(dblock->blk, read_buf, dblock->size);
H5MM_memcpy(dblock->blk, read_buf, dblock->size);
} /* end if */
} /* end if */
else {
@ -1856,7 +1856,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata,
/* Copy image to dblock->blk */
HDassert(dblock->size == len);
HDmemcpy(dblock->blk, image, dblock->size);
H5MM_memcpy(dblock->blk, image, dblock->size);
} /* end else */
/* Start decoding direct block */
@ -2146,7 +2146,7 @@ H5HF__cache_dblock_pre_serialize(H5F_t *f, void *_thing,
image = dblock->blk;
/* Magic number */
HDmemcpy(image, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
/* Version # */
@ -2201,7 +2201,7 @@ H5HF__cache_dblock_pre_serialize(H5F_t *f, void *_thing,
HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline buffer")
/* Copy the direct block's image into the buffer to compress */
HDmemcpy(write_buf, dblock->blk, write_size);
H5MM_memcpy(write_buf, dblock->blk, write_size);
/* Push direct block data through I/O filter pipeline */
nbytes = write_size;
@ -2460,7 +2460,7 @@ H5HF__cache_dblock_serialize(const H5F_t *f, void *image, size_t len,
HDassert(dblock->write_size == len);
/* Copy the image from *(dblock->write_buf) to *image */
HDmemcpy(image, dblock->write_buf, dblock->write_size);
H5MM_memcpy(image, dblock->write_buf, dblock->write_size);
/* Free *(dblock->write_buf) if it was allocated by the
* pre-serialize function

3
src/H5HFhdr.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5HFpkg.h" /* Fractal heaps */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
/****************/
@ -387,7 +388,7 @@ H5HF_hdr_create(H5F_t *f, const H5HF_create_t *cparam)
/* Set the creation parameters for the heap */
hdr->max_man_size = cparam->max_man_size;
hdr->checksum_dblocks = cparam->checksum_dblocks;
HDmemcpy(&(hdr->man_dtable.cparam), &(cparam->managed), sizeof(H5HF_dtable_cparam_t));
H5MM_memcpy(&(hdr->man_dtable.cparam), &(cparam->managed), sizeof(H5HF_dtable_cparam_t));
/* Set root table address to indicate that the heap is empty currently */
hdr->man_dtable.table_addr = HADDR_UNDEF;

4
src/H5HFhuge.c
View File

@ -355,7 +355,7 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size);
write_size = obj_size;
if(NULL == (write_buf = H5MM_malloc(write_size)))
HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline buffer")
HDmemcpy(write_buf, obj, write_size);
H5MM_memcpy(write_buf, obj, write_size);
/* Push direct block data through I/O filter pipeline */
nbytes = write_size;
@ -794,7 +794,7 @@ H5HF__huge_op_real(H5HF_hdr_t *hdr, const uint8_t *id, hbool_t is_read,
/* Copy object to user's buffer if there's filters on heap data */
/* (if there's no filters, the object was read directly into the user's buffer) */
if(hdr->filter_len > 0)
HDmemcpy(op_data, read_buf, (size_t)obj_size);
H5MM_memcpy(op_data, read_buf, (size_t)obj_size);
} /* end if */
else {
/* Call the user's 'op' callback */

2
src/H5HFman.c
View File

@ -183,7 +183,7 @@ H5HF__man_insert(H5HF_hdr_t *hdr, size_t obj_size, const void *obj, void *_id)
p = dblock->blk + blk_off;
/* Copy the object's data into the heap */
HDmemcpy(p, obj, obj_size);
H5MM_memcpy(p, obj, obj_size);
p += obj_size;
/* Sanity check */

8
src/H5HFsection.c
View File

@ -3082,7 +3082,7 @@ H5HF__sect_indirect_reduce_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect,
HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, FAIL, "allocation failed for row section pointer array")
/* Transfer row sections between current & peer sections */
HDmemcpy(&peer_sect->u.indirect.dir_rows[0],
H5MM_memcpy(&peer_sect->u.indirect.dir_rows[0],
&sect->u.indirect.dir_rows[0],
(sizeof(H5HF_free_section_t *) * peer_dir_nrows));
HDmemmove(&sect->u.indirect.dir_rows[0],
@ -3321,7 +3321,7 @@ H5HF__sect_indirect_reduce(H5HF_hdr_t *hdr, H5HF_free_section_t *sect,
HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, FAIL, "allocation failed for indirect section pointer array")
/* Transfer child indirect sections between current & peer sections */
HDmemcpy(&peer_sect->u.indirect.indir_ents[0],
H5MM_memcpy(&peer_sect->u.indirect.indir_ents[0],
&sect->u.indirect.indir_ents[sect->u.indirect.indir_nents - peer_nentries],
(sizeof(H5HF_free_section_t *) * peer_nentries));
sect->u.indirect.indir_nents -= (peer_nentries + 1); /* Transferred blocks, plus child entry */
@ -3636,7 +3636,7 @@ H5HF__sect_indirect_merge_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect1,
sect1->u.indirect.dir_rows = new_dir_rows;
/* Transfer the second section's rows to first section */
HDmemcpy(&sect1->u.indirect.dir_rows[sect1->u.indirect.dir_nrows],
H5MM_memcpy(&sect1->u.indirect.dir_rows[sect1->u.indirect.dir_nrows],
&sect2->u.indirect.dir_rows[src_row2],
(sizeof(H5HF_free_section_t *) * nrows_moved2));
@ -3682,7 +3682,7 @@ H5HF__sect_indirect_merge_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect1,
sect1->u.indirect.indir_ents = new_indir_ents;
/* Transfer the second section's entries to first section */
HDmemcpy(&sect1->u.indirect.indir_ents[sect1->u.indirect.indir_nents],
H5MM_memcpy(&sect1->u.indirect.indir_ents[sect1->u.indirect.indir_nents],
&sect2->u.indirect.indir_ents[0],
(sizeof(H5HF_free_section_t *) * sect2->u.indirect.indir_nents));
} /* end else */

4
src/H5HFtest.c
View File

@ -32,6 +32,8 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5HFpkg.h" /* Fractal heaps */
#include "H5MMprivate.h" /* Memory management */
/****************/
/* Local Macros */
@ -100,7 +102,7 @@ H5HF_get_cparam_test(const H5HF_t *fh, H5HF_create_t *cparam)
else
H5_CHECKED_ASSIGN(cparam->id_len, uint16_t, fh->hdr->id_len, unsigned);
cparam->max_man_size = fh->hdr->max_man_size;
HDmemcpy(&(cparam->managed), &(fh->hdr->man_dtable.cparam), sizeof(H5HF_dtable_cparam_t));
H5MM_memcpy(&(cparam->managed), &(fh->hdr->man_dtable.cparam), sizeof(H5HF_dtable_cparam_t));
H5O_msg_copy(H5O_PLINE_ID, &(fh->hdr->pline), &(cparam->pline));
FUNC_LEAVE_NOAPI(SUCCEED)

3
src/H5HFtiny.c
View File

@ -35,6 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5HFpkg.h" /* Fractal heaps */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -176,7 +177,7 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size);
*id++ = enc_obj_size & H5HF_TINY_MASK_EXT_2;
} /* end else */
HDmemcpy(id, obj, obj_size);
H5MM_memcpy(id, obj, obj_size);
HDmemset(id + obj_size, 0, (hdr->id_len - ((size_t)1 + (size_t)hdr->tiny_len_extended + obj_size)));
/* Update statistics about heap */

6
src/H5HG.c
View File

@ -168,7 +168,7 @@ H5HG__create(H5F_t *f, size_t size)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
/* Initialize the header */
HDmemcpy(heap->chunk, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(heap->chunk, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC);
p = heap->chunk + H5_SIZEOF_MAGIC;
*p++ = H5HG_VERSION;
*p++ = 0; /*reserved*/
@ -553,7 +553,7 @@ H5HG_insert(H5F_t *f, size_t size, void *obj, H5HG_t *hobj/*out*/)
/* Copy data into the heap */
if(size > 0) {
HDmemcpy(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f), obj, size);
H5MM_memcpy(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f), obj, size);
#ifdef OLD_WAY
/* Don't bother zeroing out the rest of the info in the heap -QAK */
HDmemset(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f) + size, 0,
@ -618,7 +618,7 @@ H5HG_read(H5F_t *f, H5HG_t *hobj, void *object/*out*/, size_t *buf_size)
/* Allocate a buffer for the object read in, if the user didn't give one */
if(!object && NULL == (object = H5MM_malloc(size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
HDmemcpy(object, p, size);
H5MM_memcpy(object, p, size);
/*
* Advance the heap in the CWFS list. We might have done this already

4
src/H5HGcache.c
View File

@ -271,7 +271,7 @@ H5HG__cache_heap_deserialize(const void *_image, size_t len, void *_udata,
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the image buffer into the newly allocate chunk */
HDmemcpy(heap->chunk, _image, len);
H5MM_memcpy(heap->chunk, _image, len);
/* Deserialize the heap's header */
if(H5HG__hdr_deserialize(heap, (const uint8_t *)heap->chunk, f) < 0)
@ -448,7 +448,7 @@ H5HG__cache_heap_serialize(const H5F_t *f, void *image, size_t len,
HDassert(heap->chunk);
/* copy the image into the buffer */
HDmemcpy(image, heap->chunk, len);
H5MM_memcpy(image, heap->chunk, len);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5HG__cache_heap_serialize() */

2
src/H5HL.c
View File

@ -725,7 +725,7 @@ H5HL_insert(H5F_t *f, H5HL_t *heap, size_t buf_size, const void *buf))
} /* end if */
/* Copy the data into the heap */
HDmemcpy(heap->dblk_image + offset, buf, buf_size);
H5MM_memcpy(heap->dblk_image + offset, buf, buf_size);
/* Set return value */
ret_value = offset;

11
src/H5HLcache.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5HLpkg.h" /* Local Heaps */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -464,7 +465,7 @@ H5HL__cache_prefix_deserialize(const void *_image, size_t len, void *_udata,
image = ((const uint8_t *)_image) + heap->prfx_size;
/* Copy the heap data from the speculative read buffer */
HDmemcpy(heap->dblk_image, image, heap->dblk_size);
H5MM_memcpy(heap->dblk_image, image, heap->dblk_size);
/* Build free list */
if(H5HL__fl_deserialize(heap) < 0)
@ -587,7 +588,7 @@ H5HL__cache_prefix_serialize(const H5F_t *f, void *_image, size_t len,
heap->free_block = heap->freelist ? heap->freelist->offset : H5HL_FREE_NULL;
/* Serialize the heap prefix */
HDmemcpy(image, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(image, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC);
image += H5_SIZEOF_MAGIC;
*image++ = H5HL_VERSION;
*image++ = 0; /*reserved*/
@ -615,7 +616,7 @@ H5HL__cache_prefix_serialize(const H5F_t *f, void *_image, size_t len,
H5HL__fl_serialize(heap);
/* Copy the heap data block into the cache image */
HDmemcpy(image, heap->dblk_image, heap->dblk_size);
H5MM_memcpy(image, heap->dblk_image, heap->dblk_size);
/* Sanity check */
HDassert((size_t)(image - (uint8_t *)_image) + heap->dblk_size == len);
@ -756,7 +757,7 @@ H5HL__cache_datablock_deserialize(const void *image, size_t len, void *_udata,
HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, NULL, "can't allocate data block image buffer");
/* copy the datablock from the read buffer */
HDmemcpy(heap->dblk_image, image, len);
H5MM_memcpy(heap->dblk_image, image, len);
/* Build free list */
if(FAIL == H5HL__fl_deserialize(heap))
@ -851,7 +852,7 @@ H5HL__cache_datablock_serialize(const H5F_t *f, void *image, size_t len,
H5HL__fl_serialize(heap);
/* Copy the heap's data block into the cache's image */
HDmemcpy(image, heap->dblk_image, heap->dblk_size);
H5MM_memcpy(image, heap->dblk_image, heap->dblk_size);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5HL__cache_datablock_serialize() */

3
src/H5I.c
View File

@ -355,6 +355,9 @@ H5Itype_exists(H5I_type_t type)
FUNC_ENTER_API(FAIL)
H5TRACE1("t", "It", type);
if(H5I_IS_LIB_TYPE(type))
HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, FAIL, "cannot call public function on library type")
if (type <= H5I_BADID || type >= H5I_next_type)
HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid type number")

4
src/H5L.c
View File

@ -1676,7 +1676,7 @@ H5L_register(const H5L_class_t *cls)
} /* end if */
/* Copy link class info into table */
HDmemcpy(H5L_table_g + i, cls, sizeof(H5L_class_t));
H5MM_memcpy(H5L_table_g + i, cls, sizeof(H5L_class_t));
done:
FUNC_LEAVE_NOAPI(ret_value)
@ -2217,7 +2217,7 @@ H5L__create_ud(const H5G_loc_t *link_loc, const char *link_name,
/* Fill in UD link-specific information in the link struct*/
if(ud_data_size > 0) {
lnk.u.ud.udata = H5MM_malloc((size_t)ud_data_size);
HDmemcpy(lnk.u.ud.udata, ud_data, (size_t) ud_data_size);
H5MM_memcpy(lnk.u.ud.udata, ud_data, (size_t) ud_data_size);
} /* end if */
else
lnk.u.ud.udata = NULL;

2
src/H5Lexternal.c
View File

@ -306,7 +306,7 @@ H5L__extern_query(const char H5_ATTR_UNUSED * link_name, const void *_udata, siz
buf_size = udata_size;
/* Copy the udata verbatim up to buf_size */
HDmemcpy(buf, udata, buf_size);
H5MM_memcpy(buf, udata, buf_size);
} /* end if */
/* Set return value */

48
src/H5MM.c
View File

@ -274,7 +274,7 @@ H5MM_malloc(size_t size)
#if defined H5_MEMORY_ALLOC_SANITY_CHECK
/* Initialize block list head singleton */
if(!H5MM_init_s) {
HDmemcpy(H5MM_block_head_s.sig, H5MM_block_signature_s, H5MM_SIG_SIZE);
H5MM_memcpy(H5MM_block_head_s.sig, H5MM_block_signature_s, H5MM_SIG_SIZE);
H5MM_block_head_s.next = &H5MM_block_head_s;
H5MM_block_head_s.prev = &H5MM_block_head_s;
H5MM_block_head_s.u.info.size = SIZET_MAX;
@ -291,15 +291,15 @@ H5MM_malloc(size_t size)
if(NULL != (block = (H5MM_block_t *)HDmalloc(alloc_size))) {
/* Set up block */
HDmemcpy(block->sig, H5MM_block_signature_s, H5MM_SIG_SIZE);
H5MM_memcpy(block->sig, H5MM_block_signature_s, H5MM_SIG_SIZE);
block->next = H5MM_block_head_s.next;
H5MM_block_head_s.next = block;
block->next->prev = block;
block->prev = &H5MM_block_head_s;
block->u.info.size = size;
block->u.info.in_use = TRUE;
HDmemcpy(block->b, H5MM_block_head_guard_s, H5MM_HEAD_GUARD_SIZE);
HDmemcpy(block->b + H5MM_HEAD_GUARD_SIZE + size, H5MM_block_tail_guard_s, H5MM_TAIL_GUARD_SIZE);
H5MM_memcpy(block->b, H5MM_block_head_guard_s, H5MM_HEAD_GUARD_SIZE);
H5MM_memcpy(block->b + H5MM_HEAD_GUARD_SIZE + size, H5MM_block_tail_guard_s, H5MM_TAIL_GUARD_SIZE);
/* Update statistics */
H5MM_total_alloc_bytes_s += size;
@ -417,7 +417,7 @@ H5MM_realloc(void *mem, size_t size)
H5MM__sanity_check(mem);
ret_value = H5MM_malloc(size);
HDmemcpy(ret_value, mem, MIN(size, old_size));
H5MM_memcpy(ret_value, mem, MIN(size, old_size));
H5MM_xfree(mem);
} /* end if */
else
@ -564,3 +564,41 @@ H5MM_xfree(void *mem)
FUNC_LEAVE_NOAPI(NULL)
} /* end H5MM_xfree() */
/*-------------------------------------------------------------------------
* Function: H5MM_memcpy
*
* Purpose: Like memcpy(3) but with sanity checks on the parameters,
* particularly buffer overlap.
*
* Return: Success: pointer to dest
* Failure: NULL
*
* Programmer: Dana Robinson
* Spring 2019
*
*-------------------------------------------------------------------------
*/
void *
H5MM_memcpy(void *dest, const void *src, size_t n)
{
void *ret = NULL;
/* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDassert(dest);
HDassert(src);
#if 0
/* Commented out while we investigate overlapping buffers in the
* parallel filter code (HDFFV-10735).
*/
HDassert((char *)dest >= (const char *)src + n || (const char *)src >= (char *)dest + n);
#endif
ret = HDmemcpy(dest, src, n);
FUNC_LEAVE_NOAPI(ret)
} /* end H5MM_memcpy() */

1
src/H5MMprivate.h
View File

@ -45,6 +45,7 @@ H5_DLL void *H5MM_realloc(void *mem, size_t size);
H5_DLL char *H5MM_xstrdup(const char *s);
H5_DLL char *H5MM_strdup(const char *s);
H5_DLL void *H5MM_xfree(void *mem);
H5_DLL void *H5MM_memcpy(void *dest, const void *src, size_t n);
#if defined H5_MEMORY_ALLOC_SANITY_CHECK
H5_DLL void H5MM_sanity_check_all(void);
H5_DLL void H5MM_final_sanity_check(void);

11
src/H5Oalloc.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free lists */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
/****************/
@ -949,7 +950,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null,
* # at the beginning of the chunk image.
*/
if(oh->version > H5O_VERSION_1) {
HDmemcpy(p, H5O_CHK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
H5MM_memcpy(p, H5O_CHK_MAGIC, (size_t)H5_SIZEOF_MAGIC);
p += H5_SIZEOF_MAGIC;
} /* end if */
@ -988,7 +989,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null,
HDassert(curr_msg->type->id != H5O_CONT_ID);
/* Copy the raw data */
HDmemcpy(p, curr_msg->raw - (size_t)H5O_SIZEOF_MSGHDR_OH(oh),
H5MM_memcpy(p, curr_msg->raw - (size_t)H5O_SIZEOF_MSGHDR_OH(oh),
curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh));
/* Update the message info */
@ -1044,7 +1045,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null,
null_msg->chunkno = oh->mesg[found_msg->msgno].chunkno;
/* Copy the message to move (& its prefix) to its new location */
HDmemcpy(p, oh->mesg[found_msg->msgno].raw - H5O_SIZEOF_MSGHDR_OH(oh),
H5MM_memcpy(p, oh->mesg[found_msg->msgno].raw - H5O_SIZEOF_MSGHDR_OH(oh),
oh->mesg[found_msg->msgno].raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh));
/* Switch moved message to point to new location */
@ -1519,7 +1520,7 @@ H5O__move_cont(H5F_t *f, H5O_t *oh, unsigned cont_u)
move_size = curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh);
/* Move message out of deleted chunk */
HDmemcpy(move_start, curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), move_size);
H5MM_memcpy(move_start, curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), move_size);
curr_msg->raw = move_start + H5O_SIZEOF_MSGHDR_OH(oh);
curr_msg->chunkno = cont_chunkno;
chk_dirtied = TRUE;
@ -1791,7 +1792,7 @@ H5O__move_msgs_forward(H5F_t *f, H5O_t *oh)
} /* end if */
/* Copy raw data for non-null message to new chunk */
HDmemcpy(null_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh));
H5MM_memcpy(null_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh));
/* Point non-null message at null message's space */
curr_msg->chunkno = null_msg->chunkno;

8
src/H5Oattr.c
View File

@ -208,7 +208,7 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags,
HGOTO_ERROR(H5E_ATTR, H5E_CANTDECODE, NULL, "can't decode attribute dataspace")
/* Copy the extent information to the dataspace */
HDmemcpy(&(attr->shared->ds->extent), extent, sizeof(H5S_extent_t));
H5MM_memcpy(&(attr->shared->ds->extent), extent, sizeof(H5S_extent_t));
/* Release temporary extent information */
extent = H5FL_FREE(H5S_extent_t, extent);
@ -240,7 +240,7 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags,
if(attr->shared->data_size) {
if(NULL == (attr->shared->data = H5FL_BLK_MALLOC(attr_buf, attr->shared->data_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
HDmemcpy(attr->shared->data, p, attr->shared->data_size);
H5MM_memcpy(attr->shared->data, p, attr->shared->data_size);
} /* end if */
/* Increment the reference count for this object header message in cache(compact
@ -336,7 +336,7 @@ H5O_attr_encode(H5F_t *f, uint8_t *p, const void *mesg)
*p++ = attr->shared->encoding;
/* Write the name including null terminator */
HDmemcpy(p, attr->shared->name, name_len);
H5MM_memcpy(p, attr->shared->name, name_len);
if(attr->shared->version < H5O_ATTR_VERSION_2) {
/* Pad to the correct number of bytes */
HDmemset(p + name_len, 0, H5O_ALIGN_OLD(name_len) - name_len);
@ -369,7 +369,7 @@ H5O_attr_encode(H5F_t *f, uint8_t *p, const void *mesg)
/* Store attribute data. If there's no data, store 0 as fill value. */
if(attr->shared->data)
HDmemcpy(p, attr->shared->data, attr->shared->data_size);
H5MM_memcpy(p, attr->shared->data, attr->shared->data_size);
else
HDmemset(p, 0, attr->shared->data_size);

2
src/H5Oattribute.c
View File

@ -862,7 +862,7 @@ H5O__attr_write_cb(H5O_t *oh, H5O_mesg_t *mesg/*in,out*/,
/* (Needs to occur before updating the shared message, or the hash
* value on the old & new messages will be the same) */
HDmemcpy(((H5A_t *)mesg->native)->shared->data, udata->attr->shared->data, udata->attr->shared->data_size);
H5MM_memcpy(((H5A_t *)mesg->native)->shared->data, udata->attr->shared->data, udata->attr->shared->data_size);
} /* end if */
/* Mark the message as modified */

7
src/H5Ocache.c
View File

@ -36,6 +36,7 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free lists */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5WBprivate.h" /* Wrapped Buffers */
@ -542,7 +543,7 @@ H5O__cache_serialize(const H5F_t *f, void *image, size_t len, void *_thing)
* Can we rework things so that the object header and the cache
* share a buffer?
*/
HDmemcpy(image, oh->chunk[0].image, len);
H5MM_memcpy(image, oh->chunk[0].image, len);
done:
FUNC_LEAVE_NOAPI(ret_value)
@ -900,7 +901,7 @@ H5O__cache_chk_serialize(const H5F_t *f, void *image, size_t len, void *_thing)
/* copy the chunk into the image -- this is potentially expensive.
* Can we rework things so that the chunk and the cache share a buffer?
*/
HDmemcpy(image, chk_proxy->oh->chunk[chk_proxy->chunkno].image, len);
H5MM_memcpy(image, chk_proxy->oh->chunk[chk_proxy->chunkno].image, len);
done:
FUNC_LEAVE_NOAPI(ret_value)
@ -1352,7 +1353,7 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
oh->chunk[chunkno].chunk_proxy = NULL;
/* Copy disk image into chunk's image */
HDmemcpy(oh->chunk[chunkno].image, image, oh->chunk[chunkno].size);
H5MM_memcpy(oh->chunk[chunkno].image, image, oh->chunk[chunkno].size);
/* Point into chunk image to decode */
chunk_image = oh->chunk[chunkno].image;

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