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Merge changes from develop for CMake and Java

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This commit is contained in:
Allen Byrne
2020-02-21 15:40:55 -06:00
parent 7daf7d4a0b
commit a6706e3a78
8 changed files with 38 additions and 31 deletions
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3
CMakeLists.txt
View File

@@ -394,9 +394,6 @@ HDF_DIR_PATHS(${HDF5_PACKAGE_NAME})
include (${HDF_RESOURCES_EXT_DIR}/HDFLibMacros.cmake)
include (${HDF_RESOURCES_DIR}/HDF5Macros.cmake)
if (HDF5_ENABLE_SANITIZERS)
include (${HDF5_SOURCE_DIR}/config/sanitizer/sanitizers.cmake)
endif ()
#-----------------------------------------------------------------------------
# Targets built within this project are exported at Install time for use

11
config/cmake/HDFCompilerFlags.cmake
View File

@@ -30,8 +30,10 @@ macro (ADD_H5_FLAGS h5_flag_var infile)
#message (STATUS "h5_flag_var=${${h5_flag_var}}")
endmacro ()
message (STATUS "Warnings Configuration:")
set (CMAKE_C_FLAGS "${CMAKE_C99_STANDARD_COMPILE_OPTION} ${CMAKE_C_FLAGS}")
set (CMAKE_C_FLAGS "${CMAKE_C_SANITIZER_FLAGS} ${CMAKE_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_SANITIZER_FLAGS} ${CMAKE_CXX_FLAGS}")
message (STATUS "Warnings Configuration: default: ${CMAKE_C_FLAGS} : ${CMAKE_CXX_FLAGS}")
#-----------------------------------------------------------------------------
# Compiler specific flags : Shouldn't there be compiler tests for these
#-----------------------------------------------------------------------------
@@ -176,7 +178,12 @@ if (NOT MSVC AND CMAKE_COMPILER_IS_GNUCC)
# Append more extra warning flags that only gcc 4.5+ know about
if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 4.5)
set (H5_CFLAGS1 "${H5_CFLAGS1} -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants")
set (H5_CFLAGS1 "${H5_CFLAGS1} -Wstrict-overflow=5 -Wjump-misses-init")
if (HDF5_ENABLE_DEV_WARNINGS)
set (H5_CFLAGS0 "${H5_CFLAGS0} -Wunsuffixed-float-constants")
else ()
set (H5_CFLAGS0 "${H5_CFLAGS0} -Wno-unsuffixed-float-constants")
endif ()
endif ()
# Append more extra warning flags that only gcc 4.6+ know about

2
config/cmake_ext_mod/CTestCustom.cmake
View File

@@ -5,7 +5,7 @@ set (CTEST_CUSTOM_WARNING_EXCEPTION
".*note.*expected.*void.*but argument is of type.*volatile.*"
".*src.SZIP.*:[ \t]*warning.*"
".*src.ZLIB.*:[ \t]*warning.*"
".*jpeg.src.*:[ \t]*warning.*"
".*src.JPEG.*:[ \t]*warning.*"
".*POSIX name for this item is deprecated.*"
".*disabling jobserver mode.*"
".*warning.*implicit declaration of function.*"

2
config/cmake_ext_mod/runTest.cmake
View File

@@ -163,7 +163,7 @@ endif ()
# if the output file needs Modified text removed
if (TEST_MASK_MOD)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
string (REGEX REPLACE "Modified:[^\n]+\n" "Modified: XXXX-XX-XX XX:XX:XX XXX\n" TEST_STREAM "${TEST_STREAM}")
string (REGEX REPLACE "Modified:[^\n]+\n" "Modified: XXXX-XX-XX XX:XX:XX XXX\n" TEST_STREAM "${TEST_STREAM}")
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
endif ()

6
config/gnu-flags
View File

@@ -251,7 +251,9 @@ if test "X-gcc" = "X-$cc_vendor"; then
# gcc 4.5
if test $cc_vers_major -ge 5 -o $cc_vers_major -eq 4 -a $cc_vers_minor -ge 5; then
H5_CFLAGS="$H5_CFLAGS -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants"
H5_CFLAGS="$H5_CFLAGS -Wstrict-overflow=5 -Wjump-misses-init"
DEVELOPER_WARNING_CFLAGS="$DEVELOPER_WARNING_CFLAGS -Wunsuffixed-float-constants"
NO_DEVELOPER_WARNING_CFLAGS="$NO_DEVELOPER_WARNING_CFLAGS -Wno-unsuffixed-float-constants"
fi
# gcc 4.6
@@ -292,7 +294,7 @@ if test "X-gcc" = "X-$cc_vendor"; then
# gcc 7
if test $cc_vers_major -ge 7; then
DEVELOPER_WARNING_CFLAGS="$DEVELOPER_WARNING_CFLAGS -Wstringop-overflow=2"
H5_CFLAGS="$H5_CFLAGS -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict"
H5_CFLAGS="$H5_CFLAGS -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict"
fi
# gcc 8

27
config/sanitizer/sanitizers.cmake
View File

@@ -28,52 +28,53 @@ function(append value)
endforeach(variable)
endfunction()
if(USE_SANITIZER AND "${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
message(STATUS "USE_SANITIZER=${USE_SANITIZER}, CMAKE_C_COMPILER_ID=${CMAKE_C_COMPILER_ID}")
if(USE_SANITIZER AND "${CMAKE_C_COMPILER_ID}" MATCHES "Clang")
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
append("-fno-omit-frame-pointer" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fno-omit-frame-pointer" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
message(STATUS "Building with sanitize, base flags=${CMAKE_C_SANITIZER_FLAGS}")
if(UNIX)
if(uppercase_CMAKE_BUILD_TYPE STREQUAL "DEBUG")
append("-O1" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-O1" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
endif()
if(USE_SANITIZER MATCHES "([Aa]ddress);([Uu]ndefined)"
OR USE_SANITIZER MATCHES "([Uu]ndefined);([Aa]ddress)")
message(STATUS "Building with Address, Undefined sanitizers")
append("-fsanitize=address,undefined" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=address,undefined" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
set(MEMCHECK_TYPE AddressSanitizer)
elseif(USE_SANITIZER MATCHES "([Aa]ddress)")
# Optional: -fno-optimize-sibling-calls -fsanitize-address-use-after-scope
message(STATUS "Building with Address sanitizer")
append("-fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=address" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
set(MEMCHECK_TYPE AddressSanitizer)
elseif(USE_SANITIZER MATCHES "([Mm]emory([Ww]ith[Oo]rigins)?)")
# Optional: -fno-optimize-sibling-calls -fsanitize-memory-track-origins=2
append("-fsanitize=memory" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=memory" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
if(USE_SANITIZER MATCHES "([Mm]emory[Ww]ith[Oo]rigins)")
message(STATUS "Building with MemoryWithOrigins sanitizer")
append("-fsanitize-memory-track-origins" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize-memory-track-origins" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
else()
message(STATUS "Building with Memory sanitizer")
endif()
set(MEMCHECK_TYPE MemorySanitizer)
elseif(USE_SANITIZER MATCHES "([Uu]ndefined)")
message(STATUS "Building with Undefined sanitizer")
append("-fsanitize=undefined" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=undefined" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
if(EXISTS "${BLACKLIST_FILE}")
append("-fsanitize-blacklist=${BLACKLIST_FILE}" CMAKE_C_FLAGS
CMAKE_CXX_FLAGS)
append("-fsanitize-blacklist=${BLACKLIST_FILE}" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
endif()
set(MEMCHECK_TYPE UndefinedBehaviorSanitizer)
elseif(USE_SANITIZER MATCHES "([Tt]hread)")
message(STATUS "Building with Thread sanitizer")
append("-fsanitize=thread" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=thread" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
set(MEMCHECK_TYPE ThreadSanitizer)
elseif(USE_SANITIZER MATCHES "([Ll]eak)")
message(STATUS "Building with Leak sanitizer")
append("-fsanitize=leak" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=leak" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
set(MEMCHECK_TYPE LeakSanitizer)
else()
message(
@@ -82,7 +83,7 @@ if(USE_SANITIZER AND "${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
elseif(MSVC)
if(USE_SANITIZER MATCHES "([Aa]ddress)")
message(STATUS "Building with Address sanitizer")
append("-fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
append("-fsanitize=address" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS)
else()
message(
FATAL_ERROR

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

@@ -3590,7 +3590,7 @@ public class H5 implements java.io.Serializable {
* - name is null.
*/
public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes,
H5O_token_t[] tokens) throws HDF5LibraryException, NullPointerException {
H5O_token_t[] tokens) throws HDF5LibraryException, NullPointerException {
if (objNames == null) {
throw new NullPointerException("H5Gget_obj_info_all(): name array is null");
}
@@ -3605,7 +3605,7 @@ public class H5 implements java.io.Serializable {
public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype,
int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException {
return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, oname.length, indx_type, -1);
return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, indx_type, -1);
}
public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype,

14
java/src/jni/h5pFAPLImp.c
View File

@@ -395,7 +395,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1hdfs
if (H5Pget_fapl_hdfs((hid_t)fapl_id, &fa) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL != fa.namenode_name) {
if (HDstrlen(fa.namenode_name) > 0) {
if (NULL == (j_namenode_name = ENVPTR->NewStringUTF(ENVONLY, fa.namenode_name))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_hdfs: out of memory - can't create namenode_name string");
@@ -405,7 +405,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1hdfs
args[1].i = (jint)fa.namenode_port;
if (NULL != fa.user_name) {
if (HDstrlen(fa.user_name) > 0) {
if (NULL == (j_user_name = ENVPTR->NewStringUTF(ENVONLY, fa.user_name))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_hdfs: out of memory - can't create user_name string");
@@ -413,7 +413,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1hdfs
}
args[2].l = j_user_name;
if (NULL != fa.kerberos_ticket_cache) {
if (HDstrlen(fa.kerberos_ticket_cache) > 0) {
if (NULL == (j_kerb_cache_path = ENVPTR->NewStringUTF(ENVONLY, fa.kerberos_ticket_cache))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_hdfs: out of memory - can't create kerberos_ticket_cache string");
@@ -820,7 +820,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1ros3
if (H5Pget_fapl_ros3((hid_t)fapl_id, &fa) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL != fa.aws_region) {
if (HDstrlen(fa.aws_region) > 0) {
if (NULL == (j_aws = ENVPTR->NewStringUTF(ENVONLY, fa.aws_region))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_ros3: out of memory - can't create aws_region string");
@@ -828,7 +828,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1ros3
}
args[0].l = j_aws;
if (NULL != fa.secret_id) {
if (HDstrlen(fa.secret_id) > 0) {
if (NULL == (j_id = ENVPTR->NewStringUTF(ENVONLY, fa.secret_id))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_ros3: out of memory - can't create secret_id string");
@@ -836,7 +836,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1fapl_1ros3
}
args[1].l = j_id;
if (NULL != fa.secret_key) {
if (HDstrlen(fa.secret_key) > 0) {
if (NULL == (j_key = ENVPTR->NewStringUTF(ENVONLY, fa.secret_key))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_fapl_ros3: out of memory - can't create secret_key string");
@@ -1685,7 +1685,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1mdc_1config
args[2].z = cacheinfo.open_trace_file;
args[3].z = cacheinfo.close_trace_file;
if (NULL != cacheinfo.trace_file_name) {
if (HDstrlen(cacheinfo.trace_file_name) > 0) {
if (NULL == (j_str = ENVPTR->NewStringUTF(ENVONLY, cacheinfo.trace_file_name))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_mdc_config: out of memory - unable to construct string from UTF characters");