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authorLarry Knox <lrknox@hdfgroup.org>2019-01-05 13:50:15 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2019-01-05 13:50:15 (GMT)
commit3be0fbd817e82b4a60b36b2b9d444a3750f2eb06 (patch)
treecc16d19b4f3fd04aa0aa70556fac36b2222daa24
parent25fe692c5c5c37a904a0d2ba3f447e60396c30da (diff)
parentcceb9f06b8f213ef1cb360a4ef900536669a8dad (diff)
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Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
-rw-r--r--MANIFEST4
-rw-r--r--c++/src/H5CppDoc.h3
-rw-r--r--config/cmake/HDF5UseFortran.cmake16
-rw-r--r--config/cmake/HDFCompilerFlags.cmake6
-rw-r--r--config/cmake_ext_mod/ConfigureChecks.cmake142
-rw-r--r--config/cmake_ext_mod/HDFUseCXX.cmake4
-rw-r--r--config/cmake_ext_mod/HDFUseFortran.cmake4
-rw-r--r--config/toolchain/GCC.cmake3
-rw-r--r--config/toolchain/PGI.cmake11
-rw-r--r--config/toolchain/crayle.cmake3
-rw-r--r--config/toolchain/intel.cmake1
-rw-r--r--configure.ac2
-rw-r--r--hl/fortran/src/Makefile.am14
-rw-r--r--java/src/hdf/hdf5lib/H5.java77
-rw-r--r--java/src/jni/h5fImp.c65
-rw-r--r--java/src/jni/h5fImp.h27
-rw-r--r--java/src/jni/h5pImp.c45
-rw-r--r--java/src/jni/h5pImp.h18
-rw-r--r--java/test/TestH5Dplist.java20
-rw-r--r--java/test/TestH5Fbasic.java30
-rw-r--r--java/test/TestH5Fparams.java49
-rw-r--r--java/test/testfiles/JUnit-TestH5Dplist.txt3
-rw-r--r--java/test/testfiles/JUnit-TestH5Fbasic.txt2
-rw-r--r--java/test/testfiles/JUnit-TestH5Fparams.txt4
-rw-r--r--release_docs/RELEASE.txt24
-rw-r--r--src/H5Adense.c35
-rw-r--r--src/H5Dchunk.c28
-rw-r--r--src/H5L.c2
-rw-r--r--test/CMakeLists.txt1
-rw-r--r--test/CMakeTests.cmake21
-rw-r--r--test/Makefile.am16
-rw-r--r--test/ShellTests.cmake3
-rw-r--r--test/del_many_dense_attrs.c203
-rw-r--r--test/dsets.c41
-rw-r--r--test/links.c6
-rw-r--r--test/ohdr.c42
-rw-r--r--test/testabort_fail.sh.in (renamed from test/test_filenotclosed.sh.in)39
-rw-r--r--testpar/CMakeTests.cmake6
-rw-r--r--testpar/t_pflush1.c247
-rw-r--r--testpar/t_pflush2.c265
40 files changed, 1099 insertions, 433 deletions
diff --git a/MANIFEST b/MANIFEST
index cb006cc..7ea34e4 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -968,6 +968,7 @@
./test/cross_read.c
./test/dangle.c
./test/deflate.h5
+./test/del_many_dense_attrs.c
./test/direct_chunk.c
./test/dsets.c
./test/dt_arith.c
@@ -1102,10 +1103,10 @@
./test/tcheck_version.c
./test/tconfig.c
./test/tcoords.c
+./test/testabort_fail.sh.in
./test/testcheck_version.sh.in
./test/testerror.sh.in
./test/testlinks_env.sh.in
-./test/test_filenotclosed.sh.in
./test/test_filter_plugin.sh.in
./test/test_filters_le.h5
./test/test_filters_be.h5
@@ -3191,6 +3192,7 @@
./config/toolchain/crayle.cmake
./config/toolchain/GCC.cmake
./config/toolchain/intel.cmake
+./config/toolchain/PGI.cmake
./config/cmake/cacheinit.cmake
./config/cmake/CMakeFindJavaCommon.cmake
diff --git a/c++/src/H5CppDoc.h b/c++/src/H5CppDoc.h
index 0da98a4..5e80408 100644
--- a/c++/src/H5CppDoc.h
+++ b/c++/src/H5CppDoc.h
@@ -53,8 +53,7 @@
* <br />
* \section install_sec Installation
*
- * The HDF5 C++ API is included with the HDF5 source code and can
- * be obtained from
+ * The HDF5 C++ API is included with the HDF5 source code.
*
* Please refer to the release_docs/INSTALL file under the top directory
* of the HDF5 source code for information about installing, building,
diff --git a/config/cmake/HDF5UseFortran.cmake b/config/cmake/HDF5UseFortran.cmake
index 157befd..a24b2e1 100644
--- a/config/cmake/HDF5UseFortran.cmake
+++ b/config/cmake/HDF5UseFortran.cmake
@@ -18,16 +18,6 @@ ENABLE_LANGUAGE (Fortran)
set (HDF_PREFIX "H5")
include (CheckFortranFunctionExists)
-## Check for non-standard extenstion quadmath.h
-
-CHECK_INCLUDE_FILES(quadmath.h C_HAVE_QUADMATH)
-
-if (${C_HAVE_QUADMATH})
- set(${HDF_PREFIX}_HAVE_QUADMATH_H 1)
-else ()
- set(${HDF_PREFIX}_HAVE_QUADMATH_H 0)
-endif ()
-
# The provided CMake Fortran macros don't provide a general compile/run function
# so this one is used.
#-----------------------------------------------------------------------------
@@ -40,7 +30,7 @@ macro (FORTRAN_RUN FUNCTION_NAME SOURCE_CODE RUN_RESULT_VAR1 COMPILE_RESULT_VAR1
TRY_RUN (RUN_RESULT_VAR COMPILE_RESULT_VAR
${CMAKE_BINARY_DIR}
${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCompiler1.f90
- LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+ LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
)
if (${COMPILE_RESULT_VAR})
@@ -367,9 +357,9 @@ ENABLE_LANGUAGE (C)
#-----------------------------------------------------------------------------
macro (C_RUN FUNCTION_NAME SOURCE_CODE RETURN_VAR)
message (STATUS "Detecting C ${FUNCTION_NAME}")
- if (CMAKE_REQUIRED_LIBRARIES)
+ if (HDF5_REQUIRED_LIBRARIES)
set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES
- "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+ "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
else ()
set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES)
endif ()
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index 93ebc3c..0a39568 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -9,16 +9,16 @@
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
+set(CMAKE_C_STANDARD 99)
+set(CMAKE_C_STANDARD_REQUIRED TRUE)
message (STATUS "Warnings Configuration:")
+set (CMAKE_C_FLAGS "${CMAKE_C99_STANDARD_COMPILE_OPTION} ${CMAKE_C_FLAGS}")
#-----------------------------------------------------------------------------
# Compiler specific flags : Shouldn't there be compiler tests for these
#-----------------------------------------------------------------------------
if (CMAKE_COMPILER_IS_GNUCC)
set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS}")
- if (NOT CYGWIN)
- set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99")
- endif ()
if (${HDF_CFG_NAME} MATCHES "Debug")
if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 5.0)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Og -ftrapv -fno-common")
diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
index 40f1440..0424ed6 100644
--- a/config/cmake_ext_mod/ConfigureChecks.cmake
+++ b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -70,7 +70,7 @@ if (WIN32)
set (CMAKE_REQUIRED_FLAGS "-DWIN32_LEAN_AND_MEAN=1 -DNOGDI=1")
endif ()
set (${HDF_PREFIX}_HAVE_WIN32_API 1)
- set (CMAKE_REQUIRED_LIBRARIES "ws2_32.lib;wsock32.lib")
+ set (HDF5_REQUIRED_LIBRARIES "ws2_32.lib;wsock32.lib")
if (NOT UNIX AND NOT MINGW)
set (WINDOWS 1)
set (CMAKE_REQUIRED_FLAGS "/DWIN32_LEAN_AND_MEAN=1 /DNOGDI=1")
@@ -109,6 +109,78 @@ endif ()
# END of WINDOWS Hard code Values
# ----------------------------------------------------------------------
+if (NOT WINDOWS)
+ TEST_BIG_ENDIAN (${HDF_PREFIX}_WORDS_BIGENDIAN)
+endif ()
+
+#-----------------------------------------------------------------------------
+# Check IF header file exists and add it to the list.
+#-----------------------------------------------------------------------------
+macro (CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
+ CHECK_INCLUDE_FILES ("${USE_INCLUDES};${FILE}" ${VARIABLE})
+ if (${VARIABLE})
+ set (USE_INCLUDES ${USE_INCLUDES} ${FILE})
+ endif ()
+endmacro ()
+
+#-----------------------------------------------------------------------------
+# Check for the existence of certain header files
+#-----------------------------------------------------------------------------
+CHECK_INCLUDE_FILE_CONCAT ("sys/file.h" ${HDF_PREFIX}_HAVE_SYS_FILE_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/ioctl.h" ${HDF_PREFIX}_HAVE_SYS_IOCTL_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/resource.h" ${HDF_PREFIX}_HAVE_SYS_RESOURCE_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/socket.h" ${HDF_PREFIX}_HAVE_SYS_SOCKET_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/stat.h" ${HDF_PREFIX}_HAVE_SYS_STAT_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/time.h" ${HDF_PREFIX}_HAVE_SYS_TIME_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/types.h" ${HDF_PREFIX}_HAVE_SYS_TYPES_H)
+CHECK_INCLUDE_FILE_CONCAT ("features.h" ${HDF_PREFIX}_HAVE_FEATURES_H)
+CHECK_INCLUDE_FILE_CONCAT ("dirent.h" ${HDF_PREFIX}_HAVE_DIRENT_H)
+CHECK_INCLUDE_FILE_CONCAT ("setjmp.h" ${HDF_PREFIX}_HAVE_SETJMP_H)
+CHECK_INCLUDE_FILE_CONCAT ("stddef.h" ${HDF_PREFIX}_HAVE_STDDEF_H)
+CHECK_INCLUDE_FILE_CONCAT ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H)
+CHECK_INCLUDE_FILE_CONCAT ("unistd.h" ${HDF_PREFIX}_HAVE_UNISTD_H)
+
+# Darwin
+CHECK_INCLUDE_FILE_CONCAT ("mach/mach_time.h" ${HDF_PREFIX}_HAVE_MACH_MACH_TIME_H)
+
+# Windows
+CHECK_INCLUDE_FILE_CONCAT ("io.h" ${HDF_PREFIX}_HAVE_IO_H)
+if (NOT CYGWIN)
+ CHECK_INCLUDE_FILE_CONCAT ("winsock2.h" ${HDF_PREFIX}_HAVE_WINSOCK2_H)
+endif ()
+CHECK_INCLUDE_FILE_CONCAT ("sys/timeb.h" ${HDF_PREFIX}_HAVE_SYS_TIMEB_H)
+
+if (CMAKE_SYSTEM_NAME MATCHES "OSF")
+ CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
+ CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h" ${HDF_PREFIX}_HAVE_SYS_PROC_H)
+else ()
+ set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
+ set (${HDF_PREFIX}_HAVE_SYS_PROC_H "" CACHE INTERNAL "" FORCE)
+endif ()
+
+CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
+CHECK_INCLUDE_FILE_CONCAT ("pdb.h" ${HDF_PREFIX}_HAVE_PDB_H)
+CHECK_INCLUDE_FILE_CONCAT ("pthread.h" ${HDF_PREFIX}_HAVE_PTHREAD_H)
+CHECK_INCLUDE_FILE_CONCAT ("srbclient.h" ${HDF_PREFIX}_HAVE_SRBCLIENT_H)
+CHECK_INCLUDE_FILE_CONCAT ("string.h" ${HDF_PREFIX}_HAVE_STRING_H)
+CHECK_INCLUDE_FILE_CONCAT ("strings.h" ${HDF_PREFIX}_HAVE_STRINGS_H)
+CHECK_INCLUDE_FILE_CONCAT ("stdlib.h" ${HDF_PREFIX}_HAVE_STDLIB_H)
+CHECK_INCLUDE_FILE_CONCAT ("memory.h" ${HDF_PREFIX}_HAVE_MEMORY_H)
+CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h" ${HDF_PREFIX}_HAVE_DLFCN_H)
+CHECK_INCLUDE_FILE_CONCAT ("inttypes.h" ${HDF_PREFIX}_HAVE_INTTYPES_H)
+CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h" ${HDF_PREFIX}_HAVE_NETINET_IN_H)
+# _Bool type support
+CHECK_INCLUDE_FILE_CONCAT (stdbool.h ${HDF_PREFIX}_HAVE_STDBOOL_H)
+
+## Check for non-standard extenstion quadmath.h
+
+CHECK_INCLUDE_FILES(quadmath.h C_HAVE_QUADMATH)
+if (${C_HAVE_QUADMATH})
+ set(${HDF_PREFIX}_HAVE_QUADMATH_H 1)
+else ()
+ set(${HDF_PREFIX}_HAVE_QUADMATH_H 0)
+endif ()
+
if (CYGWIN)
set (${HDF_PREFIX}_HAVE_LSEEK64 0)
endif ()
@@ -127,17 +199,13 @@ endif ()
CHECK_LIBRARY_EXISTS_CONCAT ("ucb" gethostname ${HDF_PREFIX}_HAVE_LIBUCB)
# For other tests to use the same libraries
-set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${LINK_LIBS})
+set (HDF5_REQUIRED_LIBRARIES ${HDF5_REQUIRED_LIBRARIES} ${LINK_LIBS})
set (USE_INCLUDES "")
if (WINDOWS)
set (USE_INCLUDES ${USE_INCLUDES} "windows.h")
endif ()
-if (NOT WINDOWS)
- TEST_BIG_ENDIAN (${HDF_PREFIX}_WORDS_BIGENDIAN)
-endif ()
-
# For other specific tests, use this MACRO.
macro (HDF_FUNCTION_TEST OTHER_TEST)
if (NOT DEFINED ${HDF_PREFIX}_${OTHER_TEST})
@@ -165,7 +233,7 @@ macro (HDF_FUNCTION_TEST OTHER_TEST)
${CMAKE_BINARY_DIR}
${HDF_RESOURCES_EXT_DIR}/HDFTests.c
COMPILE_DEFINITIONS "${MACRO_CHECK_FUNCTION_DEFINITIONS}"
- LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+ LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
OUTPUT_VARIABLE OUTPUT
)
if (${OTHER_TEST})
@@ -188,63 +256,6 @@ endmacro ()
HDF_FUNCTION_TEST (STDC_HEADERS)
#-----------------------------------------------------------------------------
-# Check IF header file exists and add it to the list.
-#-----------------------------------------------------------------------------
-macro (CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
- CHECK_INCLUDE_FILES ("${USE_INCLUDES};${FILE}" ${VARIABLE})
- if (${VARIABLE})
- set (USE_INCLUDES ${USE_INCLUDES} ${FILE})
- endif ()
-endmacro ()
-
-#-----------------------------------------------------------------------------
-# Check for the existence of certain header files
-#-----------------------------------------------------------------------------
-CHECK_INCLUDE_FILE_CONCAT ("sys/file.h" ${HDF_PREFIX}_HAVE_SYS_FILE_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/ioctl.h" ${HDF_PREFIX}_HAVE_SYS_IOCTL_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/resource.h" ${HDF_PREFIX}_HAVE_SYS_RESOURCE_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/socket.h" ${HDF_PREFIX}_HAVE_SYS_SOCKET_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/stat.h" ${HDF_PREFIX}_HAVE_SYS_STAT_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/time.h" ${HDF_PREFIX}_HAVE_SYS_TIME_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/types.h" ${HDF_PREFIX}_HAVE_SYS_TYPES_H)
-CHECK_INCLUDE_FILE_CONCAT ("features.h" ${HDF_PREFIX}_HAVE_FEATURES_H)
-CHECK_INCLUDE_FILE_CONCAT ("dirent.h" ${HDF_PREFIX}_HAVE_DIRENT_H)
-CHECK_INCLUDE_FILE_CONCAT ("setjmp.h" ${HDF_PREFIX}_HAVE_SETJMP_H)
-CHECK_INCLUDE_FILE_CONCAT ("stddef.h" ${HDF_PREFIX}_HAVE_STDDEF_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H)
-CHECK_INCLUDE_FILE_CONCAT ("unistd.h" ${HDF_PREFIX}_HAVE_UNISTD_H)
-
-# Darwin
-CHECK_INCLUDE_FILE_CONCAT ("mach/mach_time.h" ${HDF_PREFIX}_HAVE_MACH_MACH_TIME_H)
-
-# Windows
-CHECK_INCLUDE_FILE_CONCAT ("io.h" ${HDF_PREFIX}_HAVE_IO_H)
-if (NOT CYGWIN)
- CHECK_INCLUDE_FILE_CONCAT ("winsock2.h" ${HDF_PREFIX}_HAVE_WINSOCK2_H)
-endif ()
-CHECK_INCLUDE_FILE_CONCAT ("sys/timeb.h" ${HDF_PREFIX}_HAVE_SYS_TIMEB_H)
-
-if (CMAKE_SYSTEM_NAME MATCHES "OSF")
- CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
- CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h" ${HDF_PREFIX}_HAVE_SYS_PROC_H)
-else ()
- set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
- set (${HDF_PREFIX}_HAVE_SYS_PROC_H "" CACHE INTERNAL "" FORCE)
-endif ()
-
-CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
-CHECK_INCLUDE_FILE_CONCAT ("pdb.h" ${HDF_PREFIX}_HAVE_PDB_H)
-CHECK_INCLUDE_FILE_CONCAT ("pthread.h" ${HDF_PREFIX}_HAVE_PTHREAD_H)
-CHECK_INCLUDE_FILE_CONCAT ("srbclient.h" ${HDF_PREFIX}_HAVE_SRBCLIENT_H)
-CHECK_INCLUDE_FILE_CONCAT ("string.h" ${HDF_PREFIX}_HAVE_STRING_H)
-CHECK_INCLUDE_FILE_CONCAT ("strings.h" ${HDF_PREFIX}_HAVE_STRINGS_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdlib.h" ${HDF_PREFIX}_HAVE_STDLIB_H)
-CHECK_INCLUDE_FILE_CONCAT ("memory.h" ${HDF_PREFIX}_HAVE_MEMORY_H)
-CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h" ${HDF_PREFIX}_HAVE_DLFCN_H)
-CHECK_INCLUDE_FILE_CONCAT ("inttypes.h" ${HDF_PREFIX}_HAVE_INTTYPES_H)
-CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h" ${HDF_PREFIX}_HAVE_NETINET_IN_H)
-
-#-----------------------------------------------------------------------------
# Check for large file support
#-----------------------------------------------------------------------------
@@ -408,7 +419,6 @@ endif ()
#-----------------------------------------------------------------------------
# _Bool type support
-CHECK_INCLUDE_FILE_CONCAT (stdbool.h ${HDF_PREFIX}_HAVE_STDBOOL_H)
if (HAVE_STDBOOL_H)
set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
HDF_CHECK_TYPE_SIZE (bool ${HDF_PREFIX}_SIZEOF_BOOL)
@@ -580,7 +590,7 @@ if (WINDOWS)
${CMAKE_BINARY_DIR}
${HDF_RESOURCES_EXT_DIR}/HDFTests.c
COMPILE_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS} ${MACRO_CHECK_FUNCTION_DEFINITIONS}"
- LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+ LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
CMAKE_FLAGS "${CHECK_C_SOURCE_COMPILES_ADD_INCLUDES} -DCMAKE_SKIP_RPATH:BOOL=${CMAKE_SKIP_RPATH}"
COMPILE_OUTPUT_VARIABLE OUTPUT
)
diff --git a/config/cmake_ext_mod/HDFUseCXX.cmake b/config/cmake_ext_mod/HDFUseCXX.cmake
index f293ec5..efaa556 100644
--- a/config/cmake_ext_mod/HDFUseCXX.cmake
+++ b/config/cmake_ext_mod/HDFUseCXX.cmake
@@ -48,8 +48,8 @@ macro (HDF_CXX_FUNCTION_TEST OTHER_TEST)
if (NOT DEFINED ${OTHER_TEST})
set (MACRO_CHECK_FUNCTION_DEFINITIONS "-D${OTHER_TEST} ${CMAKE_REQUIRED_FLAGS}")
set (OTHER_TEST_ADD_LIBRARIES)
- if (CMAKE_REQUIRED_LIBRARIES)
- set (OTHER_TEST_ADD_LIBRARIES "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+ if (HDF5_REQUIRED_LIBRARIES)
+ set (OTHER_TEST_ADD_LIBRARIES "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
endif ()
foreach (def
diff --git a/config/cmake_ext_mod/HDFUseFortran.cmake b/config/cmake_ext_mod/HDFUseFortran.cmake
index f8f3cea..c68c921 100644
--- a/config/cmake_ext_mod/HDFUseFortran.cmake
+++ b/config/cmake_ext_mod/HDFUseFortran.cmake
@@ -48,9 +48,9 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) ${CMAKE_MATCH_1}")
#-----------------------------------------------------------------------------
macro (CHECK_FORTRAN_FEATURE FUNCTION CODE VARIABLE)
message (STATUS "Testing Fortran ${FUNCTION}")
- if (CMAKE_REQUIRED_LIBRARIES)
+ if (HDF5_REQUIRED_LIBRARIES)
set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES
- "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+ "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
else ()
set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES)
endif ()
diff --git a/config/toolchain/GCC.cmake b/config/toolchain/GCC.cmake
index ddb1641..c41d0ca 100644
--- a/config/toolchain/GCC.cmake
+++ b/config/toolchain/GCC.cmake
@@ -1,5 +1,6 @@
-# Uncomment the following to use cross-compiling
+# Uncomment the following line and the correct system name to use cross-compiling
#set(CMAKE_SYSTEM_NAME Linux)
+
set(CMAKE_COMPILER_VENDOR "GCC")
set(CMAKE_C_COMPILER cc)
diff --git a/config/toolchain/PGI.cmake b/config/toolchain/PGI.cmake
new file mode 100644
index 0000000..ec58cbb
--- /dev/null
+++ b/config/toolchain/PGI.cmake
@@ -0,0 +1,11 @@
+# Uncomment the following to use cross-compiling
+#set(CMAKE_SYSTEM_NAME Linux)
+
+set(CMAKE_COMPILER_VENDOR "PGI")
+
+set(CMAKE_C_COMPILER pgcc)
+set(CMAKE_CXX_COMPILER pgc++)
+set(CMAKE_Fortran_COMPILER pgf90)
+
+# the following is used if cross-compiling
+set(CMAKE_CROSSCOMPILING_EMULATOR "")
diff --git a/config/toolchain/crayle.cmake b/config/toolchain/crayle.cmake
index a83147b..47d8afc 100644
--- a/config/toolchain/crayle.cmake
+++ b/config/toolchain/crayle.cmake
@@ -1,5 +1,6 @@
-# Uncomment the following to use cross-compiling
+# The following line will use cross-compiling
set(CMAKE_SYSTEM_NAME Linux)
+
set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
set(CMAKE_C_COMPILER cc)
diff --git a/config/toolchain/intel.cmake b/config/toolchain/intel.cmake
index f1a5734..97f6a64 100644
--- a/config/toolchain/intel.cmake
+++ b/config/toolchain/intel.cmake
@@ -1,5 +1,6 @@
# Uncomment the following to use cross-compiling
#set(CMAKE_SYSTEM_NAME Linux)
+
set(CMAKE_COMPILER_VENDOR "intel")
set(CMAKE_C_COMPILER icc)
diff --git a/configure.ac b/configure.ac
index eb32435..21ad68b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3399,6 +3399,7 @@ AC_CONFIG_FILES([src/libhdf5.settings
src/Makefile
test/Makefile
test/H5srcdir_str.h
+ test/testabort_fail.sh
test/testcheck_version.sh
test/testerror.sh
test/testflushrefresh.sh
@@ -3406,7 +3407,6 @@ AC_CONFIG_FILES([src/libhdf5.settings
test/testlinks_env.sh
test/testswmr.sh
test/testvdsswmr.sh
- test/test_filenotclosed.sh
test/test_filter_plugin.sh
test/test_usecases.sh
test/test_vol_plugin.sh
diff --git a/hl/fortran/src/Makefile.am b/hl/fortran/src/Makefile.am
index a495e220..200a2ce 100644
--- a/hl/fortran/src/Makefile.am
+++ b/hl/fortran/src/Makefile.am
@@ -50,6 +50,19 @@ libhdf5hl_fortran_la_SOURCES=H5DSfc.c H5LTfc.c H5IMfc.c H5IMcc.c H5TBfc.c \
# HDF5 HL Fortran library depends on HDF5 Library.
libhdf5hl_fortran_la_LIBADD=$(LIBH5_HL) $(LIBH5F)
+# The name of the lib file doesn't follow the same pattern as the other hl lib
+# files, namely libhdf5_hl_*. Add a symlink with the compliant name to the
+# actual lib file.
+install-exec-hook:
+ cd $(DESTDIR)$(libdir) && \
+ if test -f libhdf5hl_fortran.a; then \
+ $(LN_S) libhdf5hl_fortran.a libhdf5_hl_fortran.a; \
+ fi; \
+ if test -f libhdf5hl_fortran.so; then \
+ $(LN_S) libhdf5hl_fortran.so libhdf5_hl_fortran.so; \
+ fi;
+
+
# Fortran module files can have different extensions and different names
# (e.g., different capitalizations) on different platforms. Write rules
# for them explicitly rather than trying to teach automake about them.
@@ -72,6 +85,7 @@ uninstall-local:
set -x; $(RM) $(includedir)/*.$(F9XMODEXT); \
fi; \
fi
+ $(RM) $(DESTDIR)$(libdir)/libhdf5_hl_fortran*
# These are the helper programs we need to build.
noinst_PROGRAMS = H5HL_buildiface
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index e354207..51b0d38 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -3229,13 +3229,56 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status)
throws HDF5LibraryException, NullPointerException;
+ /**
+ * H5Fget_dset_no_attrs_hint gets the file-level setting to create minimized dataset object headers.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native boolean H5Fget_dset_no_attrs_hint(long file_id)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Fset_dset_no_attrs_hint sets the file-level setting to create minimized dataset object headers.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ * @param minimize
+ * the minimize hint setting
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Fset_dset_no_attrs_hint(long file_id, boolean minimize)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Fset_libver_bounds sets a different low and high bounds while a file is open.
+ *
+ * @param file_id
+ * IN: Identifier of the target file.
+ * @param low
+ * IN: The earliest version of the library that will be used for writing objects
+ * @param high
+ * IN: The latest version of the library that will be used for writing objects.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Fset_libver_bounds(long file_id, int low, int high)
+ throws HDF5LibraryException;
+
// /////// unimplemented ////////
// herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
// herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
// ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
// herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info);
// ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/);
- // herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
// herr_t H5Fformat_convert(hid_t fid);
// herr_t H5Freset_page_buffering_stats(hid_t file_id);
// herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
@@ -6922,8 +6965,6 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
NullPointerException;
- // /////// Dataset creation property list (DCPL) routines ///////
-
/**
* H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
*
@@ -6952,6 +6993,36 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
+ /**
+ * H5Pget_dset_no_attrs_hint accesses the flag for whether or not datasets created by the given dcpl
+ * will be created with a "minimized" object header.
+ *
+ * @param dcpl_id
+ * IN: Dataset creation property list
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native boolean H5Pget_dset_no_attrs_hint(long dcpl_id)
+ throws HDF5LibraryException;
+
+
+ /**
+ * H5Pset_dset_no_attrs_hint sets the dcpl to minimize (or explicitly to not minimized) dataset object
+ * headers upon creation.
+ *
+ * @param dcpl_id
+ * IN: Dataset creation property list
+ *
+ * @param minimize
+ * the minimize hint setting
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ **/
+ public synchronized static native void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize)
+ throws HDF5LibraryException;
+
// /////// Dataset access property list (DAPL) routines ///////
/**
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 248e654..80adffb 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -149,6 +149,9 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
(JNIEnv *env, jclass clss, jstring name)
{
htri_t bval = JNI_FALSE;
+#ifdef H5_NO_DEPRECATED_SYMBOLS
+ h5unimplemented(env, "H5Fis_hdf5: not implemented");
+#else
const char *fileName;
PIN_JAVA_STRING(name, fileName);
@@ -162,7 +165,7 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
else if (bval < 0)
h5libraryError(env);
}
-
+#endif
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Fis_1hdf5 */
@@ -636,6 +639,66 @@ Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
} /* end else */
} /* end Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status */
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong file_id, jboolean minimize)
+{
+ herr_t retVal = -1;
+ hbool_t minimize_val;
+
+ if (minimize == JNI_TRUE)
+ minimize_val = TRUE;
+ else
+ minimize_val = FALSE;
+
+ retVal = H5Fset_dset_no_attrs_hint((hid_t)file_id, (hbool_t)minimize_val);
+ if (retVal < 0)
+ h5libraryError(env);
+}
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong file_id)
+{
+ hbool_t minimize = FALSE;
+ jboolean bval = JNI_FALSE;
+
+ if (H5Fget_dset_no_attrs_hint((hid_t)file_id, (hbool_t *)&minimize) < 0) {
+ h5libraryError(env);
+ }
+ else {
+ if (minimize == TRUE)
+ bval = JNI_TRUE;
+ } /* end else */
+
+ return bval;
+}
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fset_libver_bounds
+ * Signature: (JII)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds
+ (JNIEnv *env, jclass clss, jlong file_id, jint low, jint high)
+{
+ herr_t retVal = -1;
+
+ retVal = H5Fset_libver_bounds((hid_t)file_id, (H5F_libver_t)low, (H5F_libver_t)high);
+ if(retVal < 0)
+ h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds */
#ifdef __cplusplus
diff --git a/java/src/jni/h5fImp.h b/java/src/jni/h5fImp.h
index af0fa1d..fe253f9 100644
--- a/java/src/jni/h5fImp.h
+++ b/java/src/jni/h5fImp.h
@@ -255,6 +255,33 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
(JNIEnv *, jclass, jlong, jbooleanArray);
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint
+ (JNIEnv *, jclass, jlong, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint
+ (JNIEnv *, jclass, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Fset_libver_bounds
+ * Signature: (JII)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds
+(JNIEnv *, jclass, jlong, jint, jint);
+
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index 52008ce..19f9640 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -5946,6 +5946,51 @@ Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
return (jint)opts;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts */
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Pset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong dcpl_id, jboolean minimize)
+{
+ herr_t retVal = -1;
+ hbool_t minimize_val;
+
+ if (minimize == JNI_TRUE)
+ minimize_val = TRUE;
+ else
+ minimize_val = FALSE;
+
+ retVal = H5Pset_dset_no_attrs_hint((hid_t)dcpl_id, (hbool_t)minimize_val);
+ if (retVal < 0)
+ h5libraryError(env);
+}
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Pget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong dcpl_id)
+{
+ hbool_t minimize = FALSE;
+ jboolean bval = JNI_FALSE;
+
+ if (H5Pget_dset_no_attrs_hint((hid_t)dcpl_id, (hbool_t *)&minimize) < 0) {
+ h5libraryError(env);
+ }
+ else {
+ if (minimize == TRUE)
+ bval = JNI_TRUE;
+ } /* end else */
+
+ return bval;
+}
+
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.h b/java/src/jni/h5pImp.h
index 1d12e3d..0a603f7 100644
--- a/java/src/jni/h5pImp.h
+++ b/java/src/jni/h5pImp.h
@@ -1614,6 +1614,24 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
(JNIEnv *, jclass, jlong);
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Pset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1dset_1no_1attrs_1hint
+ (JNIEnv *, jclass, jlong, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Pget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1dset_1no_1attrs_1hint
+ (JNIEnv *, jclass, jlong);
+
#ifdef __cplusplus
} /* end extern "C" */
diff --git a/java/test/TestH5Dplist.java b/java/test/TestH5Dplist.java
index 406a1d3..1b5acfa 100644
--- a/java/test/TestH5Dplist.java
+++ b/java/test/TestH5Dplist.java
@@ -13,6 +13,7 @@
package test;
+import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -211,4 +212,23 @@ public class TestH5Dplist {
assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[4][8] == 99);
}
+ @Test
+ public void testH5P_dset_no_attrs_hint() {
+ boolean ret_val_id = true;
+
+ _createPDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DATASET_CREATE);
+
+ try {
+ ret_val_id = H5.H5Pget_dset_no_attrs_hint(H5dcpl_id);
+ assertFalse("H5P_dset_no_attrs_hint", ret_val_id);
+ H5.H5Pset_dset_no_attrs_hint(H5dcpl_id, true);
+ ret_val_id = H5.H5Pget_dset_no_attrs_hint(H5dcpl_id);
+ assertTrue("H5P_dset_no_attrs_hint", ret_val_id);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5P_dset_no_attrs_hint: " + err);
+ }
+ }
+
}
diff --git a/java/test/TestH5Fbasic.java b/java/test/TestH5Fbasic.java
index a5afb6e..72a3c23 100644
--- a/java/test/TestH5Fbasic.java
+++ b/java/test/TestH5Fbasic.java
@@ -14,6 +14,7 @@
package test;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -69,19 +70,6 @@ public class TestH5Fbasic {
}
@Test
- public void testH5Fis_hdf5() {
- boolean isH5 = false;
-
- try {
- isH5 = H5.H5Fis_hdf5(H5_FILE);
- }
- catch (Throwable err) {
- fail("H5.H5Fis_hdf5 failed on " + H5_FILE + ": " + err);
- }
- assertTrue(isH5 == true);
- }
-
- @Test
public void testH5Fis_accessible() {
boolean isH5 = false;
@@ -328,4 +316,20 @@ public class TestH5Fbasic {
fail("H5.H5Freset_mdc_hit_rate_stats: " + err);
}
}
+
+ @Test
+ public void testH5F_dset_no_attrs_hint() {
+ boolean ret_val_id = true;
+ try {
+ ret_val_id = H5.H5Fget_dset_no_attrs_hint(H5fid);
+ assertFalse("H5F_dset_no_attrs_hint", ret_val_id);
+ H5.H5Fset_dset_no_attrs_hint(H5fid, true);
+ ret_val_id = H5.H5Fget_dset_no_attrs_hint(H5fid);
+ assertTrue("H5F_dset_no_attrs_hint", ret_val_id);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5F_dset_no_attrs_hint: " + err);
+ }
+ }
}
diff --git a/java/test/TestH5Fparams.java b/java/test/TestH5Fparams.java
index 3d64aa9..40cbe4b 100644
--- a/java/test/TestH5Fparams.java
+++ b/java/test/TestH5Fparams.java
@@ -22,10 +22,12 @@ import java.io.File;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
import hdf.hdf5lib.structs.H5F_info2_t;
import org.junit.After;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
@@ -55,11 +57,6 @@ public class TestH5Fparams {
}
@Test(expected = NullPointerException.class)
- public void testH5Fis_hdf5_null() throws Throwable {
- H5.H5Fis_hdf5(null);
- }
-
- @Test(expected = NullPointerException.class)
public void testH5Fis_accessible_null() throws Throwable {
H5.H5Fis_accessible(null, -1);
}
@@ -74,7 +71,7 @@ public class TestH5Fparams {
H5.H5Funmount(-1, null);
}
- @Test
+ @Ignore
public void testH5Fis_hdf5_text() {
File txtFile = null;
boolean isH5 = false;
@@ -195,7 +192,7 @@ public class TestH5Fparams {
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
- fail("H5.H5Fopen: " + err);
+ fail("H5.H5Fcreate: " + err);
}
try {
@@ -215,4 +212,42 @@ public class TestH5Fparams {
try {H5.H5Fclose(fid);} catch (Exception ex) {}
}
}
+
+ @Ignore//(expected = HDF5FunctionArgumentException.class)
+ public void testH5Fset_libver_bounds_invalidlow() throws Throwable {
+ long fid = -1;
+
+ try {
+ try {
+ fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Throwable err) {
+ fail("H5.H5Fcreate: " + err);
+ }
+ H5.H5Fset_libver_bounds(fid, 5, HDF5Constants.H5F_LIBVER_LATEST);
+ }
+ finally {
+ try {H5.H5Fclose(fid);} catch (Exception ex) {}
+ }
+ }
+
+ @Ignore//(expected = HDF5FunctionArgumentException.class)
+ public void testH5Fset_libver_bounds_invalidhigh() throws Throwable {
+ long fid = -1;
+
+ try {
+ try {
+ fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Throwable err) {
+ fail("H5.H5Fcreate: " + err);
+ }
+ H5.H5Fset_libver_bounds(fid, HDF5Constants.H5F_LIBVER_V110, HDF5Constants.H5F_LIBVER_V110+1);
+ }
+ finally {
+ try {H5.H5Fclose(fid);} catch (Exception ex) {}
+ }
+ }
}
diff --git a/java/test/testfiles/JUnit-TestH5Dplist.txt b/java/test/testfiles/JUnit-TestH5Dplist.txt
index 1dfbed1..64e924a 100644
--- a/java/test/testfiles/JUnit-TestH5Dplist.txt
+++ b/java/test/testfiles/JUnit-TestH5Dplist.txt
@@ -1,7 +1,8 @@
JUnit version 4.11
+.testH5P_dset_no_attrs_hint
.testH5Dset_extent
Time: XXXX
-OK (1 test)
+OK (2 tests)
diff --git a/java/test/testfiles/JUnit-TestH5Fbasic.txt b/java/test/testfiles/JUnit-TestH5Fbasic.txt
index 2654624..cd4e282 100644
--- a/java/test/testfiles/JUnit-TestH5Fbasic.txt
+++ b/java/test/testfiles/JUnit-TestH5Fbasic.txt
@@ -1,7 +1,7 @@
JUnit version 4.11
.testH5Fget_mdc_size
.testH5Fget_mdc_hit_rate
-.testH5Fis_hdf5
+.testH5F_dset_no_attrs_hint
.testH5Fget_freespace
.testH5Fclose
.testH5Fget_filesize
diff --git a/java/test/testfiles/JUnit-TestH5Fparams.txt b/java/test/testfiles/JUnit-TestH5Fparams.txt
index e91cbdc..91a8435 100644
--- a/java/test/testfiles/JUnit-TestH5Fparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Fparams.txt
@@ -9,10 +9,8 @@ JUnit version 4.11
.testH5Funmount_null
.testH5Fclose_negative
.testH5Fopen_null
-.testH5Fis_hdf5_null
-.testH5Fis_hdf5_text
Time: XXXX
-OK (12 tests)
+OK (10 tests)
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 024db9a..ff18e71 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -1,4 +1,4 @@
-HDF5 version 1.11.4 currently under development
+ version 1.11.4 currently under development
================================================================================
@@ -243,6 +243,19 @@ Bug Fixes since HDF5-1.10.3 release
Library
-------
+ - Deleting attributes in dense storage
+
+ The library aborts with "infinite loop closing library" after
+ attributes in dense storage are created and then deleted.
+
+ 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
+ decoded attribute.
+
+ (VC - 2018/12/26, HDFFV-10659)
+
- Allow H5detect and H5make_libsettings to take a file as an argument.
Rather than only writing to stdout, add a command argument to name
@@ -314,6 +327,15 @@ 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
+ the next major release.
+
+ (LRK - 2019/01/04, HDFFV-10596)
+
- Made Fortran specific subroutines PRIVATE in generic procedures.
Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
diff --git a/src/H5Adense.c b/src/H5Adense.c
index 5bed82d..021fa76 100644
--- a/src/H5Adense.c
+++ b/src/H5Adense.c
@@ -300,18 +300,49 @@ static herr_t
H5A__dense_fnd_cb(const H5A_t *attr, hbool_t *took_ownership, void *_user_attr)
{
H5A_t const **user_attr = (H5A_t const **)_user_attr; /* User data from v2 B-tree attribute lookup */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_STATIC_NOERR
+ FUNC_ENTER_STATIC
/* Check arguments */
HDassert(attr);
HDassert(user_attr);
+ HDassert(took_ownership);
+ /*
+ * If there is an attribute already stored in "user_attr",
+ * we need to free the dynamially allocated spaces for the
+ * attribute, otherwise we got infinite loop closing library due to
+ * outstanding allocation. (HDFFV-10659)
+ *
+ * This callback is used by H5A__dense_remove() to close/free the
+ * attribute stored in "user_attr" (via H5O__msg_free_real()) after
+ * the attribute node is deleted from the name index v2 B-tree.
+ * The issue is:
+ * When deleting the attribute node from the B-tree,
+ * if the attribute is found in the intermediate B-tree nodes,
+ * which may be merged/redistributed, we need to free the dynamically
+ * allocated spaces for the intermediate decoded attribute.
+ */
+ if(*user_attr != NULL) {
+ H5A_t *old_attr = *user_attr;
+ if(old_attr->shared) {
+ /* Free any dynamically allocated items */
+ if(H5A__free(old_attr) < 0)
+ HGOTO_ERROR(H5E_ATTR, H5E_CANTRELEASE, FAIL, "can't release attribute info")
+
+ /* Destroy shared attribute struct */
+ old_attr->shared = H5FL_FREE(H5A_shared_t, old_attr->shared);
+ } /* end if */
+
+ old_attr = H5FL_FREE(H5A_t, old_attr);
+ } /* end if */
/* Take over attribute ownership */
*user_attr = attr;
*took_ownership = TRUE;
- FUNC_LEAVE_NOAPI(SUCCEED)
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
} /* end H5A__dense_fnd_cb() */
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 91f3b91..b5a5c39 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -1493,6 +1493,9 @@ H5D__create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Set chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
+ /* Validate this chunk dimension */
+ if(fm->layout->u.chunk.dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
HDassert(sel_start[u] == sel_end[u]);
chunk_info->scaled[u] = sel_start[u] / fm->layout->u.chunk.dim[u];
coords[u] = chunk_info->scaled[u] * fm->layout->u.chunk.dim[u];
@@ -1580,6 +1583,9 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Set initial chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
+ /* Validate this chunk dimension */
+ if(fm->layout->u.chunk.dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
scaled[u] = start_scaled[u] = sel_start[u] / fm->layout->u.chunk.dim[u];
coords[u] = start_coords[u] = scaled[u] * fm->layout->u.chunk.dim[u];
end[u] = (coords[u] + fm->chunk_dim[u]) - 1;
@@ -4043,6 +4049,9 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_
* assume here that all elements of space_dim are > 0. This is checked at
* the top of this function. */
for(op_dim=0; op_dim<space_ndims; op_dim++) {
+ /* Validate this chunk dimension */
+ if(chunk_dim[op_dim] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim)
min_unalloc[op_dim] = (old_dim[op_dim] + chunk_dim[op_dim] - 1) / chunk_dim[op_dim];
max_unalloc[op_dim] = (space_dim[op_dim] - 1) / chunk_dim[op_dim];
@@ -4484,13 +4493,17 @@ H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[])
/* Start off with this dimension marked as not needing to be modified */
new_full_dim[op_dim] = FALSE;
+ /* Validate this chunk dimension */
+ if(chunk_dim[op_dim] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim)
+
/* Calculate offset of first previously incomplete chunk in this
* dimension */
- old_edge_chunk_sc[op_dim] = (old_dim[op_dim] / chunk_dim[op_dim]);
+ old_edge_chunk_sc[op_dim] = (old_dim[op_dim] / chunk_dim[op_dim]);
/* Calculate the largest offset of chunks that might need to be
* modified in this dimension */
- max_edge_chunk_sc[op_dim] = MIN((old_dim[op_dim] - 1) / chunk_dim[op_dim],
+ max_edge_chunk_sc[op_dim] = MIN((old_dim[op_dim] - 1) / chunk_dim[op_dim],
MAX((space_dim[op_dim] / chunk_dim[op_dim]), 1) - 1);
/* Check for old_dim aligned with chunk boundary in this dimension, if
@@ -4626,6 +4639,8 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size")
/* Distribute evenly the number of blocks between processes. */
+ if(mpi_size == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Resulted in division by zero")
num_blocks = chunk_info->num_io / mpi_size; /* value should be the same on all procs */
/* after evenly distributing the blocks between processes, are
@@ -5066,6 +5081,10 @@ H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim)
HDmemset(min_mod_chunk_sc, 0, sizeof(min_mod_chunk_sc));
HDmemset(max_mod_chunk_sc, 0, sizeof(max_mod_chunk_sc));
for(op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) {
+ /* Validate this chunk dimension */
+ if(chunk_dim[op_dim] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", op_dim)
+
/* Calculate the largest offset of chunks that might need to be
* modified in this dimension */
max_mod_chunk_sc[op_dim] = (old_dim[op_dim] - 1) / chunk_dim[op_dim];
@@ -5721,9 +5740,12 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
/* (background buffer has already been zeroed out, if not expanding) */
if(udata->cpy_info->expand_ref) {
size_t ref_count;
+ size_t dt_size;
/* Determine # of reference elements to copy */
- ref_count = nbytes / H5T_get_size(udata->dt_src);
+ if((dt_size = H5T_get_size(udata->dt_src)) == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "size must not be 0")
+ ref_count = nbytes / dt_size;
/* Copy the reference elements */
if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0)
diff --git a/src/H5L.c b/src/H5L.c
index 33e561a..1f45740 100644
--- a/src/H5L.c
+++ b/src/H5L.c
@@ -648,6 +648,8 @@ H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t link_type,
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no link name specified")
if(link_type < H5L_TYPE_UD_MIN || link_type > H5L_TYPE_MAX)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid link class")
+ if(!udata && udata_size)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "udata cannot be NULL if udata_size is non-zero")
/* Check the group access property list */
if(H5P_DEFAULT == lcpl_id)
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 69afb85..0d67485 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -374,6 +374,7 @@ set (H5_CHECK_TESTS
atomic_reader
links_env
filenotclosed
+ del_many_dense_attrs
flushrefresh
)
diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 9816543..c0d4813 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -520,6 +520,7 @@ set (test_CLEANFILES
flushrefresh_VERIFICATION_CHECKPOINT2
flushrefresh_VERIFICATION_DONE
filenotclosed.h5
+ del_many_dense_attrs.h5
atomic_data
accum_swmr_big.h5
ohdr_swmr.h5
@@ -796,6 +797,7 @@ set_tests_properties (H5TEST-tcheck_version-release PROPERTIES
# atomic_reader
# links_env
# filenotclosed
+# del_many_dense_attrs
# flushrefresh
##############################################################################
# autotools script tests
@@ -803,7 +805,7 @@ set_tests_properties (H5TEST-tcheck_version-release PROPERTIES
# NOT CONVERTED accum_swmr_reader is used by accum.c.
# NOT CONVERTED atomic_writer and atomic_reader are standalone programs.
# links_env is used by testlinks_env.sh
-# filenotclosed is used by test_filenotclosed.sh
+# filenotclosed and del_many_dense_attrs are used by testabort_fail.sh
# NOT CONVERTED flushrefresh is used by testflushrefresh.sh.
# NOT CONVERTED use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh
# NOT CONVERTED swmr_* files (besides swmr.c) are used by testswmr.sh.
@@ -830,6 +832,23 @@ set_tests_properties (H5TEST-filenotclosed PROPERTIES
WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST
)
+#-- Adding test for del_many_dense_attrs
+add_test (
+ NAME H5TEST-clear-del_many_dense_attrs-objects
+ COMMAND ${CMAKE_COMMAND}
+ -E remove
+ del_many_dense_attrs.h5
+ WORKING_DIRECTORY
+ ${HDF5_TEST_BINARY_DIR}/H5TEST
+)
+set_tests_properties (H5TEST-clear-del_many_dense_attrs-objects PROPERTIES FIXTURES_SETUP del_many_dense_attrs_clear_objects)
+add_test (NAME H5TEST-del_many_dense_attrs COMMAND $<TARGET_FILE:del_many_dense_attrs>)
+set_tests_properties (H5TEST-del_many_dense_attrs PROPERTIES
+ FIXTURES_REQUIRED del_many_dense_attrs_clear_objects
+ ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/H5TEST"
+ WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST
+)
+
#-- Adding test for err_compat
if (HDF5_ENABLE_DEPRECATED_SYMBOLS)
add_test (NAME H5TEST-clear-err_compat-objects
diff --git a/test/Makefile.am b/test/Makefile.am
index 1a232ab..88dc542 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -29,12 +29,13 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_builddir)/src
# testflushrefresh.sh: flushrefresh
# testswmr.sh: swmr*
# testvdsswmr.sh: vds_swmr*
-# test_filenotclosed.sh: filenotclosed.c
+# testabort_fail.sh: filenotclosed.c and del_many_dense_attrs.c
# test_filter_plugin.sh: filter_plugin.c
# test_usecases.sh: use_append_chunk, use_append_mchunks, use_disable_mdc_flushes
-TEST_SCRIPT = testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh test_filenotclosed.sh\
- testswmr.sh testvdsswmr.sh testflushrefresh.sh test_usecases.sh
-SCRIPT_DEPEND = error_test$(EXEEXT) err_compat$(EXEEXT) links_env$(EXEEXT) filenotclosed$(EXEEXT) \
+TEST_SCRIPT = testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh \
+ testswmr.sh testvdsswmr.sh testflushrefresh.sh test_usecases.sh testabort_fail.sh
+SCRIPT_DEPEND = error_test$(EXEEXT) err_compat$(EXEEXT) links_env$(EXEEXT) \
+ filenotclosed$(EXEEXT) del_many_dense_attrs$(EXEEXT) \
flushrefresh$(EXEEXT) use_append_chunk$(EXEEXT) use_append_mchunks$(EXEEXT) use_disable_mdc_flushes$(EXEEXT) \
swmr_generator$(EXEEXT) swmr_reader$(EXEEXT) swmr_writer$(EXEEXT) \
swmr_remove_reader$(EXEEXT) swmr_remove_writer$(EXEEXT) swmr_addrem_writer$(EXEEXT) \
@@ -68,7 +69,7 @@ TEST_PROG= testhdf5 \
# accum_swmr_reader is used by accum.c.
# atomic_writer and atomic_reader are standalone programs.
# links_env is used by testlinks_env.sh
-# filenotclosed is used by test_filenotclosed.sh
+# filenotclosed and del_many_dense_attrs are used by testabort_fail.sh
# flushrefresh is used by testflushrefresh.sh.
# use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh
# swmr_* files (besides swmr.c) are used by testswmr.sh.
@@ -78,7 +79,8 @@ TEST_PROG= testhdf5 \
# and this lets automake keep all its test programs in one place.
check_PROGRAMS=$(TEST_PROG) error_test err_compat tcheck_version \
testmeta accum_swmr_reader atomic_writer atomic_reader \
- links_env filenotclosed flushrefresh use_append_chunk use_append_mchunks use_disable_mdc_flushes \
+ links_env filenotclosed del_many_dense_attrs flushrefresh \
+ use_append_chunk use_append_mchunks use_disable_mdc_flushes \
swmr_generator swmr_start_write swmr_reader swmr_writer swmr_remove_reader \
swmr_remove_writer swmr_addrem_writer swmr_sparse_reader swmr_sparse_writer \
swmr_check_compat_vfd vds_swmr_gen vds_swmr_reader vds_swmr_writer
@@ -221,7 +223,7 @@ use_disable_mdc_flushes_SOURCES=use_disable_mdc_flushes.c
# Temporary files.
DISTCLEANFILES=testerror.sh testlibinfo.sh testcheck_version.sh testlinks_env.sh test_filter_plugin.sh \
- testswmr.sh testvdsswmr.sh test_usecases.sh testflushrefresh.sh test_filenotclosed.sh \
+ testswmr.sh testvdsswmr.sh test_usecases.sh testflushrefresh.sh testabort_fail.sh \
test_vol_plugin.sh
include $(top_srcdir)/config/conclude.am
diff --git a/test/ShellTests.cmake b/test/ShellTests.cmake
index 58dc85d..98f3daf 100644
--- a/test/ShellTests.cmake
+++ b/test/ShellTests.cmake
@@ -171,6 +171,7 @@ if (UNIX)
# atomic_writer
# atomic_reader
# filenotclosed
+ # del_many_dense_attrs
# flushrefresh
##############################################################################
# autotools script tests
@@ -178,7 +179,7 @@ if (UNIX)
# NOT CONVERTED accum_swmr_reader is used by accum.c.
# NOT CONVERTED atomic_writer and atomic_reader are standalone programs.
# links_env is used by testlinks_env.sh
- # filenotclosed is used by test_filenotclosed.sh
+ # filenotclosed and del_many_dense_attrs are used by testabort_fail.sh
# NOT CONVERTED flushrefresh is used by testflushrefresh.sh.
# NOT CONVERTED use_append_chunk, use_append_mchunks and use_disable_mdc_flushes are used by test_usecases.sh
# NOT CONVERTED swmr_* files (besides swmr.c) are used by testswmr.sh.
diff --git a/test/del_many_dense_attrs.c b/test/del_many_dense_attrs.c
new file mode 100644
index 0000000..bbae48d
--- /dev/null
+++ b/test/del_many_dense_attrs.c
@@ -0,0 +1,203 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Purpose: Test to verify that the infinite loop closing library/abort failure
+ * is fixed when the application creates and removes dense attributes
+ * (See HDFFV-10659).
+ */
+
+
+#include "h5test.h"
+
+/* The test file name */
+const char *FILENAME[] = {
+ "del_many_dense_attrs",
+ NULL
+};
+
+#define ATTR_COUNT 64 /* The number of attributes */
+
+/*-------------------------------------------------------------------------
+ * Function: catch_signal
+ *
+ * Purpose: The signal handler to catch the SIGABRT signal.
+ *
+ * Return: No return
+ *
+ * Programmer: Vailin Choi
+ *
+ *-------------------------------------------------------------------------
+ */
+static void catch_signal(int H5_ATTR_UNUSED signo)
+{
+ HDexit(1);
+} /* catch_signal() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: Test to verify that the infinite loop closing library/abort failure
+ * is fixed when the application creates and removes dense attributes
+ * (See HDFFV-10659).
+ *
+ * Return: Success: exit(EXIT_SUCCESS)
+ * Failure: exit(EXIT_FAILURE)
+ *
+ * Programmer: Vailin Choi; Dec 2018
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(void)
+{
+ hid_t fid = -1; /* HDF5 File ID */
+ hid_t gid = -1; /* Group ID */
+ hid_t sid = -1; /* Dataspace ID */
+ hid_t aid = -1; /* Attribute ID */
+ hid_t tid = -1; /* Datatype ID */
+ hid_t fapl = -1; /* File access property lists */
+ hid_t gcpl = -1; /* Group creation property list */
+ char aname[50]; /* Name of attribute */
+ char *basename="attr"; /* Name prefix for attribute */
+ char filename[100]; /* File name */
+ int i; /* Local index variable */
+
+ /* Testing setup */
+ h5_reset();
+
+ /* To exit from the file for SIGABRT signal */
+ if(HDsignal(SIGABRT, catch_signal) == SIG_ERR)
+ TEST_ERROR
+
+ fapl = h5_fileaccess();
+ h5_fixname(FILENAME[0], fapl, filename, sizeof(filename));
+
+ /* Set to latest format */
+ if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
+ TEST_ERROR
+
+ /* Create the file */
+ if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
+ TEST_ERROR
+
+ /* Close the file */
+ if(H5Fclose(fid) < 0)
+ TEST_ERROR
+
+ /* Re-open the file */
+ if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
+ TEST_ERROR
+
+ /* Create the group creation property list */
+ if((gcpl = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+ TEST_ERROR
+
+ /* Set to use dense storage for all attributes on the group */
+ if(H5Pset_attr_phase_change(gcpl, 0, 0) < 0)
+ TEST_ERROR
+
+ /* Create the group in the file */
+ if((gid = H5Gcreate2(fid, "group", H5P_DEFAULT, gcpl, H5P_DEFAULT)) < 0)
+ TEST_ERROR
+
+ /* Create dataspace */
+ if((sid = H5Screate(H5S_SCALAR)) < 0)
+ TEST_ERROR
+
+ /* Get a copy of the datatype */
+ if((tid = H5Tcopy(H5T_NATIVE_FLOAT)) < 0)
+ TEST_ERROR
+
+ /* Create attributes in the group */
+ for(i = ATTR_COUNT; i >= 0; i--) {
+ /* Set up the attribute name */
+ HDsprintf(aname, "%s%d", basename, i);
+
+ /* Create the attribute */
+ if((aid = H5Acreate2(gid, aname, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ TEST_ERROR
+
+ /* Write to the attribute */
+ if(H5Awrite(aid, tid, &i) < 0)
+ TEST_ERROR
+
+ /* Close the attribute */
+ if(H5Aclose(aid) < 0)
+ TEST_ERROR
+ }
+
+ /* Close the datatype */
+ if(H5Tclose(tid) < 0)
+ TEST_ERROR
+
+ /* Close the dataspace */
+ if(H5Sclose(sid) < 0)
+ TEST_ERROR
+
+ /* Close the group */
+ if(H5Gclose(gid) < 0)
+ TEST_ERROR
+
+ /* Close the group creation property list */
+ if(H5Pclose(gcpl) < 0)
+ TEST_ERROR
+
+ /* Close the file */
+ if(H5Fclose(fid) < 0)
+ TEST_ERROR
+
+ /* Re-open the file */
+ if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
+ TEST_ERROR
+
+ /* Open the group */
+ if((gid = H5Gopen(fid, "group", H5P_DEFAULT)) < 0)
+ TEST_ERROR
+
+ /* Delete the attributes */
+ for (i = 0; i <= ATTR_COUNT; i++) {
+ /* Set up the attribute name */
+ HDsprintf(aname, "%s%d", basename, i);
+
+ /* Delete the attribute */
+ if(H5Adelete(gid, aname) < 0)
+ TEST_ERROR
+ } /* end for */
+
+ /* Close the group */
+ if(H5Gclose(gid) < 0)
+ TEST_ERROR
+
+ /* Close the file */
+ if(H5Fclose(fid) < 0)
+ TEST_ERROR
+
+ h5_cleanup(FILENAME, fapl);
+
+ return(EXIT_SUCCESS);
+
+error:
+ H5E_BEGIN_TRY {
+ H5Gclose(gid);
+ H5Sclose(sid);
+ H5Tclose(tid);
+ H5Aclose(aid);
+ H5Fclose(fid);
+ H5Pclose(gcpl);
+ H5Pclose(fapl);
+ } H5E_END_TRY
+
+ return EXIT_FAILURE;
+}
diff --git a/test/dsets.c b/test/dsets.c
index e63878c..5de9cfa 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -13072,15 +13072,13 @@ test_object_header_minimization_dcpl(void)
/*********/
if(NULL == h5_fixname(OHMIN_FILENAME_A, H5P_DEFAULT, filename, sizeof(filename)))
- FAIL_PUTS_ERROR("unable to prepare filename")
+ TEST_ERROR
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- if (0 > file_id)
- FAIL_PUTS_ERROR("unable to create test file\n");
+ if (0 > file_id) TEST_ERROR
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
- if (0 > dcpl_id)
- FAIL_PUTS_ERROR("unable to create DCPL\n");
+ if (0 > dcpl_id) TEST_ERROR
/*********/
/* TESTS */
@@ -13088,28 +13086,23 @@ test_object_header_minimization_dcpl(void)
/* default value (not set explicitly)
*/
- if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL)
- FAIL_PUTS_ERROR("unable to get minimize value\n");
+ if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL) TEST_ERROR
if (FALSE != minimize)
- FAIL_PUTS_ERROR("Expected FALSE default but was not!\n");
+ TEST_ERROR
/* FALSE-set value
*/
- if (H5Pset_dset_no_attrs_hint(dcpl_id, FALSE) == FAIL)
- FAIL_PUTS_ERROR("unable to set minimize value to FALSE\n");
- if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL)
- FAIL_PUTS_ERROR("unable to get minimize value\n");
+ if (H5Pset_dset_no_attrs_hint(dcpl_id, FALSE) == FAIL) TEST_ERROR
+ if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL) TEST_ERROR
if (FALSE != minimize)
- FAIL_PUTS_ERROR("Expected FALSE default but was not!\n");
+ TEST_ERROR
/* TRUE-set value
*/
- if (H5Pset_dset_no_attrs_hint(dcpl_id, TRUE) == FAIL)
- FAIL_PUTS_ERROR("unable to set minimize value to TRUE\n");
- if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL)
- FAIL_PUTS_ERROR("unable to get minimize value\n");
+ if (H5Pset_dset_no_attrs_hint(dcpl_id, TRUE) == FAIL) TEST_ERROR
+ if (H5Pget_dset_no_attrs_hint(dcpl_id, &minimize) == FAIL) TEST_ERROR
if (TRUE != minimize)
- FAIL_PUTS_ERROR("Expected TRUE default but was not!\n");
+ TEST_ERROR
/* error cases
*/
@@ -13117,35 +13110,35 @@ test_object_header_minimization_dcpl(void)
ret = H5Pget_dset_no_attrs_hint(-1, &minimize);
} H5E_END_TRY;
if (ret == SUCCEED)
- FAIL_PUTS_ERROR("Invalid DCPL ID should fail\n");
+ TEST_ERROR /* Invalid DCPL ID should fail */
H5E_BEGIN_TRY {
ret = H5Pset_dset_no_attrs_hint(-1, FALSE);
} H5E_END_TRY;
if (ret == SUCCEED)
- FAIL_PUTS_ERROR("Invalid DCPL ID should fail\n");
+ TEST_ERROR /* Invalid DCPL ID should fail */
H5E_BEGIN_TRY {
ret = H5Pset_dset_no_attrs_hint(-1, TRUE);
} H5E_END_TRY;
if (ret == SUCCEED)
- FAIL_PUTS_ERROR("Invalid DCPL ID should fail\n");
+ TEST_ERROR /* Invalid DCPL ID should fail */
H5E_BEGIN_TRY {
ret = H5Pget_dset_no_attrs_hint(dcpl_id, NULL);
} H5E_END_TRY;
if (ret == SUCCEED)
- FAIL_PUTS_ERROR("NULL out pointer should fail\n");
+ TEST_ERROR /* NULL out pointer should fail */
/************/
/* TEARDOWN */
/************/
if (H5Fclose(file_id) == FAIL)
- FAIL_PUTS_ERROR("can't close FILE");
+ TEST_ERROR
if (H5Pclose(dcpl_id) == FAIL)
- FAIL_PUTS_ERROR("unable to close DCPL\n");
+ TEST_ERROR
PASSED();
return SUCCEED;
diff --git a/test/links.c b/test/links.c
index b09ddb1..520f784 100644
--- a/test/links.c
+++ b/test/links.c
@@ -8823,6 +8823,12 @@ ud_link_errors(hid_t fapl, hbool_t new_format)
TEST_ERROR
} H5E_END_TRY
+ /* Try to create a link with H5Lcreate_ud that has a NULL udata pointer, but a non-zero udata_size value */
+ H5E_BEGIN_TRY {
+ if(H5Lcreate_ud(fid, "/ud_link", (H5L_type_t)UD_CBFAIL_TYPE, NULL, 1, H5P_DEFAULT, H5P_DEFAULT) >= 0)
+ TEST_ERROR
+ } H5E_END_TRY;
+
/* Create a user-defined link to the group. */
strcpy(group_name, "/group");
if(H5Lcreate_ud(fid, "/ud_link", (H5L_type_t)UD_CBFAIL_TYPE, &group_name, HDstrlen(group_name) + 1, H5P_DEFAULT, H5P_DEFAULT) < 0) FAIL_STACK_ERROR
diff --git a/test/ohdr.c b/test/ohdr.c
index 042a81b..57edaf5 100644
--- a/test/ohdr.c
+++ b/test/ohdr.c
@@ -753,7 +753,7 @@ put_attribute(hid_t loc_id, const char *attrname, const void *attrvalue, hid_t d
{
if((*attribute_id) < 0) {
hid_t id = -1;
- id = H5Acreate(loc_id, attrname, datatype_id, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
+ id = H5Acreate2(loc_id, attrname, datatype_id, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
if(id < 0)
return FAIL;
*attribute_id = id;
@@ -770,7 +770,7 @@ count_attributes(hid_t dset_id)
{
H5O_info_t info;
- if(H5Oget_info(dset_id, &info, H5O_INFO_ALL) < 0)
+ if(H5Oget_info2(dset_id, &info, H5O_INFO_ALL) < 0)
return -1;
else
return (int)info.num_attrs; /* should never exceed int bounds */
@@ -879,10 +879,10 @@ test_minimized_dset_ohdr_attribute_addition(hid_t fapl_id)
} H5E_END_TRY;
if(count != -1) TEST_ERROR
- dset_id = H5Dcreate(file_id, "dataset", int_type_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ dset_id = H5Dcreate2(file_id, "dataset", int_type_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dset_id < 0) TEST_ERROR
- mindset_id = H5Dcreate(file_id, "mindataset", int_type_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ mindset_id = H5Dcreate2(file_id, "mindataset", int_type_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
if(mindset_id < 0) TEST_ERROR
/********************
@@ -1121,13 +1121,13 @@ test_minimized_dset_ohdr_size_comparisons(hid_t fapl_id)
file_f_id = H5Fcreate(filename_a, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
if(file_f_id < 0) TEST_ERROR
- dset_f_x_id = H5Dcreate(file_f_id, "default", int_type_id, dspace_id, H5P_DEFAULT, dcpl_default, H5P_DEFAULT);
+ dset_f_x_id = H5Dcreate2(file_f_id, "default", int_type_id, dspace_id, H5P_DEFAULT, dcpl_default, H5P_DEFAULT);
if(dset_f_x_id < 0) TEST_ERROR
- dset_f_N_id = H5Dcreate(file_f_id, "dsetNOT", int_type_id, dspace_id, H5P_DEFAULT, dcpl_dontmin, H5P_DEFAULT);
+ dset_f_N_id = H5Dcreate2(file_f_id, "dsetNOT", int_type_id, dspace_id, H5P_DEFAULT, dcpl_dontmin, H5P_DEFAULT);
if(dset_f_N_id < 0) TEST_ERROR
- dset_f_Y_id = H5Dcreate(file_f_id, "dsetMIN", int_type_id, dspace_id, H5P_DEFAULT, dcpl_minimize, H5P_DEFAULT);
+ dset_f_Y_id = H5Dcreate2(file_f_id, "dsetMIN", int_type_id, dspace_id, H5P_DEFAULT, dcpl_minimize, H5P_DEFAULT);
if(dset_f_x_id < 0) TEST_ERROR
file_F_id = H5Fcreate(filename_b, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
@@ -1135,13 +1135,13 @@ test_minimized_dset_ohdr_size_comparisons(hid_t fapl_id)
ret = H5Fset_dset_no_attrs_hint(file_F_id, TRUE);
if(ret < 0) TEST_ERROR
- dset_F_x_id = H5Dcreate(file_F_id, "default", int_type_id, dspace_id, H5P_DEFAULT, dcpl_default, H5P_DEFAULT);
+ dset_F_x_id = H5Dcreate2(file_F_id, "default", int_type_id, dspace_id, H5P_DEFAULT, dcpl_default, H5P_DEFAULT);
if(dset_F_x_id < 0) TEST_ERROR
- dset_F_N_id = H5Dcreate(file_F_id, "dsetNOT", int_type_id, dspace_id, H5P_DEFAULT, dcpl_dontmin, H5P_DEFAULT);
+ dset_F_N_id = H5Dcreate2(file_F_id, "dsetNOT", int_type_id, dspace_id, H5P_DEFAULT, dcpl_dontmin, H5P_DEFAULT);
if(dset_F_N_id < 0) TEST_ERROR
- dset_F_Y_id = H5Dcreate(file_F_id, "dsetMIN", int_type_id, dspace_id, H5P_DEFAULT, dcpl_minimize, H5P_DEFAULT);
+ dset_F_Y_id = H5Dcreate2(file_F_id, "dsetMIN", int_type_id, dspace_id, H5P_DEFAULT, dcpl_minimize, H5P_DEFAULT);
if(dset_F_Y_id < 0) TEST_ERROR
/*********
@@ -1276,16 +1276,16 @@ test_minimized_dset_ohdr_with_filter(hid_t fapl_id)
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
if(file_id < 0) TEST_ERROR
- dset_xx_id = H5Dcreate(file_id, "xx", dtype_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ dset_xx_id = H5Dcreate2(file_id, "xx", dtype_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dset_xx_id < 0) TEST_ERROR
- dset_mx_id = H5Dcreate(file_id, "Mx", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mx_id, H5P_DEFAULT);
+ dset_mx_id = H5Dcreate2(file_id, "Mx", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mx_id, H5P_DEFAULT);
if(dset_mx_id < 0) TEST_ERROR
- dset_xZ_id = H5Dcreate(file_id, "xZ", dtype_id, dspace_id, H5P_DEFAULT, dcpl_xZ_id, H5P_DEFAULT);
+ dset_xZ_id = H5Dcreate2(file_id, "xZ", dtype_id, dspace_id, H5P_DEFAULT, dcpl_xZ_id, H5P_DEFAULT);
if(dset_xZ_id < 0) TEST_ERROR
- dset_mZ_id = H5Dcreate(file_id, "MZ", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mZ_id, H5P_DEFAULT);
+ dset_mZ_id = H5Dcreate2(file_id, "MZ", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mZ_id, H5P_DEFAULT);
if(dset_mZ_id < 0) TEST_ERROR
/*********
@@ -1435,18 +1435,18 @@ test_minimized_dset_ohdr_modification_times(hid_t _fapl_id)
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
if(file_id < 0) TEST_ERROR
- dset_xx_id = H5Dcreate( file_id, "xx", dtype_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ dset_xx_id = H5Dcreate2( file_id, "xx", dtype_id, dspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dset_xx_id < 0) TEST_ERROR
- dset_mx_id = H5Dcreate(file_id, "mx", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mx_id, H5P_DEFAULT);
+ dset_mx_id = H5Dcreate2(file_id, "mx", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mx_id, H5P_DEFAULT);
if(dset_mx_id < 0) TEST_ERROR
- dset_xT_id = H5Dcreate(file_id, "xT", dtype_id, dspace_id, H5P_DEFAULT, dcpl_xT_id, H5P_DEFAULT);
+ dset_xT_id = H5Dcreate2(file_id, "xT", dtype_id, dspace_id, H5P_DEFAULT, dcpl_xT_id, H5P_DEFAULT);
if(dset_xT_id < 0) TEST_ERROR
- dset_mT_id = H5Dcreate(file_id, "mT", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mT_id, H5P_DEFAULT);
+ dset_mT_id = H5Dcreate2(file_id, "mT", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mT_id, H5P_DEFAULT);
if(dset_mT_id < 0) TEST_ERROR
- dset_mN_id = H5Dcreate(file_id, "mN", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mN_id, H5P_DEFAULT);
+ dset_mN_id = H5Dcreate2(file_id, "mN", dtype_id, dspace_id, H5P_DEFAULT, dcpl_mN_id, H5P_DEFAULT);
if(dset_mN_id < 0) TEST_ERROR
/* ----- *
@@ -1561,7 +1561,7 @@ test_minimized_dset_ohdr_fillvalue_backwards_compatability(hid_t _fapl_id)
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
if(file_id < 0) TEST_ERROR
- dset_0_id = H5Dcreate(file_id, "fullrange", dtype_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ dset_0_id = H5Dcreate2(file_id, "fullrange", dtype_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
if(dset_0_id < 0) TEST_ERROR
/* Close file and re-open with different libver bounds.
@@ -1576,7 +1576,7 @@ test_minimized_dset_ohdr_fillvalue_backwards_compatability(hid_t _fapl_id)
file_id = H5Fopen(filename, H5F_ACC_RDWR, fapl_id);
if(file_id < 0) TEST_ERROR
- dset_1_id = H5Dcreate(file_id, "upperrange", dtype_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ dset_1_id = H5Dcreate2(file_id, "upperrange", dtype_id, dspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
if(dset_1_id < 0) TEST_ERROR
/* re-open "fullrange" dataset
diff --git a/test/test_filenotclosed.sh.in b/test/testabort_fail.sh.in
index 0b43c5b..925d8a4 100644
--- a/test/test_filenotclosed.sh.in
+++ b/test/testabort_fail.sh.in
@@ -13,6 +13,9 @@
#
# Test to verify that the assertion/abort failure is fixed when the application
# does not close the file. (See HDFFV-10160)
+#
+# Test to verify that the infinite loop closing library/abort failure is fixed
+# when the application creates and removes dense attributes (See HDFFV-10659)
srcdir=@srcdir@
@@ -20,22 +23,44 @@ nerrors=0
##############################################################################
##############################################################################
-### T H E T E S T ###
+### T H E T E S T S ###
##############################################################################
##############################################################################
-
+#
+#
echo "Testing file not closed assertion/abort failure"
TEST_NAME=filenotclosed # The test name
-TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary
+TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary
#
# Run the test
-#$RUNSERIAL $TEST_BIN >/dev/null 2>&1
-$RUNSERIAL $TEST_BIN 2>&1
+$RUNSERIAL $TEST_BIN >/dev/null 2>&1
exitcode=$?
if [ $exitcode -eq 0 ]; then
echo "Test PASSED"
else
+ echo "Test FAILED"
nerrors="`expr $nerrors + 1`"
- echo "***Error encountered***"
fi
-exit $nerrors
+#
+#
+echo "Testing infinite loop closing library/abort failure"
+TEST_NAME=del_many_dense_attrs # The test name
+TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary
+# Run the test
+$RUNSERIAL $TEST_BIN >/dev/null 2>&1
+exitcode=$?
+if [ $exitcode -eq 0 ]; then
+ echo "Test PASSED"
+else
+ echo "Test FAILED"
+ nerrors="`expr $nerrors + 1`"
+fi
+#
+#
+if test $nerrors -eq 0 ; then
+ echo "All tests for abort failure passed."
+ exit 0
+else
+ echo "Tests for abort failure failed with $nerrors errors."
+ exit 1
+fi
diff --git a/testpar/CMakeTests.cmake b/testpar/CMakeTests.cmake
index dffb813..a0d7f59 100644
--- a/testpar/CMakeTests.cmake
+++ b/testpar/CMakeTests.cmake
@@ -22,9 +22,9 @@ foreach (testp ${H5P_TESTS})
add_test (NAME TEST_PAR_${testp} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${testp}> ${MPIEXEC_POSTFLAGS})
endforeach ()
-# The following will only be correct on windows shared
-#set_tests_properties (TEST_PAR_t_pflush1 PROPERTIES WILL_FAIL "true")
-set_property (TEST TEST_PAR_t_pflush1 PROPERTY PASS_REGULAR_EXPRESSION "PASSED")
+# The t_pflush1 test is hard-coded to fail.
+set_tests_properties (TEST_PAR_t_pflush1 PROPERTIES WILL_FAIL "true")
+#set_property (TEST TEST_PAR_t_pflush1 PROPERTY PASS_REGULAR_EXPRESSION "PASSED")
set_tests_properties (TEST_PAR_t_pflush2 PROPERTIES DEPENDS TEST_PAR_t_pflush1)
##############################################################################
diff --git a/testpar/t_pflush1.c b/testpar/t_pflush1.c
index 4677bfe..27b561b 100644
--- a/testpar/t_pflush1.c
+++ b/testpar/t_pflush1.c
@@ -15,11 +15,11 @@
* Programmer: Leon Arber <larber@uiuc.edu>
* Sept. 28, 2006.
*
- * Purpose: This is the first half of a two-part test that makes sure
- * that a file can be read after a parallel application crashes as long
- * as the file was flushed first. We simulate a crash by
- * calling _exit(0) since this doesn't flush HDF5 caches but
- * still exits with success.
+ * Purpose: This is the first half of a two-part test that makes sure
+ * that a file can be read after a parallel application crashes
+ * as long as the file was flushed first. We simulate a crash by
+ * calling _exit() since this doesn't flush HDF5 caches but
+ * still exits with success.
*/
#include "h5test.h"
@@ -29,171 +29,190 @@ const char *FILENAME[] = {
NULL
};
-static double the_data[100][100];
+static int data_g[100][100];
+#define N_GROUPS 100
+
+
/*-------------------------------------------------------------------------
- * Function: create_file
- *
- * Purpose: Creates file used in part 1 of the test
+ * Function: create_test_file
*
- * Return: Success: 0
+ * Purpose: Creates the file used in part 1 of the test
*
- * Failure: 1
+ * Return: Success: A valid file ID
+ * Failure: H5I_INVALID_HID
*
- * Programmer: Leon Arber
+ * Programmer: Leon Arber
* Sept. 26, 2006
*
- * Modifications:
- *
*-------------------------------------------------------------------------
*/
static hid_t
-create_file(char* name, hid_t fapl)
+create_test_file(char *name, hid_t fapl_id)
{
- hid_t file, dcpl, space, dset, groups, grp, plist;
- hsize_t ds_size[2] = {100, 100};
- hsize_t ch_size[2] = {5, 5};
- hsize_t i, j;
-
-
-
- if((file=H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) goto error;
+ hid_t fid = H5I_INVALID_HID;
+ hid_t dcpl_id = H5I_INVALID_HID;
+ hid_t sid = H5I_INVALID_HID;
+ hid_t did = H5I_INVALID_HID;
+ hid_t top_level_gid = H5I_INVALID_HID;
+ hid_t gid = H5I_INVALID_HID;
+ hid_t dxpl_id = H5I_INVALID_HID;
+ hsize_t dims[2] = {100, 100};
+ hsize_t chunk_dims[2] = {5, 5};
+ hsize_t i, j;
+
+ if((fid = H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id)) < 0)
+ goto error;
/* Create a chunked dataset */
- if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) goto error;
- if(H5Pset_chunk(dcpl, 2, ch_size) < 0) goto error;
- if((space = H5Screate_simple(2, ds_size, NULL)) < 0) goto error;
- if((dset = H5Dcreate2(file, "dset", H5T_NATIVE_FLOAT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- goto error;
-
- plist = H5Pcreate(H5P_DATASET_XFER);
- H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);
-
+ if((dcpl_id = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+ if(H5Pset_chunk(dcpl_id, 2, chunk_dims) < 0)
+ goto error;
+ if((sid = H5Screate_simple(2, dims, NULL)) < 0)
+ goto error;
+ if((did = H5Dcreate2(fid, "dset", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+
+ if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+ if(H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) < 0)
+ goto error;
/* Write some data */
- for(i = 0; i < ds_size[0]; i++) {
- /*
- * The extra cast in the following statement is a bug workaround
- * for the Win32 version 5.0 compiler.
- * 1998-11-06 ptl
- */
- for(j = 0; j < ds_size[1]; j++)
- the_data[i][j] = (double)(hssize_t)i/(hssize_t)(j+1);
- }
- if(H5Dwrite(dset, H5T_NATIVE_DOUBLE, space, space, plist, the_data) < 0) goto error;
+ for(i = 0; i < dims[0]; i++)
+ for(j = 0; j < dims[1]; j++)
+ data_g[i][j] = (int)(i + (i * j) + j);
+
+ if(H5Dwrite(did, H5T_NATIVE_INT, sid, sid, dxpl_id, data_g) < 0)
+ goto error;
/* Create some groups */
- if((groups = H5Gcreate2(file, "some_groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error;
- for(i = 0; i < 100; i++) {
- sprintf(name, "grp%02u", (unsigned)i);
- if((grp = H5Gcreate2(groups, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error;
- if(H5Gclose(grp) < 0) goto error;
+ if((top_level_gid = H5Gcreate2(fid, "some_groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+ for(i = 0; i < N_GROUPS; i++) {
+ HDsprintf(name, "grp%02u", (unsigned)i);
+ if((gid = H5Gcreate2(top_level_gid, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+ if(H5Gclose(gid) < 0)
+ goto error;
}
- return file;
+ return fid;
error:
- HD_exit(1);
-}
+ return H5I_INVALID_HID;
+} /* end create_test_file() */
+
/*-------------------------------------------------------------------------
* Function: main
*
- * Purpose: Part 1 of a two-part H5Fflush() test.
- *
- * Return: Success: 0
+ * Purpose: Part 1 of a two-part parallel H5Fflush() test.
*
- * Failure: 1
+ * Return: EXIT_FAILURE (always)
*
- * Programmer: Robb Matzke
+ * Programmer: Robb Matzke
* Friday, October 23, 1998
*
- * Modifications:
- * Leon Arber
- * Sept. 26, 2006, expand test to check for failure if H5Fflush is not called.
- *
- *
*-------------------------------------------------------------------------
*/
int
main(int argc, char* argv[])
{
- hid_t file1, file2, fapl;
- MPI_File *mpifh_p = NULL;
- char name[1024];
- const char *envval = NULL;
- int mpi_size, mpi_rank;
- MPI_Comm comm = MPI_COMM_WORLD;
- MPI_Info info = MPI_INFO_NULL;
+ hid_t fid1 = H5I_INVALID_HID;
+ hid_t fid2 = H5I_INVALID_HID;
+ hid_t fapl_id = H5I_INVALID_HID;
+ MPI_File *mpifh_p = NULL;
+ char name[1024];
+ const char *envval = NULL;
+ int mpi_size;
+ int mpi_rank;
+ MPI_Comm comm = MPI_COMM_WORLD;
+ MPI_Info info = MPI_INFO_NULL;
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
- fapl = H5Pcreate(H5P_FILE_ACCESS);
- H5Pset_fapl_mpio(fapl, comm, info);
-
if(mpi_rank == 0)
- TESTING("H5Fflush (part1)");
+ TESTING("H5Fflush (part1)");
+
+ /* Don't run using the split VFD */
envval = HDgetenv("HDF5_DRIVER");
if(envval == NULL)
envval = "nomatch";
- if(HDstrcmp(envval, "split")) {
+
+ if(!HDstrcmp(envval, "split")) {
+ if(mpi_rank == 0) {
+ SKIPPED();
+ HDputs(" Test not compatible with current Virtual File Driver");
+ }
+ MPI_Finalize();
+ HDexit(EXIT_FAILURE);
+ }
+
+ if((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ goto error;
+ if(H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
+ goto error;
+
/* Create the file */
- h5_fixname(FILENAME[0], fapl, name, sizeof name);
- file1 = create_file(name, fapl);
+ h5_fixname(FILENAME[0], fapl_id, name, sizeof(name));
+ if((fid1 = create_test_file(name, fapl_id)) < 0)
+ goto error;
/* Flush and exit without closing the library */
- if(H5Fflush(file1, H5F_SCOPE_GLOBAL) < 0) goto error;
+ if(H5Fflush(fid1, H5F_SCOPE_GLOBAL) < 0)
+ goto error;
/* Create the other file which will not be flushed */
- h5_fixname(FILENAME[1], fapl, name, sizeof name);
- file2 = create_file(name, fapl);
-
+ h5_fixname(FILENAME[1], fapl_id, name, sizeof(name));
+ if((fid2 = create_test_file(name, fapl_id)) < 0)
+ goto error;
if(mpi_rank == 0)
PASSED();
- fflush(stdout);
- fflush(stderr);
- } /* end if */
- else {
- SKIPPED();
- puts(" Test not compatible with current Virtual File Driver");
- } /* end else */
-
- /*
- * Some systems like AIX do not like files not closed when MPI_Finalize
+
+ HDfflush(stdout);
+ HDfflush(stderr);
+
+ /* Some systems like AIX do not like files not being closed when MPI_Finalize
* is called. So, we need to get the MPI file handles, close them by hand.
* Then the _exit is still needed to stop at_exit from happening in some systems.
* Note that MPIO VFD returns the address of the file-handle in the VFD struct
* because MPI_File_close wants to modify the file-handle variable.
*/
- /* close file1 */
- if(H5Fget_vfd_handle(file1, fapl, (void **)&mpifh_p) < 0) {
- printf("H5Fget_vfd_handle for file1 failed\n");
- goto error;
- } /* end if */
- if(MPI_File_close(mpifh_p) != MPI_SUCCESS) {
- printf("MPI_File_close for file1 failed\n");
- goto error;
- } /* end if */
- /* close file2 */
- if(H5Fget_vfd_handle(file2, fapl, (void **)&mpifh_p) < 0) {
- printf("H5Fget_vfd_handle for file2 failed\n");
- goto error;
- } /* end if */
- if(MPI_File_close(mpifh_p) != MPI_SUCCESS) {
- printf("MPI_File_close for file2 failed\n");
- goto error;
- } /* end if */
-
- fflush(stdout);
- fflush(stderr);
- HD_exit(0);
+ /* Close file 1 */
+ if(H5Fget_vfd_handle(fid1, fapl_id, (void **)&mpifh_p) < 0)
+ goto error;
+ if(MPI_File_close(mpifh_p) != MPI_SUCCESS)
+ goto error;
+
+ /* Close file 2 */
+ if(H5Fget_vfd_handle(fid2, fapl_id, (void **)&mpifh_p) < 0)
+ goto error;
+ if(MPI_File_close(mpifh_p) != MPI_SUCCESS)
+ goto error;
+
+ HDfflush(stdout);
+ HDfflush(stderr);
+
+ /* Always exit with a failure code!
+ *
+ * In accordance with the standard, not having all processes
+ * call MPI_Finalize() can be considered an error, so mpiexec
+ * et al. may indicate failure on return. It's much easier to
+ * always ignore the failure condition than to handle some
+ * platforms returning success and others failure.
+ */
+ HD_exit(EXIT_FAILURE);
error:
- fflush(stdout);
- fflush(stderr);
- HD_exit(1);
-}
+ HDfflush(stdout);
+ HDfflush(stderr);
+ HDprintf("*** ERROR ***\n");
+ HDprintf("THERE WAS A REAL ERROR IN t_pflush1.\n");
+ HD_exit(EXIT_FAILURE);
+} /* end main() */
diff --git a/testpar/t_pflush2.c b/testpar/t_pflush2.c
index 2051f4e..f58e5a5 100644
--- a/testpar/t_pflush2.c
+++ b/testpar/t_pflush2.c
@@ -30,116 +30,124 @@ const char *FILENAME[] = {
NULL
};
-static double the_data[100][100];
+static int data_g[100][100];
+#define N_GROUPS 100
/*-------------------------------------------------------------------------
- * Function: check_file
+ * Function: check_test_file
*
- * Purpose: Part 2 of a two-part H5Fflush() test.
+ * Purpose: Part 2 of a two-part H5Fflush() test.
*
- * Return: Success: 0
+ * Return: SUCCEED/FAIL
*
- * Failure: 1
- *
- * Programmer: Leon Arber
+ * Programmer: Leon Arber
* Sept. 26, 2006.
*
*-------------------------------------------------------------------------
*/
-static int
-check_file(char* name, hid_t fapl)
+static herr_t
+check_test_file(char* name, hid_t fapl_id)
{
- hid_t file, space, dset, groups, grp, plist;
- hsize_t ds_size[2];
- double error;
- hsize_t i, j;
-
- plist = H5Pcreate(H5P_DATASET_XFER);
- H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);
- if((file = H5Fopen(name, H5F_ACC_RDONLY, fapl)) < 0) goto error;
+ hid_t fid = H5I_INVALID_HID;
+ hid_t sid = H5I_INVALID_HID;
+ hid_t did = H5I_INVALID_HID;
+ hid_t top_level_gid = H5I_INVALID_HID;
+ hid_t gid = H5I_INVALID_HID;
+ hid_t dxpl_id = H5I_INVALID_HID;
+ hsize_t dims[2];
+ int val;
+ hsize_t i, j;
+
+ if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+ if(H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) < 0)
+ goto error;
+ if((fid = H5Fopen(name, H5F_ACC_RDONLY, fapl_id)) < 0)
+ goto error;
/* Open the dataset */
- if((dset = H5Dopen2(file, "dset", H5P_DEFAULT)) < 0) goto error;
- if((space = H5Dget_space(dset)) < 0) goto error;
- if(H5Sget_simple_extent_dims(space, ds_size, NULL) < 0) goto error;
- assert(100==ds_size[0] && 100==ds_size[1]);
+ if((did = H5Dopen2(fid, "dset", H5P_DEFAULT)) < 0)
+ goto error;
+ if((sid = H5Dget_space(did)) < 0)
+ goto error;
+ if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+ goto error;
+ HDassert(100 == dims[0] && 100 == dims[1]);
/* Read some data */
- if (H5Dread(dset, H5T_NATIVE_DOUBLE, space, space, plist,
- the_data) < 0) goto error;
- for (i=0; i<ds_size[0]; i++) {
- for (j=0; j<ds_size[1]; j++) {
- /*
- * The extra cast in the following statement is a bug workaround
- * for the Win32 version 5.0 compiler.
- * 1998-11-06 ptl
- */
- error = fabs(the_data[i][j]-(double)(hssize_t)i/((hssize_t)j+1));
- if (error>0.0001) {
- H5_FAILED();
- printf(" dset[%lu][%lu] = %g\n",
- (unsigned long)i, (unsigned long)j, the_data[i][j]);
- printf(" should be %g\n",
- (double)(hssize_t)i/(hssize_t)(j+1));
- goto error;
- }
- }
+ if(H5Dread(did, H5T_NATIVE_INT, sid, sid, dxpl_id, data_g) < 0)
+ goto error;
+ for(i = 0; i < dims[0]; i++) {
+ for(j = 0; j < dims[1]; j++) {
+ val = (int)(i + (i * j) + j);
+ if(data_g[i][j] != val) {
+ H5_FAILED();
+ HDprintf(" data_g[%lu][%lu] = %d\n", (unsigned long)i, (unsigned long)j, data_g[i][j]);
+ HDprintf(" should be %d\n", val);
+ }
+ }
}
/* Open some groups */
- if((groups = H5Gopen2(file, "some_groups", H5P_DEFAULT)) < 0) goto error;
- for(i = 0; i < 100; i++) {
- sprintf(name, "grp%02u", (unsigned)i);
- if((grp = H5Gopen2(groups, name, H5P_DEFAULT)) < 0) goto error;
- if(H5Gclose(grp) < 0) goto error;
+ if((top_level_gid = H5Gopen2(fid, "some_groups", H5P_DEFAULT)) < 0)
+ goto error;
+ for(i = 0; i < N_GROUPS; i++) {
+ HDsprintf(name, "grp%02u", (unsigned)i);
+ if((gid = H5Gopen2(top_level_gid, name, H5P_DEFAULT)) < 0)
+ goto error;
+ if(H5Gclose(gid) < 0)
+ goto error;
}
- if(H5Gclose(groups) < 0) goto error;
- if(H5Dclose(dset) < 0) goto error;
- if(H5Fclose(file) < 0) goto error;
- if(H5Pclose(plist) < 0) goto error;
- if(H5Sclose(space) < 0) goto error;
+ if(H5Gclose(top_level_gid) < 0)
+ goto error;
+ if(H5Dclose(did) < 0)
+ goto error;
+ if(H5Fclose(fid) < 0)
+ goto error;
+ if(H5Pclose(dxpl_id) < 0)
+ goto error;
+ if(H5Sclose(sid) < 0)
+ goto error;
- return 0;
+ return SUCCEED;
error:
H5E_BEGIN_TRY {
- H5Pclose(plist);
- H5Gclose(groups);
- H5Dclose(dset);
- H5Fclose(file);
- H5Sclose(space);
+ H5Pclose(dxpl_id);
+ H5Gclose(top_level_gid);
+ H5Dclose(did);
+ H5Fclose(fid);
+ H5Sclose(sid);
+ H5Gclose(gid);
} H5E_END_TRY;
- return 1;
-}
+ return FAIL;
+} /* end check_test_file() */
/*-------------------------------------------------------------------------
- * Function: main
+ * Function: main
*
- * Purpose: Part 2 of a two-part H5Fflush() test.
+ * Purpose: Part 2 of a two-part H5Fflush() test.
*
- * Return: Success: 0
+ * Return: EXIT_SUCCESS/EXIT_FAIL
*
- * Failure: 1
- *
- * Programmer: Robb Matzke
+ * Programmer: Robb Matzke
* Friday, October 23, 1998
*
- * Modifications:
- * Leon Arber
- * Sept. 26, 2006, expand to check for case where the was file not flushed.
- *
*-------------------------------------------------------------------------
*/
int
-main(int argc, char* argv[])
+main(int argc, char *argv[])
{
+ hid_t fapl_id1 = H5I_INVALID_HID;
+ hid_t fapl_id2 = H5I_INVALID_HID;
H5E_auto2_t func;
- char name[1024];
+ char name[1024];
const char *envval = NULL;
- int mpi_size, mpi_rank;
+ int mpi_size;
+ int mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
@@ -148,69 +156,70 @@ main(int argc, char* argv[])
MPI_Comm_rank(comm, &mpi_rank);
if(mpi_rank == 0)
- TESTING("H5Fflush (part2 with flush)");
+ TESTING("H5Fflush (part2 with flush)");
- /* Don't run this test using the core or split file drivers */
+ /* Don't run using the split VFD */
envval = HDgetenv("HDF5_DRIVER");
- if (envval == NULL)
+ if(envval == NULL)
envval = "nomatch";
- if (HDstrcmp(envval, "core") && HDstrcmp(envval, "split")) {
- hid_t fapl1, fapl2;
-
- fapl1 = H5Pcreate(H5P_FILE_ACCESS);
- H5Pset_fapl_mpio(fapl1, comm, info);
-
- fapl2 = H5Pcreate(H5P_FILE_ACCESS);
- H5Pset_fapl_mpio(fapl2, comm, info);
-
- /* Check the case where the file was flushed */
- h5_fixname(FILENAME[0], fapl1, name, sizeof name);
- if(check_file(name, fapl1))
- {
- H5_FAILED()
- goto error;
- }
- else if(mpi_rank == 0)
- {
- PASSED()
- }
-
- /* Check the case where the file was not flushed. This should give an error
- * so we turn off the error stack temporarily */
- if(mpi_rank == 0)
- TESTING("H5Fflush (part2 without flush)");
- H5Eget_auto2(H5E_DEFAULT,&func,NULL);
- H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
- h5_fixname(FILENAME[1], fapl2, name, sizeof name);
- if(check_file(name, fapl2))
- {
- if(mpi_rank == 0)
- {
- PASSED()
- }
- }
- else
- {
- H5_FAILED()
- goto error;
- }
- H5Eset_auto2(H5E_DEFAULT, func, NULL);
-
-
- h5_clean_files(&FILENAME[0], fapl1);
- h5_clean_files(&FILENAME[1], fapl2);
+
+ if(!HDstrcmp(envval, "split")) {
+ if(mpi_rank == 0) {
+ SKIPPED();
+ HDputs(" Test not compatible with current Virtual File Driver");
+ }
+ MPI_Finalize();
+ HDexit(EXIT_FAILURE);
+ }
+
+ if((fapl_id1 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ goto error;
+ if(H5Pset_fapl_mpio(fapl_id1, comm, info) < 0)
+ goto error;
+
+ if((fapl_id2 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ goto error;
+ if(H5Pset_fapl_mpio(fapl_id2, comm, info) < 0)
+ goto error;
+
+ /* Check the case where the file was flushed */
+ h5_fixname(FILENAME[0], fapl_id1, name, sizeof(name));
+ if(check_test_file(name, fapl_id1)) {
+ H5_FAILED()
+ goto error;
}
- else
- {
- SKIPPED();
- puts(" Test not compatible with current Virtual File Driver");
+ else if(mpi_rank == 0) {
+ PASSED()
}
+ /* Check the case where the file was not flushed. This should give an error
+ * so we turn off the error stack temporarily.
+ */
+ if(mpi_rank == 0)
+ TESTING("H5Fflush (part2 without flush)");
+ H5Eget_auto2(H5E_DEFAULT,&func, NULL);
+ H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+ h5_fixname(FILENAME[1], fapl_id2, name, sizeof(name));
+ if(check_test_file(name, fapl_id2)) {
+ if(mpi_rank == 0)
+ PASSED()
+ }
+ else {
+ H5_FAILED()
+ goto error;
+ }
+
+ H5Eset_auto2(H5E_DEFAULT, func, NULL);
+
+ h5_clean_files(&FILENAME[0], fapl_id1);
+ h5_clean_files(&FILENAME[1], fapl_id2);
+
MPI_Finalize();
- return 0;
- error:
- return 1;
-}
+ HDexit(EXIT_SUCCESS);
+
+error:
+ HDexit(EXIT_FAILURE);
+} /* end main() */