diff options
| author | Larry Knox <lrknox@hdfgroup.org> | 2019-01-05 13:50:15 (GMT) |
|---|---|---|
| committer | Larry Knox <lrknox@hdfgroup.org> | 2019-01-05 13:50:15 (GMT) |
| commit | 3be0fbd817e82b4a60b36b2b9d444a3750f2eb06 (patch) | |
| tree | cc16d19b4f3fd04aa0aa70556fac36b2222daa24 | |
| parent | 25fe692c5c5c37a904a0d2ba3f447e60396c30da (diff) | |
| parent | cceb9f06b8f213ef1cb360a4ef900536669a8dad (diff) | |
| download | hdf5-3be0fbd817e82b4a60b36b2b9d444a3750f2eb06.zip hdf5-3be0fbd817e82b4a60b36b2b9d444a3750f2eb06.tar.gz hdf5-3be0fbd817e82b4a60b36b2b9d444a3750f2eb06.tar.bz2 | |
Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
40 files changed, 1099 insertions, 433 deletions
@@ -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) @@ -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() */ |