diff options
104 files changed, 1605 insertions, 403 deletions
@@ -1390,6 +1390,9 @@ ./tools/testfiles/tgrp_comments.ls ./tools/testfiles/tgrp_comments.ddl ./tools/testfiles/tgrp_comments.h5 +./tools/testfiles/tgrpnullspace.h5 +./tools/testfiles/tgrpnullspace.ddl +./tools/testfiles/tgrpnullspace.ls ./tools/testfiles/thlink-1.ddl ./tools/testfiles/thlink-2.ddl ./tools/testfiles/thlink-3.ddl @@ -1445,6 +1448,7 @@ ./tools/testfiles/tno-subset.h5 ./tools/testfiles/tno-subset.ddl ./tools/testfiles/tnullspace.h5 +./tools/testfiles/tnullspace.h5.xml ./tools/testfiles/tnullspace.ddl ./tools/testfiles/tobjref.h5 ./tools/testfiles/topaque.h5 @@ -1713,6 +1717,8 @@ ./tools/testfiles/tdset2.h5.xml ./tools/testfiles/tempty.h5.xml ./tools/testfiles/tenum.h5.xml +./tools/testfiles/test35.nc +./tools/testfiles/test35.nc.xml ./tools/testfiles/tfpformat.h5.xml ./tools/testfiles/tgroup.h5.xml ./tools/testfiles/thlink.h5.xml @@ -2021,6 +2027,7 @@ ./tools/h5diff/testfiles/h5diff_udfail.txt ./tools/h5diff/testfiles/diff_strings1.h5 ./tools/h5diff/testfiles/diff_strings2.h5 +./tools/h5diff/testfiles/h5diff_vlstr.txt #test files for h5repack ./tools/h5repack/testfiles/README diff --git a/Makefile.in b/Makefile.in index 3b8f4d6..06eb5b8 100644 --- a/Makefile.in +++ b/Makefile.in @@ -422,6 +422,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ @@ -1,4 +1,4 @@ -HDF5 version 1.8.19 released on 2017-06-15 +HDF5 version 1.8.20-snap2 currently under development Please refer to the release_docs/INSTALL file for installation instructions. ------------------------------------------------------------------------------ diff --git a/c++/Makefile.in b/c++/Makefile.in index 6165684..4a2eb21 100644 --- a/c++/Makefile.in +++ b/c++/Makefile.in @@ -583,6 +583,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/c++/examples/Makefile.in b/c++/examples/Makefile.in index 863765f..88f92e8 100644 --- a/c++/examples/Makefile.in +++ b/c++/examples/Makefile.in @@ -530,6 +530,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in index cbfb7c4..b096c9f 100644 --- a/c++/src/Makefile.in +++ b/c++/src/Makefile.in @@ -595,6 +595,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/c++/src/cpp_doc_config b/c++/src/cpp_doc_config index 6413f86..38a6fe4 100644 --- a/c++/src/cpp_doc_config +++ b/c++/src/cpp_doc_config @@ -49,7 +49,7 @@ PROJECT_NAME = "HDF5 C++ API" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "1.8.19" +PROJECT_NUMBER = "1.8.20-snap2, currently under development" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/c++/test/Makefile.in b/c++/test/Makefile.in index 686df18..841a797 100644 --- a/c++/test/Makefile.in +++ b/c++/test/Makefile.in @@ -585,6 +585,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/config/cmake/CTestCustom.cmake b/config/cmake/CTestCustom.cmake index 4091687..9f5262f 100644 --- a/config/cmake/CTestCustom.cmake +++ b/config/cmake/CTestCustom.cmake @@ -8,7 +8,7 @@ # 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. - +# set (CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS 3000) # Allow full output to go to CDash set to 0 SET(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE 50000) diff --git a/config/cmake/CTestScript.cmake b/config/cmake/CTestScript.cmake index bf9e633..c59b10c 100644 --- a/config/cmake/CTestScript.cmake +++ b/config/cmake/CTestScript.cmake @@ -8,7 +8,7 @@ # 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. - +# cmake_minimum_required (VERSION 3.2.2 FATAL_ERROR) ######################################################## # For any comments please contact cdashhelp@hdfgroup.org diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake index 7068345..77918a4 100644 --- a/config/cmake/ConfigureChecks.cmake +++ b/config/cmake/ConfigureChecks.cmake @@ -8,7 +8,7 @@ # 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. - +# #----------------------------------------------------------------------------- # Include all the necessary files for macros #----------------------------------------------------------------------------- diff --git a/config/cmake/ConversionTests.c b/config/cmake/ConversionTests.c index 022a296..082dbd4 100644 --- a/config/cmake/ConversionTests.c +++ b/config/cmake/ConversionTests.c @@ -9,7 +9,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #ifdef H5_LDOUBLE_TO_LONG_SPECIAL_TEST #include <string.h> diff --git a/config/cmake/H5cxx_config.h.in b/config/cmake/H5cxx_config.h.in index 098a5d8..82e85c6 100644 --- a/config/cmake/H5cxx_config.h.in +++ b/config/cmake/H5cxx_config.h.in @@ -9,7 +9,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - /* src/H5cxx_config.h.in Created manually. */ /* Define if offsetof extension is present */ diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in index f413832..4d106aa 100644 --- a/config/cmake/H5pubconf.h.in +++ b/config/cmake/H5pubconf.h.in @@ -9,7 +9,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - /* H5pubconf.h Generated By CMake during the configuration */ #ifndef H5_CONFIG_H_ diff --git a/config/cmake/HDF518_Examples.cmake.in b/config/cmake/HDF518_Examples.cmake.in index 6214b9f..a239ded 100644 --- a/config/cmake/HDF518_Examples.cmake.in +++ b/config/cmake/HDF518_Examples.cmake.in @@ -8,7 +8,7 @@ # 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. - +# cmake_minimum_required(VERSION 3.2.2 FATAL_ERROR) ############################################################################################################### # This script will build and run the examples from a folder diff --git a/config/cmake/HDF5_Examples_options.cmake b/config/cmake/HDF5_Examples_options.cmake index f6e8dd2..b108b5b 100644 --- a/config/cmake/HDF5_Examples_options.cmake +++ b/config/cmake/HDF5_Examples_options.cmake @@ -8,7 +8,7 @@ # 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. - +# ############################################################################################# #### Change default configuration of options in config/cmake/cacheinit.cmake file ### #### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ### diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake index 35c05fa..98a2a23 100644 --- a/config/cmake/cacheinit.cmake +++ b/config/cmake/cacheinit.cmake @@ -8,7 +8,7 @@ # 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. - +# # This is the CMakeCache file. ######################## diff --git a/config/cmake/hdf5-config-version.cmake.in b/config/cmake/hdf5-config-version.cmake.in index 5697ead..8e16725 100644 --- a/config/cmake/hdf5-config-version.cmake.in +++ b/config/cmake/hdf5-config-version.cmake.in @@ -8,7 +8,7 @@ # 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. - +# #----------------------------------------------------------------------------- # HDF5 Version file for install directory #----------------------------------------------------------------------------- diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in index 7fe71e8..14859c1 100644 --- a/config/cmake/hdf5-config.cmake.in +++ b/config/cmake/hdf5-config.cmake.in @@ -8,7 +8,7 @@ # 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. - +# #----------------------------------------------------------------------------- # HDF5 Config file for compiling against hdf5 build/install directory #----------------------------------------------------------------------------- diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index 3d3fb27..e7e11ee 100755 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -37,8 +37,8 @@ cmake_minimum_required (VERSION 3.2.2 FATAL_ERROR) # NO_MAC_FORTRAN - Yes to be SHARED on a Mac
##############################################################################
-set (CTEST_SOURCE_VERSION "1.8.19")
-set (CTEST_SOURCE_VERSEXT "")
+set (CTEST_SOURCE_VERSION "1.8.20")
+set (CTEST_SOURCE_VERSEXT "-snap2")
##############################################################################
# handle input parameters to script.
diff --git a/config/cmake_ext_mod/CheckTypeSize.cmake b/config/cmake_ext_mod/CheckTypeSize.cmake index 116560a..c14c2f2 100644 --- a/config/cmake_ext_mod/CheckTypeSize.cmake +++ b/config/cmake_ext_mod/CheckTypeSize.cmake @@ -8,7 +8,7 @@ # 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. - +# # # Check if the type exists and determine size of type. if the type # exists, the size will be stored to the variable. diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index 7db1ec3..56d45f9 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -8,7 +8,7 @@ # 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. - +# #----------------------------------------------------------------------------- # Include all the necessary files for macros #----------------------------------------------------------------------------- diff --git a/config/cmake_ext_mod/FindSZIP.cmake b/config/cmake_ext_mod/FindSZIP.cmake index 68d2080..699be85 100644 --- a/config/cmake_ext_mod/FindSZIP.cmake +++ b/config/cmake_ext_mod/FindSZIP.cmake @@ -8,7 +8,7 @@ # 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. - +# # - Find SZIP library # - Derived from the FindTiff.cmake that is included with cmake diff --git a/config/cmake_ext_mod/GetTimeOfDayTest.cpp b/config/cmake_ext_mod/GetTimeOfDayTest.cpp index 8871ebc..5fd7c04 100644 --- a/config/cmake_ext_mod/GetTimeOfDayTest.cpp +++ b/config/cmake_ext_mod/GetTimeOfDayTest.cpp @@ -9,7 +9,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #if defined (TRY_SYS_TIME_H) #include <sys/time.h> /* #include <time.h> */ diff --git a/config/cmake_ext_mod/HDFLibMacros.cmake b/config/cmake_ext_mod/HDFLibMacros.cmake index 9de5339..54e408b 100644 --- a/config/cmake_ext_mod/HDFLibMacros.cmake +++ b/config/cmake_ext_mod/HDFLibMacros.cmake @@ -8,7 +8,7 @@ # 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. - +# #------------------------------------------------------------------------------- macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic) # May need to build JPEG with PIC on x64 machines with gcc @@ -74,14 +74,14 @@ macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic) HDF_IMPORT_SET_LIB_OPTIONS (jpeg-static "jpeg" STATIC "") add_dependencies (JPEG jpeg-static) set (JPEG_STATIC_LIBRARY "jpeg-static") - set (JPEG_LIBRARIES ${JPEG_static_LIBRARY}) + set (JPEG_LIBRARIES ${JPEG_STATIC_LIBRARY}) if (BUILD_SHARED_LIBS) # Create imported target jpeg-shared add_library(jpeg-shared SHARED IMPORTED) HDF_IMPORT_SET_LIB_OPTIONS (jpeg-shared "jpeg" SHARED "") add_dependencies (JPEG jpeg-shared) set (JPEG_SHARED_LIBRARY "jpeg-shared") - set (JPEG_LIBRARIES ${JPEG_LIBRARIES} ${JPEG_shared_LIBRARY}) + set (JPEG_LIBRARIES ${JPEG_LIBRARIES} ${JPEG_SHARED_LIBRARY}) endif () set (JPEG_INCLUDE_DIR_GEN "${BINARY_DIR}") @@ -167,14 +167,14 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding) HDF_IMPORT_SET_LIB_OPTIONS (szip-static "szip" STATIC "") add_dependencies (SZIP szip-static) set (SZIP_STATIC_LIBRARY "szip-static") - set (SZIP_LIBRARIES ${SZIP_static_LIBRARY}) + set (SZIP_LIBRARIES ${SZIP_STATIC_LIBRARY}) if (BUILD_SHARED_LIBS) # Create imported target szip-shared add_library(szip-shared SHARED IMPORTED) HDF_IMPORT_SET_LIB_OPTIONS (szip-shared "szip" SHARED "") add_dependencies (SZIP szip-shared) set (SZIP_SHARED_LIBRARY "szip-shared") - set (SZIP_LIBRARIES ${SZIP_LIBRARIES} ${SZIP_shared_LIBRARY}) + set (SZIP_LIBRARIES ${SZIP_LIBRARIES} ${SZIP_SHARED_LIBRARY}) endif () set (SZIP_INCLUDE_DIR_GEN "${BINARY_DIR}") @@ -262,7 +262,7 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type) HDF_IMPORT_SET_LIB_OPTIONS (zlib-static ${ZLIB_LIB_NAME} STATIC "") add_dependencies (ZLIB zlib-static) set (ZLIB_STATIC_LIBRARY "zlib-static") - set (ZLIB_LIBRARIES ${ZLIB_static_LIBRARY}) + set (ZLIB_LIBRARIES ${ZLIB_STATIC_LIBRARY}) if (BUILD_SHARED_LIBS) # Create imported target zlib-shared add_library(zlib-shared SHARED IMPORTED) diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index 64f6f8d..602b6bf 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -8,7 +8,7 @@ # distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. - +# #------------------------------------------------------------------------------- macro (SET_GLOBAL_VARIABLE name value) set (${name} ${value} CACHE INTERNAL "Used to pass variables between directories" FORCE) diff --git a/config/cmake_ext_mod/HDFTests.c b/config/cmake_ext_mod/HDFTests.c index e8353f5..60ac744 100644 --- a/config/cmake_ext_mod/HDFTests.c +++ b/config/cmake_ext_mod/HDFTests.c @@ -9,7 +9,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #define SIMPLE_TEST(x) int main(){ x; return 0; } #ifdef HAVE_C99_DESIGNATED_INITIALIZER diff --git a/config/cmake_ext_mod/HDFUseFortran.cmake b/config/cmake_ext_mod/HDFUseFortran.cmake index 5a2885a..7bf4d81 100644 --- a/config/cmake_ext_mod/HDFUseFortran.cmake +++ b/config/cmake_ext_mod/HDFUseFortran.cmake @@ -8,7 +8,7 @@ # 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. - +# # # This file provides functions for Fortran support. # diff --git a/config/cmake_ext_mod/grepTest.cmake b/config/cmake_ext_mod/grepTest.cmake index 82ac090..5b0e8fd 100644 --- a/config/cmake_ext_mod/grepTest.cmake +++ b/config/cmake_ext_mod/grepTest.cmake @@ -8,7 +8,7 @@ # 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. - +# # grepTest.cmake executes a command and captures the output in a file. File is then compared # against a reference file. Exit status of command can also be compared. diff --git a/config/cmake_ext_mod/runTest.cmake b/config/cmake_ext_mod/runTest.cmake index 0a9ebd1..3a02614 100644 --- a/config/cmake_ext_mod/runTest.cmake +++ b/config/cmake_ext_mod/runTest.cmake @@ -8,7 +8,7 @@ # 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. - +# # runTest.cmake executes a command and captures the output in a file. File is then compared # against a reference file. Exit status of command can also be compared. cmake_policy(SET CMP0007 NEW) diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 index ea12a88..ce07853 100644 --- a/config/linux-gnulibc1 +++ b/config/linux-gnulibc1 @@ -84,6 +84,20 @@ else $RM $tmpfile fc_version_info=`$FC -V | grep Absoft` ;; + # The NAG compiler + nagfor*|nagftn*) + RM='rm -f' + tmpfile=/tmp/cmpver.$$ + $FC -V >& $tmpfile + if test -s "$tmpfile"; then + if( grep -s 'NAG Fortran' $tmpfile > /dev/null) then + FC_BASENAME=nagfor + fi + fi + fc_version_info=`grep "NAG Fortran" $tmpfile` + echo "compiler '$FC' is $fc_version_info" + $RM $tmpfile + ;; *) ;; @@ -117,6 +131,37 @@ case $FC_BASENAME in PROFILE_FCFLAGS="-g -pg" f9x_flags_set=yes ;; +# +# NAG compiler +# + nagfor) + + F9XSUFFIXFLAG="" +# We force compiler to use upper case for external names +# (just in case since this should be a default EIP) + H5_FCFLAGS="$H5_FCFLAGS" + FSEARCH_DIRS="" + + # Production + PROD_FCFLAGS= + + # Debug + DEBUG_FCFLAGS="-C" + + # Symbols + SYMBOLS_FCFLAGS="-g" + NO_SYMBOLS_FCFLAGS="-s" + + # Profiling + PROFILE_FCFLAGS="-pg" + + # Optimization + HIGH_OPT_FCFLAGS="-O" + DEBUG_OPT_FCFLAGS="-O0" + NO_OPT_FCFLAGS="-O0" + + f9x_flags_set=yes + ;; esac @@ -208,6 +253,19 @@ case $FC in *pgf90*) fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -V 2>&1 | grep 'pgf90'` ;; + *nagfor*|*nagftn*) + RM='rm -f' + tmpfile=/tmp/cmpver.$$ + $FC -V >& $tmpfile + if test -s "$tmpfile"; then + if( grep -s 'NAG Fortran' $tmpfile > /dev/null) then + FC_BASENAME=nagfor + fi + fi + fc_version_info=`grep "NAG Fortran" $tmpfile` + $RM $tmpfile + echo "compiler '$FC' is $fc_version_info" + ;; *) echo "No match to get fc_version_info for $FC" @@ -1,7 +1,7 @@ #! /bin/sh # From configure.ac Id. # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for HDF5 1.8.19. +# Generated by GNU Autoconf 2.69 for HDF5 1.8.20-snap2. # # Report bugs to <help@hdfgroup.org>. # @@ -591,8 +591,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='HDF5' PACKAGE_TARNAME='hdf5' -PACKAGE_VERSION='1.8.19' -PACKAGE_STRING='HDF5 1.8.19' +PACKAGE_VERSION='1.8.20-snap2' +PACKAGE_STRING='HDF5 1.8.20-snap2' PACKAGE_BUGREPORT='help@hdfgroup.org' PACKAGE_URL='' @@ -640,6 +640,7 @@ LTLIBOBJS LIBOBJS HAVE_SHARED_CONDITIONAL_FALSE HAVE_SHARED_CONDITIONAL_TRUE +fortran_linux_linker_option SEARCH BUILD_HDF5_HL_CONDITIONAL_FALSE BUILD_HDF5_HL_CONDITIONAL_TRUE @@ -1479,7 +1480,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures HDF5 1.8.19 to adapt to many kinds of systems. +\`configure' configures HDF5 1.8.20-snap2 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1549,7 +1550,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of HDF5 1.8.19:";; + short | recursive ) echo "Configuration of HDF5 1.8.20-snap2:";; esac cat <<\_ACEOF @@ -1744,7 +1745,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -HDF5 configure 1.8.19 +HDF5 configure 1.8.20-snap2 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -2681,7 +2682,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by HDF5 $as_me 1.8.19, which was +It was created by HDF5 $as_me 1.8.20-snap2, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -3552,7 +3553,7 @@ fi # Define the identity of the package. PACKAGE='hdf5' - VERSION='1.8.19' + VERSION='1.8.20-snap2' cat >>confdefs.h <<_ACEOF @@ -22394,7 +22395,7 @@ fi case "X-$enable_production" in - X-|X-yes) + X-yes) enable_production="yes" { $as_echo "$as_me:${as_lineno-$LINENO}: result: production" >&5 $as_echo "production" >&6; } @@ -22404,7 +22405,7 @@ $as_echo "production" >&6; } H5_CXXFLAGS="$H5_CXXFLAGS $PROD_CXXFLAGS" H5_FCFLAGS="$H5_FCFLAGS $PROD_FCFLAGS" ;; - X-no) + X-|X-no) enable_production="no" { $as_echo "$as_me:${as_lineno-$LINENO}: result: development" >&5 $as_echo "development" >&6; } @@ -29312,7 +29313,7 @@ Usage: $0 [OPTIONS] Report bugs to <bug-libtool@gnu.org>." lt_cl_version="\ -HDF5 config.lt 1.8.19 +HDF5 config.lt 1.8.20-snap2 configured by $0, generated by GNU Autoconf 2.69. Copyright (C) 2011 Free Software Foundation, Inc. @@ -30733,6 +30734,27 @@ else STATIC_SHARED="none" fi +if test "X$HDF_FORTRAN" = "Xyes"; then + + ### libtool does not pass the correct argument linking (-Wl,-Wl,,) for the NAG Fortran compiler + ### on Linux (other OSs have not been tested). + ### Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to + ### wl="-Wl,-Wl,," in the libtool file. (HDFFV-10037) + case "`uname`" in + Linux*) + + fortran_linux_linker_option="-Wl," + if test "X$FC_BASENAME" = "Xnagfor"; then + fortran_linux_linker_option="-Wl,-Wl,," + fi + + ## Set the correct linker option for use in h5fc.in markup + + ;; + esac + +fi + ## ---------------------------------------------------------------------- ## Set a macro if shared library is enabled. ## @@ -31351,7 +31373,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by HDF5 $as_me 1.8.19, which was +This file was extended by HDF5 $as_me 1.8.20-snap2, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -31417,7 +31439,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -HDF5 config.status 1.8.19 +HDF5 config.status 1.8.20-snap2 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" @@ -33705,6 +33727,10 @@ fi chmod 755 tools/misc/h5cc +if test "X$HDF_CXX" = "Xyes"; then + chmod 755 c++/src/h5c++ +fi + if test "X$HDF_FORTRAN" = "Xyes"; then chmod 755 fortran/src/h5fc @@ -33716,10 +33742,18 @@ if test "X$HDF_FORTRAN" = "Xyes"; then cat libtool | awk '/wl=\"/{c++;if(c==3){sub("wl=\"\"","wl=\"-Wl,\"");c=0}}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool ;; esac -fi -if test "X$HDF_CXX" = "Xyes"; then - chmod 755 c++/src/h5c++ + ### libtool does not pass the correct argument linking (-WL,-Wl,,) for the NAG Fortran compiler + ### on Linux (other OSs have not been tested). + ### Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to + ### wl="-Wl,-Wl,," in the libtool file. (HDFFV-10037) + case "`uname`" in + Linux*) + if test "X$FC_BASENAME" = "Xnagfor"; then + cat libtool | awk '/NAG_Fortran/{flag=1}flag&&/wl=/{$NF="wl=\"-Wl,Wl,,\"";flag=0}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool + fi + ;; + esac fi ## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic diff --git a/configure.ac b/configure.ac index 796352f..e5590bd 100644 --- a/configure.ac +++ b/configure.ac @@ -24,7 +24,7 @@ AC_PREREQ([2.69]) ## NOTE: Do not forget to change the version number here when we do a ## release!!! ## -AC_INIT([HDF5], [1.8.19], [help@hdfgroup.org]) +AC_INIT([HDF5], [1.8.20-snap2], [help@hdfgroup.org]) AC_CONFIG_SRCDIR([src/H5.c]) AC_CONFIG_HEADERS([src/H5config.h]) @@ -784,7 +784,7 @@ AC_ARG_ENABLE([production], [Determines how to run the compiler.])]) case "X-$enable_production" in - X-|X-yes) + X-yes) enable_production="yes" AC_MSG_RESULT([production]) CONFIG_MODE=production @@ -793,7 +793,7 @@ case "X-$enable_production" in H5_CXXFLAGS="$H5_CXXFLAGS $PROD_CXXFLAGS" H5_FCFLAGS="$H5_FCFLAGS $PROD_FCFLAGS" ;; - X-no) + X-|X-no) enable_production="no" AC_MSG_RESULT([development]) CONFIG_MODE=development @@ -2916,6 +2916,27 @@ else STATIC_SHARED="none" fi +if test "X$HDF_FORTRAN" = "Xyes"; then + + ### libtool does not pass the correct argument linking (-Wl,-Wl,,) for the NAG Fortran compiler + ### on Linux (other OSs have not been tested). + ### Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to + ### wl="-Wl,-Wl,," in the libtool file. (HDFFV-10037) + case "`uname`" in + Linux*) + + fortran_linux_linker_option="-Wl," + if test "X$FC_BASENAME" = "Xnagfor"; then + fortran_linux_linker_option="-Wl,-Wl,," + fi + + ## Set the correct linker option for use in h5fc.in markup + AC_SUBST([fortran_linux_linker_option]) + ;; + esac + +fi + ## ---------------------------------------------------------------------- ## Set a macro if shared library is enabled. ## @@ -3004,6 +3025,10 @@ AC_CONFIG_FILES([src/libhdf5.settings AC_OUTPUT chmod 755 tools/misc/h5cc +if test "X$HDF_CXX" = "Xyes"; then + chmod 755 c++/src/h5c++ +fi + if test "X$HDF_FORTRAN" = "Xyes"; then chmod 755 fortran/src/h5fc @@ -3015,10 +3040,18 @@ if test "X$HDF_FORTRAN" = "Xyes"; then cat libtool | awk '/wl=\"/{c++;if(c==3){sub("wl=\"\"","wl=\"-Wl,\"");c=0}}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool ;; esac -fi -if test "X$HDF_CXX" = "Xyes"; then - chmod 755 c++/src/h5c++ + ### libtool does not pass the correct argument linking (-WL,-Wl,,) for the NAG Fortran compiler + ### on Linux (other OSs have not been tested). + ### Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to + ### wl="-Wl,-Wl,," in the libtool file. (HDFFV-10037) + case "`uname`" in + Linux*) + if test "X$FC_BASENAME" = "Xnagfor"; then + cat libtool | awk '/NAG_Fortran/{flag=1}flag&&/wl=/{$NF="wl=\"-Wl,Wl,,\"";flag=0}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool + fi + ;; + esac fi ## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic diff --git a/examples/Makefile.in b/examples/Makefile.in index e91f11a..3d1a9c5 100644 --- a/examples/Makefile.in +++ b/examples/Makefile.in @@ -530,6 +530,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/fortran/Makefile.in b/fortran/Makefile.in index 49c0172..d46c86d 100644 --- a/fortran/Makefile.in +++ b/fortran/Makefile.in @@ -587,6 +587,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/fortran/examples/Makefile.am b/fortran/examples/Makefile.am index 3428a9e..d78cbb3 100644 --- a/fortran/examples/Makefile.am +++ b/fortran/examples/Makefile.am @@ -68,10 +68,10 @@ h5_crtatt.chkexe_: h5_rdwt.chkexe_ # Additional dependencies for the examples are listed below if BUILD_PARALLEL_CONDITIONAL $(EXTRA_PROG): $(H5FC_PP) - $(H5FC_PP) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; + $(H5FC_PP) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; else $(EXTRA_PROG): $(H5FC) - $(H5FC) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; + $(H5FC) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; endif # Tell automake how to install examples diff --git a/fortran/examples/Makefile.in b/fortran/examples/Makefile.in index 30f8755..208bd44 100644 --- a/fortran/examples/Makefile.in +++ b/fortran/examples/Makefile.in @@ -538,6 +538,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ @@ -1052,9 +1053,9 @@ h5_crtatt.chkexe_: h5_rdwt.chkexe_ # Tell automake how to build examples using h5fc # Additional dependencies for the examples are listed below @BUILD_PARALLEL_CONDITIONAL_TRUE@$(EXTRA_PROG): $(H5FC_PP) -@BUILD_PARALLEL_CONDITIONAL_TRUE@ $(H5FC_PP) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; +@BUILD_PARALLEL_CONDITIONAL_TRUE@ $(H5FC_PP) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; @BUILD_PARALLEL_CONDITIONAL_FALSE@$(EXTRA_PROG): $(H5FC) -@BUILD_PARALLEL_CONDITIONAL_FALSE@ $(H5FC) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; +@BUILD_PARALLEL_CONDITIONAL_FALSE@ $(H5FC) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; # List dependencies for each example. Normally, automake would take # care of this for us, but if we tell automake about the programs it diff --git a/fortran/src/Makefile.in b/fortran/src/Makefile.in index c896ea0..300cb0b 100644 --- a/fortran/src/Makefile.in +++ b/fortran/src/Makefile.in @@ -647,6 +647,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/fortran/src/h5fc.in b/fortran/src/h5fc.in index 47642c9..29ef83f 100644 --- a/fortran/src/h5fc.in +++ b/fortran/src/h5fc.in @@ -307,7 +307,7 @@ if test "x$do_link" = "xyes"; then link_args="$link_args -L${libdir}" case "$host_os" in - linux*) flag="-Wl,-rpath -Wl," ;; + linux*) flag="@fortran_linux_linker_option@-rpath -Wl," ;; hpux*) flag="-Wl,+b -Wl," ;; freebsd*|solaris*) flag="-R" ;; rs6000*|aix*) flag="-L" ;; diff --git a/fortran/test/Makefile.in b/fortran/test/Makefile.in index df8f9e4..4764b8f 100644 --- a/fortran/test/Makefile.in +++ b/fortran/test/Makefile.in @@ -655,6 +655,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/fortran/testpar/Makefile.in b/fortran/testpar/Makefile.in index c23b730..f318ce6 100644 --- a/fortran/testpar/Makefile.in +++ b/fortran/testpar/Makefile.in @@ -583,6 +583,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/Makefile.in b/hl/Makefile.in index d203a60..825621a 100644 --- a/hl/Makefile.in +++ b/hl/Makefile.in @@ -587,6 +587,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/c++/Makefile.in b/hl/c++/Makefile.in index dd52b3e..840696a 100644 --- a/hl/c++/Makefile.in +++ b/hl/c++/Makefile.in @@ -583,6 +583,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/c++/examples/Makefile.in b/hl/c++/examples/Makefile.in index 82f94ce..de7f8c1 100644 --- a/hl/c++/examples/Makefile.in +++ b/hl/c++/examples/Makefile.in @@ -530,6 +530,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in index c3be749..fc57136 100644 --- a/hl/c++/src/Makefile.in +++ b/hl/c++/src/Makefile.in @@ -586,6 +586,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/c++/test/Makefile.in b/hl/c++/test/Makefile.in index fc30db8..05742b6 100644 --- a/hl/c++/test/Makefile.in +++ b/hl/c++/test/Makefile.in @@ -583,6 +583,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/examples/Makefile.in b/hl/examples/Makefile.in index 961a701..d6e4acd 100644 --- a/hl/examples/Makefile.in +++ b/hl/examples/Makefile.in @@ -530,6 +530,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/fortran/Makefile.in b/hl/fortran/Makefile.in index c8dcddf..f3f2dc2 100644 --- a/hl/fortran/Makefile.in +++ b/hl/fortran/Makefile.in @@ -587,6 +587,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/fortran/examples/Makefile.am b/hl/fortran/examples/Makefile.am index b8ed434..71c2866 100644 --- a/hl/fortran/examples/Makefile.am +++ b/hl/fortran/examples/Makefile.am @@ -43,10 +43,10 @@ FORTRAN_API=yes # Tell automake how to build examples using h5fc if BUILD_PARALLEL_CONDITIONAL $(EXTRA_PROG): $(H5FC_PP) - $(H5FC_PP) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; + $(H5FC_PP) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; else $(EXTRA_PROG): $(H5FC) - $(H5FC) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; + $(H5FC) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; endif # Tell automake how to install examples diff --git a/hl/fortran/examples/Makefile.in b/hl/fortran/examples/Makefile.in index a473467..fbf6d58 100644 --- a/hl/fortran/examples/Makefile.in +++ b/hl/fortran/examples/Makefile.in @@ -531,6 +531,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ @@ -1027,9 +1028,9 @@ help: # Tell automake how to build examples using h5fc @BUILD_PARALLEL_CONDITIONAL_TRUE@$(EXTRA_PROG): $(H5FC_PP) -@BUILD_PARALLEL_CONDITIONAL_TRUE@ $(H5FC_PP) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; +@BUILD_PARALLEL_CONDITIONAL_TRUE@ $(H5FC_PP) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; @BUILD_PARALLEL_CONDITIONAL_FALSE@$(EXTRA_PROG): $(H5FC) -@BUILD_PARALLEL_CONDITIONAL_FALSE@ $(H5FC) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90; +@BUILD_PARALLEL_CONDITIONAL_FALSE@ $(H5FC) $(H5CCFLAGS) -o $@ $(srcdir)/$@.f90; # How to create EXAMPLEDIR if it doesn't already exist $(EXAMPLEDIR): diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in index a995b72..2399369 100644 --- a/hl/fortran/src/Makefile.in +++ b/hl/fortran/src/Makefile.in @@ -604,6 +604,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/fortran/test/Makefile.in b/hl/fortran/test/Makefile.in index e188470..67cd706 100644 --- a/hl/fortran/test/Makefile.in +++ b/hl/fortran/test/Makefile.in @@ -595,6 +595,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in index fbf5c9f..965457f 100644 --- a/hl/src/Makefile.in +++ b/hl/src/Makefile.in @@ -585,6 +585,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in index 005e51d..f9b3c73 100644 --- a/hl/test/Makefile.in +++ b/hl/test/Makefile.in @@ -622,6 +622,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/tools/Makefile.in b/hl/tools/Makefile.in index 8c1eab7..1416a66 100644 --- a/hl/tools/Makefile.in +++ b/hl/tools/Makefile.in @@ -584,6 +584,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/hl/tools/gif2h5/Makefile.in b/hl/tools/gif2h5/Makefile.in index 611c912..05cb213 100644 --- a/hl/tools/gif2h5/Makefile.in +++ b/hl/tools/gif2h5/Makefile.in @@ -597,6 +597,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt index 87b6c73..a7aad02 100644 --- a/release_docs/HISTORY-1_8.txt +++ b/release_docs/HISTORY-1_8.txt @@ -3,6 +3,7 @@ HDF5 History This file contains development history of HDF5 1.8 branch +21. Release Information for hdff5-1.8.19 20. Release Information for hdf5-1.8.18 19. Release Information for hdf5-1.8.17 18. Release Information for hdf5-1.8.16 @@ -26,6 +27,435 @@ This file contains development history of HDF5 1.8 branch [Search on the string '%%%%' for section breaks of each release.] +%%%%1.8.19%%%% + + +HDF5 version 1.8.19 released on 2017-06-15 +================================================================================ + +INTRODUCTION +============ + +This document describes the differences between HDF5-1.8.18 and +HDF5-1.8.19, and contains information on the platforms tested and +known problems in HDF5-1.8.19. +For more details, see the files HISTORY-1_0-1_8_0_rc3.txt +and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. + +Links to the HDF5 1.8.19 source code, documentation, and additional materials +can be found on the HDF5 web page at: + + https://support.hdfgroup.org/HDF5/ + +The HDF5 1.8.19 release can be obtained from: + + https://support.hdfgroup.org/HDF5/release/obtain518.html + +User documentation for 1.8.19 can be accessed directly at this location: + + https://support.hdfgroup.org/HDF5/doc1.8/ + +New features in the HDF5-1.8.x release series, including brief general +descriptions of some new and modified APIs, are described in the "What's New +in 1.8.0?" document: + + https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html + +All new and modified APIs are listed in detail in the "HDF5 Software Changes +from Release to Release" document, in the section "Release 1.8.19 (current +release) versus Release 1.8.18 + + https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for New Platforms, Languages, and Compilers +- Bug Fixes since HDF5-1.8.19 +- Supported Platforms +- Supported Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration + -------------- + - CMake in the Tools + + User-defined filters on Windows require that tools be built + with shared libraries. + + CMake command code added to build tools with + shared libraries as well as with static libraries. + + (ADB - 2017/02/07, HDFFV-10123) + + + Library + ------- + - H5PL package + + Users would like to be able to set the plugin path programmatically + instead of through the environment variable. + + H5PL package obtained new APIs for manipulating the entries of + the plugin path table. The new APIs are; + H5PLappend - Insert a plugin path at the end of the list. + H5PLprepend - Insert a plugin path at the beginning of the list. + H5PLreplace - Replace the path at the specified index. + H5PLinsert - Insert a plugin path at the specified index, moving + other paths after the index. + H5PLremove - Remove the plugin path at the specifed index and + compacting the list. + H5PLget - Query the plugin path at the specified index. + H5PLsize - Query the size of the current list of plugin paths. + + (ADB - 2017/04/04, HDFFV-10143) + + - H5Dget_chunk_storage_size + + The storage size of a chunk in the file is needed to determine the size + of the buffer to be allocated for reading a chunk directly from a file. + + New API function gets the size in bytes currently allocated within a + file for a raw data chunk in a dataset. This function was added to get + the chunk size in support of the implementation of H5DOread_chunks, but + may also be useful for other purposes. + + (VC - 2017/05/02, HDFFV-9934) + + C++ API + ------- + - The following C++ API wrappers have been added to the C++ Library: + // Determines if a name exists. + H5Location::nameExists() - C API H5Lexists() + + // Checks if an ID is valid. + IdComponent::isValid() - C API H5Iis_valid() + + // Sets the number of soft or user-defined links that can be + // traversed before a failure occurs. + LinkAccPropList::setNumLinks() - C API H5Pset_nlinks() + + // Gets the number of soft or user-defined link traversals allowed + LinkAccPropList::getNumLinks() - C API H5Pget_nlinks() + + // Returns a copy of the creation property list of a datatype. + DataType::getCreatePlist() - C API H5Tget_create_plist() + + // Opens an object within a location, regarless its type. + H5Location::openObjId() - C API H5Oopen() + H5Location::openObjId() - C API H5Oopen() + + // Closes an object opened by openObjId(). + H5Location::closeObjId() - C API H5Oclose() + + // Gets general information about a file. + H5File::getFileInfo() - C API H5Fget_info() + + // Returns the header version of an HDF5 object. + H5Object::objVersion() - C API H5Oget_info() + + (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156) + + - New class LinkAccPropList is added for link access proprety list + + (BMR, 2017/05/13, HDFFV-10156) + + High-Level APIs + --------------- + - H5DOread_chunk + + Users wanted to read compressed data directly from a file without any + processing by the HDF5 data transfer pipeline, just as they were able + to write it directly to a file with H5DOwrite_chunk. + + New API function, corresponding to existing function H5DOwrite_chunk. + H5DOread_chunk reads a raw data chunk directly from a chunked dataset + in the file into the application buffer, bypassing the library’s internal + data transfer pipeline, including filters. + + (VC - 2017/05/02, HDFFV-9934) + + +Support for New Platforms, Languages, and Compilers +=================================================== + + - Added OpenMPI 2.0.1 compiled with GCC 4.9.3 + + +Bug Fixes since HDF5-1.8.18 +=========================== + + Configuration + ------------- + - Support for Fortran shared libraries on OS X with autotools now + works. Cmake builds still disables Fortran shared libraries on OS X. + (MSB - 2017/04/30, HDFFV-2772) + + + Library + ------- + - bitfield datatypes + + bitfield datatypes did not fully support endianness of the data. + + Improved the endianness of bitfield datatypes by adding missing functional + code. This code used integer types as a template. + + (ADB - 2017/05/12, HDFFV-10186) + + - Newly created datasets with H5D_COMPACT layout failed to open after + several H5Dopen/H5Dclose cycles. + + The layout "dirty" flag for a compact dataset is now properly reset + before flushing the message. + + (VC - 2017/05/11, HDFFV-10051) + - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file. + + (DER - 2017/04/25, HDFFV-9638) + + + Tools + ----- + - h5repack + + h5repack did not maintain the creation order flag of the root + group. + + Improved h5repack by reading the creation order and applying the + flag to the new root group. Also added arguments to set the + order and index direction, which applies to the traversing of the + original file, on the command line. + + (ADB - 2017/05/26, HDFFV-8611) + + - h5diff + + h5diff failed to account for strpad type and null terminators + of char strings. Also, h5diff failed to account for string length + differences and would give a different result depending on file + order in the command line. + + Improved h5diff compare of strings and arrays by adding a check for + string lengths and if the strpad was null filled. + + (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) + + - h5diff + + h5diff help text about epsilon comparison was confusing. + + Changed h5diff help text to indicate that the 'a' refers to the + datapoint in file1 and 'b' refers to the datapoint value in file2. + + (ADB - 2017/05/16, HDFFV-9995) + + - h5diff + + h5diff did not report user-defined filter data differences correctly. + + Improved h5diff compare of user-defined filter data by reporting an + error if the user-defined filter plugin cannot be found. + + (ADB - 2017/01/18, HDFFV-9994) + C++ API + ------- + - The class hierarchy is revised to better reflect the HDF5 model. + Class H5File is now derived from class Group instead of H5Location. + Class Attribute is now derived from H5Location instead of IdComponent. + Wrappers of H5A APIs in H5Location are now duplicated in H5Object, + the original wrappers in H5Location will be deprecated in future + releases. + + (BMR - 2017/05/15, HDFFV-10156) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus/mayll) Version 4.4.7 20120313 + Versions 4.9.3, 5.2.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 16.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + OpenMPI 2.0.1 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Versions 4.9.3, 5.3.0, 6.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) + gcc and gfortran compilers (GCC 5.4.0) + (cmake and autotools) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (mayll) + + Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) + (cmake and autotools) + + CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) + (cmake and autotools) + + Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 + (cmake and autotools) + + +Known Problems +============== + + The dynamically loaded plugin test libraries require undefined references + to HDF5 functions to be resolved at runtime in order to function properly. + With autotools on CYGWIN this results in build errors, and we have not + found a solution that satisfies both. Therefore the dynamically loaded + plugin tests have been disabled on CYGWIN. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + %%%%1.8.18%%%% diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index f7a7f34..4349311 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,4 +1,4 @@ -HDF5 version 1.8.19 released on 2017-06-15 +HDF5 version 1.8.20-snap2 currently under development ================================================================================ INTRODUCTION @@ -56,88 +56,38 @@ New Features ============ Configuration - -------------- - - CMake in the Tools - - User-defined filters on Windows require that tools be built - with shared libraries. - - CMake command code added to build tools with - shared libraries as well as with static libraries. - - (ADB - 2017/02/07, HDFFV-10123) + ------------- + - None Library ------- - - H5PL package - - Users would like to be able to set the plugin path programmatically - instead of through the environment variable. + - None - H5PL package obtained new APIs for manipulating the entries of - the plugin path table. The new APIs are; - H5PLappend - Insert a plugin path at the end of the list. - H5PLprepend - Insert a plugin path at the beginning of the list. - H5PLreplace - Replace the path at the specified index. - H5PLinsert - Insert a plugin path at the specified index, moving - other paths after the index. - H5PLremove - Remove the plugin path at the specifed index and - compacting the list. - H5PLget - Query the plugin path at the specified index. - H5PLsize - Query the size of the current list of plugin paths. - (ADB - 2017/04/04, HDFFV-10143) + Parallel Library + ---------------- + - None - - H5Dget_chunk_storage_size - - The storage size of a chunk in the file is needed to determine the size - of the buffer to be allocated for reading a chunk directly from a file. - - New API function gets the size in bytes currently allocated within a - file for a raw data chunk in a dataset. This function was added to get - the chunk size in support of the implementation of H5DOread_chunks, but - may also be useful for other purposes. - - (VC - 2017/05/02, HDFFV-9934) - C++ API - ------- - - The following C++ API wrappers have been added to the C++ Library: - // Determines if a name exists. - H5Location::nameExists() - C API H5Lexists() - - // Checks if an ID is valid. - IdComponent::isValid() - C API H5Iis_valid() - - // Sets the number of soft or user-defined links that can be - // traversed before a failure occurs. - LinkAccPropList::setNumLinks() - C API H5Pset_nlinks() - - // Gets the number of soft or user-defined link traversals allowed - LinkAccPropList::getNumLinks() - C API H5Pget_nlinks() - - // Returns a copy of the creation property list of a datatype. - DataType::getCreatePlist() - C API H5Tget_create_plist() - - // Opens an object within a location, regarless its type. - H5Location::openObjId() - C API H5Oopen() - H5Location::openObjId() - C API H5Oopen() + Tools + ----- + - None - // Closes an object opened by openObjId(). - H5Location::closeObjId() - C API H5Oclose() - // Gets general information about a file. - H5File::getFileInfo() - C API H5Fget_info() + High-Level APIs + --------------- + - None - // Returns the header version of an HDF5 object. - H5Object::objVersion() - C API H5Oget_info() - (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156) + Fortran API + ----------- + - None - - New class LinkAccPropList is added for link access proprety list - (BMR, 2017/05/13, HDFFV-10156) + C++ API + ------- + - None High-Level APIs @@ -159,98 +109,81 @@ New Features Support for New Platforms, Languages, and Compilers =================================================== - - Added OpenMPI 2.0.1 compiled with GCC 4.9.3 -Bug Fixes since HDF5-1.8.18 +Bug Fixes since HDF5-1.8.19 =========================== Configuration ------------- - - Support for Fortran shared libraries on OS X with autotools now - works. Cmake builds still disables Fortran shared libraries on OS X. - (MSB - 2017/04/30, HDFFV-2772) + - None Library ------- - - bitfield datatypes - - bitfield datatypes did not fully support endianness of the data. - - Improved the endianness of bitfield datatypes by adding missing functional - code. This code used integer types as a template. - - (ADB - 2017/05/12, HDFFV-10186) + - None - - Newly created datasets with H5D_COMPACT layout failed to open after - several H5Dopen/H5Dclose cycles. - The layout "dirty" flag for a compact dataset is now properly reset - before flushing the message. + Parallel Library + ---------------- + - None - (VC - 2017/05/11, HDFFV-10051) - - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file. - - (DER - 2017/04/25, HDFFV-9638) + Performance + ------------- + - None Tools ----- - - h5repack + - h5ls - h5repack did not maintain the creation order flag of the root - group. + h5ls generated error on stack when it encountered a H5S_NULL + dataspace. - Improved h5repack by reading the creation order and applying the - flag to the new root group. Also added arguments to set the - order and index direction, which applies to the traversing of the - original file, on the command line. + Adding checks for H5S_NULL before calling H5Sis_simple (located + in the h5tools_dump_mem function) fixed the issue. - (ADB - 2017/05/26, HDFFV-8611) + (ADB - 2017/08/17, HDFFV-10188) - - h5diff + - h5dump - h5diff failed to account for strpad type and null terminators - of char strings. Also, h5diff failed to account for string length - differences and would give a different result depending on file - order in the command line. + h5dump segfaulted on output of XML file. - Improved h5diff compare of strings and arrays by adding a check for - string lengths and if the strpad was null filled. + Function that escape'd strings used the full buffer length + instead of just the length of the replacement string in a + strncpy call. Using the correct length fixed the issue. - (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) + (ADB - 2017/08/01, HDFFV-10256) - h5diff - h5diff help text about epsilon comparison was confusing. - - Changed h5diff help text to indicate that the 'a' refers to the - datapoint in file1 and 'b' refers to the datapoint value in file2. + h5diff segfaulted on compare of a NULL variable length string. - (ADB - 2017/05/16, HDFFV-9995) + Improved h5diff compare of strings by adding a check for + NULL strings and setting the lengths to zero. - - h5diff + (ADB - 2017/07/25, HDFFV-10246) - h5diff did not report user-defined filter data differences correctly. - Improved h5diff compare of user-defined filter data by reporting an - error if the user-defined filter plugin cannot be found. + Fortran API + ----------- + - None - (ADB - 2017/01/18, HDFFV-9994) C++ API ------- - - The class hierarchy is revised to better reflect the HDF5 model. - Class H5File is now derived from class Group instead of H5Location. - Class Attribute is now derived from H5Location instead of IdComponent. - Wrappers of H5A APIs in H5Location are now duplicated in H5Object, - the original wrappers in H5Location will be deprecated in future - releases. + - None + + + High-Level APIs: + --------------- + - None - (BMR - 2017/05/15, HDFFV-10156) + Packet Table APIs: + ------------------ + - None Supported Platforms diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index fcc752c..021335f 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -150,6 +150,10 @@ typedef struct H5D_chunk_it_ud3_t { /* needed for copy object pointed by refs */ H5O_copy_t *cpy_info; /* Copy options */ + + /* needed for getting raw data from chunk cache */ + hbool_t chunk_in_cache; + uint8_t *chunk; /* the unfiltered chunk data */ } H5D_chunk_it_ud3_t; /* Callback info for iteration to dump index */ @@ -324,7 +328,6 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsiz H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ unsigned space_ndims; /* Dataset's space rank */ - hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -414,7 +417,6 @@ H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset, const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ unsigned space_ndims; /* Dataset's space rank */ - hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Dataset's chunk offset */ hsize_t chunk_idx; /* Index of chunk cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ @@ -521,7 +523,6 @@ H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, h const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ unsigned space_ndims; /* Dataset's space rank */ - hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Dataset's chunk offset */ hsize_t chunk_idx; /* Index of chunk cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ @@ -4836,12 +4837,57 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) udata->buf_size = buf_size = nbytes; } /* end if */ - /* read chunk data from the source file */ - if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") + if(udata->chunk_in_cache && udata->chunk) { + HDassert(!H5F_addr_defined(chunk_rec->chunk_addr)); + HDmemcpy(buf, udata->chunk, nbytes); + udata->chunk = NULL; + } else { + H5D_rdcc_ent_t *ent = NULL; /* Cache entry */ + unsigned idx; /* Index of chunk in cache, if present */ + unsigned u; /* Counter */ + H5D_shared_t *shared_fo = udata->cpy_info->shared_fo; + + /* See if the written chunk is in the chunk cache */ + if(shared_fo && shared_fo->cache.chunk.nslots > 0) { + hsize_t chunk_idx; /* Index of chunk cache entry */ + H5O_layout_t *layout = &shared_fo->layout; + + /* Calculate the index of this chunk */ + if(H5VM_chunk_index(layout->u.chunk.ndims - 1, chunk_rec->offset, + layout->u.chunk.dim, layout->u.chunk.down_chunks, &chunk_idx) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") + idx = H5D_CHUNK_HASH(shared_fo, chunk_idx); + + /* Get the chunk cache entry for that location */ + ent = shared_fo->cache.chunk.slot[idx]; + if(ent) { + /* Speculatively set the 'found' flag */ + udata->chunk_in_cache = TRUE; + + /* Verify that the cache entry is the correct chunk */ + for(u = 0; u < (layout->u.chunk.ndims -1); u++) + if(chunk_rec->offset[u] != ent->offset[u]) { + udata->chunk_in_cache = FALSE; + break; + } /* end if */ + } /* end if */ + } /* end if */ + + if(udata->chunk_in_cache) { + HDassert(H5F_addr_defined(chunk_rec->chunk_addr)); + HDassert(H5F_addr_defined(ent->chunk_addr)); + + H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t); + HDmemcpy(buf, ent->chunk, nbytes); + } else { + /* read chunk data from the source file */ + if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") + } + } /* Need to uncompress variable-length & reference data elements */ - if(has_filters && (is_vlen || fix_ref)) { + if(has_filters && (is_vlen || fix_ref) && !udata->chunk_in_cache) { unsigned filter_mask = chunk_rec->filter_mask; if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0) @@ -4906,7 +4952,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) udata_dst.addr = HADDR_UNDEF; /* Need to compress variable-length & reference data elements before writing to file */ - if(has_filters && (is_vlen || fix_ref) ) { + if(has_filters && (is_vlen || fix_ref || udata->chunk_in_cache) ) { if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 @@ -4971,6 +5017,7 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, uint32_t nelmts = 0; /* Number of elements in buffer */ hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */ hbool_t copy_setup_done = FALSE; /* Indicate that 'copy setup' is done */ + H5D_shared_t *shared_fo = (H5D_shared_t *)cpy_info->shared_fo; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -5157,11 +5204,39 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, udata.nelmts = nelmts; udata.pline = pline; udata.cpy_info = cpy_info; + udata.chunk_in_cache = FALSE; + udata.chunk = NULL; + + if(!H5F_addr_defined(idx_info_src.storage->idx_addr)) + idx_info_src.storage = &shared_fo->layout.storage.u.chunk; + + HDassert(H5F_addr_defined(idx_info_src.storage->idx_addr)); /* Iterate over chunks to copy data */ if((storage_src->ops->iterate)(&idx_info_src, H5D__chunk_copy_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data") + /* Iterate over the chunk cache to copy data for chunks with undefined address */ + if(shared_fo) { + H5D_rdcc_ent_t *ent, *next; + H5D_chunk_rec_t chunk_rec; + + chunk_rec.nbytes = layout_src->size; + chunk_rec.filter_mask = 0; + chunk_rec.chunk_addr = HADDR_UNDEF; + + for(ent = shared_fo->cache.chunk.head; ent; ent = next) { + if(!H5F_addr_defined(ent->chunk_addr)) { + HDmemcpy(chunk_rec.offset, ent->offset, sizeof(chunk_rec.offset)); + udata.chunk = ent->chunk; + udata.chunk_in_cache = TRUE; + if(H5D__chunk_copy_cb(&chunk_rec, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy chunk data in cache") + } + next = ent->next; + } /* end for */ + } + /* I/O buffers may have been re-allocated */ buf = udata.buf; bkg = udata.bkg; diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index b142f3b..4b61442 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -396,7 +396,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst, +H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_dst, H5O_storage_compact_t *storage_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, hid_t dxpl_id) { @@ -407,6 +407,8 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst void *bkg = NULL; /* Temporary buffer for copying data */ void *reclaim_buf = NULL; /* Buffer for reclaiming data */ hid_t buf_sid = -1; /* ID for buffer dataspace */ + H5D_shared_t *shared_fo = cpy_info->shared_fo; /* Pointer to the shared struct for dataset object */ + H5O_storage_compact_t *storage_src = _storage_src; /* Pointer to storage_src */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -418,6 +420,10 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst HDassert(storage_dst); HDassert(dt_src); + /* If the dataset is open in the file, point to "layout" in the shared struct */ + if(shared_fo != NULL) + storage_src = &(shared_fo->layout.storage.u.compact); + /* Allocate space for destination data */ if(NULL == (storage_dst->buf = H5MM_malloc(storage_src->size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate memory for compact dataset") diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index c6cef57..9516d53 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -1298,6 +1298,10 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, hsize_t buf_dim[1] = {0}; /* Dimension for buffer */ hbool_t is_vlen = FALSE; /* Flag to indicate that VL type conversion should occur */ hbool_t fix_ref = FALSE; /* Flag to indicate that ref values should be fixed */ + H5D_shared_t *shared_fo = cpy_info->shared_fo; /* Pointer to the shared struct for dataset object */ + hbool_t try_sieve = FALSE; /* Try to get data from the sieve buffer */ + haddr_t sieve_start = HADDR_UNDEF; /* Start location of sieve buffer */ + haddr_t sieve_end = HADDR_UNDEF; /* End locations of sieve buffer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -1418,9 +1422,32 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer") } /* end if */ - /* Loop over copying data */ addr_src = storage_src->addr; addr_dst = storage_dst->addr; + + /* If data sieving is enabled and the dataset is open in the file, + set up to copy data out of the sieve buffer if deemed possible later */ + if(H5F_HAS_FEATURE(f_src, H5FD_FEAT_DATA_SIEVE) && + shared_fo && shared_fo->cache.contig.sieve_buf) { + try_sieve = TRUE; + sieve_start = shared_fo->cache.contig.sieve_loc; + sieve_end = sieve_start + shared_fo->cache.contig.sieve_size; + /* + * It is possble for addr_src to be undefined when: + * (a) The dataset is created and data is written to it. + * (b) The dataset is then copied via H5Ocopy(). + * H5D_mark() in H5Dint.c is different between + * 1.8 and develop branches: + * 1.8--it just sets dataset->shared->layout_dirty as TRUE + * to be flushed later. + * develop--it will flush the layout message if it has been changed. + */ + if(!H5F_addr_defined(addr_src)) + addr_src = sieve_start; + } + + HDassert(H5F_addr_defined(addr_src)); + /* Loop over copying data */ while(total_src_nbytes > 0) { /* Check if we should reduce the number of bytes to transfer */ if(total_src_nbytes < src_nbytes) { @@ -1446,14 +1473,20 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, dst_nbytes = mem_nbytes = src_nbytes; } /* end if */ - /* Read raw data from source file */ - if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, src_nbytes, H5P_DATASET_XFER_DEFAULT, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data") + /* If the entire copy is within the sieve buffer, copy data from the sieve buffer */ + if(try_sieve && (addr_src >= sieve_start) && ((addr_src + src_nbytes -1) < sieve_end)) { + unsigned char *base_sieve_buf = shared_fo->cache.contig.sieve_buf + (addr_src - sieve_start); + + HDmemcpy(buf, base_sieve_buf, src_nbytes); + } else + /* Read raw data from source file */ + if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, src_nbytes, H5P_DATASET_XFER_DEFAULT, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data") /* Perform datatype conversion, if necessary */ if(is_vlen) { /* Convert from source file to memory */ - if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) + if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ @@ -1463,13 +1496,13 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, HDmemset(bkg, 0, buf_size); /* Convert from memory to destination file */ - if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) + if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Reclaim space from variable length data */ if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data") - } /* end if */ + } /* end if */ else if(fix_ref) { /* Check for expanding references */ if(cpy_info->expand_ref) { diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c index 9193a4c..31beb0e 100644 --- a/src/H5Ocopy.c +++ b/src/H5Ocopy.c @@ -357,24 +357,8 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out*/, if((obj_class = H5O_obj_class(oloc_src, dxpl_id)) == NULL) HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to determine object type") - /* Check if the object at the address is already open in the file */ - if(H5FO_opened(oloc_src->file, oloc_src->addr) != NULL) { - - H5G_loc_t tmp_loc; /* Location of object */ - H5O_loc_t tmp_oloc; /* Location of object */ - H5G_name_t tmp_path; /* Object's path */ - - tmp_loc.oloc = &tmp_oloc; - tmp_loc.path = &tmp_path; - tmp_oloc.file = oloc_src->file; - tmp_oloc.addr = oloc_src->addr; - tmp_oloc.holding_file = oloc_src->holding_file; - H5G_name_reset(tmp_loc.path); - - /* Flush the object of this class */ - if(obj_class->flush && obj_class->flush(&tmp_loc, dxpl_id) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object") - } + /* Set the pointer to the shared struct for the object if opened in the file */ + cpy_info->shared_fo = H5FO_opened(oloc_src->file, oloc_src->addr); /* Get source object header */ if(NULL == (oh_src = H5O_protect(oloc_src, dxpl_id, H5AC_READ))) diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 95d66ab..17385c2 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -592,6 +592,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, H5O_layout_t *layout_src = (H5O_layout_t *) mesg_src; H5O_layout_t *layout_dst = NULL; hbool_t copied = FALSE; /* Whether the data was copied */ + H5D_shared_t *shared_fo = (H5D_shared_t *)cpy_info->shared_fo; void *ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT @@ -628,7 +629,9 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, layout_dst->storage.u.contig.size = H5S_extent_nelem(udata->src_space_extent) * H5T_get_size(udata->src_dtype); - if(H5D__contig_is_space_alloc(&layout_src->storage)) { + if(H5D__contig_is_space_alloc(&layout_src->storage) || + (H5F_HAS_FEATURE(file_src, H5FD_FEAT_DATA_SIEVE) && + shared_fo && shared_fo->cache.contig.sieve_buf)) { /* copy contiguous raw data */ if(H5D__contig_copy(file_src, &layout_src->storage.u.contig, file_dst, &layout_dst->storage.u.contig, udata->src_dtype, cpy_info, dxpl_id) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy contiguous storage") @@ -637,7 +640,8 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, break; case H5D_CHUNKED: - if(H5D__chunk_is_space_alloc(&layout_src->storage)) { + if(H5D__chunk_is_space_alloc(&layout_src->storage) || + (shared_fo && H5D__chunk_is_space_alloc(&shared_fo->layout.storage))) { /* Create chunked layout */ if(H5D__chunk_copy(file_src, &layout_src->storage.u.chunk, &layout_src->u.chunk, file_dst, &layout_dst->storage.u.chunk, udata->src_space_extent, udata->src_dtype, udata->common.src_pline, cpy_info, dxpl_id) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage") diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 9b24977..ca0fc8e 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -169,6 +169,7 @@ typedef struct H5O_copy_t { H5SL_t *dst_dt_list; /* Skip list to hold committed datatypes in dest file */ hbool_t dst_dt_list_complete; /* Whether the destination datatype list is complete (i.e. not only populated with "suggestions" from H5Padd_merge_committed_dtype_path) */ H5O_t *oh_dst; /* The destination object header */ + void *shared_fo; /* The shared pointer for the object */ H5O_mcdt_search_cb_t mcdt_cb; /* The callback to invoke before searching the global list of committed datatypes at destination */ void *mcdt_ud; /* User data passed to callback */ } H5O_copy_t; diff --git a/src/H5public.h b/src/H5public.h index a479123..9fb864d 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -92,10 +92,10 @@ extern "C" { /* Version numbers */ #define H5_VERS_MAJOR 1 /* For major interface/format changes */ #define H5_VERS_MINOR 8 /* For minor interface/format changes */ -#define H5_VERS_RELEASE 19 /* For tweaks, bug-fixes, or development */ -#define H5_VERS_SUBRELEASE "" /* For pre-releases like snap0 */ +#define H5_VERS_RELEASE 20 /* For tweaks, bug-fixes, or development */ +#define H5_VERS_SUBRELEASE "snap2" /* For pre-releases like snap0 */ /* Empty string for real releases. */ -#define H5_VERS_INFO "HDF5 library version: 1.8.19" /* Full version string */ +#define H5_VERS_INFO "HDF5 library version: 1.8.20-snap2" /* Full version string */ #define H5check() H5check_version(H5_VERS_MAJOR,H5_VERS_MINOR, \ H5_VERS_RELEASE) diff --git a/src/Makefile.in b/src/Makefile.in index 33e4a08..9af0c2f 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -643,6 +643,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/test/Makefile.in b/test/Makefile.in index 473622e..d2de02d 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -967,6 +967,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/test/objcopy.c b/test/objcopy.c index 33f43d3..e679007 100644 --- a/test/objcopy.c +++ b/test/objcopy.c @@ -2179,6 +2179,9 @@ error: * Purpose: Create a simple dataset in SRC file and copy it to DST file * (Note: dataset has no data) * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -2188,7 +2191,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_simple_empty(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_simple_empty(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t sid = -1; /* Dataspace ID */ @@ -2197,7 +2200,11 @@ test_copy_dataset_simple_empty(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): empty contiguous dataset"); + if(test_open) { + TESTING("H5Ocopy(): empty and opened contiguous dataset"); + } else { + TESTING("H5Ocopy(): empty contiguous dataset"); + } /* Initialize the filenames */ h5_fixname(FILENAME[0], src_fapl, src_filename, sizeof src_filename); @@ -2225,15 +2232,18 @@ test_copy_dataset_simple_empty(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h /* attach attributes to the dataset */ if(test_copy_attach_attributes(did, H5T_NATIVE_INT) < 0) TEST_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) TEST_ERROR + if(!test_open) { - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -2244,8 +2254,10 @@ test_copy_dataset_simple_empty(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset for copy */ - if((did = H5Dopen2(fid_src, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset for copy */ + if((did = H5Dopen2(fid_src, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR @@ -3092,6 +3104,9 @@ error: * * Purpose: Create a compact dataset in SRC file and copy it to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -3101,7 +3116,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_compact(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_compact(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t sid = -1; /* Dataspace ID */ @@ -3113,7 +3128,11 @@ test_copy_dataset_compact(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): compact dataset"); + if(test_open) { + TESTING("H5Ocopy(): compact and opened dataset"); + } else { + TESTING("H5Ocopy(): compact dataset"); + } /* set initial data values */ for (i=0; i<DIM_SIZE_1; i++) @@ -3156,15 +3175,17 @@ test_copy_dataset_compact(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t /* attach attributes to the dataset */ if(test_copy_attach_attributes(did, H5T_NATIVE_INT) < 0) TEST_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) TEST_ERROR + if(!test_open) { + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -3175,8 +3196,10 @@ test_copy_dataset_compact(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_COMPACT, fid_dst, NAME_DATASET_COMPACT, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset for copy */ - if((did = H5Dopen2(fid_src, NAME_DATASET_COMPACT, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset for copy */ + if((did = H5Dopen2(fid_src, NAME_DATASET_COMPACT, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_COMPACT, H5P_DEFAULT)) < 0) TEST_ERROR @@ -3744,6 +3767,9 @@ error: * creates lots of object header chunks in SRC file and copy * datasets to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -3753,7 +3779,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_multi_ohdr_chunks(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_multi_ohdr_chunks(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t sid = -1; /* Dataspace ID */ @@ -3765,7 +3791,11 @@ test_copy_dataset_multi_ohdr_chunks(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fa char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): datasets that have multiple ohdr chunks"); + if(test_open) { + TESTING("H5Ocopy(): openend datasets that have multiple ohdr chunks"); + } else{ + TESTING("H5Ocopy(): datasets that have multiple ohdr chunks"); + } /* set initial data values */ for (i=0; i<DIM_SIZE_1; i++) @@ -3805,24 +3835,27 @@ test_copy_dataset_multi_ohdr_chunks(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fa /* Add attributes to datasets in a way that creates lots of chunks */ if(test_copy_attach_paired_attributes(did, did2, H5T_NATIVE_INT) < 0) TEST_ERROR + /* close dataspace */ + if(H5Sclose(sid) < 0) TEST_ERROR + /* close the first dataset */ if(H5Dclose(did) < 0) TEST_ERROR - /* close the second dataset */ - if(H5Dclose(did2) < 0) TEST_ERROR + if(!test_open) { - /* close dataspace */ - if(H5Sclose(sid) < 0) TEST_ERROR + /* close the second dataset */ + if(H5Dclose(did2) < 0) TEST_ERROR - /* close group */ - if(H5Gclose(gid) < 0) TEST_ERROR + /* close group */ + if(H5Gclose(gid) < 0) TEST_ERROR - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -3833,8 +3866,14 @@ test_copy_dataset_multi_ohdr_chunks(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fa /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_GROUP_TOP, fid_dst, NAME_GROUP_TOP, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the group for copy */ - if((gid = H5Gopen2(fid_src, NAME_GROUP_TOP, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR + if(test_open) { + + /* close the second dataset */ + if(H5Dclose(did2) < 0) TEST_ERROR + + } else + /* open the group for copy */ + if((gid = H5Gopen2(fid_src, NAME_GROUP_TOP, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR /* open the destination group */ if((gid2 = H5Gopen2(fid_dst, NAME_GROUP_TOP, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR @@ -5999,6 +6038,9 @@ error: * Purpose: Create a soft link in SRC file and copy it to DST file * copy a datast pointed by a soft link to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -6008,7 +6050,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_soft_link(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_soft_link(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t sid = -1; /* Dataspace ID */ @@ -6020,7 +6062,11 @@ test_copy_soft_link(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fa char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): object through soft link"); + if(test_open) { + TESTING("H5Ocopy(): opened object through soft link"); + } else { + TESTING("H5Ocopy(): object through soft link"); + } /* set initial data values */ for (i=0; i<DIM_SIZE_1; i++) @@ -6057,21 +6103,22 @@ test_copy_soft_link(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fa /* close dataspace */ if(H5Sclose(sid) < 0) FAIL_STACK_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) FAIL_STACK_ERROR + /* close the group */ + if(H5Gclose(gid) < 0) FAIL_STACK_ERROR /* make a soft link to the dataset */ if(H5Lcreate_soft(NAME_LINK_DATASET, fid_src, NAME_LINK_SOFT, H5P_DEFAULT, H5P_DEFAULT) < 0) FAIL_STACK_ERROR - /* close the group */ - if(H5Gclose(gid) < 0) FAIL_STACK_ERROR - - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) FAIL_STACK_ERROR + if(!test_open) { + /* close the dataset */ + if(H5Dclose(did) < 0) FAIL_STACK_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) FAIL_STACK_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -6082,8 +6129,10 @@ test_copy_soft_link(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fa /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_LINK_SOFT, fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset through the soft link for copy */ - if((did = H5Dopen2(fid_src, NAME_LINK_SOFT, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset through the soft link for copy */ + if((did = H5Dopen2(fid_src, NAME_LINK_SOFT, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR @@ -6572,9 +6621,12 @@ error: * Purpose: Copy dataset that uses the "old" layout version (pre version 3) * format. * - * Note: This test uses the "fill_old.h5" file for convenience, since it + * Note: This test uses the "fill_old.h5" file for convenience, since it * has a dataset with the old layout format. * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -6584,7 +6636,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_old_layout(hid_t fcpl_dst, hid_t fapl) +test_copy_old_layout(hid_t fcpl_dst, hid_t fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t did = -1, did2 = -1; /* Dataset IDs */ @@ -6592,7 +6644,11 @@ test_copy_old_layout(hid_t fcpl_dst, hid_t fapl) char src_filename[NAME_BUF_SIZE] = ""; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): dataset with old layout format"); + if(test_open) { + TESTING("H5Ocopy(): opened dataset with old layout format"); + } else { + TESTING("H5Ocopy(): dataset with old layout format"); + } /* Generate correct name for source file by prepending the source path */ if(srcdir && ((HDstrlen(srcdir) + HDstrlen(FILE_OLD_LAYOUT) + 1) < sizeof(src_filename))) { @@ -6616,11 +6672,18 @@ test_copy_old_layout(hid_t fcpl_dst, hid_t fapl) /* Create an uncopied object in destination file so that addresses in source and destination files aren't the same */ if(H5Gclose(H5Gcreate2(fid_dst, NAME_GROUP_UNCOPIED, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR + if(test_open) { + /* open the source dataset */ + if((did = H5Dopen2(fid_src, NAME_OLD_FORMAT, H5P_DEFAULT)) < 0) TEST_ERROR + } + /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_OLD_FORMAT, fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the source dataset */ - if((did = H5Dopen2(fid_src, NAME_OLD_FORMAT, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the source dataset */ + if((did = H5Dopen2(fid_src, NAME_OLD_FORMAT, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR @@ -6947,6 +7010,9 @@ error: * Purpose: Create a dataset that uses a named variable length datatype * in SRC file and copy it to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -6956,7 +7022,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_chunked_named_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_chunked_named_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t tid = -1, tid_copy=-1; /* Datatype ID */ @@ -6970,7 +7036,11 @@ test_copy_dataset_chunked_named_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): chunked dataset with named VLEN datatype"); + if(test_open) { + TESTING("H5Ocopy(): chunked and opened dataset with named VLEN datatype"); + } else { + TESTING("H5Ocopy(): chunked dataset with named VLEN datatype"); + } /* set initial data values */ for(i = 0; i < DIM_SIZE_1; i++) { @@ -7021,15 +7091,18 @@ test_copy_dataset_chunked_named_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap /* close the datatype */ if(H5Tclose(tid) < 0) TEST_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) TEST_ERROR + if(!test_open) { - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -7040,8 +7113,10 @@ test_copy_dataset_chunked_named_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_VL, fid_dst, NAME_DATASET_VL, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset for copy */ - if((did = H5Dopen2(fid_src, NAME_DATASET_VL, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset for copy */ + if((did = H5Dopen2(fid_src, NAME_DATASET_VL, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_VL, H5P_DEFAULT)) < 0) TEST_ERROR @@ -7401,6 +7476,9 @@ error: * Purpose: Create a compact dataset w/nested VLEN datatype * in SRC file and copy it to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -7410,7 +7488,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_contig_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_contig_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t tid=-1, tid2=-1; /* Datatype ID */ @@ -7424,7 +7502,11 @@ test_copy_dataset_contig_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): contigous dataset with nested VLEN datatype"); + if(test_open) { + TESTING("H5Ocopy(): contigous and opened dataset with nested VLEN datatype"); + } else { + TESTING("H5Ocopy(): contigous dataset with nested VLEN datatype"); + } /* set initial data values */ for(i=0; i<DIM_SIZE_1; i++) { @@ -7481,15 +7563,17 @@ test_copy_dataset_contig_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h /* close compact plist */ if(H5Pclose(pid) < 0) TEST_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) TEST_ERROR + if(!test_open) { + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -7500,8 +7584,10 @@ test_copy_dataset_contig_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_VL_VL, fid_dst, NAME_DATASET_VL_VL, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset for copy */ - if((did = H5Dopen2(fid_src, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset for copy */ + if((did = H5Dopen2(fid_src, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR @@ -7711,6 +7797,9 @@ error: * Purpose: Create a dataset that uses a named variable length datatype * in SRC file and copy it to DST file * + * Note: The parameter "test_open" is added to test for H5Ocopy when + * the dataset is open in the file (HDFFV-7853). + * * Return: Success: 0 * Failure: number of errors * @@ -7720,7 +7809,7 @@ error: *------------------------------------------------------------------------- */ static int -test_copy_dataset_compressed_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +test_copy_dataset_compressed_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl, hbool_t test_open) { hid_t fid_src = -1, fid_dst = -1; /* File IDs */ hid_t tid = -1, tid2=-1; /* Datatype ID */ @@ -7735,7 +7824,11 @@ test_copy_dataset_compressed_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap char src_filename[NAME_BUF_SIZE]; char dst_filename[NAME_BUF_SIZE]; - TESTING("H5Ocopy(): compressed dataset with nested VLEN datatype"); + if(test_open) { + TESTING("H5Ocopy(): compressed and opened dataset with nested VLEN datatype"); + } else { + TESTING("H5Ocopy(): compressed dataset with nested VLEN datatype"); + } /* set initial data values */ for(i=0; i<DIM_SIZE_1; i++) { @@ -7793,15 +7886,17 @@ test_copy_dataset_compressed_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap /* close compact plist */ if(H5Pclose(pid) < 0) TEST_ERROR - /* close the dataset */ - if(H5Dclose(did) < 0) TEST_ERROR + if(!test_open) { + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR - /* close the SRC file */ - if(H5Fclose(fid_src) < 0) TEST_ERROR + /* close the SRC file */ + if(H5Fclose(fid_src) < 0) TEST_ERROR - /* open the source file with read-only */ - if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + /* open the source file with read-only */ + if((fid_src = H5Fopen(src_filename, H5F_ACC_RDONLY, src_fapl)) < 0) TEST_ERROR + } /* create destination file */ if((fid_dst = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) TEST_ERROR @@ -7811,8 +7906,10 @@ test_copy_dataset_compressed_vl_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fap /* copy the dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_VL_VL, fid_dst, NAME_DATASET_VL_VL, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the dataset for copy */ - if((did = H5Dopen2(fid_src, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR + if(!test_open) { + /* open the dataset for copy */ + if((did = H5Dopen2(fid_src, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR + } /* open the destination dataset */ if((did2 = H5Dopen2(fid_dst, NAME_DATASET_VL_VL, H5P_DEFAULT)) < 0) TEST_ERROR @@ -8464,6 +8561,188 @@ error: /*------------------------------------------------------------------------- + * Function: test_copy_null_ref_open + * + * Purpose: Creates 2 datasets with references, one with object and + * the other with region references. Copies these datasets + * to a new file without expanding references, causing them + * to become NULL. Next, copies these references to a third + * file with expanding references, to verify that NULL + * references are handled correctly. + * + * Note: this is copied from test_copy_null_ref() with modifications + * to test for opened datasets in the files. + * + * Return: Success: 0 + * Failure: number of errors + * + * Programmer: Neil Fortner + * Wednesday, March 31, 2010 + * + *------------------------------------------------------------------------- + */ +static int +test_copy_null_ref_open(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst_fapl) +{ + hid_t fid1 = -1, fid2 = -1, fid3 = -1; /* File IDs */ + hid_t sid = -1; /* Dataspace ID */ + hid_t pid = -1; /* Object copy property list ID */ + hid_t did1 = -1, did2 = -1; /* Dataset IDs */ + hid_t did3 = -1, did4 = -1; /* Dataset IDs */ + hid_t did5 = -1, did6 = -1; /* Dataset IDs */ + hid_t dcpl = -1; /* Dataset creation property list */ + hsize_t chunk_dim1d[1] = {2}; /* Chunk dimensions */ + hsize_t dim1d[1] = {3}; /* Dataset dimensions */ + hobj_ref_t obj_buf[3]; /* Buffer for object refs */ + hdset_reg_ref_t reg_buf[3]; /* Buffer for region refs */ + char zeros[MAX(sizeof(obj_buf),sizeof(reg_buf))]; /* Array of zeros, for memcmp */ + char src_filename[NAME_BUF_SIZE]; + char mid_filename[NAME_BUF_SIZE]; + char dst_filename[NAME_BUF_SIZE]; + + TESTING("H5Ocopy(): NULL references for opened datasets"); + + /* Initialize "zeros" array */ + HDmemset(zeros, 0, sizeof(zeros)); + + /* Initialize the filenames */ + h5_fixname(FILENAME[0], src_fapl, src_filename, sizeof src_filename); + h5_fixname(FILENAME[1], src_fapl, mid_filename, sizeof mid_filename); + h5_fixname(FILENAME[2], dst_fapl, dst_filename, sizeof dst_filename); + + /* Reset file address checking info */ + addr_reset(); + + /* Create source file */ + if((fid1 = H5Fcreate(src_filename, H5F_ACC_TRUNC, fcpl_src, src_fapl)) < 0) + TEST_ERROR + + /* Create dataspace */ + if((sid = H5Screate_simple(1, dim1d, NULL)) < 0) TEST_ERROR + + /* create and set chunk plist */ + if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR + if(H5Pset_chunk(dcpl, 1, chunk_dim1d) < 0) TEST_ERROR + if(H5Pset_deflate(dcpl, 9) < 0) TEST_ERROR + + /* Create object reference dataset at SRC file */ + if((did1 = H5Dcreate2(fid1, "obj_ref_dset", H5T_STD_REF_OBJ, sid, + H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR + + /* Create region reference dataset at SRC file */ + if((did2 = H5Dcreate2(fid1, "reg_ref_dset", H5T_STD_REF_DSETREG, + sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR + + /* Create references */ + if(H5Rcreate(&obj_buf[0], did1, ".", H5R_OBJECT, (hid_t)-1) < 0) TEST_ERROR + if(H5Rcreate(&obj_buf[1], did2, ".", H5R_OBJECT, (hid_t)-1) < 0) TEST_ERROR + if(H5Rcreate(®_buf[0], did1, ".", H5R_DATASET_REGION, sid) < 0) + TEST_ERROR + if(H5Rcreate(®_buf[1], did2, ".", H5R_DATASET_REGION, sid) < 0) + TEST_ERROR + + /* Write data into file */ + if(H5Dwrite(did1, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf) + < 0) TEST_ERROR + if(H5Dwrite(did2, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, + reg_buf) < 0) TEST_ERROR + + + /* Create middle file */ + if((fid2 = H5Fcreate(mid_filename, H5F_ACC_TRUNC, fcpl_src, src_fapl)) < 0) + TEST_ERROR + + /* Copy the source file to the middle file. Note the expand references + * flag is not set. */ + if(H5Ocopy(fid1, "/", fid2, "/A", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + + /* Close datasets in source file */ + if(H5Dclose(did1) < 0) TEST_ERROR + if(H5Dclose(did2) < 0) TEST_ERROR + + /* Close source file */ + if(H5Fclose(fid1) < 0) TEST_ERROR + + /* Open copied datasets */ + if((did3 = H5Dopen2(fid2, "/A/obj_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR + if((did4 = H5Dopen2(fid2, "/A/reg_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR + + /* Read copied datasets */ + if(H5Dread(did3, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf) + < 0) TEST_ERROR + if(H5Dread(did4, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, + reg_buf) < 0) TEST_ERROR + + /* Verify that the references contain only "0" bytes */ + if(HDmemcmp(obj_buf, zeros, sizeof(obj_buf))) TEST_ERROR + if(HDmemcmp(reg_buf, zeros, sizeof(reg_buf))) TEST_ERROR + + /* Create destination file */ + if((fid3 = H5Fcreate(dst_filename, H5F_ACC_TRUNC, fcpl_dst, dst_fapl)) < 0) + TEST_ERROR + + /* Create object copy property list */ + if((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) TEST_ERROR + + /* Set the "expand references" flag */ + if(H5Pset_copy_object(pid, H5O_COPY_EXPAND_REFERENCE_FLAG) < 0) TEST_ERROR + + /* Copy the middle file to the destination file. Note the expand references + * flag *is* set, even though the references are now NULL. */ + if(H5Ocopy(fid2, "/", fid3, "/AA", pid, H5P_DEFAULT) < 0) TEST_ERROR + + /* Close datasets in middle file */ + if(H5Dclose(did3) < 0) TEST_ERROR + if(H5Dclose(did4) < 0) TEST_ERROR + + /* Close the middle file */ + if(H5Fclose(fid2) < 0) TEST_ERROR + + /* Open copied datasets */ + if((did5 = H5Dopen2(fid3, "/AA/A/obj_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR + if((did6 = H5Dopen2(fid3, "/AA/A/reg_ref_dset", H5P_DEFAULT)) < 0) TEST_ERROR + + /* Read copied datasets */ + if(H5Dread(did5, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_buf) + < 0) TEST_ERROR + if(H5Dread(did6, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, + reg_buf) < 0) TEST_ERROR + + /* Verify that the references contain only "0" bytes */ + if(HDmemcmp(obj_buf, zeros, sizeof(obj_buf))) TEST_ERROR + if(HDmemcmp(reg_buf, zeros, sizeof(reg_buf))) TEST_ERROR + + /* Close */ + if(H5Pclose(pid) < 0) TEST_ERROR + if(H5Pclose(dcpl) < 0) TEST_ERROR + if(H5Dclose(did5) < 0) TEST_ERROR + if(H5Dclose(did6) < 0) TEST_ERROR + if(H5Fclose(fid3) < 0) TEST_ERROR + if(H5Sclose(sid) < 0) TEST_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Pclose(pid); + H5Pclose(dcpl); + H5Sclose(sid); + H5Dclose(did1); + H5Dclose(did2); + H5Dclose(did3); + H5Dclose(did4); + H5Dclose(did5); + H5Dclose(did6); + H5Fclose(fid1); + H5Fclose(fid2); + H5Fclose(fid3); + } H5E_END_TRY; + return 1; +} /* end test_copy_null_ref_open */ + + +/*------------------------------------------------------------------------- * Function: test_copy_attr_crt_order * * Purpose: Tests copying attributes with creation order tracked, with @@ -12189,9 +12468,12 @@ test_copy_dataset_open(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst hid_t sid = -1; /* Dataspace ID */ hid_t tid = -1; /* Datatype ID */ hid_t did = -1, did2 = -1; /* Dataset IDs */ + hid_t did3 = -1, did4 = -1; /* Dataset IDs */ hid_t gid = -1, gid2 = -1; /* Group IDs */ int buf[DIM_SIZE_1][DIM_SIZE_2]; /* Buffer for writing data */ - int newbuf[DIM_SIZE_1][DIM_SIZE_2]; /* Buffer for writing data */ + int newbuf[DIM_SIZE_1][DIM_SIZE_2]; /* Buffer for writing data */ + hid_t pid = -1; /* Dataset creation property list */ + hsize_t chunk_dim2d[2] ={CHUNK_SIZE_1, CHUNK_SIZE_2}; /* Chunk dimension sizes */ hsize_t dim2d[2]; /* Dataset dimensions */ int i, j; /* local index variables */ char src_filename[NAME_BUF_SIZE]; @@ -12232,14 +12514,23 @@ test_copy_dataset_open(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst /* create 2D dataspace */ if((sid = H5Screate_simple(2, dim2d, NULL)) < 0) TEST_ERROR - /* create 2D int dataset in SRC file */ + /* create and set chunk plist */ + if((pid = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR + if(H5Pset_chunk(pid, 2, chunk_dim2d) < 0) TEST_ERROR + + /* create 2D dataset in SRC file */ if((did = H5Dcreate2(fid_src, NAME_DATASET_SIMPLE, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR + /* create 2D chunked dataset in SRC file */ + if((did2 = H5Dcreate2(fid_src, NAME_DATASET_CHUNKED, H5T_NATIVE_INT, sid, H5P_DEFAULT, pid, H5P_DEFAULT)) < 0) TEST_ERROR + /* write data to the dataset */ if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) TEST_ERROR + if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) TEST_ERROR /* attach attributes to the dataset */ if(test_copy_attach_attributes(did, H5T_NATIVE_INT) < 0) TEST_ERROR + if(test_copy_attach_attributes(did2, H5T_NATIVE_INT) < 0) TEST_ERROR /* * Test case 1 @@ -12250,74 +12541,94 @@ test_copy_dataset_open(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid_t dst */ /* copy the opened dataset to another location in SRC file */ if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_src, NAME_DATASET_SIMPLE2, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_CHUNKED, fid_src, NAME_DATASET_CHUNKED2, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR - /* open the copied dataset */ - if((did2 = H5Dopen2(fid_src, NAME_DATASET_SIMPLE2, H5P_DEFAULT)) < 0) TEST_ERROR + /* open the copied datasets */ + if((did3 = H5Dopen2(fid_src, NAME_DATASET_SIMPLE2, H5P_DEFAULT)) < 0) TEST_ERROR + if((did4 = H5Dopen2(fid_src, NAME_DATASET_CHUNKED2, H5P_DEFAULT)) < 0) TEST_ERROR /* Check if the datasets are equal */ - if(compare_datasets(did, did2, H5P_DEFAULT, buf) != TRUE) TEST_ERROR + if(compare_datasets(did, did3, H5P_DEFAULT, buf) != TRUE) TEST_ERROR + if(compare_datasets(did2, did4, H5P_DEFAULT, buf) != TRUE) TEST_ERROR /* close the copied dataset */ - if(H5Dclose(did2) < 0) TEST_ERROR + if(H5Dclose(did3) < 0) TEST_ERROR + if(H5Dclose(did4) < 0) TEST_ERROR /* * Copy to another file */ /* copy the opened dataset from SRC to DST */ if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_CHUNKED, fid_dst, NAME_DATASET_CHUNKED, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR /* open the copied dataset in DST file */ - if((did2 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + if((did3 = H5Dopen2(fid_dst, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + if((did4 = H5Dopen2(fid_dst, NAME_DATASET_CHUNKED, H5P_DEFAULT)) < 0) TEST_ERROR /* Check if the datasets are equal */ - if(compare_datasets(did, did2, H5P_DEFAULT, buf) != TRUE) TEST_ERROR + if(compare_datasets(did, did3, H5P_DEFAULT, buf) != TRUE) TEST_ERROR + if(compare_datasets(did2, did4, H5P_DEFAULT, buf) != TRUE) TEST_ERROR /* close the copied dataset in DST file */ - if(H5Dclose(did2) < 0) TEST_ERROR + if(H5Dclose(did3) < 0) TEST_ERROR + if(H5Dclose(did4) < 0) TEST_ERROR /* close the dataset in SRC file */ if(H5Dclose(did) < 0) TEST_ERROR + if(H5Dclose(did2) < 0) TEST_ERROR /* * Test case 2 */ /* reopen the dataset in SRC file */ if((did = H5Dopen2(fid_src, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + if((did2 = H5Dopen2(fid_src, NAME_DATASET_CHUNKED, H5P_DEFAULT)) < 0) TEST_ERROR /* write another set of data to the dataset */ if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, newbuf) < 0) TEST_ERROR + if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, newbuf) < 0) TEST_ERROR /* * Copy within the same file */ /* copy the opened dataset to another location in SRC file */ - if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_src, "NEW_DATASET", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_src, "NEW_DATASET_SIMPLE", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_CHUNKED, fid_src, "NEW_DATASET_CHUNKED", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR /* open the copied dataset */ - if((did2 = H5Dopen2(fid_src, "NEW_DATASET", H5P_DEFAULT)) < 0) TEST_ERROR + if((did3 = H5Dopen2(fid_src, "NEW_DATASET_SIMPLE", H5P_DEFAULT)) < 0) TEST_ERROR + if((did4 = H5Dopen2(fid_src, "NEW_DATASET_CHUNKED", H5P_DEFAULT)) < 0) TEST_ERROR /* Check if the datasets are equal */ - if(compare_datasets(did, did2, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR + if(compare_datasets(did, did3, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR + if(compare_datasets(did2, did4, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR /* close the copied dataset in SRC file */ - if(H5Dclose(did2) < 0) TEST_ERROR + if(H5Dclose(did3) < 0) TEST_ERROR + if(H5Dclose(did4) < 0) TEST_ERROR /* * Copy to another file */ /* copy the opened dataset from SRC to DST */ - if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_dst, "NEW_DATASET", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_SIMPLE, fid_dst, "NEW_DATASET_SIMPLE", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + if(H5Ocopy(fid_src, NAME_DATASET_CHUNKED, fid_dst, "NEW_DATASET_CHUNKED", H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR /* open the copied dataset in DST file */ - if((did2 = H5Dopen2(fid_dst, "NEW_DATASET", H5P_DEFAULT)) < 0) TEST_ERROR + if((did3 = H5Dopen2(fid_dst, "NEW_DATASET_SIMPLE", H5P_DEFAULT)) < 0) TEST_ERROR + if((did4 = H5Dopen2(fid_dst, "NEW_DATASET_CHUNKED", H5P_DEFAULT)) < 0) TEST_ERROR /* Check if the datasets are equal */ - if(compare_datasets(did, did2, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR + if(compare_datasets(did, did3, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR + if(compare_datasets(did2, did4, H5P_DEFAULT, newbuf) != TRUE) TEST_ERROR /* close the copied dataset in DST file */ - if(H5Dclose(did2) < 0) TEST_ERROR + if(H5Dclose(did3) < 0) TEST_ERROR + if(H5Dclose(did4) < 0) TEST_ERROR /* close the dataset at SRC file */ if(H5Dclose(did) < 0) TEST_ERROR + if(H5Dclose(did2) < 0) TEST_ERROR /* * Test case 3 @@ -12576,14 +12887,25 @@ main(void) /* The tests... */ nerrors += test_copy_dataset_simple(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_simple_samefile(fcpl_src, src_fapl); - nerrors += test_copy_dataset_simple_empty(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_simple_empty(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_simple_empty(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_dataset_compound(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_chunked(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_chunked_empty(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_chunked_sparse(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compressed(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_dataset_compact(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_dataset_multi_ohdr_chunks(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_compact(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_compact(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_multi_ohdr_chunks(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_multi_ohdr_chunks(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_dataset_attr_named_dtype(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_group_empty(fcpl_src, fcpl_dst, src_fapl, dst_fapl); @@ -12593,7 +12915,11 @@ main(void) nerrors += test_copy_group_loop(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_group_wide_loop(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_group_links(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_soft_link(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_soft_link(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_soft_link(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_ext_link(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_exist(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_path(fcpl_src, fcpl_dst, src_fapl, dst_fapl); @@ -12673,19 +12999,39 @@ main(void) nerrors += test_copy_attribute_compound_vlstr(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compact_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_contig_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_dataset_compressed_named_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compact_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_dataset_contig_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_contig_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_contig_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_dataset_chunked_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); - nerrors += test_copy_dataset_compressed_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_dataset_compressed_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, FALSE); + nerrors += test_copy_dataset_compressed_vl_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl, TRUE); + nerrors += test_copy_dataset_contig_cmpd_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_chunked_cmpd_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_dataset_compact_cmpd_vl(fcpl_src, fcpl_dst, src_fapl, dst_fapl); nerrors += test_copy_same_file_named_datatype(fcpl_src, src_fapl); - nerrors += test_copy_old_layout(fcpl_dst, dst_fapl); + + /* Test with dataset opened in the file or not */ + nerrors += test_copy_old_layout(fcpl_dst, dst_fapl, FALSE); + nerrors += test_copy_old_layout(fcpl_dst, dst_fapl, TRUE); + + /* Test with dataset opened in the file or not */ nerrors += test_copy_null_ref(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + nerrors += test_copy_null_ref_open(fcpl_src, fcpl_dst, src_fapl, dst_fapl); + nerrors += test_copy_iterate(fcpl_src, fcpl_dst, src_fapl, dst_fapl); } diff --git a/test/plugin.c b/test/plugin.c index b662476..0de8839 100644 --- a/test/plugin.c +++ b/test/plugin.c @@ -731,7 +731,10 @@ test_filter_path_apis(void) if(H5Zfilter_avail(H5Z_FILTER_DYNLIB1) != TRUE) TEST_ERROR + TESTING(" initialize"); H5PLsize(&ndx); + if(ndx!=2) TEST_ERROR + PASSED(); TESTING(" remove"); /* Remove all existing paths*/ diff --git a/testpar/Makefile.in b/testpar/Makefile.in index b23d704..6d17ef2 100644 --- a/testpar/Makefile.in +++ b/testpar/Makefile.in @@ -616,6 +616,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/Makefile.in b/tools/Makefile.in index 15a6547..d5b5ef8 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -584,6 +584,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5copy/Makefile.in b/tools/h5copy/Makefile.in index 5f93ffc..981c7a2 100644 --- a/tools/h5copy/Makefile.in +++ b/tools/h5copy/Makefile.in @@ -591,6 +591,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5diff/CMakeTests.cmake b/tools/h5diff/CMakeTests.cmake index 7f6f8c3..aa620ef 100644 --- a/tools/h5diff/CMakeTests.cmake +++ b/tools/h5diff/CMakeTests.cmake @@ -66,6 +66,8 @@ ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/tudfilter2.h5 ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/diff_strings1.h5 ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/diff_strings2.h5 + # tools/testfiles + ${HDF5_TOOLS_DIR}/testfiles/tvlstr.h5 ) set (LIST_OTHER_TEST_FILES @@ -251,6 +253,7 @@ ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_90.txt ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_ud.txt ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_udfail.txt + ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_vlstr.txt ) set (LIST_WIN_TEST_FILES @@ -276,6 +279,11 @@ HDFTEST_COPY_FILE("${h5_tstfiles}" "${PROJECT_BINARY_DIR}/PAR/testfiles/${fname}" "h5diff_files") endif () endforeach () + # copy second version of tvlstr.h5 + HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tvlstr.h5" "${PROJECT_BINARY_DIR}/testfiles/tvlstr2.h5" "h5diff_files") + if (H5_HAVE_PARALLEL) + HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tvlstr.h5" "${PROJECT_BINARY_DIR}/PAR/testfiles/tvlstr2.h5" "h5diff_files") + endif () # @@ -839,6 +847,8 @@ h5diff_801.out.err h5diff_90.out h5diff_90.out.err + h5diff_vlstr.out + h5diff_vlstr.out.err ) set_tests_properties (H5DIFF-clearall-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles") if (NOT "${last_test}" STREQUAL "") @@ -1403,6 +1413,7 @@ ADD_H5_TEST (h5diff_487 1 -v --exclude-path "/group1/dset" h5diff_exclude3-1.h5 # # diff various multiple vlen and fixed strings in a compound type dataset # ############################################################################## ADD_H5_TEST (h5diff_530 0 -v ${COMP_VL_STRS_FILE} ${COMP_VL_STRS_FILE} /group /group_copy) +ADD_H5_TEST (h5diff_vlstr 0 -v tvlstr.h5 tvlstr2.h5) # ############################################################################## # # Test container types (array,vlen) with multiple nested compound types diff --git a/tools/h5diff/Makefile.in b/tools/h5diff/Makefile.in index 5371541..5f44cfd 100644 --- a/tools/h5diff/Makefile.in +++ b/tools/h5diff/Makefile.in @@ -611,6 +611,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5diff/testfiles/h5diff_vlstr.txt b/tools/h5diff/testfiles/h5diff_vlstr.txt new file mode 100644 index 0000000..67141f1 --- /dev/null +++ b/tools/h5diff/testfiles/h5diff_vlstr.txt @@ -0,0 +1,16 @@ + +file1 file2 +--------------------------------------- + x x / + x x /Dataset1 + x x /vl_string_type + +group : </> and </> +0 differences found +attribute: <test_scalar of </>> and <test_scalar of </>> +0 differences found +dataset: </Dataset1> and </Dataset1> +0 differences found +datatype: </vl_string_type> and </vl_string_type> +0 differences found +EXIT CODE: 0 diff --git a/tools/h5diff/testh5diff.sh.in b/tools/h5diff/testh5diff.sh.in index 45a7a45..ff370a9 100644 --- a/tools/h5diff/testh5diff.sh.in +++ b/tools/h5diff/testh5diff.sh.in @@ -120,6 +120,7 @@ $SRC_H5DIFF_TESTFILES/non_comparables1.h5 $SRC_H5DIFF_TESTFILES/non_comparables2.h5 $SRC_H5DIFF_TESTFILES/diff_strings1.h5 $SRC_H5DIFF_TESTFILES/diff_strings2.h5 +$SRC_TOOLS_TESTFILES/tvlstr.h5 " LIST_OTHER_TEST_FILES=" @@ -308,6 +309,7 @@ $SRC_H5DIFF_TESTFILES/h5diff_80.txt $SRC_H5DIFF_TESTFILES/h5diff_90.txt $SRC_H5DIFF_TESTFILES/h5diff_tmp1.txt $SRC_H5DIFF_TESTFILES/h5diff_tmp2.txt +$SRC_H5DIFF_TESTFILES/h5diff_vlstr.txt $SRC_H5DIFF_TESTFILES/tmptest.he5 $SRC_H5DIFF_TESTFILES/tmptest2.he5 $SRC_H5DIFF_TESTFILES/tmpSingleSiteBethe.reference.h5 @@ -522,6 +524,8 @@ SKIP() { ############################################################################## # prepare for test COPY_TESTFILES_TO_TESTDIR +# second copy of tvlstr.h5 +$CP -f $SRC_TOOLS_TESTFILES/tvlstr.h5 $TESTDIR/tvlstr2.h5 # ############################################################################ # # Common usage @@ -1097,6 +1101,7 @@ TOOLTEST h5diff_487.txt -v --exclude-path "/group1/dset" h5diff_exclude3-1.h5 h5 # # diff various multiple vlen and fixed strings in a compound type dataset # ############################################################################## TOOLTEST h5diff_530.txt -v h5diff_comp_vl_strs.h5 h5diff_comp_vl_strs.h5 /group /group_copy +TOOLTEST h5diff_vlstr.txt -v tvlstr.h5 tvlstr2.h5 # ############################################################################## # # Test container types (array,vlen) with multiple nested compound types diff --git a/tools/h5dump/CMakeTests.cmake b/tools/h5dump/CMakeTests.cmake index 0978265..d930edd 100644 --- a/tools/h5dump/CMakeTests.cmake +++ b/tools/h5dump/CMakeTests.cmake @@ -103,6 +103,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup-1.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup-2.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrp_comments.ddl + ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrpnullspace.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink-1.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink-2.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink-3.ddl @@ -270,6 +271,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tfvalues.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrp_comments.h5 + ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrpnullspace.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/thyperslab.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tints4dims.h5 @@ -883,6 +885,8 @@ tgroup-2.out.err tgrp_comments.out tgrp_comments.out.err + tgrpnullspace.out + tgrpnullspace.out.err thlink-1.out thlink-1.out.err thlink-2.out @@ -1389,6 +1393,7 @@ # test for displaying dataset and attribute of null space ADD_H5_TEST (tnullspace 0 --enable-error-stack tnullspace.h5) + ADD_H5_TEST (tgrpnullspace 0 -p --enable-error-stack tgrpnullspace.h5) # test for displaying dataset and attribute of space with 0 dimension size ADD_H5_TEST (zerodim 0 --enable-error-stack zerodim.h5) diff --git a/tools/h5dump/CMakeTestsXML.cmake b/tools/h5dump/CMakeTestsXML.cmake index 49adc6f..9a3b511 100644 --- a/tools/h5dump/CMakeTestsXML.cmake +++ b/tools/h5dump/CMakeTestsXML.cmake @@ -50,8 +50,10 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tname-quot.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tname-sp.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tnamed_dtype_attr.h5 + ${HDF5_TOOLS_SRC_DIR}/testfiles/test35.nc ${HDF5_TOOLS_SRC_DIR}/testfiles/tnestedcomp.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tnodata.h5 + ${HDF5_TOOLS_SRC_DIR}/testfiles/tnullspace.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tobjref.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/topaque.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/torderattr.h5 @@ -99,6 +101,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tempty-ns.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tempty-ns-2.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tenum.h5.xml + ${HDF5_TOOLS_SRC_DIR}/testfiles/test35.nc.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/textlink.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tfpformat.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup.h5.xml @@ -115,6 +118,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tname-sp.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tnestedcomp.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tnodata.h5.xml + ${HDF5_TOOLS_SRC_DIR}/testfiles/tnullspace.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/tobjref.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/topaque.h5.xml ${HDF5_TOOLS_SRC_DIR}/testfiles/torderattr1.h5.xml @@ -258,6 +262,8 @@ tempty.h5.out.err tenum.h5.out tenum.h5.out.err + test35.nc.out + test35.nc.out.err textlink.h5.out textlink.h5.out.err tfpformat.h5.out @@ -292,6 +298,8 @@ tnodata.h5.out.err tnoname.h5.out tnoname.h5.out.err + tnullspace.h5.out + tnullspace.h5.out.err tobjref.h5.out tobjref.h5.out.err topaque.h5.out @@ -398,9 +406,7 @@ ADD_XML_H5_TEST (tsaf.h5 0 tsaf.h5) ADD_XML_H5_TEST (tempty.h5 0 tempty.h5) ADD_XML_H5_TEST (tnamed_dtype_attr.h5 0 tnamed_dtype_attr.h5) - ##Test dataset and attribute of null space. Commented out: - ## wait until the XML schema is updated for null space. - ## ADD_XML_H5_TEST (tnullspace.h5 0 tnulspace.h5) + ADD_XML_H5_TEST (tnullspace.h5 0 tnullspace.h5) ## So is dataspace with 0 dimension size. ## ADD_XML_H5_TEST (zerodim.h5 0 zerodim.h5) @@ -430,3 +436,6 @@ # tests for floating point user defined printf format ADD_XML_H5_TEST (tfpformat.h5 0 -u -m %.7f tfpformat.h5) + # test for HDFFV-10256 issue + ADD_XML_H5_TEST (test35.nc 0 test35.nc) + diff --git a/tools/h5dump/Makefile.in b/tools/h5dump/Makefile.in index bca81ed..a48e5ba 100644 --- a/tools/h5dump/Makefile.in +++ b/tools/h5dump/Makefile.in @@ -613,6 +613,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5dump/h5dump_xml.c b/tools/h5dump/h5dump_xml.c index 8f6dd86..089419b 100644 --- a/tools/h5dump/h5dump_xml.c +++ b/tools/h5dump/h5dump_xml.c @@ -10,8 +10,6 @@ * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#include <stdio.h> -#include <stdlib.h> #include "H5private.h" #include "h5tools.h" @@ -781,20 +779,20 @@ xml_escape_the_string(const char *str, int slen) esc_len = 1; } else if (*cp == '\'') { - HDstrncpy(ncp, apos, ncp_len); esc_len = HDstrlen(apos); + HDstrncpy(ncp, apos, esc_len); } else if (*cp == '<') { - HDstrncpy(ncp, lt, ncp_len); esc_len = HDstrlen(lt); + HDstrncpy(ncp, lt, esc_len); } else if (*cp == '>') { - HDstrncpy(ncp, gt, ncp_len); esc_len = HDstrlen(gt); + HDstrncpy(ncp, gt, esc_len); } else if (*cp == '&') { - HDstrncpy(ncp, amp, ncp_len); esc_len = HDstrlen(amp); + HDstrncpy(ncp, amp, esc_len); } else { *ncp = *cp; @@ -1960,28 +1958,32 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, H5Tclose(type); space = H5Aget_space(obj_id); + if(space == H5S_NULL || space == H5S_NO_CLASS) { + status = SUCCEED; + } + else { + ndims = H5Sget_simple_extent_dims(space, size, NULL); - ndims = H5Sget_simple_extent_dims(space, size, NULL); + for (i = 0; i < ndims; i++) + nelmts *= size[i]; - for (i = 0; i < ndims; i++) - nelmts *= size[i]; + buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)))); + HDassert(buf); - buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)))); - HDassert(buf); + if (H5Aread(obj_id, p_type, buf) >= 0) { + h5tools_context_t datactx; + HDmemset(&datactx, 0, sizeof(datactx)); + datactx.need_prefix = TRUE; + datactx.indent_level = ctx.indent_level; + datactx.cur_column = ctx.cur_column; + status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf); + } + /* Reclaim any VL memory, if necessary */ + if (vl_data) + H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); - if (H5Aread(obj_id, p_type, buf) >= 0) { - h5tools_context_t datactx; - HDmemset(&datactx, 0, sizeof(datactx)); - datactx.need_prefix = TRUE; - datactx.indent_level = ctx.indent_level; - datactx.cur_column = ctx.cur_column; - status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf); + HDfree(buf); } - /* Reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); - - HDfree(buf); H5Tclose(p_type); H5Sclose(space); H5Tclose(type); diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c index c74e800..f9450cb 100644 --- a/tools/h5dump/h5dumpgentest.c +++ b/tools/h5dump/h5dumpgentest.c @@ -112,6 +112,7 @@ #define FILE82 "tcompound_complex2.h5" #define FILE83 "tvlenstr_array.h5" #define FILE84 "tudfilter.h5" +#define FILE85 "tgrpnullspace.h5" /*------------------------------------------------------------------------- * prototypes @@ -10289,6 +10290,43 @@ H5Z_filter_dynlibud(unsigned int flags, size_t cd_nelmts, *------------------------------------------------------------------------- */ +/*------------------------------------------------------------------------- + * Function: gent_null_space_group + * + * Purpose: generates dataset and attribute of null dataspace in a group + *------------------------------------------------------------------------- + */ +static void gent_null_space_group(void) +{ + hid_t fid, root, group, dataset, space, attr; + int dset_buf = 10; + int point = 4; + + fid = H5Fcreate(FILE85, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + root = H5Gopen2(fid, "/", H5P_DEFAULT); + + group = H5Gcreate2(fid, "/g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* null space */ + space = H5Screate(H5S_NULL); + + /* dataset */ + dataset = H5Dcreate2(group, "dset", H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* nothing should be written */ + H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &dset_buf); + + /* attribute */ + attr = H5Acreate2(group, "attr", H5T_NATIVE_UINT, space, H5P_DEFAULT, H5P_DEFAULT); + H5Awrite(attr, H5T_NATIVE_INT, &point); /* Nothing can be written */ + + H5Dclose(dataset); + H5Aclose(attr); + H5Gclose(group); + H5Gclose(root); + H5Sclose(space); + H5Fclose(fid); +} + int main(void) { gent_group(); @@ -10376,6 +10414,7 @@ int main(void) gent_bitnopaquefields(); gent_intsfourdims(); + gent_null_space_group(); gent_udfilter(); diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in index f941afc..9ceffa5 100644 --- a/tools/h5dump/testh5dump.sh.in +++ b/tools/h5dump/testh5dump.sh.in @@ -131,6 +131,7 @@ $SRC_H5DUMP_TESTFILES/tfpformat.h5 $SRC_H5DUMP_TESTFILES/tfvalues.h5 $SRC_H5DUMP_TESTFILES/tgroup.h5 $SRC_H5DUMP_TESTFILES/tgrp_comments.h5 +$SRC_H5DUMP_TESTFILES/tgrpnullspace.h5 $SRC_H5DUMP_TESTFILES/thlink.h5 $SRC_H5DUMP_TESTFILES/thyperslab.h5 $SRC_H5DUMP_TESTFILES/tintsattrs.h5 @@ -258,6 +259,7 @@ $SRC_H5DUMP_TESTFILES/tfpformat.ddl $SRC_H5DUMP_TESTFILES/tgroup-1.ddl $SRC_H5DUMP_TESTFILES/tgroup-2.ddl $SRC_H5DUMP_TESTFILES/tgrp_comments.ddl +$SRC_H5DUMP_TESTFILES/tgrpnullspace.ddl $SRC_H5DUMP_TESTFILES/thlink-1.ddl $SRC_H5DUMP_TESTFILES/thlink-2.ddl $SRC_H5DUMP_TESTFILES/thlink-3.ddl @@ -1265,6 +1267,7 @@ TOOLTEST thyperslab.ddl --enable-error-stack thyperslab.h5 # test for displaying dataset and attribute of null space TOOLTEST tnullspace.ddl --enable-error-stack tnullspace.h5 +TOOLTEST tgrpnullspace.ddl -p --enable-error-stack tgrpnullspace.h5 # test for displaying dataset and attribute of space with 0 dimension size TOOLTEST zerodim.ddl --enable-error-stack zerodim.h5 diff --git a/tools/h5dump/testh5dumpxml.sh.in b/tools/h5dump/testh5dumpxml.sh.in index 81201b7..8aa8811 100644 --- a/tools/h5dump/testh5dumpxml.sh.in +++ b/tools/h5dump/testh5dumpxml.sh.in @@ -80,6 +80,7 @@ $SRC_H5DUMP_TESTFILES/tdset.h5 $SRC_H5DUMP_TESTFILES/tdset2.h5 $SRC_H5DUMP_TESTFILES/tempty.h5 $SRC_H5DUMP_TESTFILES/tenum.h5 +$SRC_H5DUMP_TESTFILES/test35.nc $SRC_H5DUMP_TESTFILES/textlink.h5 $SRC_H5DUMP_TESTFILES/tfpformat.h5 $SRC_H5DUMP_TESTFILES/tgroup.h5 @@ -96,6 +97,7 @@ $SRC_H5DUMP_TESTFILES/tname-sp.h5 $SRC_H5DUMP_TESTFILES/tnamed_dtype_attr.h5 $SRC_H5DUMP_TESTFILES/tnestedcomp.h5 $SRC_H5DUMP_TESTFILES/tnodata.h5 +$SRC_H5DUMP_TESTFILES/tnullspace.h5 $SRC_H5DUMP_TESTFILES/tobjref.h5 $SRC_H5DUMP_TESTFILES/topaque.h5 $SRC_H5DUMP_TESTFILES/torderattr.h5 @@ -144,6 +146,7 @@ $SRC_H5DUMP_TESTFILES/tempty-nons-uri.h5.xml $SRC_H5DUMP_TESTFILES/tempty-ns.h5.xml $SRC_H5DUMP_TESTFILES/tempty-ns-2.h5.xml $SRC_H5DUMP_TESTFILES/tenum.h5.xml +$SRC_H5DUMP_TESTFILES/test35.nc.xml $SRC_H5DUMP_TESTFILES/textlink.h5.xml $SRC_H5DUMP_TESTFILES/tfpformat.h5.xml $SRC_H5DUMP_TESTFILES/tgroup.h5.xml @@ -160,6 +163,7 @@ $SRC_H5DUMP_TESTFILES/tname-quot.h5.xml $SRC_H5DUMP_TESTFILES/tname-sp.h5.xml $SRC_H5DUMP_TESTFILES/tnestedcomp.h5.xml $SRC_H5DUMP_TESTFILES/tnodata.h5.xml +$SRC_H5DUMP_TESTFILES/tnullspace.h5.xml $SRC_H5DUMP_TESTFILES/tobjref.h5.xml $SRC_H5DUMP_TESTFILES/topaque.h5.xml $SRC_H5DUMP_TESTFILES/torderattr1.h5.xml @@ -353,9 +357,7 @@ TOOLTEST tvlstr.h5.xml --xml tvlstr.h5 TOOLTEST tsaf.h5.xml --xml tsaf.h5 TOOLTEST tempty.h5.xml --xml tempty.h5 TOOLTEST tnamed_dtype_attr.h5.xml --xml tnamed_dtype_attr.h5 -##Test dataset and attribute of null space. Commented out: -## wait until the XML schema is updated for null space. -##TOOLTEST tnullspace.h5.xml --xml tnulspace.h5 +TOOLTEST tnullspace.h5.xml --xml tnullspace.h5 # other options for xml @@ -383,6 +385,9 @@ TOOLTEST torderattr4.h5.xml --xml -H --sort_by=creation_order --sort_order=desce # tests for floating point user defined printf format TOOLTEST tfpformat.h5.xml -u -m %.7f tfpformat.h5 +# test for HDFFV-10256 issue +TOOLTEST test35.nc.xml --xml test35.nc + # Clean up temporary files/directories CLEAN_TESTFILES_AND_TESTDIR diff --git a/tools/h5import/Makefile.in b/tools/h5import/Makefile.in index 866cc76..fa4dceb 100644 --- a/tools/h5import/Makefile.in +++ b/tools/h5import/Makefile.in @@ -592,6 +592,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in index 5613fa0..0939991 100644 --- a/tools/h5jam/Makefile.in +++ b/tools/h5jam/Makefile.in @@ -603,6 +603,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5ls/CMakeTests.cmake b/tools/h5ls/CMakeTests.cmake index 343949a..a839518 100644 --- a/tools/h5ls/CMakeTests.cmake +++ b/tools/h5ls/CMakeTests.cmake @@ -33,6 +33,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/textlinktar.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrp_comments.h5 + ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrpnullspace.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tloop.h5 ${HDF5_TOOLS_SRC_DIR}/testfiles/tnestedcomp.h5 @@ -88,6 +89,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup-1.ls ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup-2.ls ${HDF5_TOOLS_SRC_DIR}/testfiles/tgroup-3.ls + ${HDF5_TOOLS_SRC_DIR}/testfiles/tgrpnullspace.ls ${HDF5_TOOLS_SRC_DIR}/testfiles/thlink-1.ls ${HDF5_TOOLS_SRC_DIR}/testfiles/tloop-1.ls ${HDF5_TOOLS_SRC_DIR}/testfiles/tmultifile.ls @@ -239,6 +241,8 @@ textlinksrc-7-old.out.err tgrp_comments.out tgrp_comments.out.err + tgrpnullspace.out + tgrpnullspace.out.err tsoftlinks-1.out tsoftlinks-1.out.err tsoftlinks-2.out @@ -413,6 +417,9 @@ # test for empty data ADD_H5_TEST (tempty 0 -w80 -d tempty.h5) + # test for displaying dataset and attribute of null space + ADD_H5_TEST (tgrpnullspace 0 -w80 -v -S tgrpnullspace.h5) + # test for all dataset types written to attributes # enable -S for avoiding printing NATIVE types ADD_H5_TEST (tattr2 0 -w80 -v -S tattr2.h5) diff --git a/tools/h5ls/Makefile.in b/tools/h5ls/Makefile.in index b9dbcf4..1ea9bb3 100644 --- a/tools/h5ls/Makefile.in +++ b/tools/h5ls/Makefile.in @@ -596,6 +596,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c index 7daf7e3..a58b96b 100644 --- a/tools/h5ls/h5ls.c +++ b/tools/h5ls/h5ls.c @@ -1616,38 +1616,40 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain info = &outputformat; - if(hexdump_g) - p_type = H5Tcopy(type); - else - p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); - - if(p_type >= 0) { - /* VL data special information */ - unsigned int vl_data = 0; /* contains VL datatypes */ - - /* Check if we have VL data in the dataset's datatype */ - if (h5tools_detect_vlen(p_type) == TRUE) - vl_data = TRUE; - - temp_need= nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); - HDassert(temp_need == (hsize_t)((size_t)temp_need)); - need = (size_t)temp_need; - buf = HDmalloc(need); - HDassert(buf); - if(H5Aread(attr, p_type, buf) >= 0) { - ctx.need_prefix = TRUE; - ctx.indent_level = 2; - ctx.cur_column = (size_t)curr_pos; - h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf); - } + if(space_type != H5S_NULL && space_type != H5S_NO_CLASS) { + if(hexdump_g) + p_type = H5Tcopy(type); + else + p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); + + if(p_type >= 0) { + /* VL data special information */ + unsigned int vl_data = 0; /* contains VL datatypes */ + + /* Check if we have VL data in the dataset's datatype */ + if (h5tools_detect_vlen(p_type) == TRUE) + vl_data = TRUE; + + temp_need= nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); + HDassert(temp_need == (hsize_t)((size_t)temp_need)); + need = (size_t)temp_need; + buf = HDmalloc(need); + HDassert(buf); + if(H5Aread(attr, p_type, buf) >= 0) { + ctx.need_prefix = TRUE; + ctx.indent_level = 2; + ctx.cur_column = (size_t)curr_pos; + h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf); + } - /* Reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); + /* Reclaim any VL memory, if necessary */ + if (vl_data) + H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); - HDfree(buf); - H5Tclose(p_type); - } /* end if */ + HDfree(buf); + H5Tclose(p_type); + } /* end if */ + } H5Sclose(space); H5Tclose(type); diff --git a/tools/h5ls/testh5ls.sh.in b/tools/h5ls/testh5ls.sh.in index 4b57acc..40bb529 100644 --- a/tools/h5ls/testh5ls.sh.in +++ b/tools/h5ls/testh5ls.sh.in @@ -80,6 +80,7 @@ $SRC_H5LS_TESTFILES/textlinksrc.h5 $SRC_H5LS_TESTFILES/textlinktar.h5 $SRC_H5LS_TESTFILES/tgroup.h5 $SRC_H5LS_TESTFILES/tgrp_comments.h5 +$SRC_H5LS_TESTFILES/tgrpnullspace.h5 $SRC_H5LS_TESTFILES/thlink.h5 $SRC_H5LS_TESTFILES/tloop.h5 $SRC_H5LS_TESTFILES/tnestedcomp.h5 @@ -134,6 +135,7 @@ $SRC_H5LS_TESTFILES/tgroup.ls $SRC_H5LS_TESTFILES/tgroup-1.ls $SRC_H5LS_TESTFILES/tgroup-2.ls $SRC_H5LS_TESTFILES/tgroup-3.ls +$SRC_H5LS_TESTFILES/tgrpnullspace.ls $SRC_H5LS_TESTFILES/thlink-1.ls $SRC_H5LS_TESTFILES/tloop-1.ls $SRC_H5LS_TESTFILES/tmultifile.ls @@ -390,6 +392,9 @@ TOOLTEST tarray1.ls 0 -w80 -r -d tarray1.h5 # test for empty data TOOLTEST tempty.ls 0 -w80 -d tempty.h5 +# test for displaying dataset and attribute of null space +TOOLTEST tgrpnullspace.ls 0 -w80 -v -S tgrpnullspace.h5 + # test for all dataset types written to attributes # enable -S for avoiding printing NATIVE types TOOLTEST tattr2.ls 0 -w80 -v -S tattr2.h5 diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in index f2518f0..2031191 100644 --- a/tools/h5repack/Makefile.in +++ b/tools/h5repack/Makefile.in @@ -629,6 +629,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl index 09b2484..4bdd7f8 100644 --- a/tools/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl +++ b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl @@ -11,7 +11,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -33,7 +33,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -55,7 +55,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -77,7 +77,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -99,7 +99,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -121,7 +121,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { @@ -143,7 +143,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 8 19 } + PARAMS { 9 1 8 20 } } } FILLVALUE { diff --git a/tools/h5stat/Makefile.in b/tools/h5stat/Makefile.in index 11d5ecd..adbc776 100644 --- a/tools/h5stat/Makefile.in +++ b/tools/h5stat/Makefile.in @@ -593,6 +593,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/lib/Makefile.in b/tools/lib/Makefile.in index 8ee8348..342b4e8 100644 --- a/tools/lib/Makefile.in +++ b/tools/lib/Makefile.in @@ -581,6 +581,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c index 1b17382..6480cf6 100644 --- a/tools/lib/h5diff_array.c +++ b/tools/lib/h5diff_array.c @@ -674,21 +674,33 @@ static hsize_t diff_datum(void *_mem1, h5difftrace("diff_datum H5T_STRING variable\n"); /* Get pointer to first string */ s1 = *(char**) mem1; - size1 = HDstrlen(s1); + if(s1) + size1 = HDstrlen(s1); + else + size1 = 0; /* Get pointer to second string */ s2 = *(char**) mem2; - size2 = HDstrlen(s2); + if(s2) + size2 = HDstrlen(s2); + else + size2 = 0; } else if (H5T_STR_NULLTERM == pad) { h5difftrace("diff_datum H5T_STRING null term\n"); /* Get pointer to first string */ s1 = (char*) mem1; - size1 = HDstrlen(s1); + if(s1) + size1 = HDstrlen(s1); + else + size1 = 0; if (size1 > size_mtype) size1 = size_mtype; /* Get pointer to second string */ s2 = (char*) mem2; - size2 = HDstrlen(s2); + if(s2) + size2 = HDstrlen(s2); + else + size2 = 0; if (size2 > size_mtype) size2 = size_mtype; } diff --git a/tools/lib/h5tools_ref.c b/tools/lib/h5tools_ref.c index 85850e3..16a949d 100644 --- a/tools/lib/h5tools_ref.c +++ b/tools/lib/h5tools_ref.c @@ -11,8 +11,6 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#include <stdio.h> -#include <stdlib.h> #include "h5tools_ref.h" #include "H5private.h" #include "H5SLprivate.h" @@ -166,7 +164,8 @@ haddr_t ref_path_table_lookup(const char *thepath) { H5O_info_t oi; - + if((HDstrlen(thepath) == 0) || (thepath == NULL)) + return HADDR_UNDEF; /* Allow lookups on the root group, even though it doesn't have any link info */ if(HDstrcmp(thepath, "/")) { H5L_info_t li; diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in index 6a54bd8..7075597 100644 --- a/tools/misc/Makefile.in +++ b/tools/misc/Makefile.in @@ -618,6 +618,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/perform/CMakeTests.cmake b/tools/perform/CMakeTests.cmake index 5c4b54f..5468b0d 100644 --- a/tools/perform/CMakeTests.cmake +++ b/tools/perform/CMakeTests.cmake @@ -55,6 +55,7 @@ add_test (NAME PERFORM_perf_meta COMMAND $<TARGET_FILE:perf_meta>) add_test (NAME PERFORM_zip_perf_help COMMAND $<TARGET_FILE:zip_perf> "-h") add_test (NAME PERFORM_zip_perf COMMAND $<TARGET_FILE:zip_perf> tfilters.h5) +set_tests_properties (PERFORM_zip_perf PROPERTIES DEPENDS PERFORM_zip_perf_help) if (H5_HAVE_PARALLEL) add_test (NAME PERFORM_h5perf COMMAND ${MPIEXEC} ${MPIEXEC_PREFLAGS} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_POSTFLAGS} $<TARGET_FILE:h5perf>) diff --git a/tools/perform/Makefile.in b/tools/perform/Makefile.in index 5dbe4e9..1baa196 100644 --- a/tools/perform/Makefile.in +++ b/tools/perform/Makefile.in @@ -622,6 +622,7 @@ dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ exec_prefix = @exec_prefix@ +fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ host_alias = @host_alias@ host_cpu = @host_cpu@ diff --git a/tools/testfiles/test35.nc b/tools/testfiles/test35.nc Binary files differnew file mode 100644 index 0000000..4bd5d7f --- /dev/null +++ b/tools/testfiles/test35.nc diff --git a/tools/testfiles/test35.nc.xml b/tools/testfiles/test35.nc.xml new file mode 100644 index 0000000..a38ed8a --- /dev/null +++ b/tools/testfiles/test35.nc.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<hdf5:HDF5-File xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> +<hdf5:RootGroup OBJ-XID="xid_48" H5Path="/"> + <hdf5:Attribute Name="aaa"> + <hdf5:Dataspace> + <hdf5:ScalarDataspace /> + </hdf5:Dataspace> + <hdf5:DataType> + <hdf5:AtomicType> + <hdf5:StringType Cset="H5T_CSET_ASCII" StrSize="14108" StrPad="H5T_STR_NULLTERM"/> + </hdf5:AtomicType> + </hdf5:DataType> + <hdf5:Data> + <hdf5:DataFromFile> + 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+ </hdf5:DataFromFile> + </hdf5:Data> + </hdf5:Attribute> +</hdf5:RootGroup> +</hdf5:HDF5-File> diff --git a/tools/testfiles/tgrpnullspace.ddl b/tools/testfiles/tgrpnullspace.ddl new file mode 100644 index 0000000..2b91527 --- /dev/null +++ b/tools/testfiles/tgrpnullspace.ddl @@ -0,0 +1,33 @@ +HDF5 "tgrpnullspace.h5" { +GROUP "/" { + GROUP "g1" { + ATTRIBUTE "attr" { + DATATYPE H5T_STD_U32LE + DATASPACE NULL + DATA { + } + } + DATASET "dset" { + DATATYPE H5T_STD_I32BE + DATASPACE NULL + STORAGE_LAYOUT { + CONTIGUOUS + SIZE 0 + OFFSET 18446744073709551615 + } + FILTERS { + NONE + } + FILLVALUE { + FILL_TIME H5D_FILL_TIME_IFSET + VALUE H5D_FILL_VALUE_DEFAULT + } + ALLOCATION_TIME { + H5D_ALLOC_TIME_LATE + } + DATA { + } + } + } +} +} diff --git a/tools/testfiles/tgrpnullspace.h5 b/tools/testfiles/tgrpnullspace.h5 Binary files differnew file mode 100644 index 0000000..82a405e --- /dev/null +++ b/tools/testfiles/tgrpnullspace.h5 diff --git a/tools/testfiles/tgrpnullspace.ls b/tools/testfiles/tgrpnullspace.ls new file mode 100644 index 0000000..439414c --- /dev/null +++ b/tools/testfiles/tgrpnullspace.ls @@ -0,0 +1,7 @@ +Opened "tgrpnullspace.h5" with sec2 driver. +g1 Group + Attribute: attr null + Type: 32-bit little-endian unsigned integer + + Location: 1:800 + Links: 1 diff --git a/tools/testfiles/tnullspace.h5.xml b/tools/testfiles/tnullspace.h5.xml new file mode 100644 index 0000000..b1c1974 --- /dev/null +++ b/tools/testfiles/tnullspace.h5.xml @@ -0,0 +1,39 @@ +<?xml version="1.0" encoding="UTF-8"?> +<hdf5:HDF5-File xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> +<hdf5:RootGroup OBJ-XID="xid_928" H5Path="/"> + <hdf5:Attribute Name="attr"> + <hdf5:Dataspace> + <!-- unknown dataspace --> + </hdf5:Dataspace> + <hdf5:DataType> + <hdf5:AtomicType> + <hdf5:IntegerType ByteOrder="LE" Sign="false" Size="4" /> + </hdf5:AtomicType> + </hdf5:DataType> + <hdf5:Data> + <hdf5:NoData/> + </hdf5:Data> + </hdf5:Attribute> + <hdf5:Dataset Name="dset" OBJ-XID="xid_976" H5Path= "/dset" Parents="xid_928" H5ParentPaths="/"> + <hdf5:StorageLayout> + <hdf5:ContiguousLayout/> + </hdf5:StorageLayout> + <hdf5:FillValueInfo FillTime="FillIfSet" AllocationTime="Late"> + <hdf5:FillValue> + <hdf5:NoFill/> + </hdf5:FillValue> + </hdf5:FillValueInfo> + <hdf5:Dataspace> + <!-- unknown dataspace --> + </hdf5:Dataspace> + <hdf5:DataType> + <hdf5:AtomicType> + <hdf5:IntegerType ByteOrder="BE" Sign="true" Size="4" /> + </hdf5:AtomicType> + </hdf5:DataType> + <hdf5:Data> + <hdf5:NoData/> + </hdf5:Data> + </hdf5:Dataset> +</hdf5:RootGroup> +</hdf5:HDF5-File> |