mirror of
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* Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Reorg tools perform to provide h5perf for installation * Correct file paths * Correct path * Add new src folder to makefile list * Remove bin_PROGRAMS from TEST_PROG * Default h5perf executables to static build * Remove test lib dependency from h5perf * format adjustments * Remove test lib from autotools makefile * Add note * h5perf needs the math library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
1537 lines
60 KiB
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1537 lines
60 KiB
Plaintext
HDF5 version 1.13.0 currently under development
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================================================================================
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INTRODUCTION
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============
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This document describes the differences between this release and the previous
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HDF5 release. It contains information on the platforms tested and known
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problems in this release. For more details check the HISTORY*.txt files in the
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HDF5 source.
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Note that documentation in the links below will be updated at the time of each
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final release.
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Links to HDF5 documentation can be found on The HDF5 web page:
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https://portal.hdfgroup.org/display/HDF5/HDF5
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The official HDF5 releases can be obtained from:
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https://www.hdfgroup.org/downloads/hdf5/
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Changes from Release to Release and New Features in the HDF5-1.13.x release series
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can be found at:
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https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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========
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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.12.0
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- Supported Platforms
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- Tested Configuration Features Summary
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- More Tested Platforms
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- Known Problems
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- CMake vs. Autotools installations
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New Features
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============
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Configuration:
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-------------
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- Adds C++ Autotools configuration file for Intel
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* Checks for icpc as the compiler
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* Sets std=c++11
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* Copies most non-warning flags from intel-flags
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(DER - 2021/06/02)
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- Adds C++ Autotools configuration file for PGI
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* Checks for pgc++ as the compiler name (was: pgCC)
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* Sets -std=c++11
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* Other options basically match new C options (below)
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(DER - 2021/06/02)
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- Updates PGI C options
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* -Minform set to warn (was: inform) to suppress spurious messages
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* Sets -gopt -O2 as debug options
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* Sets -O4 as 'high optimization' option
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* Sets -O0 as 'no optimization' option
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* Removes specific settings for PGI 9 and 10
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(DER - 2021/06/02)
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- A C++11-compliant compiler is now required to build the C++ wrappers
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CMAKE_CXX_STANDARD is now set to 11 when building with CMake and
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-std=c++11 is added when building with clang/gcc via the Autotools.
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(DER - 2021/05/27)
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- CMake will now run the shell script tests in test/ by default
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The test directory includes several shell script tests that previously
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were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS
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has been set to ON and SH_PROGRAM has been set to bash (some test
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scripts use bash-isms). Platforms without bash (e.g., Windows) will
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ignore the script tests.
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(DER - 2021/05/23)
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- Removed unused HDF5_ENABLE_HSIZET option from CMake
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This has been unused for some time and has no effect.
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(DER - 2021/05/23)
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- CMake no longer builds the C++ library by default
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HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the
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Autotools build defaults.
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(DER - 2021/04/20)
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- Removal of pre-VS2015 work-arounds
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HDF5 now requires Visual Studio 2015 or greater, so old work-around
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code and definitions have been removed, including:
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* <inttypes.h>
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* snprintf and vsnprintf
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* llround, llroundf, lround, lroundf, round, roundf
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* strtoll and strtoull
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* va_copy
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* struct timespec
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(DER - 2021/03/22)
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- Add CMake variable HDF5_LIB_INFIX
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This infix is added to all library names after 'hdf5'.
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e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
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This name is used in packages on debian based systems.
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(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)
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(barcode - 2021/03/22)
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- On macOS, Universal Binaries can now be built, allowing native execution on
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both Intel and Apple Silicon (ARM) based Macs.
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To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64"
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(SAM - 2021/02/07, github-311)
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- Added a configure-time option to control certain compiler warnings
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diagnostics
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A new configure-time option was added that allows some compiler warnings
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diagnostics to have the default operation. This is mainly intended for
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library developers and currently only works for gcc 10 and above. The
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diagnostics flags apply to C, C++ and Fortran compilers and will appear
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in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They
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will NOT be exported to h5cc, etc.
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The default is OFF, which will disable the warnings URL and color attributes
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for the warnings output. ON will not add the flags and allow default behavior.
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Autotools: --enable-diags
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CMake: HDF5_ENABLE_BUILD_DIAGS
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(ADB - 2021/02/05, HDFFV-11213)
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- CMake option to build the HDF filter plugins project as an external project
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The HDF filter plugins project is a collection of registered compression
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filters that can be dynamically loaded when needed to access data stored
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in a hdf5 file. This CMake-only option allows the plugins to be built and
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distributed with the hdf5 library and tools. Like the options for szip and
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zlib, either a tgz file or a git repository can be specified for the source.
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The option was refactored to use the CMake FetchContent process. This allows
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more control over the filter targets, but required external project command
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options to be moved to a CMake include file, HDF5PluginCache.cmake. Also
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enabled the filter examples to be used as tests for operation of the
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filter plugins.
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(ADB - 2020/12/10, OESS-98)
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- FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers
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On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did
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not process C++ options. Since FreeBSD 10, the default compiler has
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been clang (via 'cc').
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The default compilers have been set to 'cc' for C and 'c++' for C++,
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which will pick up clang and clang++ respectively on FreeBSD 10+.
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Additionally, clang options are now set correctly for both C and C++
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and g++ options will now be set if that compiler is being used (an
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omission from the former functionality).
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(DER - 2020/11/28, HDFFV-11193)
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- Fixed POSIX problems when building w/ gcc on Solaris
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When building on Solaris using gcc, the POSIX symbols were not
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being set correctly, which could lead to issues like clock_gettime()
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not being found.
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The standard is now set to gnu99 when building with gcc on Solaris,
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which allows POSIX things to be #defined and linked correctly. This
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differs slightly from the gcc norm, where we set the standard to c99
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and manually set POSIX #define symbols.
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(DER - 2020/11/25, HDFFV-11191)
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- Added a configure-time option to consider certain compiler warnings
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as errors
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A new configure-time option was added that converts some compiler warnings
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to errors. This is mainly intended for library developers and currently
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only works for gcc and clang. The warnings that are considered errors
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will appear in the generated libhdf5.settings file. These warnings apply
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to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags",
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respectively. They will NOT be exported to h5cc, etc.
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The default is OFF. Building with this option may fail when compiling
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on operating systems and with compiler versions not commonly used by
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the library developers. Compilation may also fail when headers not
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under the control of the library developers (e.g., mpi.h, hdfs.h) raise
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warnings.
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Autotools: --enable-warnings-as-errors
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CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS
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(DER - 2020/11/23, HDFFV-11189)
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- Autotools and CMake target added to produce doxygen generated documentation
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The default is OFF or disabled.
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Autoconf option is '--enable-doxygen'
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autotools make target is 'doxygen' and will build all doxygen targets
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CMake configure option is 'HDF5_BUILD_DOC'.
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CMake target is 'doxygen' for all available doxygen targets
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CMake target is 'hdf5lib_doc' for the src subdirectory
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(ADB - 2020/11/03)
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- CMake option to use MSVC naming conventions with MinGW
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HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions
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when using a MinGW toolchain
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(xan - 2020/10/30)
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- CMake option to statically link gcc libs with MinGW
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HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++
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with the MinGW toolchain
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(xan - 2020/10/30)
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- CMake option to build the HDF filter plugins project as an external project
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The HDF filter plugins project is a collection of registered compression
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filters that can be dynamically loaded when needed to access data stored
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in a hdf5 file. This CMake-only option allows the plugins to be built and
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distributed with the hdf5 library and tools. Like the options for szip and
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zlib, either a tgz file or a git repository can be specified for the source.
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The necessary options are (see the INSTALL_CMake.txt file):
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HDF5_ENABLE_PLUGIN_SUPPORT
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PLUGIN_TGZ_NAME or PLUGIN_GIT_URL
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There are more options necessary for various filters and the plugin project
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documents should be referenced.
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(ADB - 2020/09/27, OESS-98)
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- Added CMake option to format source files
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HDF5_ENABLE_FORMATTERS option will enable creation of targets using the
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pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder
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or tool folder. All sources can be formatted by executing the format target;
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make format
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(ADB - 2020/08/24)
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- Add file locking configure and CMake options
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HDF5 1.10.0 introduced a file locking scheme, primarily to help
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enforce SWMR setup. Formerly, the only user-level control of the scheme
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was via the HDF5_USE_FILE_LOCKING environment variable.
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This change introduces configure-time options that control whether
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or not file locking will be used and whether or not the library
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ignores errors when locking has been disabled on the file system
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(useful on some HPC Lustre installations).
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In both the Autotools and CMake, the settings have the effect of changing
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the default property list settings (see the H5Pset/get_file_locking()
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entry, below).
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The yes/no/best-effort file locking configure setting has also been
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added to the libhdf5.settings file.
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Autotools:
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An --enable-file-locking=(yes|no|best-effort) option has been added.
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yes: Use file locking.
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no: Do not use file locking.
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best-effort: Use file locking and ignore "disabled" errors.
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CMake:
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Two self-explanatory options have been added:
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HDF5_USE_FILE_LOCKING
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HDF5_IGNORE_DISABLED_FILE_LOCKS
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Setting both of these to ON is the equivalent to the Autotools'
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best-effort setting.
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NOTE:
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The precedence order of the various file locking control mechanisms is:
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1) HDF5_USE_FILE_LOCKING environment variable (highest)
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2) H5Pset_file_locking()
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3) configure/CMake options (which set the property list defaults)
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4) library defaults (currently best-effort)
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(DER - 2020/07/30, HDFFV-11092)
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- CMake option to link the generated Fortran MOD files into the include
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directory.
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The Fortran generation of MOD files by a Fortran compile can produce
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different binary files between SHARED and STATIC compiles with different
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compilers and/or different platforms. Note that it has been found that
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different versions of Fortran compilers will produce incompatible MOD
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files. Currently, CMake will locate these MOD files in subfolders of
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the include directory and add that path to the Fortran library target
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in the CMake config file, which can be used by the CMake find library
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process. For other build systems using the binary from a CMake install,
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a new CMake configuration can be used to copy the pre-chosen version
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of the Fortran MOD files into the install include directory.
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The default will depend on the configuration of
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BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
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YES YES Default to SHARED
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YES NO Default to STATIC
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NO YES Default to SHARED
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NO NO Default to SHARED
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The defaults can be overridden by setting the config option
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HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
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(ADB - 2020/07/09, HDFFV-11116)
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- CMake option to use AEC (open source SZip) library instead of SZip
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The open source AEC library is a replacement library for SZip. In
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order to use it for hdf5 the libaec CMake source was changed to add
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"-fPIC" and exclude test files. Autotools does not build the
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compression libraries within hdf5 builds. New option USE_LIBAEC is
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required to compensate for the different files produced by AEC build.
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(ADB - 2020/04/22, OESS-65)
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- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
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Some handcrafted tests in HDFTests.c has been removed and the CMake
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CHECK_STRUCT_HAS_MEMBER module has been used.
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(ADB - 2020/03/24, TRILAB-24)
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- Both build systems use same set of warnings flags
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GNU C, C++ and gfortran warnings flags were moved to files in a config
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sub-folder named gnu-warnings. Flags that only are available for a specific
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version of the compiler are in files named with that version.
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Clang C warnings flags were moved to files in a config sub-folder
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named clang-warnings.
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Intel C, Fortran warnings flags were moved to files in a config sub-folder
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named intel-warnings.
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There are flags in named "error-xxx" files with warnings that may
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be promoted to errors. Some source files may still need fixes.
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There are also pairs of files named "developer-xxx" and "no-developer-xxx"
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that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
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configure option:--enable-developer-warnings.
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In addition, CMake no longer applies these warnings for examples.
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(ADB - 2020/03/24, TRILAB-192)
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- Added test script for file size compare
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If CMake minimum version is at least 3.14, the fileCompareTest.cmake
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script will compare file sizes.
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(ADB - 2020/02/24, HDFFV-11036)
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- Update CMake minimum version to 3.12
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Updated CMake minimum version to 3.12 and added version checks
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for Windows features.
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(ADB - 2020/02/05, TRILABS-142)
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- Fixed CMake include properties for Fortran libraries
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Corrected the library properties for Fortran to use the
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correct path for the Fortran module files.
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(ADB - 2020/02/04, HDFFV-11012)
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- Added common warnings files for gnu and intel
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Added warnings files to use one common set of flags
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during configure for both autotools and CMake build
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systems. The initial implementation only affects a
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general set of flags for gnu and intel compilers.
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(ADB - 2020/01/17)
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- Added new options to CMake for control of testing
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Added CMake options (default ON);
|
|
HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
|
|
combined with:
|
|
HDF5_TEST_TOOLS
|
|
HDF5_TEST_EXAMPLES
|
|
HDF5_TEST_SWMR
|
|
HDF5_TEST_FORTRAN
|
|
HDF5_TEST_CPP
|
|
HDF5_TEST_JAVA
|
|
|
|
(ADB - 2020/01/15, HDFFV-11001)
|
|
|
|
- Added Clang sanitizers to CMake for analyzer support if compiler is clang.
|
|
|
|
Added CMake code and files to execute the Clang sanitizers if
|
|
HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
|
|
is set to one of the following:
|
|
Address
|
|
Memory
|
|
MemoryWithOrigins
|
|
Undefined
|
|
Thread
|
|
Leak
|
|
'Address;Undefined'
|
|
|
|
(ADB - 2019/12/12, TRILAB-135)
|
|
|
|
- Update CMake for VS2019 support
|
|
|
|
CMake added support for VS2019 in version 3.15. Changes to the CMake
|
|
generator setting required changes to scripts. Also updated version
|
|
references in CMake files as necessary.
|
|
|
|
(ADB - 2019/11/18, HDFFV-10962)
|
|
|
|
- Update CMake options to match new autotools options
|
|
|
|
Add configure options (autotools - CMake):
|
|
enable-asserts HDF5_ENABLE_ASSERTS
|
|
enable-symbols HDF5_ENABLE_SYMBOLS
|
|
enable-profiling HDF5_ENABLE_PROFILING
|
|
enable-optimization HDF5_ENABLE_OPTIMIZATION
|
|
In addition NDEBUG is no longer forced defined and relies on the CMake
|
|
process.
|
|
|
|
(ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
|
|
|
|
|
|
Library:
|
|
--------
|
|
- Change how the release part of version, in major.minor.release is checked
|
|
for compatibility
|
|
|
|
The HDF5 library uses a function, H5check_version, to check that
|
|
the version defined in the header files, which is used to compile an
|
|
application is compatible with the version codified in the library, which
|
|
the application loads at runtime. This previously required an exact match
|
|
or the library would print a warning, dump the build settings and then
|
|
abort or continue. An environment variable controlled the logic.
|
|
|
|
Now the function first checks that the library release version, in
|
|
major.minor.release, is not older than the version in the headers.
|
|
Secondly, if the release version is different, it checks if either
|
|
the library version or the header version is in the exception list, in
|
|
which case the release part of version, in major.minor.release, must
|
|
be exact. An environment variable still controls the logic.
|
|
|
|
(ADB - 2021/07/27)
|
|
|
|
- gcc warning suppression macros were moved out of H5public.h
|
|
|
|
The HDF5 library uses a set of macros to suppress warnings on gcc.
|
|
These warnings were originally located in H5public.h so that the
|
|
multi VFD (which only uses public headers) could also make use of them
|
|
but internal macros should not be publicly exposed like this.
|
|
|
|
These macros have now been moved to H5private.h. Pending future multi
|
|
VFD refactoring, the macros have been duplicated in H5FDmulti.c to
|
|
suppress the format string warnings there.
|
|
|
|
(DER - 2021/06/03)
|
|
|
|
- H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX
|
|
|
|
The size_hint value is ultimately stored in a uint32_t struct field,
|
|
so specifying a value larger than this on a 64-bit machine can cause
|
|
undefined behavior including crashing the system.
|
|
|
|
The documentation for this API call was also incorrect, stating that
|
|
passing a negative value would cause the library to use a default
|
|
value. Instead, passing a "negative" value actually passes a very large
|
|
value, which is probably not what the user intends and can cause
|
|
crashes on 64-bit systems.
|
|
|
|
The Doxygen documentation has been updated and passing values larger
|
|
than UINT32_MAX for size_hint will now produce a normal HDF5 error.
|
|
|
|
(DER - 2021/04/29, HDFFV-11241)
|
|
|
|
|
|
- H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID
|
|
|
|
When passed an invalid fapl ID, H5Pset_fapl_log() would usually
|
|
segfault when attempting to free an uninitialized pointer in the error
|
|
handling code. This behavior is more common in release builds or
|
|
when the memory sanitization checks were not selected as a build
|
|
option.
|
|
|
|
The pointer is now correctly initialized and the API call now
|
|
produces a normal HDF5 error when fed an invalid fapl ID.
|
|
|
|
(DER - 2021/04/28, HDFFV-11240)
|
|
|
|
- Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
|
|
|
|
The call incorrectly attempts to free an internal copy of the previous
|
|
log location string, which causes a segfault. This only happens
|
|
when the call is invoked multiple times on the same property list.
|
|
On the first call to a given fapl, the log location is set to NULL so
|
|
the segfault does not occur.
|
|
|
|
The string is now handled properly and the segfault no longer occurs.
|
|
|
|
(DER - 2021/04/27, HDFFV-11239)
|
|
|
|
- HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows
|
|
|
|
HSYS_GOTO_ERROR is an internal macro that is used to produce error
|
|
messages when system calls fail. These strings include errno and the
|
|
the associated strerror() value, which are not particularly useful
|
|
when a Win32 API call fails.
|
|
|
|
On Windows, this macro has been updated to include the result of
|
|
GetLastError(). When a system call fails on Windows, usually only
|
|
one of errno and GetLastError() will be useful, however we emit both
|
|
for the user to parse. The Windows error message is not emitted as
|
|
it would be awkward to free the FormatMessage() buffer given the
|
|
existing HDF5 error framework. Users will have to look up the error
|
|
codes in MSDN.
|
|
|
|
The format string on Windows has been changed from:
|
|
|
|
"%s, errno = %d, error message = '%s'"
|
|
|
|
to:
|
|
|
|
"%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32""
|
|
|
|
for those inclined to parse it for error values.
|
|
|
|
(DER - 2021/03/21)
|
|
|
|
- File locking now works on Windows
|
|
|
|
Since version 1.10.0, the HDF5 library has used a file locking scheme
|
|
to help enforce one reader at a time accessing an HDF5 file, which can
|
|
be helpful when setting up readers and writers to use the single-
|
|
writer/multiple-readers (SWMR) access pattern.
|
|
|
|
In the past, this was only functional on POSIX systems where flock() or
|
|
fcntl() were present. Windows used a no-op stub that always succeeded.
|
|
|
|
HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the
|
|
same scheme as POSIX systems. We lock the entire file when we set up the
|
|
locks (by passing DWORDMAX as both size parameters to LockFileEx()).
|
|
|
|
(DER - 2021/03/19, HDFFV-10191)
|
|
|
|
- H5Epush_ret() now requires a trailing semicolon
|
|
|
|
H5Epush_ret() is a function-like macro that has been changed to
|
|
contain a `do {} while(0)` loop. Consequently, a trailing semicolon
|
|
is now required to end the `while` statement. Previously, a trailing
|
|
semi would work, but was not mandatory. This change was made to allow
|
|
clang-format to correctly format the source code.
|
|
|
|
(SAM - 2021/03/03)
|
|
|
|
- Improved performance of H5Sget_select_elem_pointlist
|
|
|
|
Modified library to cache the point after the last block of points
|
|
retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the
|
|
same function to retrieve the next block of points from the list can
|
|
proceed immediately without needing to iterate over the point list.
|
|
|
|
(NAF - 2021/01/19)
|
|
|
|
- Replaced H5E_ATOM with H5E_ID in H5Epubgen.h
|
|
|
|
The term "atom" is archaic and not in line with current HDF5 library
|
|
terminology, which uses "ID" instead. "Atom" has mostly been purged
|
|
from the library internals and this change removes H5E_ATOM from
|
|
the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with
|
|
H5E_ID.
|
|
|
|
(DER - 2020/11/24, HDFFV-11190)
|
|
|
|
- Add a new public function H5Ssel_iter_reset
|
|
|
|
This function resets a dataspace selection iterator back to an
|
|
initial state so that it may be used for iteration once more.
|
|
This can be useful when needing to iterate over a selection
|
|
multiple times without having to repeatedly create/destroy
|
|
a selection iterator for that dataspace selection.
|
|
|
|
(JTH - 2020/09/18)
|
|
|
|
- Remove HDFS VFD stubs
|
|
|
|
The original implementation of the HDFS VFD included non-functional
|
|
versions of the following public API calls when the HDFS VFD is
|
|
not built as a part of the HDF5 library:
|
|
|
|
* H5FD_hdfs_init()
|
|
* H5Pget_fapl_hdfs()
|
|
* H5Pset_fapl_hdfs()
|
|
|
|
They will remain present in HDF5 1.10 and HDF5 1.12 releases
|
|
for binary compatibility purposes but have been removed as of 1.14.0.
|
|
|
|
Note that this has nothing to do with the real HDFS VFD API calls
|
|
that are fully functional when the HDFS VFD is configured and built.
|
|
|
|
We simply changed:
|
|
|
|
#ifdef LIBHDFS
|
|
<real API call>
|
|
#else
|
|
<useless stub>
|
|
#endif
|
|
|
|
to:
|
|
|
|
#ifdef LIBHDFS
|
|
<real API call>
|
|
#endif
|
|
|
|
Which is how the other optional VFDs are handled.
|
|
|
|
(DER - 2020/08/27)
|
|
|
|
- Add Mirror VFD
|
|
|
|
Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
|
|
machine. Must be used in conjunction with the Splitter VFD.
|
|
|
|
(JOS - 2020/03/13, TBD)
|
|
|
|
- Add Splitter VFD
|
|
|
|
Maintain separate R/W and W/O channels for "concurrent" file writes
|
|
to two files using a single HDF5 file handle.
|
|
|
|
(JOS - 2020/03/13, TBD)
|
|
|
|
- Refactored public exposure of haddr_t type in favor of "object tokens"
|
|
|
|
To better accommodate HDF5 VOL connectors where "object addresses in a file"
|
|
may not make much sense, the following changes were made to the library:
|
|
|
|
* Introduced new H5O_token_t "object token" type, which represents a
|
|
unique and permanent identifier for referencing an HDF5 object within
|
|
a container; these "object tokens" are meant to replace object addresses.
|
|
Along with the new type, a new H5Oopen_by_token API call was introduced
|
|
to open an object by a token, similar to how object addresses were
|
|
previously used with H5Oopen_by_addr.
|
|
|
|
* Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
|
|
H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
|
|
struct and H5L_iterate2_t callback function, which work with the newly-introduced
|
|
object tokens, instead of object addresses. The original functions have been
|
|
renamed to version 1 functions and are deprecated in favor of the new version 2
|
|
functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
|
|
types and are now deprecated in favor of their version 2 counterparts. For each of
|
|
the functions and types, compatibility macros take place of the original symbols.
|
|
|
|
* Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
|
|
H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
|
|
struct and H5O_iterate2_t callback function, which work with the newly-introduced
|
|
object tokens, instead of object addresses. The version 2 functions are now
|
|
deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
|
|
types have been renamed to version 1 types and are now deprecated in favor of their
|
|
version 2 counterparts. For each, compatibility macros take place of the original
|
|
symbols.
|
|
|
|
* Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
|
|
H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
|
|
struct, which are used to retrieve the native HDF5 file format-specific information
|
|
about an object. This information (such as object header info and B-tree/heap info)
|
|
has been removed from the new H5O_info2_t struct so that the more generic
|
|
H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
|
|
VOL connectors.
|
|
|
|
* Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
|
|
two object tokens, convert an object token into a nicely-readable string format and
|
|
to convert an object token string back into a real object token, respectively.
|
|
|
|
(DER, QAK, JTH - 2020/01/16)
|
|
|
|
- Add new public function H5Sselect_adjust.
|
|
|
|
This function shifts a dataspace selection by a specified logical offset
|
|
within the dataspace extent. This can be useful for VOL developers to
|
|
implement chunked datasets.
|
|
|
|
(NAF - 2019/11/18)
|
|
|
|
- Add new public function H5Sselect_project_intersection.
|
|
|
|
This function computes the intersection between two dataspace selections
|
|
and projects that intersection into a third selection. This can be useful
|
|
for VOL developers to implement chunked or virtual datasets.
|
|
|
|
(NAF - 2019/11/13, ID-148)
|
|
|
|
- Add new public function H5VLget_file_type.
|
|
|
|
This function returns a datatype equivalent to the supplied datatype but
|
|
with the location set to be in the file. This datatype can then be used
|
|
with H5Tconvert to convert data between file and in-memory representation.
|
|
This function is intended for use only by VOL connector developers.
|
|
|
|
(NAF - 2019/11/08, ID-127)
|
|
|
|
|
|
Parallel Library:
|
|
-----------------
|
|
-
|
|
|
|
|
|
Fortran Library:
|
|
----------------
|
|
- Add wrappers for H5Pset/get_file_locking() API calls
|
|
|
|
h5pget_file_locking_f()
|
|
h5pset_file_locking_f()
|
|
|
|
See the configure option discussion for HDFFV-11092 (above) for more
|
|
information on the file locking feature and how it's controlled.
|
|
|
|
(DER - 2020/07/30, HDFFV-11092)
|
|
|
|
C++ Library:
|
|
------------
|
|
- Add wrappers for H5Pset/get_file_locking() API calls
|
|
|
|
FileAccPropList::setFileLocking()
|
|
FileAccPropList::getFileLocking()
|
|
|
|
See the configure option discussion for HDFFV-11092 (above) for more
|
|
information on the file locking feature and how it's controlled.
|
|
|
|
(DER - 2020/07/30, HDFFV-11092)
|
|
|
|
|
|
Java Library:
|
|
-------------
|
|
- Replaced HDF5AtomException with HDF5IdException
|
|
|
|
Since H5E_ATOM changed to H5E_ID in the C library, the Java exception
|
|
that wraps the error category was also renamed. Its functionality
|
|
remains unchanged aside from the name.
|
|
|
|
(See also the HDFFV-11190 note in the C library section)
|
|
|
|
(DER - 2020/11/24, HDFFV-11190)
|
|
|
|
- Added new H5S functions.
|
|
|
|
H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
|
|
H5Sselect_intersect_block, H5Sselect_project_intersection,
|
|
H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
|
|
wrapper functions added.
|
|
|
|
(ADB - 2020/10/27, HDFFV-10868)
|
|
|
|
- Add wrappers for H5Pset/get_file_locking() API calls
|
|
|
|
H5Pset_file_locking()
|
|
H5Pget_use_file_locking()
|
|
H5Pget_ignore_disabled_file_locking()
|
|
|
|
Unlike the C++ and Fortran wrappers, there are separate getters for the
|
|
two file locking settings, each of which returns a boolean value.
|
|
|
|
See the configure option discussion for HDFFV-11092 (above) for more
|
|
information on the file locking feature and how it's controlled.
|
|
|
|
(DER - 2020/07/30, HDFFV-11092)
|
|
|
|
- Added ability to test java library with VOLs.
|
|
|
|
Created a new CMake script that combines the java and vol test scripts.
|
|
|
|
(ADB - 2020/02/03, HDFFV-10996)
|
|
|
|
- Tests fail for non-English locales.
|
|
|
|
In the JUnit tests with a non-English locale, only the part before
|
|
the decimal comma is replaced by XXXX and this leads to a comparison
|
|
error. Changed the regex for the Time substitution.
|
|
|
|
(ADB - 2020/01/09, HDFFV-10995)
|
|
|
|
|
|
Tools:
|
|
------
|
|
- Refactored the perform tools and removed depends on test library.
|
|
|
|
Moved the perf and h5perf tools from tools/test/perform to
|
|
tools/src/h5perf so that they can be installed. This required
|
|
that the test library dependency be removed by copying the
|
|
needed functions from h5test.c.
|
|
The standalone scripts and other perform tools remain in the
|
|
tools/test/perform folder.
|
|
|
|
(ADB - 2021/08/10)
|
|
|
|
- Removed partial long exceptions
|
|
|
|
Some of the tools accepted shortened versions of the long options
|
|
(ex: --datas instead of --dataset). These were implemented inconsistently,
|
|
are difficult to maintian, and occasionally block useful long option
|
|
names. These partial long options have been removed from all the tools.
|
|
|
|
(DER - 2021/08/03)
|
|
|
|
- h5repack added help text for user-defined filters.
|
|
|
|
Added help text line that states the valid values of the filter flag
|
|
for user-defined filters;
|
|
filter_flag: 1 is OPTIONAL or 0 is MANDATORY
|
|
|
|
(ADB - 2021/01/14, HDFFV-11099)
|
|
|
|
- Added h5delete tool
|
|
|
|
Deleting HDF5 storage when using the VOL can be tricky when the VOL
|
|
does not create files. The h5delete tool is a simple wrapper around
|
|
the H5Fdelete() API call that uses the VOL specified in the
|
|
HDF5_VOL_CONNECTOR environment variable to delete a "file". If
|
|
the call to H5Fdelete() fails, the tool will attempt to use
|
|
the POSIX remove(3) call to remove the file.
|
|
|
|
Note that the HDF5 library does currently have support for
|
|
H5Fdelete() in the native VOL connector.
|
|
|
|
(DER - 2020/12/16)
|
|
|
|
- h5repack added options to control how external links are handled.
|
|
|
|
Currently h5repack preserves external links and cannot copy and merge
|
|
data from the external files. Two options, merge and prune, were added to
|
|
control how to merge data from an external link into the resulting file.
|
|
--merge Follow external soft link recursively and merge data.
|
|
--prune Do not follow external soft links and remove link.
|
|
--merge --prune Follow external link, merge data and remove dangling link.
|
|
|
|
(ADB - 2020/08/05, HDFFV-9984)
|
|
|
|
- h5repack was fixed to repack the reference attributes properly.
|
|
The code line that checks if the update of reference inside a compound
|
|
datatype is misplaced outside the code block loop that carries out the
|
|
check. In consequence, the next attribute that is not the reference
|
|
type was repacked again as the reference type and caused the failure of
|
|
repacking. The fix is to move the corresponding code line to the correct
|
|
code block.
|
|
|
|
(KY -2020/02/07, HDFFV-11014)
|
|
|
|
- h5diff was updated to use the new reference APIs.
|
|
|
|
h5diff uses the new reference APIs to compare references.
|
|
Attribute references can also be compared.
|
|
|
|
(ADB - 2019/12/19, HDFFV-10980)
|
|
|
|
- h5dump and h5ls were updated to use the new reference APIs.
|
|
|
|
The tools library now use the new reference APIs to inspect a
|
|
file. Also the DDL spec was updated to reflect the format
|
|
changes produced with the new APIs. The export API and support
|
|
functions in the JNI were updated to match.
|
|
|
|
(ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
|
|
|
|
|
|
High-Level APIs:
|
|
----------------
|
|
-
|
|
|
|
C Packet Table API:
|
|
-------------------
|
|
-
|
|
|
|
Internal header file:
|
|
---------------------
|
|
-
|
|
|
|
Documentation:
|
|
--------------
|
|
-
|
|
|
|
Support for new platforms, languages and compilers
|
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==================================================
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-
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Bug Fixes since HDF5-1.12.0 release
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===================================
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Library
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-------
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- Fixed CVE-2018-14460
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The tool h5repack produced a segfault when the rank in dataspace
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message was corrupted, causing invalid read while decoding the
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dimension sizes.
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The problem was fixed by ensuring that decoding the dimension sizes
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and max values will not go beyong the end of the buffer.
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(BMR - 2021/05/12, HDFFV-11223)
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- Fixed CVE-2018-11206
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The tool h5dump produced a segfault when the size of a fill value
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message was corrupted and caused a buffer overflow.
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The problem was fixed by verifying the fill value's size
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against the buffer size before attempting to access the buffer.
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(BMR - 2021/03/15, HDFFV-10480)
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- Fixed CVE-2018-14033 (same issue as CVE-2020-10811)
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The tool h5dump produced a segfault when the storage size message
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was corrupted and caused a buffer overflow.
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The problem was fixed by verifying the storage size against the
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buffer size before attempting to access the buffer.
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(BMR - 2021/03/15, HDFFV-11159/HDFFV-11049)
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- Remove underscores on header file guards
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Header file guards used a variety of underscores at the beginning of the define.
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Removed all leading (some trailing) underscores from header file guards.
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(ADB - 2021/03/03, #361)
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- Fixed issue with MPI communicator and info object not being
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copied into new FAPL retrieved from H5F_get_access_plist
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Added logic to copy the MPI communicator and info object into
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the output FAPL. MPI communicator is retrieved from the VFD, while
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the MPI info object is retrieved from the file's original FAPL.
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(JTH - 2021/02/15, HDFFV-11109)
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- Fixed problems with vlens and refs inside compound using
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H5VLget_file_type()
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Modified library to properly ref count H5VL_object_t structs and only
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consider file vlen and reference types to be equal if their files are
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the same.
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(NAF - 2021/01/22)
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- Creation of dataset with optional filter
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When the combination of type, space, etc doesn't work for filter
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and the filter is optional, it was supposed to be skipped but it was
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not skipped and the creation failed.
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Allowed the creation of the dataset in such a situation.
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(BMR - 2020/08/13, HDFFV-10933)
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- Explicitly declared dlopen to use RTLD_LOCAL
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dlopen documentation states that if neither RTLD_GLOBAL nor
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RTLD_LOCAL are specified, then the default behavior is unspecified.
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The default on linux is usually RTLD_LOCAL while macos will default
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to RTLD_GLOBAL.
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(ADB - 2020/08/12, HDFFV-11127)
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- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
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causes asserts/errors when passed to other dataspace API calls.
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H5S_NO_CLASS is an internal class value that should not have been
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exposed via a public API call.
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In debug builds of the library, this can cause assert() function to
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trip. In non-debug builds, it will produce normal library errors.
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The new library behavior is for H5Sset_extent_none() to convert
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the dataspace into one of type H5S_NULL, which is better handled
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by the library and easier for developers to reason about.
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(DER - 2020/07/27, HDFFV-11027)
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- Fixed issues CVE-2018-13870 and CVE-2018-13869
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When a buffer overflow occurred because a name length was corrupted
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and became very large, h5dump crashed on memory access violation.
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A check for reading pass the end of the buffer was added to multiple
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locations to prevent the crashes and h5dump now simply fails with an
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error message when this error condition occurs.
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(BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121)
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- Fixed the segmentation fault when reading attributes with multiple threads
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It was reported that the reading of attributes with variable length string
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datatype will crash with segmentation fault particularly when the number of
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threads is high (>16 threads). The problem was due to the file pointer that
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was set in the variable length string datatype for the attribute. That file
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pointer was already closed when the attribute was accessed.
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The problem was fixed by setting the file pointer to the current opened file pointer
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when the attribute was accessed. Similar patch up was done before when reading
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dataset with variable length string datatype.
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(VC - 2020/07/13, HDFFV-11080)
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- Fixed CVE-2020-10810
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The tool h5clear produced a segfault during an error recovery in
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the superblock decoding. An internal pointer was reset to prevent
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further accessing when it is not assigned with a value.
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(BMR - 2020/06/29, HDFFV-11053)
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- Fixed CVE-2018-17435
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The tool h52gif produced a segfault when the size of an attribute
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message was corrupted and caused a buffer overflow.
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The problem was fixed by verifying the attribute message's size
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against the buffer size before accessing the buffer. h52gif was
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also fixed to display the failure instead of silently exiting
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after the segfault was eliminated.
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(BMR - 2020/06/19, HDFFV-10591)
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Java Library
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------------
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- JNI utility function does not handle new references.
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The JNI utility function for converting reference data to string did
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not use the new APIs. In addition to fixing that function, added new
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java tests for using the new APIs.
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(ADB - 2021/02/16, HDFFV-11212)
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- The H5FArray.java class, in which virtually the entire execution time
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is spent using the HDFNativeData method that converts from an array
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of bytes to an array of the destination Java type.
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1. Convert the entire byte array into a 1-d array of the desired type,
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rather than performing 1 conversion per row;
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2. Use the Java Arrays method copyOfRange to grab the section of the
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array from (1) that is desired to be inserted into the destination array.
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(PGT,ADB - 2020/12/13, HDFFV-10865)
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- Added ability to test java library with VOLs.
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Created a new CMake script that combines the java and vol test scripts.
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(ADB - 2020/02/03, HDFFV-10996)
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- Tests fail for non-English locales.
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In the JUnit tests with a non-English locale, only the part before
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the decimal comma is replaced by XXXX and this leads to a comparison
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error. Changed the regex for the Time substitution.
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(ADB - 2020/01/09, HDFFV-10995)
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Configuration
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-------------
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- Better support for libaec (open-source Szip library) in CMake
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Implemented better support for libaec 1.0.5 (or later) library. This version
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of libaec contains improvements for better integration with HDF5. Furthermore,
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the variable USE_LIBAEC_STATIC has been introduced to allow to make use of
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static version of libaec library. Use libaec_DIR or libaec_ROOT to set
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the location in which libaec can be found.
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Be aware, the Szip library of libaec 1.0.4 depends on another library within
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libaec library. This dependency is not specified in the current CMake
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configuration which means that one can not use the static Szip library of
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libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5.
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(JWSB - 2021/06/22)
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- Refactor CMake configure for Fortran
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The Fortran configure tests for KINDs reused a single output file that was
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read to form the Integer and Real Kinds defines. However, if config was run
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more then once, the CMake completed variable prevented the tests from executing
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again and the last value saved in the file was used to create the define.
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Creating separate files for each KIND solved the issue.
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In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in
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defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION
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correctly for a zero value. This was fixed by supplying the required defines.
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In addition it was moved from the Fortran specific HDF5UseFortran.camke file
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to the C centric ConfigureChecks.cmake file.
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(ADB - 2021/06/03)
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- Move emscripten flag to compile flags
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The emscripten flag, -O0, was removed from target_link_libraries command
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to the correct target_compile_options command.
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(ADB - 2021/04/26 HDFFV-11083)
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- Remove arbitrary warning flag groups from CMake builds
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The arbitrary groups were created to reduce the quantity of warnings being
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reported that overwhelmed testing report systems. Considerable work has
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been accomplished to reduce the warning count and these arbitrary groups
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are no longer needed.
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Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON.
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Visual Studio warnings C4100, C4706, and C4127 have been moved to
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developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds.
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(ADB - 2021/03/22, HDFFV-11228)
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- Reclassify CMake messages, to allow new modes and --log-level option
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CMake message commands have a mode argument. By default, STATUS mode
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was chosen for any non-error message. CMake version 3.15 added additional
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modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode
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of STATUS were reviewed and most were reclassified as VERBOSE. The new
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mode was protected by a check for a CMake version of at least 3.15. If CMake
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version 3.17 or above is used, the user can use the command line option
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of "--log-level" to further restrict which message commands are displayed.
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(ADB - 2021/01/11, HDFFV-11144)
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- Fixes Autotools determination of the stat struct having an st_blocks field
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A missing parenthesis in an autoconf macro prevented building the test
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code used to determine if the stat struct contains the st_blocks field.
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Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define
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found in H5pubconf.h will be defined correctly on both the Autotools and
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CMake. This #define is only used in the tests and does not affect the
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HDF5 C library.
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(DER - 2021/01/07, HDFFV-11201)
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- Add missing ENV variable line to hdfoptions.cmake file
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Using the build options to use system SZIP/ZLIB libraries need to also
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specify the library root directory. Setting the {library}_ROOT ENV
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variable was added to the hdfoptions.cmake file.
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(ADB - 2020/10/19 HDFFV-11108)
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Tools
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-----
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- Changed how h5dump and h5ls identify long double.
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Long double support is not consistent across platforms. Tools will always
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identify long double as 128-bit [little/big]-endian float nn-bit precision.
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New test file created for datasets with attributes for float, double and
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long double. In addition any unknown integer or float datatype will now
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also show the number of bits for precision.
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These files are also used in the java tests.
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(ADB - 2021/03/24, HDFFV-11229,HDFFV-11113)
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- Fixed tools argument parsing.
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Tools parsing used the length of the option from the long array to match
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the option from the command line. This incorrectly matched a shorter long
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name option that happened to be a subset of another long option.
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Changed to match whole names.
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(ADB - 2021/01/19, HDFFV-11106)
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- The tools library was updated by standardizing the error stack process.
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General sequence is:
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h5tools_setprogname(PROGRAMNAME);
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h5tools_setstatus(EXIT_SUCCESS);
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h5tools_init();
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... process the command-line (check for error-stack enable) ...
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h5tools_error_report();
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... (do work) ...
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h5diff_exit(ret);
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(ADB - 2020/07/20, HDFFV-11066)
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- h5diff fixed a command line parsing error.
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h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
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The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used.
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(ADB - 2020/07/20, HDFFV-10897)
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- h5diff added a command line option to ignore attributes.
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h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
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Adding the exclude-attribute argument will only exclude attributes, with the supplied path,
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from comparison.
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(ADB - 2020/07/20, HDFFV-5935)
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- h5diff added another level to the verbose argument to print filenames.
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Added verbose level 3 that is level 2 plus the filenames. The levels are:
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0 : Identical to '-v' or '--verbose'
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1 : All level 0 information plus one-line attribute status summary
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2 : All level 1 information plus extended attribute status report
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3 : All level 2 information plus file names
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(ADB - 2020/07/20, HDFFV-1005)
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- h5repack was fixed to repack the reference attributes properly.
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The code line that checks if the update of reference inside a compound
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datatype is misplaced outside the code block loop that carries out the
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check. In consequence, the next attribute that is not the reference
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type was repacked again as the reference type and caused the failure of
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repacking. The fix is to move the corresponding code line to the correct
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code block.
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(KY -2020/02/10, HDFFV-11014)
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- h5diff was updated to use the new reference APIs.
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h5diff uses the new reference APIs to compare references.
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Attribute references can also be compared.
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(ADB - 2019/12/19, HDFFV-10980)
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- h5dump and h5ls were updated to use the new reference APIs.
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The tools library now use the new reference APIs to inspect a
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file. Also the DDL spec was updated to reflect the format
|
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changes produced with the new APIs. The export API and support
|
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functions in the JNI were updated to match.
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(ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
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Performance
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-------------
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-
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Fortran API
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-----------
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- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
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(MSB - 2020/02/18, HDFFV-11029)
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High-Level Library
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------------------
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-
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Fortran High-Level APIs
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-----------------------
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-
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Documentation
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-------------
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-
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F90 APIs
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--------
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-
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C++ APIs
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--------
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- Added DataSet::operator=
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Some compilers complain if the copy constructor is given explicitly
|
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but the assignment operator is implicitly set to default.
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(2021/05/19)
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Testing
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-------
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- Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
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|
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Lib files needed are now copied to a subdirectory in the java/test
|
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directory, and on Macs the loader path for libhdf5.xxxs.so is changed
|
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in the temporary copy of libhdf5_java.dylib.
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(LRK, 2020/07/02, HDFFV-11063)
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Supported Platforms
|
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===================
|
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|
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Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
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#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
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(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
|
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IBM XL C/C++ V13.1
|
|
IBM XL Fortran V15.1
|
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|
|
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)
|
|
Version 4.9.3, Version 5.2.0,
|
|
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
|
|
|
|
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 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
|
|
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
|
|
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
|
|
Visual Studio 2019 w/ MSMPI 10.1 (cmake)
|
|
|
|
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
|
|
64-bit gfortran GNU Fortran (GCC) 4.9.2
|
|
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
|
|
|
|
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
|
|
|
|
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
|
|
64-bit gfortran GNU Fortran (GCC) 7.1.0
|
|
(swallow/kite) Intel icc/icpc/ifort version 17.0.2
|
|
|
|
|
|
Tested Configuration Features Summary
|
|
=====================================
|
|
|
|
In the tables below
|
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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
|
|
Solaris2.11 32-bit n y/y n y y y
|
|
Solaris2.11 64-bit 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 ?
|
|
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ?
|
|
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y ?
|
|
CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
|
|
CentOS 6.7 Linux 2.6.18 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 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
|
|
Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
|
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|
|
|
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Platform Shared Shared Shared Thread-
|
|
C libs F90 libs C++ libs safe
|
|
Solaris2.11 32-bit y y y y
|
|
Solaris2.11 64-bit y y y 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
|
|
Mac OS X El Capitan 10.11.6 64-bit y n y y
|
|
CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
|
|
CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n
|
|
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
|
|
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
|
|
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
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Linux 2.6.32-573.18.1.el6.ppc64 y y y n
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Compiler versions for each platform are listed in the preceding
|
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"Supported Platforms" table.
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|
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More Tested Platforms
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|
=====================
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The following platforms are not supported but have been tested for this release.
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|
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Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
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#1 SMP x86_64 GNU/Linux compilers:
|
|
(mayll/platypus) Version 4.4.7 20120313
|
|
Version 4.9.3, 5.3.0, 6.2.0
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
x86-64;
|
|
Version 17.10-0
|
|
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
|
|
|
|
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
|
|
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
|
|
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
|
|
GCC Version 7.1.0
|
|
OpenMPI 3.0.0-GCC-7.2.0-2.29
|
|
Intel(R) C (icc) and C++ (icpc) compilers
|
|
Version 17.0.0.098 Build 20160721
|
|
with NAG Fortran Compiler Release 6.1(Tozai)
|
|
|
|
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
|
|
#1 SMP x86_64 GNU/Linux
|
|
(moohan)
|
|
|
|
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
|
|
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
|
|
(ostrich) and IBM XL Fortran for Linux, V15.1
|
|
|
|
Fedora33 5.11.18-200.fc33.x86_64
|
|
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1)
|
|
GNU Fortran (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1)
|
|
clang version 11.0.0 (Fedora 11.0.0-2.fc33)
|
|
(cmake and autotools)
|
|
|
|
Ubuntu20.04 5.8.0-53-generic-x86_64
|
|
#60~20.04-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 9.3.0-17ubuntu1
|
|
GNU Fortran (GCC) 9.3.0-17ubuntu1
|
|
clang version 10.0.0-4ubuntu1
|
|
(cmake and autotools)
|
|
|
|
Ubuntu20.10 5.8.0-53-generic-x86_64
|
|
#60-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1
|
|
GNU Fortran (GCC) 10.2.0-13ubuntu1
|
|
Ubuntu clang version 11.0.0-2
|
|
(cmake and autotools)
|
|
|
|
SUSE15sp2 5.3.18-22-default
|
|
#1 SMP x86_64 GNU/Linux GNU gcc (SUSE Linux) 7.5.0
|
|
GNU Fortran (SUSE Linux) 7.5.0
|
|
clang version 7.0.1 (tags/RELEASE_701/final 349238)
|
|
(cmake and autotools)
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
Setting a variable-length dataset fill value will leak the memory allocated
|
|
for the p field of the hvl_t struct. A fix is in progress for this.
|
|
HDFFV-10840
|
|
|
|
CMake files do not behave correctly with paths containing spaces.
|
|
Do not use spaces in paths because the required escaping for handling spaces
|
|
results in very complex and fragile build files.
|
|
ADB - 2019/05/07
|
|
|
|
At present, metadata cache images may not be generated by parallel
|
|
applications. Parallel applications can read files with metadata cache
|
|
images, but since this is a collective operation, a deadlock is possible
|
|
if one or more processes do not participate.
|
|
|
|
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
|
|
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
|
|
|
|
The subsetting option in ph5diff currently will fail and should be avoided.
|
|
The subsetting option works correctly in serial h5diff.
|
|
|
|
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.
|
|
|
|
|
|
CMake vs. Autotools installations
|
|
=================================
|
|
While both build systems produce similar results, there are differences.
|
|
Each system produces the same set of folders on linux (only CMake works
|
|
on standard Windows); bin, include, lib and share. Autotools places the
|
|
COPYING and RELEASE.txt file in the root folder, CMake places them in
|
|
the share folder.
|
|
|
|
The bin folder contains the tools and the build scripts. Additionally, CMake
|
|
creates dynamic versions of the tools with the suffix "-shared". Autotools
|
|
installs one set of tools depending on the "--enable-shared" configuration
|
|
option.
|
|
build scripts
|
|
-------------
|
|
Autotools: h5c++, h5cc, h5fc
|
|
CMake: h5c++, h5cc, h5hlc++, h5hlcc
|
|
|
|
The include folder holds the header files and the fortran mod files. CMake
|
|
places the fortran mod files into separate shared and static subfolders,
|
|
while Autotools places one set of mod files into the include folder. Because
|
|
CMake produces a tools library, the header files for tools will appear in
|
|
the include folder.
|
|
|
|
The lib folder contains the library files, and CMake adds the pkgconfig
|
|
subfolder with the hdf5*.pc files used by the bin/build scripts created by
|
|
the CMake build. CMake separates the C interface code from the fortran code by
|
|
creating C-stub libraries for each Fortran library. In addition, only CMake
|
|
installs the tools library. The names of the szip libraries are different
|
|
between the build systems.
|
|
|
|
The share folder will have the most differences because CMake builds include
|
|
a number of CMake specific files for support of CMake's find_package and support
|
|
for the HDF5 Examples CMake project.
|
|
|