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2102 lines
84 KiB
Plaintext
HDF5 History
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============
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This file contains development history of the HDF5 1.10 branch
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03. Release Information for hdf5-1.10.1
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02. Release Information for hdf5-1.10.0-patch1
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01. Release Information for hdf5-1.10.0
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[Search on the string '%%%%' for section breaks of each release.]
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%%%%1.10.1%%%%
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HDF5 version 1.10.1 released on 2017-04-27
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================================================================================
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INTRODUCTION
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This document describes the differences between HDF5-1.10.0-patch1 and
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HDF5 1.10.1, and contains information on the platforms tested and known
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problems in HDF5-1.10.1. For more details check the HISTORY*.txt files
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in the HDF5 source.
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Links to HDF5 1.10.1 source code, documentation, and additional materials can
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be found on The HDF5 web page at:
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https://support.hdfgroup.org/HDF5/
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The HDF5 1.10.1 release can be obtained from:
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https://support.hdfgroup.org/HDF5/release/obtain5.html
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User documentation for the snapshot can be accessed directly at this location:
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https://support.hdfgroup.org/HDF5/doc/
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New features in the HDF5-1.10.x release series, including brief general
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descriptions of some new and modified APIs, are described in the "New Features
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in HDF5 Release 1.10" document:
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https://support.hdfgroup.org/HDF5/docNewFeatures/index.html
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All new and modified APIs are listed in detail in the "HDF5 Software Changes
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from Release to Release" document, in the section "Release 10.1 (current
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release) versus Release 1.10.0
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https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
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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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- Major New Features Introduced in HDF5 1.10.1
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- Other New Features and Enhancements
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- Support for New Platforms, Languages, and Compilers
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- Bug Fixes since HDF5-1.10.0-patch1
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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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Major New Features Introduced in HDF5 1.10.1
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============================================
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For links to the RFCs and documentation in this section please view
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https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser.
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________________________________________
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Metadata Cache Image
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________________________________________
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HDF5 metadata is typically small, and scattered throughout the HDF5 file.
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This can affect performance, particularly on large HPC systems. The
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Metadata Cache Image feature can improve performance by writing the
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metadata cache in a single block on file close, and then populating the
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cache with the contents of this block on file open, thus avoiding the many
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small I/O operations that would otherwise be required on file open and
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close. See the RFC for complete details regarding this feature. Also,
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see the Fine Tuning the Metadata Cache documentation.
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At present, metadata cache images may not be generated by parallel
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applications. Parallel applications can read files with metadata cache
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images, but since this is a collective operation, a deadlock is possible
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if one or more processes do not participate.
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________________________________________
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Metadata Cache Evict on Close
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________________________________________
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The HDF5 library's metadata cache is fairly conservative about holding on
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to HDF5 object metadata (object headers, chunk index structures, etc.),
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which can cause the cache size to grow, resulting in memory pressure on
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an application or system. The "evict on close" property will cause all
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metadata for an object to be evicted from the cache as long as metadata
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is not referenced from any other open object. See the Fine Tuning the
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Metadata Cache documentation for information on the APIs.
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At present, evict on close is disabled in parallel builds.
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________________________________________
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Paged Aggregation
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________________________________________
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The current HDF5 file space allocation accumulates small pieces of metadata
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and raw data in aggregator blocks which are not page aligned and vary
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widely in sizes. The paged aggregation feature was implemented to provide
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efficient paged access of these small pieces of metadata and raw data.
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See the RFC for details. Also, see the File Space Management documentation.
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________________________________________
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Page Buffering
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________________________________________
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Small and random I/O accesses on parallel file systems result in poor
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performance for applications. Page buffering in conjunction with paged
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aggregation can improve performance by giving an application control of
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minimizing HDF5 I/O requests to a specific granularity and alignment.
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See the RFC for details. Also, see the Page Buffering documentation.
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At present, page buffering is disabled in parallel builds.
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Other New Features and Enhancements
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===================================
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Library
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-------
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- Added a mechanism for disabling the SWMR file locking scheme.
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The file locking calls used in HDF5 1.10.0 (including patch1)
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will fail when the underlying file system does not support file
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locking or where locks have been disabled. To disable all file
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locking operations, an environment variable named
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HDF5_USE_FILE_LOCKING can be set to the five-character string
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'FALSE'. This does not fundamentally change HDF5 library
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operation (aside from initial file open/create, SWMR is lock-free),
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but users will have to be more careful about opening files
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to avoid problematic access patterns (i.e.: multiple writers)
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that the file locking was designed to prevent.
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Additionally, the error message that is emitted when file lock
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operations set errno to ENOSYS (typical when file locking has been
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disabled) has been updated to describe the problem and potential
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resolution better.
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(DER, 2016/10/26, HDFFV-9918)
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- The return type of H5Pget_driver_info() has been changed from void *
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to const void *.
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The pointer returned by this function points to internal library
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memory and should not be freed by the user.
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(DER, 2016/11/04, HDFFV-10017)
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- The direct I/O VFD has been removed from the list of VFDs that
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support SWMR.
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This configuration was never officially tested and several SWMR
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tests fail when this VFD is set.
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(DER, 2016/11/03, HDFFV-10169)
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Configuration:
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--------------
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- The minimum version of CMake required to build HDF5 is now 3.2.2.
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(ADB, 2017/01/10)
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- An --enable/disable-developer-warnings option has been added to
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configure.
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This disables warnings that do not indicate poor code quality such
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as -Winline and gcc's -Wsuggest-attribute. Developer warnings are
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disabled by default.
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(DER, 2017/01/10)
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- A bin/restore.sh script was added that reverts autogen.sh processing.
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(DER, 2016/11/08)
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- CMake: Added NAMESPACE hdf5:: to package configuration files to allow
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projects using installed HDF5 binaries built with CMake to link with
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them without specifying the HDF5 library location via IMPORTED_LOCATION.
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(ABD, 2016/10/17, HDFFV-10003)
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- CMake: Changed the CTEST_BUILD_CONFIGURATION option to
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CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
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(ABD, 2016/10/17, HDFFV-9971)
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Fortran Library:
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----------------
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- The HDF5 Fortran library can now be compiled with the NAG compiler.
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(MSB, 2017/2/10, HDFFV-9973)
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C++ Library:
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------------
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- The following C++ API wrappers have been added to the C++ Library:
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// Sets/Gets the strategy and the threshold value that the library
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// will employ in managing file space.
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FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy
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FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy
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// Sets/Gets the file space page size for paged aggregation.
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FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size
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FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size
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// Checks if the given ID is valid.
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IdComponent::isValid - H5Iis_valid
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// Sets/Gets the number of soft or user-defined links that can be
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// traversed before a failure occurs.
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LinkAccPropList::setNumLinks - H5Pset_nlinks
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LinkAccPropList::getNumLinks - H5Pget_nlinks
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// Returns a copy of the creation property list of a datatype.
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DataType::getCreatePlist - H5Tget_create_plist
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// Opens/Closes an object within a group or a file, regardless of object
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// type
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Group::getObjId - H5Oopen
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Group::closeObjId - H5Oclose
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// Maps elements of a virtual dataset to elements of the source dataset.
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DSetCreatPropList::setVirtual - H5Pset_virtual
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// Gets general information about this file.
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H5File::getFileInfo - H5Fget_info2
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// Returns the number of members in a type.
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IdComponent::getNumMembers - H5Inmembers
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// Determines if an element type exists.
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IdComponent::typeExists - H5Itype_exists
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// Determines if an object exists.
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H5Location::exists - H5Lexists.
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// Returns the header version of an HDF5 object.
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H5Object::objVersion - H5Oget_info for version
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(BMR, 2017/03/20, HDFFV-10004, HDFFV-10139, HDFFV-10145)
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- New exception: ObjHeaderIException for H5O interface.
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(BMR, 2017/03/15, HDFFV-10145)
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- New class LinkAccPropList for link access property list, to be used by
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wrappers of H5Lexists.
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(BMR, 2017/01/04, HDFFV-10145)
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- New constructors to open datatypes in ArrayType, CompType, DataType,
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EnumType, FloatType, IntType, StrType, and VarLenType.
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(BMR, 2016/12/26, HDFFV-10056)
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- New member functions:
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DSetCreatPropList::setNbit() to setup N-bit compression for a dataset.
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ArrayType::getArrayNDims() const
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ArrayType::getArrayDims() const
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both to replace the non-const versions.
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(BMR, 2016/04/25, HDFFV-8623, HDFFV-9725)
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Tools:
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------
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- The following options have been added to h5clear:
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-s: clear the status_flags field in the file's superblock
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-m: Remove the metadata cache image from the file
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(QAK, 2017/03/22, PR#361)
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High-Level APIs:
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---------------
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- Added New Fortran 2003 API for h5tbmake_table_f.
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(MSB, 2017/02/10, HDFFV-8486)
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Support for New Platforms, Languages, and Compilers
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===================================================
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- Added NAG compiler
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Bug Fixes since HDF5-1.10.0-patch1 release
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==================================
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Library
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-------
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- Outdated data structure was used in H5D_CHUNK_DEBUG blocks, causing
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compilation errors when H5D_CHUNK_DEBUG was defined. This is fixed.
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(BMR, 2017/04/04, HDFFV-8089)
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- SWMR implementation in the HDF5 1.10.0 and 1.10.0-patch1 releases has a
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broken metadata flush dependency that manifested itself with the following
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error at the end of the HDF5 error stack:
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H5Dint.c line 846 in H5D__swmr_setup(): dataspace chunk index must be 0
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for SWMR access, chunkno = 1
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major: Dataset
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minor: Bad value
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It was also reported at https://github.com/areaDetector/ADCore/issues/203
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The flush dependency is fixed in this release.
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- Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY
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(ABD, 2016/12/12, PR#201)
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- A number of issues were fixed when reading/writing from/to corrupted
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files to ensure that the library fails gracefully in these cases:
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* Writing to a corrupted file that has an object message which is
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incorrectly marked as sharable on disk results in a buffer overflow /
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invalid write instead of a clean error message.
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* Decoding data from a corrupted file with a dataset encoded with the
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H5Z_NBIT decoding can result in a code execution vulnerability under
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the context of the application using the HDF5 library.
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* When decoding an array datatype from a corrupted file, the HDF5 library
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fails to return an error in production if the number of dimensions
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decoded is greater than the maximum rank.
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* When decoding an "old style" array datatype from a corrupted file, the
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HDF5 library fails to return an error in production if the number of
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dimensions decoded is greater than the maximum rank.
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(NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
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- Fixed an error that would occur when copying an object with an attribute
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which is a compound datatype consisting of a variable length string.
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(VC, 2016/08/24, HDFFV-7991)
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- H5DOappend will no longer fail if a dataset has no append callback
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registered.
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(VC, 2016/08/14, HDFFV-9960)
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- Fixed an issue where H5Pset_alignment could result in misaligned blocks
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with some input combinations, causing an assertion failure in debug mode.
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(NAF, 2016/08/11, HDFFV-9948)
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- Fixed a problem where a plugin compiled into a DLL in the default plugin
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directory could not be found by the HDF5 library at runtime on Windows
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when the HDF5_PLUGIN_PATH environment variable was not set.
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(ABD, 2016/08/01, HDFFV-9706)
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- Fixed an error that would occur when calling H5Adelete on an attribute
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which is attached to an externally linked object in the target file and
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whose datatype is a committed datatype in the main file.
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(VC, 2016/07/06, HDFFV-9940)
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- (a) Throw an error instead of assertion when v1 btree level hits the 1
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byte limit.
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(b) Modifications to better handle error recovery when conversion by
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h5format_convert fails.
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(VC, 2016/05/29, HDFFV-9434)
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- Fixed a memory leak where an array used by the library to track SWMR
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read retries was unfreed.
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The leaked memory was small (on the order of a few tens of ints) and
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allocated per-file. The memory was allocated (and lost) only when a
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file was opened for SWMR access.
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(DER, 2016/04/27, HDFFV-9786)
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- Fixed a memory leak that could occur when opening a file for the first
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time (including creating) and the call fails.
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This occurred when the file-driver-specific info was not cleaned up.
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The amount of memory leaked varied with the file driver, but would
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normally be less than 1 kB.
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(DER, 2016/12/06, HDFFV-10168)
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- Fixed a failure in collective metadata writes.
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This failure only appeared when collective metadata writes
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were enabled (via H5Pset_coll_metadata_write()).
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(JRM, 2017/04/10, HDFFV-10055)
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Parallel Library
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----------------
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- Fixed a bug that could occur when allocating a chunked dataset in parallel
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with an alignment set and an alignment threshold greater than the chunk
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size but less than or equal to the raw data aggregator size.
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(NAF, 2016/08/11, HDFFV-9969)
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Configuration
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-------------
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- Configuration will check for the strtoll and strtoull functions
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before using alternatives
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(ABD, 2017/03/17, PR#340)
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- CMake uses a Windows pdb directory variable if available and
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will generate both static and shared pdb files.
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(ABD, 2017/02/06, HDFFV-9875)
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- CMake now builds shared versions of tools.
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(ABD, 2017/02/01, HDFFV-10123)
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- Makefiles and test scripts have been updated to correctly remove files
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created when running "make check" and to avoid removing any files under
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source control. In-source builds followed by "make clean" and "make
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distclean" should result in the original source files.
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(LRK, 2017/01/17, HDFFV-10099)
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- The tools directory has been divided into two separate source and test
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directories. This resolves a build dependency and, as a result,
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'make check' will no longer fail in the tools directory if 'make' was
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not executed first.
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(ABD, 2016/10/27, HDFFV-9719)
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- CMake: Fixed a timeout error that would occasionally occur when running
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the virtual file driver tests simultaneously due to test directory
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and file name collisions.
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(ABD, 2016/09/19, HDFFV-9431)
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- CMake: Fixed a command length overflow error by converting custom
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commands inside CMakeTest.cmake files into regular dependencies and
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targets.
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(ABD, 2016/07/12, HDFFV-9939)
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- Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
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condensing cygwin configuration files into a single file and
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removing outdated compiler settings.
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(ABD, 2016/07/12, HDFFV-9946)
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Fortran
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--------
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- Changed H5S_ALL_F from INTEGER to INTEGER(HID_T)
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(MSB, 2016/10/14, HDFFV-9987)
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Tools
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-----
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- h5diff now correctly ignores strpad in comparing strings.
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(ABD, 2017/03/03, HDFFV-10128)
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- h5repack now correctly parses the command line filter options.
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(ABD, 2017/01/24, HDFFV-10046)
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- h5diff now correctly returns an error when it cannot read data due
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to an unavailable filter plugin.
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(ADB 2017/01/18, HDFFV-9994 )
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- Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
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in which they would erroneously drop the file argument specified via
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the -o flag when the -o flag was specified before the -c flag on the
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command line, resulting in a failure to compile.
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(LRK, 2016/11/04, HDFFV-9938, HDFFV-9530)
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- h5repack User Defined (UD) filter parameters were not parsed correctly.
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The UD filter parameters were not being parsed correctly. Reworked coding
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section to parse the correct values and verify number of parameters.
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(ABD, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039)
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- h5repack allows the --enable-error-stack option on the command line.
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(ADB, 2016/08/08, HDFFV-9775)
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C++ APIs
|
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--------
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- The member function H5Location::getNumObjs() is moved to
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class Group because the objects are in a group or a file only,
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and H5Object::getNumAttrs to H5Location to get the number of
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attributes at a given location.
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|
(BMR, 2017/03/17, PR#466)
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|
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- Due to the change in the C API, the overloaded functions of
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PropList::setProperty now need const for some arguments. They are
|
|
planned for deprecation and are replaced by new versions with proper
|
|
consts.
|
|
|
|
(BMR, 2017/03/17, PR#344)
|
|
|
|
- The high-level API Packet Table (PT) did not write data correctly when
|
|
the datatype is a compound type that has string type as one of the
|
|
members. This problem started in 1.8.15, after the fix of HDFFV-9042
|
|
was applied, which caused the Packet Table to use native type to access
|
|
the data. It should be up to the application to specify whether the
|
|
buffer to be read into memory is in the machine's native architecture.
|
|
Thus, the PT is fixed to not use native type but to make a copy of the
|
|
user's provided datatype during creation or the packet table's datatype
|
|
during opening. If an application wishes to use native type to read the
|
|
data, then the application will request that. However, the Packet Table
|
|
doesn't provide a way to specify memory datatype in this release. This
|
|
feature will be available in future releases.
|
|
|
|
(BMR, 2016/10/27, HDFFV-9758)
|
|
|
|
- The obsolete macros H5_NO_NAMESPACE and H5_NO_STD have been removed from
|
|
the HDF5 C++ API library.
|
|
|
|
(BMR, 2016/10/23, HDFFV-9532)
|
|
|
|
- The problem where a user-defined function cannot access both, attribute
|
|
and dataset, using only one argument is now fixed.
|
|
|
|
(BMR, 2016/10/11, HDFFV-9920)
|
|
|
|
- In-memory array information, ArrayType::rank and
|
|
ArrayType::dimensions, were removed. This is an implementation
|
|
detail and should not affect applications.
|
|
|
|
(BMR, 2016/04/25, HDFFV-9725)
|
|
|
|
|
|
Testing
|
|
-------
|
|
- Fixed a problem that caused tests using SWMR to occasionally fail when
|
|
running "make check" using parallel make.
|
|
|
|
(LRK, 2016/03/22, PR#338, PR#346, PR#358)
|
|
|
|
|
|
Supported Platforms
|
|
===================
|
|
|
|
Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
|
|
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
|
|
(ostrich) GNU Fortran (GCC) 4.4.7 20120313
|
|
(Red Hat 4.4.7-4)
|
|
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)
|
|
Version 4.9.3, Version 5.2.0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 15.0.3.187 Build 20150407
|
|
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/ 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 clang/clang++ version 5.1 from Xcode 5.1
|
|
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 clang/clang++ version 6.0 from Xcode 6.2
|
|
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 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 from Xcode 7.3
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
(osx1010dev/osx1010test) 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
|
|
Solaris2.11 32-bit n y/y n y y y
|
|
Solaris2.11 64-bit n y/n n y y y
|
|
Windows 7 y y/y n y y y
|
|
Windows 7 x64 y y/y y 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
|
|
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
|
|
CentOS 7.2 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/y n y y y
|
|
|
|
|
|
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 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
|
|
Mac OS X El Capitan 10.11.6 64-bit y n y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
|
|
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
|
|
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
|
|
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
|
|
|
|
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 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
(mayll/platypus) Version 4.4.7 20120313
|
|
Version 4.8.4
|
|
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 15.0.3.187 (Build 20150407)
|
|
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)
|
|
Intel(R) C (icc) and C++ (icpc) compilers
|
|
Version 15.0.3.187 (Build 20150407)
|
|
with NAG Fortran Compiler Release 6.1(Tozai)
|
|
|
|
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
|
|
|
|
Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
|
|
gcc, g++ (Debian 4.9.2-10) 4.9.2
|
|
GNU Fortran (Debian 4.9.2-10) 4.9.2
|
|
(cmake and autotools)
|
|
|
|
Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc, g++ (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)
|
|
|
|
Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
|
|
gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
|
|
5.4.0 20160609
|
|
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
|
|
5.4.0 20160609
|
|
(cmake and autotools)
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
|
|
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.
|
|
|
|
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.
|
|
|
|
|
|
%%%%1.10.0-patch1%%%%
|
|
|
|
|
|
HDF5 version 1.10.0-patch1 released on 2016-05-23
|
|
================================================================================
|
|
|
|
INTRODUCTION
|
|
|
|
This document describes the differences between HDF5-1.8 series and
|
|
HDF5 1.10.0 releases, and contains information on the platforms
|
|
tested.
|
|
|
|
Links to HDF5 1.10.0 source code can be found on The HDF Group's
|
|
development FTP server at the following location:
|
|
|
|
https://www.hdfgroup.org/HDF5/release/obtain5110.html
|
|
|
|
User documentation can be accessed directly at this location:
|
|
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/
|
|
|
|
For more information, see the HDF5 home page:
|
|
|
|
https://www.hdfgroup.org/HDF5/
|
|
|
|
If you have any questions or comments, please send them to the HDF
|
|
Help Desk:
|
|
|
|
help@hdfgroup.org
|
|
|
|
|
|
|
|
CONTENTS
|
|
|
|
- New Features
|
|
- Issues Addressed in this Release
|
|
- Supported Platforms
|
|
- Tested Configuration Features Summary
|
|
- More Tested Platforms
|
|
- Known Problems and Limitations
|
|
|
|
|
|
|
|
New Features
|
|
============
|
|
This release supports the following features:
|
|
|
|
Configuration
|
|
-------------
|
|
- API Compatibility with HDF5 1.8 Flag Was Added
|
|
|
|
The 1.10 version of the HDF5 Library can be configured to operate
|
|
identically to the 1.8 library with the --with-default-api-version=v18
|
|
configure flag. This allows existing code to be compiled with the 1.10
|
|
library without requiring immediate changes to the application source
|
|
code. For addtional configuration options and other details, see
|
|
"API Compatibility Macros in HDF5" at
|
|
https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
|
|
|
|
- Autotools Configuration Has Been Extensively Reworked
|
|
|
|
The autotools configuration options have been updated to allow more
|
|
fine-grained control of the build options and to correct some bugs.
|
|
See configure --help for comprehensive information on each option.
|
|
|
|
Specific changes:
|
|
|
|
* --enable-debug and --enable-production are no longer accepted.
|
|
Use --enable-build-mode=(debug | production) instead. These set
|
|
appropriate defaults for symbols, optimizations, and other
|
|
configuration options. These defaults can be overridden by the
|
|
user.
|
|
|
|
* Extra debug output messages are no longer enabled with
|
|
--enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
|
|
instead.
|
|
|
|
* A new --enable-symbols option allows symbols to be generated
|
|
independently of the build mode. --disable-symbols can be used
|
|
to strip symbols from the binary.
|
|
|
|
* A new --enable-asserts option sets/unsets NDEBUG. This is
|
|
independent of the build mode. This also enables some extra
|
|
low-overhead debug checks in the library.
|
|
|
|
* A new --enable-profiling option sets profiling flags. This is
|
|
independent of the build mode.
|
|
|
|
* A new --enable-optimization option sets the optimization level.
|
|
This is independent of the build mode.
|
|
|
|
* Many of these options can take a flags string that will be used
|
|
to build the library. This can be useful for specifying custom
|
|
optimization flags such as -Os and -Ofast.
|
|
|
|
* gnu C++ and Fortran use configure sub-files that update the
|
|
build flags and turn on warnings. The increase in warnings when
|
|
building these wrapper libraries is due to these flag changes
|
|
and not to a decrease in code quality.
|
|
|
|
* The option to clear file buffers has been removed. Any buffer that
|
|
will eventually be written to disk will now always be memset
|
|
to zero. This prevents the previous contents of the buffer from
|
|
being written to the disk if the buffer contents are not
|
|
completely overwritten, which has security implications.
|
|
|
|
- LFS Changes
|
|
|
|
The way the autotools handle large file support (LFS) has been
|
|
overhauled in this release.
|
|
|
|
* We assume ftello and fseeko exist
|
|
|
|
* We no longer explicitly use the *64 I/O functions. Instead, we
|
|
rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
|
|
|
|
* _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
|
|
|
|
|
|
|
|
Parallel Library
|
|
-----------------
|
|
- Collective Metadata I/O
|
|
|
|
Calls for HDF5 metadata can result in many small reads and writes.
|
|
On metadata reads, collective metadata I/O can improve performance
|
|
by allowing the library to perform optimizations when reading the
|
|
metadata by having one rank read the data and broadcasting it to
|
|
all other ranks.
|
|
|
|
Collective metadata I/O improves metadata write performance through
|
|
the construction of an MPI derived datatype that is then written
|
|
collectively in a single call. For more information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
|
|
|
|
|
|
|
|
Library
|
|
--------
|
|
- Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR)
|
|
|
|
The Single Writer/ Multiple Reader or SWMR feature enables users to
|
|
read data concurrently while writing it. Communications between the
|
|
processes and file locking are not required. The processes can run
|
|
on the same or on different platforms as long as they share a common
|
|
file system that is POSIX compliant. For more information, see the
|
|
Single-Writer/Multiple-Reader (SWMR) documentation at
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
|
|
|
|
- Virtual Dataset (VDS)
|
|
|
|
The VDS feature enables data to be accessed across HDF5 files
|
|
using standard HDF5 objects such as groups and datasets without
|
|
rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
|
|
is an HDF5 dataset that is composed of source HDF5 datasets in
|
|
a predefined mapping. VDS can be used with the SWMR feature. For
|
|
documentation, check
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
|
|
|
|
- Persistent Free File Space Tracking
|
|
|
|
Usage patterns when working with an HDF5 file sometimes result in
|
|
wasted space within the file. This can also impair access times
|
|
when working with the resulting files. The new file space management
|
|
feature provides strategies for managing space in a file to improve
|
|
performance in both of these areas. For more information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
|
|
|
|
- Version 3 Metadata Cache
|
|
|
|
The version 3 metadata cache moves management of metadata I/O from
|
|
the clients to the metadata cache proper. This change is essential for
|
|
SWMR and other features that have yet to be released.
|
|
|
|
|
|
|
|
C++ Library
|
|
------------
|
|
- New Member Function Added to H5::ArrayType
|
|
|
|
The assignment operator ArrayType::operator= was added because
|
|
ArrayType has pointer data members.
|
|
|
|
(BMR - 2016/03/07, HDFFV-9562)
|
|
|
|
|
|
|
|
Tools
|
|
------
|
|
- h5watch
|
|
|
|
The h5watch tool allows users to output new records appended to
|
|
a dataset under SWMR access as it grows. The functionality is
|
|
similar to the Unix user command "tail" with the follow option,
|
|
which outputs appended data as the file grows. For more
|
|
information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
|
|
|
|
- h5format_convert
|
|
|
|
The h5format_convert tool allows users to convert the indexing
|
|
type of a chunked dataset made with a 1.10.x version of the HDF5
|
|
Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
|
|
type. For example, datasets created using SWMR access, can be
|
|
converted to be accessed by the HDF5 1.18 library and tools. The
|
|
tool does not rewrite raw data, but it does rewrite HDF5 metadata.
|
|
|
|
|
|
|
|
High-Level APIs
|
|
----------------
|
|
- H5DOappend
|
|
|
|
The function appends data to a dataset along a specified dimension.
|
|
|
|
|
|
C Packet Table API
|
|
------------------
|
|
- Replacement of a Public Function with H5PTcreate
|
|
|
|
The existing function H5PTcreate_fl limits applications so they
|
|
can use the deflate compression only. The public function
|
|
H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
|
|
takes a property list identifier to provide flexibility on
|
|
creation properties.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- New Public Functions: H5PTget_dataset and H5PTget_type
|
|
|
|
Two accessor functions have been added. H5PTget_dataset returns
|
|
the identifier of the dataset associated with the packet table,
|
|
and H5PTget_type returns the identifier of the datatype used by
|
|
the packet table.
|
|
|
|
(BMR, 2016/03/04, HDFFV-8623)
|
|
|
|
- Regarding #ifdef VLPT_REMOVED
|
|
|
|
The #ifdef VLPT_REMOVED blocks have been removed from the packet
|
|
table (PT) library source except for the following functions:
|
|
+ H5PTis_varlen() has been made available again
|
|
+ H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
|
|
|
|
(BMR - 2016/03/04, HDFFV-442)
|
|
|
|
C++ Packet Table API
|
|
--------------------
|
|
- New Constructor Added to FL_PacketTable
|
|
|
|
An overloaded constructor has been added to FL_PacketTable and
|
|
takes a property list identifier to provide flexibility on
|
|
creation properties.
|
|
|
|
(BMR - 2016/03/08, HDFFV-8623)
|
|
|
|
- New Public Functions
|
|
|
|
Two accessor wrappers are added to class PacketTable.
|
|
PacketTable::GetDataset() returns the identifier of the dataset
|
|
associated with the packet table, and PacketTable::GetDatatype()
|
|
returns the identifier of the datatype that the packet table uses.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- Member Functions with "char*" as an Argument
|
|
|
|
Overloaded functions were added to provide the "const char*"
|
|
argument; the existing version will be deprecated in future
|
|
releases.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- Regarding #ifdef VLPT_REMOVED
|
|
|
|
The #ifdef VLPT_REMOVED blocks have been removed from the packet
|
|
table library source code except for the following functions:
|
|
+ VL_PacketTable::IsVariableLength() was moved to PacketTable
|
|
+ VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
|
|
|
|
(BMR - 2016/03/04, HDFFV-442)
|
|
|
|
|
|
|
|
Java Wrapper Library
|
|
--------------------
|
|
|
|
The Java HDF5 JNI library has been integrated into the HDF5 repository.
|
|
The configure option is "--enable-java", and the CMake option is
|
|
HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
|
|
HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
|
|
"hdf.hdflib.hdf5".
|
|
|
|
A number of new APIs were added including some for VDS and SWMR.
|
|
|
|
|
|
|
|
Other Important Changes
|
|
-----------------------
|
|
|
|
The hid_t type was changed from 32-bit to a 64-bit value.
|
|
|
|
|
|
|
|
Issues Addressed in this Release Since 1.10.0
|
|
=============================================
|
|
|
|
- h5diff would return from a compare attributes abnormally if one of the datatypes
|
|
was a vlen. This resulted in a memory leak as well as an incorrect report of
|
|
attribute comparison.
|
|
|
|
Fixed.
|
|
(ADB - 2016/04/26, HDFFV-9784)
|
|
|
|
- The JUnit-interface test may fail on Solaris platforms. The result of
|
|
a test for verifying the content of the error stack to stdout is
|
|
in a different order on Solaris then other platforms.
|
|
|
|
This test is skipped on Solaris
|
|
(ADB - 2016/04/21, HDFFV-9734)
|
|
|
|
- When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
|
|
there was a missing command argument for the tests of the examples.
|
|
|
|
Fixed.
|
|
(ADB - 2016/04/21, HDFFV-9743)
|
|
|
|
- Changed h5diff to print a warning when a dataset is virtual, enabling
|
|
the data to be compared. In addition h5repack failed to copy the data
|
|
of a virtual dataset to the new file. Function H5D__get_space_status changed
|
|
to correctly determine the H5D_space_status_t allocation value.
|
|
|
|
CMake added the Fixed Array indexing tests that were only in the autotools
|
|
test scripts.
|
|
|
|
Fixed and tests added for vds issues.
|
|
(ADB,NAF - 2016/04/21, HDFFV-9756)
|
|
|
|
- CMake added the h5format_convert tool and tests that were only in the autotools
|
|
build and test scripts. The autotools test script was reworked to allow CMake
|
|
to execute the test suite in parallel.
|
|
|
|
Also, h5clear tool and tests were added to the misc folder.
|
|
|
|
Fixed.
|
|
(ADB - 2016/04/21, HDFFV-9766)
|
|
|
|
- CMake added the h5watch tool and argument tests that were only in the autotools
|
|
build and test scripts. The POSIX only tests were not added to CMake.
|
|
|
|
CMake HL tools files were refactored to move the CMake test scripts into each tool folder.
|
|
|
|
Fixed.
|
|
(ADB - 2016/04/21, HDFFV-9770)
|
|
|
|
- Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled.
|
|
|
|
Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish
|
|
KINDs of same precision
|
|
(MSB - 2016/05/14,HDFFV-9912)
|
|
|
|
|
|
- Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN).
|
|
(MSB - 2016/05/14)
|
|
|
|
- Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled.
|
|
|
|
Fixed.
|
|
(MSB - 2016/05/14,HDFFV-9912)
|
|
|
|
- Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran
|
|
enabled.
|
|
|
|
Fixed.
|
|
(MSB - 2016/05/16,HDFFV-9917)
|
|
|
|
- A cmake build with Fortran enabled does not install module h5fortkit
|
|
|
|
Fixed.
|
|
(MSB - 2016/05/23,HDFFV-9923)
|
|
|
|
|
|
Issues Addressed in this Release Since alpha1
|
|
=============================================
|
|
|
|
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
|
|
|
|
The correct access property list settings from the
|
|
H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
|
|
H5Pget_efile_prefix function calls could not be retrieved
|
|
using H5Dget_access_plist().
|
|
|
|
Fixed.
|
|
|
|
(DER and NAF - 2016/03/14, HDFFV-9716)
|
|
|
|
- h5dump
|
|
|
|
When h5dump was provided with the name of a non-existing file or
|
|
when optional arguments were the last option on the command line,
|
|
h5dump would segfault.
|
|
|
|
Fixed.
|
|
|
|
(ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
|
|
|
|
- No Error Message for Corrupt Metadata
|
|
|
|
The HDF5 Library did not propagate an error when it encountered
|
|
corrupt metadata in an HDF5 file. The issue was fixed for a
|
|
specific file provided by a user. If you still see the problem,
|
|
please contact help@hdfgroup.org
|
|
|
|
Fixed.
|
|
|
|
(MC - 2016/02/18, HDFFV-9670)
|
|
|
|
- Problem Reading Chunked Datasets with a String Datatype Larger
|
|
Than the Chunk Size in Bytes
|
|
|
|
When the latest file format was used and when a chunked dataset
|
|
was created with a datatype with the size bigger than a chunk
|
|
size, the data could not be read back. The issue was reported
|
|
for chunked datasets with a string datatype and was confirmed
|
|
for other datatypes with the sizes bigger than the chunk size in
|
|
bytes.
|
|
|
|
Fixed.
|
|
|
|
(JM - 2016/02/13, HDFFV-9672)
|
|
|
|
- Control over the Location of External Files
|
|
|
|
Users were unable to specify the locations of external files.
|
|
|
|
Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
|
|
added so that users could specify the locations of external files.
|
|
|
|
(DER - 2016/02/04, HDFFV-8740)
|
|
|
|
|
|
|
|
Issues Addressed in this Release Since alpha0
|
|
=============================================
|
|
- h5format_convert
|
|
|
|
The h5format_convert tool did not downgrade the version of the
|
|
superblock.
|
|
|
|
Fixed. The tool now will downgrade the version of the superblock.
|
|
|
|
(EIP 2016/01/11)
|
|
|
|
- Crashes with multiple threads: invalid pointers
|
|
|
|
It was reported that alpha0 crashed when used with multiple
|
|
threads. The issue exists in the HDF5 Library versions 1.8 and
|
|
1.9. The problem is related to a shared file pointer used in some
|
|
miscellaneous data structures. The thread-safe library exposed
|
|
paths in the library where a file pointer became invalid.
|
|
|
|
The alpha1 release contains the fixes for the specific use case
|
|
as described in HDFFV-9643. We will keep working on identifying
|
|
and fixing other paths in the library with similar problems.
|
|
|
|
(EIP - 2016/01/15, HDFFV-9643)
|
|
|
|
|
|
|
|
Supported Platforms
|
|
===================
|
|
The following platforms are supported and have been tested for this release.
|
|
They are built with the configure process unless specified otherwise.
|
|
|
|
AIX 6.1 xlc/xlc_r 10.1.0.5
|
|
(NASA G-ADA) xlC/xlC_r 10.1.0.5
|
|
xlf90/xlf90_r 12.1.0.6
|
|
|
|
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
(mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16)
|
|
Version 4.9.3, Version 5.2.0
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
x86-64;
|
|
Version 15.7-0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 15.0.3.187 Build 20150407
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
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)
|
|
Version 4.9.3, Version 5.2.0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 15.0.3.187 Build 20150407
|
|
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)
|
|
Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
|
|
(cmake and autotools)
|
|
|
|
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)
|
|
|
|
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
|
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
|
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
|
|
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 clang/clang++ version 6.0 from Xcode 6.2
|
|
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 clang/clang++ version 6.0 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 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
|
|
|
|
|
|
|
|
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/y n y y n
|
|
Windows 8.1 n y/y n y y y
|
|
Windows 8.1 x64 n 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 Yosemeti 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 8.1 y y y y
|
|
Windows 8.1 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 Yosemeti 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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
|
|
#1 SMP x86_64 GNU/Linux
|
|
(platypus)
|
|
|
|
Windows 7 Visual Studio 2008 (cmake)
|
|
|
|
Windows 7 x64 Visual Studio 2008 (cmake)
|
|
|
|
Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
|
|
|
|
Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
|
|
gcc (Debian 4.7.2-5) 4.7.2
|
|
GNU Fortran (Debian 4.7.2-5) 4.7.2
|
|
(cmake and autotools)
|
|
|
|
Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
|
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
|
(cmake and autotools)
|
|
|
|
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc (SUSE Linux) 4.8.1
|
|
GNU Fortran (SUSE Linux) 4.8.1
|
|
(cmake and autotools)
|
|
|
|
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
|
|
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
|
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
|
(cmake and autotools)
|
|
|
|
hopper.nersc.gov PrgEnv-gnu/5.2.40
|
|
gcc (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
g++ (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
|
|
|
|
|
|
Known Problems and Limitations
|
|
==============================
|
|
This section contains the list of known problems and limitations introduced
|
|
in this release of HDF5.
|
|
|
|
Note: this list is not exhaustive of all known issues discovered in HDF5
|
|
software to date. For a list of significant problems and known workarounds
|
|
identified in past releases, please refer to:
|
|
|
|
https://www.hdfgroup.org/HDF5/release/known_problems/
|
|
|
|
The HDF Group also maintains a JIRA issue-tracking database which is used to
|
|
capture all known issues which are too numerous to reasonably list in this
|
|
document. The HDF Group is taking steps to make our JIRA issue database
|
|
open to the public, and this section will refer to that database in a future
|
|
release. In the meantime, please contact help@hdfgroup.org if you come across
|
|
an issue not listed here or at the link above, and we will provide any
|
|
information about known workarounds that we have or add it to our list of
|
|
known issues if it is a new issue.
|
|
|
|
- The flush/refresh test occasionally fails on OS X platforms. This is
|
|
being investigated but no fix or workaround is available at this time.
|
|
(DER - 2016/03/22, HDFFV-9731)
|
|
|
|
- The VDS/SWMR test will fail with a segmentation fault if the library
|
|
is built with --enable-using-memchecker. The is due to a VDS shutdown
|
|
procedure freeing a shared resource too early when the memory
|
|
checker changes are built. This problem does not arise when the
|
|
memory checker changes are not used since the internal library free
|
|
lists behave differently. The memory checker configure option should
|
|
normally only be used under special circumstances so this should not
|
|
affect most users. Users should be aware that the --enable-using-memchecker
|
|
+ VDS combination may cause a segfault, however, so Valgrind et al. may
|
|
have to be used with an HDF5 library built without the feature if this
|
|
proves to be a problem.
|
|
(DER - 2016/03/21, HDFFV-9732)
|
|
|
|
- SWMR feature limitations
|
|
The SWMR feature will only work if an HDF5 file under SWMR access resides
|
|
on a file system that obeys POSIX write() ordering semantics. Because of
|
|
this, SWMR will not work on network file systems such as NFS or SMB/Windows
|
|
file shares since those systems do not guarantee write odering. SWMR
|
|
regression tests are likely to fail if run on a network file system. SWMR
|
|
is currently not tested on Windows though it can be tested manually
|
|
(some of the SWMR test programs are built by CMake), and there are no
|
|
obvious reasons for it to not work on NTFS or GPFS.
|
|
(EIP - 2016/03/20, HDFFV-9733)
|
|
|
|
- VDS feature limitation
|
|
Currently, the path to a VDS source file is interpreted as relative to the
|
|
directory where the executable program runs and not to the HDF5 file with
|
|
the VDS dataset unless a full path to the source file is specified during
|
|
the mapping.
|
|
(EIP - 2016/03/20, HDFFV-9724)
|
|
|
|
- The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
|
|
and root group name ("/"):
|
|
|
|
H5Lexists(fileid, "/")
|
|
|
|
In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
|
|
The documentation will be updated with information regarding this change.
|
|
(LRK - 2016/03/30, HDFFV-8746)
|
|
|
|
|
|
%%%%1.10.0%%%%
|
|
|
|
HDF5 version 1.10.0 released on 2016-03-30
|
|
================================================================================
|
|
|
|
|
|
|
|
INTRODUCTION
|
|
|
|
This document describes the differences between HDF5-1.8 series and
|
|
HDF5 1.10.0 releases, and contains information on the platforms
|
|
tested.
|
|
|
|
Links to HDF5 1.10.0 source code can be found on The HDF Group's
|
|
development FTP server at the following location:
|
|
|
|
https://www.hdfgroup.org/HDF5/release/obtain5110.html
|
|
|
|
User documentation can be accessed directly at this location:
|
|
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/
|
|
|
|
For more information, see the HDF5 home page:
|
|
|
|
https://www.hdfgroup.org/HDF5/
|
|
|
|
If you have any questions or comments, please send them to the HDF
|
|
Help Desk:
|
|
|
|
help@hdfgroup.org
|
|
|
|
|
|
|
|
CONTENTS
|
|
|
|
- New Features
|
|
- Issues Addressed in this Release
|
|
- Supported Platforms
|
|
- Tested Configuration Features Summary
|
|
- More Tested Platforms
|
|
- Known Problems and Limitations
|
|
|
|
|
|
|
|
New Features
|
|
============
|
|
This release supports the following features:
|
|
|
|
Configuration
|
|
-------------
|
|
- API Compatibility with HDF5 1.8 Flag Was Added
|
|
|
|
The 1.10 version of the HDF5 Library can be configured to operate
|
|
identically to the 1.8 library with the --with-default-api-version=v18
|
|
configure flag. This allows existing code to be compiled with the 1.10
|
|
library without requiring immediate changes to the application source
|
|
code. For addtional configuration options and other details, see
|
|
"API Compatibility Macros in HDF5" at
|
|
https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
|
|
|
|
- Autotools Configuration Has Been Extensively Reworked
|
|
|
|
The autotools configuration options have been updated to allow more
|
|
fine-grained control of the build options and to correct some bugs.
|
|
See configure --help for comprehensive information on each option.
|
|
|
|
Specific changes:
|
|
|
|
* --enable-debug and --enable-production are no longer accepted.
|
|
Use --enable-build-mode=(debug | production) instead. These set
|
|
appropriate defaults for symbols, optimizations, and other
|
|
configuration options. These defaults can be overridden by the
|
|
user.
|
|
|
|
* Extra debug output messages are no longer enabled with
|
|
--enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
|
|
instead.
|
|
|
|
* A new --enable-symbols option allows symbols to be generated
|
|
independently of the build mode. --disable-symbols can be used
|
|
to strip symbols from the binary.
|
|
|
|
* A new --enable-asserts option sets/unsets NDEBUG. This is
|
|
independent of the build mode. This also enables some extra
|
|
low-overhead debug checks in the library.
|
|
|
|
* A new --enable-profiling option sets profiling flags. This is
|
|
independent of the build mode.
|
|
|
|
* A new --enable-optimization option sets the optimization level.
|
|
This is independent of the build mode.
|
|
|
|
* Many of these options can take a flags string that will be used
|
|
to build the library. This can be useful for specifying custom
|
|
optimization flags such as -Os and -Ofast.
|
|
|
|
* gnu C++ and Fortran use configure sub-files that update the
|
|
build flags and turn on warnings. The increase in warnings when
|
|
building these wrapper libraries is due to these flag changes
|
|
and not to a decrease in code quality.
|
|
|
|
* The option to clear file buffers has been removed. Any buffer that
|
|
will eventually be written to disk will now always be memset
|
|
to zero. This prevents the previous contents of the buffer from
|
|
being written to the disk if the buffer contents are not
|
|
completely overwritten, which has security implications.
|
|
|
|
- LFS Changes
|
|
|
|
The way the autotools handle large file support (LFS) has been
|
|
overhauled in this release.
|
|
|
|
* We assume ftello and fseeko exist
|
|
|
|
* We no longer explicitly use the *64 I/O functions. Instead, we
|
|
rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
|
|
|
|
* _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
|
|
|
|
|
|
|
|
Parallel Library
|
|
-----------------
|
|
- Collective Metadata I/O
|
|
|
|
Calls for HDF5 metadata can result in many small reads and writes.
|
|
On metadata reads, collective metadata I/O can improve performance
|
|
by allowing the library to perform optimizations when reading the
|
|
metadata by having one rank read the data and broadcasting it to
|
|
all other ranks.
|
|
|
|
Collective metadata I/O improves metadata write performance through
|
|
the construction of an MPI derived datatype that is then written
|
|
collectively in a single call. For more information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
|
|
|
|
|
|
|
|
Library
|
|
--------
|
|
- Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR)
|
|
|
|
The Single Writer/ Multiple Reader or SWMR feature enables users to
|
|
read data concurrently while writing it. Communications between the
|
|
processes and file locking are not required. The processes can run
|
|
on the same or on different platforms as long as they share a common
|
|
file system that is POSIX compliant. For more information, see the
|
|
Single-Writer/Multiple-Reader (SWMR) documentation at
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
|
|
|
|
- Virtual Dataset (VDS)
|
|
|
|
The VDS feature enables data to be accessed across HDF5 files
|
|
using standard HDF5 objects such as groups and datasets without
|
|
rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
|
|
is an HDF5 dataset that is composed of source HDF5 datasets in
|
|
a predefined mapping. VDS can be used with the SWMR feature. For
|
|
documentation, check
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
|
|
|
|
- Persistent Free File Space Tracking
|
|
|
|
Usage patterns when working with an HDF5 file sometimes result in
|
|
wasted space within the file. This can also impair access times
|
|
when working with the resulting files. The new file space management
|
|
feature provides strategies for managing space in a file to improve
|
|
performance in both of these areas. For more information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
|
|
|
|
- Version 3 Metadata Cache
|
|
|
|
The version 3 metadata cache moves management of metadata I/O from
|
|
the clients to the metadata cache proper. This change is essential for
|
|
SWMR and other features that have yet to be released.
|
|
|
|
|
|
|
|
C++ Library
|
|
------------
|
|
- New Member Function Added to H5::ArrayType
|
|
|
|
The assignment operator ArrayType::operator= was added because
|
|
ArrayType has pointer data members.
|
|
|
|
(BMR - 2016/03/07, HDFFV-9562)
|
|
|
|
|
|
|
|
Tools
|
|
------
|
|
- h5watch
|
|
|
|
The h5watch tool allows users to output new records appended to
|
|
a dataset under SWMR access as it grows. The functionality is
|
|
similar to the Unix user command "tail" with the follow option,
|
|
which outputs appended data as the file grows. For more
|
|
information, see
|
|
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
|
|
|
|
- h5format_convert
|
|
|
|
The h5format_convert tool allows users to convert the indexing
|
|
type of a chunked dataset made with a 1.10.x version of the HDF5
|
|
Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
|
|
type. For example, datasets created using SWMR access, can be
|
|
converted to be accessed by the HDF5 1.18 library and tools. The
|
|
tool does not rewrite raw data, but it does rewrite HDF5 metadata.
|
|
|
|
|
|
|
|
High-Level APIs
|
|
----------------
|
|
- H5DOappend
|
|
|
|
The function appends data to a dataset along a specified dimension.
|
|
|
|
|
|
C Packet Table API
|
|
------------------
|
|
- Replacement of a Public Function with H5PTcreate
|
|
|
|
The existing function H5PTcreate_fl limits applications so they
|
|
can use the deflate compression only. The public function
|
|
H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
|
|
takes a property list identifier to provide flexibility on
|
|
creation properties.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- New Public Functions: H5PTget_dataset and H5PTget_type
|
|
|
|
Two accessor functions have been added. H5PTget_dataset returns
|
|
the identifier of the dataset associated with the packet table,
|
|
and H5PTget_type returns the identifier of the datatype used by
|
|
the packet table.
|
|
|
|
(BMR, 2016/03/04, HDFFV-8623)
|
|
|
|
- Regarding #ifdef VLPT_REMOVED
|
|
|
|
The #ifdef VLPT_REMOVED blocks have been removed from the packet
|
|
table (PT) library source except for the following functions:
|
|
+ H5PTis_varlen() has been made available again
|
|
+ H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
|
|
|
|
(BMR - 2016/03/04, HDFFV-442)
|
|
|
|
C++ Packet Table API
|
|
--------------------
|
|
- New Constructor Added to FL_PacketTable
|
|
|
|
An overloaded constructor has been added to FL_PacketTable and
|
|
takes a property list identifier to provide flexibility on
|
|
creation properties.
|
|
|
|
(BMR - 2016/03/08, HDFFV-8623)
|
|
|
|
- New Public Functions
|
|
|
|
Two accessor wrappers are added to class PacketTable.
|
|
PacketTable::GetDataset() returns the identifier of the dataset
|
|
associated with the packet table, and PacketTable::GetDatatype()
|
|
returns the identifier of the datatype that the packet table uses.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- Member Functions with "char*" as an Argument
|
|
|
|
Overloaded functions were added to provide the "const char*"
|
|
argument; the existing version will be deprecated in future
|
|
releases.
|
|
|
|
(BMR - 2016/03/04, HDFFV-8623)
|
|
|
|
- Regarding #ifdef VLPT_REMOVED
|
|
|
|
The #ifdef VLPT_REMOVED blocks have been removed from the packet
|
|
table library source code except for the following functions:
|
|
+ VL_PacketTable::IsVariableLength() was moved to PacketTable
|
|
+ VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
|
|
|
|
(BMR - 2016/03/04, HDFFV-442)
|
|
|
|
|
|
|
|
Java Wrapper Library
|
|
--------------------
|
|
|
|
The Java HDF5 JNI library has been integrated into the HDF5 repository.
|
|
The configure option is "--enable-java", and the CMake option is
|
|
HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
|
|
HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
|
|
"hdf.hdflib.hdf5".
|
|
|
|
A number of new APIs were added including some for VDS and SWMR.
|
|
|
|
|
|
|
|
Other Important Changes
|
|
-----------------------
|
|
|
|
The hid_t type was changed from 32-bit to a 64-bit value.
|
|
|
|
|
|
|
|
Issues Addressed in this Release Since alpha1
|
|
=============================================
|
|
|
|
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
|
|
|
|
The correct access property list settings from the
|
|
H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
|
|
H5Pget_efile_prefix function calls could not be retrieved
|
|
using H5Dget_access_plist().
|
|
|
|
Fixed.
|
|
|
|
(DER and NAF - 2016/03/14, HDFFV-9716)
|
|
|
|
- h5dump
|
|
|
|
When h5dump was provided with the name of a non-existing file or
|
|
when optional arguments were the last option on the command line,
|
|
h5dump would segfault.
|
|
|
|
Fixed.
|
|
|
|
(ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
|
|
|
|
- No Error Message for Corrupt Metadata
|
|
|
|
The HDF5 Library did not propagate an error when it encountered
|
|
corrupt metadata in an HDF5 file. The issue was fixed for a
|
|
specific file provided by a user. If you still see the problem,
|
|
please contact help@hdfgroup.org
|
|
|
|
Fixed.
|
|
|
|
(MC - 2016/02/18, HDFFV-9670)
|
|
|
|
- Problem Reading Chunked Datasets with a String Datatype Larger
|
|
Than the Chunk Size in Bytes
|
|
|
|
When the latest file format was used and when a chunked dataset
|
|
was created with a datatype with the size bigger than a chunk
|
|
size, the data could not be read back. The issue was reported
|
|
for chunked datasets with a string datatype and was confirmed
|
|
for other datatypes with the sizes bigger than the chunk size in
|
|
bytes.
|
|
|
|
Fixed.
|
|
|
|
(JM - 2016/02/13, HDFFV-9672)
|
|
|
|
- Control over the Location of External Files
|
|
|
|
Users were unable to specify the locations of external files.
|
|
|
|
Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
|
|
added so that users could specify the locations of external files.
|
|
|
|
(DER - 2016/02/04, HDFFV-8740)
|
|
|
|
|
|
|
|
Issues Addressed in this Release Since alpha0
|
|
=============================================
|
|
- h5format_convert
|
|
|
|
The h5format_convert tool did not downgrade the version of the
|
|
superblock.
|
|
|
|
Fixed. The tool now will downgrade the version of the superblock.
|
|
|
|
(EIP 2016/01/11)
|
|
|
|
- Crashes with multiple threads: invalid pointers
|
|
|
|
It was reported that alpha0 crashed when used with multiple
|
|
threads. The issue exists in the HDF5 Library versions 1.8 and
|
|
1.9. The problem is related to a shared file pointer used in some
|
|
miscellaneous data structures. The thread-safe library exposed
|
|
paths in the library where a file pointer became invalid.
|
|
|
|
The alpha1 release contains the fixes for the specific use case
|
|
as described in HDFFV-9643. We will keep working on identifying
|
|
and fixing other paths in the library with similar problems.
|
|
|
|
(EIP - 2016/01/15, HDFFV-9643)
|
|
|
|
|
|
|
|
Supported Platforms
|
|
===================
|
|
The following platforms are supported and have been tested for this release.
|
|
They are built with the configure process unless specified otherwise.
|
|
|
|
AIX 6.1 xlc/xlc_r 10.1.0.5
|
|
(NASA G-ADA) xlC/xlC_r 10.1.0.5
|
|
xlf90/xlf90_r 12.1.0.6
|
|
|
|
Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
(mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16)
|
|
Version 4.9.3, Version 5.2.0
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
x86-64;
|
|
Version 15.7-0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 15.0.3.187 Build 20150407
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
|
|
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)
|
|
Version 4.9.3, Version 5.2.0
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
compilers:
|
|
Version 15.0.3.187 Build 20150407
|
|
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)
|
|
Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
|
|
(cmake and autotools)
|
|
|
|
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)
|
|
|
|
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
|
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
|
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
|
|
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 clang/clang++ version 6.0 from Xcode 6.2.0
|
|
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 clang/clang++ version 6.0 from Xcode 7.0.0
|
|
64-bit gfortran GNU Fortran (GCC) 4.9.2
|
|
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
|
|
|
|
Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
|
|
|
|
|
|
|
|
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/y n y y n
|
|
Windows 8.1 n y/y n y y y
|
|
Windows 8.1 x64 n 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 Yosemeti 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 8.1 y y y y
|
|
Windows 8.1 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 Yosemeti 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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
|
|
#1 SMP x86_64 GNU/Linux
|
|
(platypus)
|
|
|
|
Windows 7 Visual Studio 2008 (cmake)
|
|
|
|
Windows 7 x64 Visual Studio 2008 (cmake)
|
|
|
|
Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
|
|
|
|
Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
|
|
|
Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
|
|
gcc (Debian 4.7.2-5) 4.7.2
|
|
GNU Fortran (Debian 4.7.2-5) 4.7.2
|
|
(cmake and autotools)
|
|
|
|
Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
|
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
|
(cmake and autotools)
|
|
|
|
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
|
|
gcc (SUSE Linux) 4.8.1
|
|
GNU Fortran (SUSE Linux) 4.8.1
|
|
(cmake and autotools)
|
|
|
|
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
|
|
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
|
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
|
(cmake and autotools)
|
|
|
|
hopper.nersc.gov PrgEnv-gnu/5.2.40
|
|
gcc (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
g++ (GCC) 4.9.2 20141030 (Cray Inc.)
|
|
|
|
|
|
|
|
Known Problems and Limitations
|
|
==============================
|
|
This section contains the list of known problems and limitations introduced
|
|
in this release of HDF5.
|
|
|
|
Note: this list is not exhaustive of all known issues discovered in HDF5
|
|
software to date. For a list of significant problems and known workarounds
|
|
identified in past releases, please refer to:
|
|
|
|
https://www.hdfgroup.org/HDF5/release/known_problems/
|
|
|
|
The HDF Group also maintains a JIRA issue-tracking database which is used to
|
|
capture all known issues which are too numerous to reasonably list in this
|
|
document. The HDF Group is taking steps to make our JIRA issue database
|
|
open to the public, and this section will refer to that database in a future
|
|
release. In the meantime, please contact help@hdfgroup.org if you come across
|
|
an issue not listed here or at the link above, and we will provide any
|
|
information about known workarounds that we have or add it to our list of
|
|
known issues if it is a new issue.
|
|
|
|
- The JUnit-interface test may fail on Solaris platforms. The result of
|
|
a test for verifying the content of the error stack to stdout is
|
|
in a different order on Solaris then other platforms. Use make -i option
|
|
to test beyond the java/test folder.
|
|
(ADB - 2016/03/22, HDFFV-9734)
|
|
|
|
- The flush/refresh test occasionally fails on OS X platforms. This is
|
|
being investigated but no fix or workaround is available at this time.
|
|
(DER - 2016/03/22, HDFFV-9731)
|
|
|
|
- The VDS/SWMR test will fail with a segmentation fault if the library
|
|
is built with --enable-using-memchecker. The is due to a VDS shutdown
|
|
procedure freeing a shared resource too early when the memory
|
|
checker changes are built. This problem does not arise when the
|
|
memory checker changes are not used since the internal library free
|
|
lists behave differently. The memory checker configure option should
|
|
normally only be used under special circumstances so this should not
|
|
affect most users. Users should be aware that the --enable-using-memchecker
|
|
+ VDS combination may cause a segfault, however, so Valgrind et al. may
|
|
have to be used with an HDF5 library built without the feature if this
|
|
proves to be a problem.
|
|
(DER - 2016/03/21, HDFFV-9732)
|
|
|
|
- SWMR feature limitations
|
|
The SWMR feature will only work if an HDF5 file under SWMR access resides
|
|
on a file system that obeys POSIX write() ordering semantics. Because of
|
|
this, SWMR will not work on network file systems such as NFS or SMB/Windows
|
|
file shares since those systems do not guarantee write odering. SWMR
|
|
regression tests are likely to fail if run on a network file system. SWMR
|
|
is currently not tested on Windows though it can be tested manually
|
|
(some of the SWMR test programs are built by CMake), and there are no
|
|
obvious reasons for it to not work on NTFS or GPFS.
|
|
(EIP - 2016/03/20, HDFFV-9733)
|
|
|
|
- VDS feature limitation
|
|
Currently, the path to a VDS source file is interpreted as relative to the
|
|
directory where the executable program runs and not to the HDF5 file with
|
|
the VDS dataset unless a full path to the source file is specified during
|
|
the mapping.
|
|
(EIP - 2016/03/20, HDFFV-9724)
|
|
|
|
- When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
|
|
there is a missing command argument for the tests of the examples.
|
|
|
|
This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF,
|
|
or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF.
|
|
(LRK - 2016/03/30, HDFFV-9743)
|
|
|
|
- The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
|
|
and root group name ("/"):
|
|
|
|
H5Lexists(fileid, "/")
|
|
|
|
In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
|
|
The documentation will be updated with information regarding this change.
|
|
(LRK - 2016/03/30, HDFFV-8746)
|
|
|