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|
HDF5 version 1.10.0-pre1 released on 2016-03-16
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.8.* and
HDF5 1.10.0 release, 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:
http://www.hdfgroup.org/HDF5/release/obtain5110.html
User documentation be accessed directly at this location:
http://www.hdfgroup.org/HDF5/docNewFeatures/
For more information, see the HDF5 home page:
http://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
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
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 v1.8 library with the --with-default-api-version=v18 configure flag.
This allows existing code to be compiled with the v1.10 library without
requiring immediate changes to the application source code. For addtional
configuration options and other details, see "API Compatibility Macros in HDF5":
http://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 the other configuration options (symbols, optimization,
etc.). 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 (e.g., -Os, -Ofast), etc.
* 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, not 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 file - 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
http://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html
C++ Library:
------------
- New member function added to H5::ArrayType
The assignment operator ArrayType::operator= is added because ArrayType
has pointer data members.
(BMR, 2016/03/07, HDFFV-9562)
Tools:
------
- h5watch
Allows users to output new records appended to a dataset iunder 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
http://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools
- h5format_convert
The 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 tools doesn't rewrite raw data, but HDF5 metadata only.
High-Level APIs:
----------------
- H5DOappend
The function appends data to a dataset along a specified dimension.
C Packet Table API
------------------
- Replacement of a public function
The existing function H5PTcreate_fl limits applications to deflate
compression only. The public function H5PTcreate is added to replace
H5PTcreate_fl. H5PTcreate takes a property list ID to provide
flexibility on creation properties.
hid_t H5PTcreate(hid_t loc_id, const char *dset_name,
hid_t dtype_id, hsize_t chunk_size, hid_t plist_id);
(BMR, 2016/03/04, HDFFV-8623)
- New public functions
Two accessor functions were added per HDFFV-8623/patch 003.
/* Returns the ID of the dataset associated with the packet table */
hid_t H5PTget_dataset(hid_t table_id);
/* Returns the ID of the datatype the packet table uses */
hid_t H5PTget_type(hid_t table_id);
(BMR, 2016/03/04, HDFFV-8623)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks are removed from the PT library source
except the following functions:
+ H5PTis_varlen() is made available again.
+ H5PTfree_vlen_readbuff() now became H5PTfree_vlen_buff()
(BMR, 2016/03/04, HDFFV-442)
C++ Packet Table API
--------------------
- New constructor
An overloaded constructor is added to FL_PacketTable and takes a property
list ID to provide flexibility on creation properties.
FL_PacketTable(hid_t fileID, hid_t plist_id, const char* name, hid_t dtypeID, hsize_t chunkSize);
(BMR, 2016/03/08, HDFFV-8623)
- New public functions
Two accessor wrappers are added to class PacketTable, per HDFFV-8623/patch 004.
/* Returns the ID of the dataset associated with the packet table */
hid_t PacketTable::GetDataset()
/* Returns the ID of the datatype that the packet table uses */
hid_t PacketTable::GetDatatype()
(BMR, 2016/03/04, HDFFV-8623)
- Member functions having "char*" as an argument
Overloaded functions were added to provide "const char*" argument, the
existing version will be deprecated in future releases.
(BMR, 2016/03/04)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks are removed from the PT library source
except the following functions:
+ VL_PacketTable::IsVariableLength() is moved to PacketTable
+ VL_PacketTable::FreeReadBuff() now became PacketTable::FreeBuff()
(BMR, 2016/03/04, HDFFV-442)
Java wrapper library
--------------------
Java HDF5 JNI library has been integrated into the HDF5 repo, 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".
Also there are a number of new APIs added, including those for VDS and SWMR.
Other important changes:
-----------------------
hid_t type was changed from 32-bit to a 64-bit value.
Documentation
-------------
See http://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools
Issues Addressed in this Release since alpha1
=============================================
- Wrong settings returned for a dataset access property list.
One couldn't get the correct access property setting with the following functions calls
H5Pget_virtual_printf_gap
H5Pget_virtual_view
H5Pget_efile_prefix
when a dataset access property list was obtained from H5Dget_access_plist(). Fixed.
(DER and NAF 2016-03-14 HDFFV-9716)
- h5dump segfaulted when provided with invalid arguments or when optional aruments are last option
on command line.
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 failed. Fixed.
(ADB 2016-02-28 HDFFV-9639, HDFFV-9684)
- HDF5 library segfaults on a corrupted file.
The HDF5 library didn't propagate an error when encounting a corruped metadata in an HDF5 file.
The issue was fixed for a specific filei porvided by a user. If you still see the problem,
please contact help@hdfgroup.org
(MC 2016-02-18 HDFFV-9670)
- When the latest file format is used, and when a chunked dataset is created with a datatype with the size
bigger than a chunk size, the data cannot be read back.
The issue was reported for the chunked datasets with a string datatype, and was confirmed for other i
datatypes with the sizes bigger than the chunk size in bytes. Fixed.
(JM 2016-02-13 HDFFV-9672)
- Control over the location of the external files
New API H5Pset_efile_prefix was added to specify locations of the external files.
(DER 2016-02-04 HDFFV-8740)
Issues Addressed in this Release since alpha0
=============================================
- h5format_convert tool didn't downgrade version of the superblock. Fixed.
(EIP 2016-01-11)
- 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 the misc. data
structures. The thread-safe library exposed paths in the library where
file pointer became invalid. Alpha1 release contains the fixes for the specific
use case as decribed in HDFFV-9643.
We will keep working on identifying other paths in the library with similar problem
and fixing the issue.
(EIP 2016-01-15)
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
==============================
Please contact help@hdfgroup.org if an issue found is not listed here.
- SWMR feature
SWMR feature will work only if an HDF5 file uner SWMR access resides on
the file systems that obey POSIX write() semantics. SWMR will not work on
the network file systems (e.g., NFS, SMB/Windows file shares), since
those systems do not guarantee write odering. SWMR regression tests will
fail if run on a network file system.
(EIP - 2016-03-20)
- VDS feature
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)
- On Windows platforms in debug configurations, the VFD flush1 tests will
fail with the split and multi VFD drivers. These tests will display a
modal debug dialog which must be answered or wait for the test timeout
to expire.
(ADB - 2014/06/23 - HDFFV-8851)
- CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
catches some undefined behavior in the alignment algorithm of the macro
DETECT_I in H5detect.c. Since the algorithm is trying to detect the
alignment of integers, ideally the flag -fcatch-undefined-behavior
shouldn't to be used for H5detect.c.
(SLU - 2013/10/16 - HDFFV-8147)
- The STDIO VFD does not work on some architectures, possibly due to 32/64
bit or large file issues. The basic STDIO VFD test is known to fail on
64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
10.7.0. The STDIO VFD test has been disabled while we investigate and
a fix should appear in a future release.
(DER - 2011/10/14 - HDFFV-8235)
- h5diff can report inconsistent results when comparing datasets of enum type
that contain invalid values. This is due to how enum types are handled in
the library and will be addressed in a future release.
(DER - 2011/10/14 - HDFFV-7527)
- The links test can fail under the stdio VFD due to some issues with external
links. This will be investigated and fixed in a future release.
(DER - 2011/10/14 - HDFFV-7768)
- After the shared library support was fixed for some bugs, it was discovered
that "make prefix=XXX install" no longer works for shared libraries. It
still works correctly for static libraries. Therefore, if you want to
install the HDF5 shared libraries in a location such as /usr/local/hdf5,
you need to specify the location via the --prefix option during configure
time. E.g, ./configure --prefix=/usr/local/hdf5 ...
(AKC - 2011/05/07 - HDFFV-7583)
- The parallel test, t_shapesame, in testpar/, may run for a long time and may
be terminated by the alarm signal. If that happens, one can increase the
alarm seconds (default is 1200 seconds = 20 minutes) by setting the
environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
(60 minutes). Note that the t_shapesame test may fail in some systems
(see the "While working on the 1.8.6 release..." problem below). If
it does, it will waste more time if $HDF5_ALARM_SECONDS is set
to a larger value.
(AKC - 2011/05/07)
- Shared Fortran libraries are not working on AIX. While they are
generated when --enable-shared is specified, the Fortran and HL/Fortran
tests fail. HL and C++ shared libraries should now be working as intended,
however.
(MAM - 2011/04/20)
- While working on the 1.8.6 release of HDF5, a bug was discovered that can
occur when reading from a dataset in parallel shortly after it has been
written to collectively. The issue was exposed by a new test in the parallel
HDF5 test suite, but had existed before that. We believe the problem lies
with certain MPI implementations and/or file systems.
We have provided a pure MPI test program, as well as a standalone HDF5
program, that can be used to determine if this is an issue on your system.
They should be run across multiple nodes with a varying number of processes.
These programs can be found at:
http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
(NAF - 2011/01/19)
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