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New Features
Configuration:
- Added some initial support for making purify (or similar memory
checking products) happier by initializing buffers to zero and
disabling the internal free list code. To take advantage of this,
define 'H5_USING_PURIFY' in your CFLAGS when building the library.
- WINDOWS building,testing and installing improvements
- On Windows, FORTRAN,C++ and C projects are merged into one zip file,
users can choose an option to build either FORTRAN or C++ or both
with basic C library.For detailed information,
please read INSTALL_Windows.txt.
- On Windows, szip compression library with or without encoder can be easily
turned off or on when building HDF5. For detailed information,
please read INSTALL_Windows.txt, especially section V.
- On Windows, an optional procedure for building,testing and installing
HDF5 from command line is provided. This procedure is supposed to be
convenient for experienced users, please read
INSTALL_windows_From_Command_Line.txt for details.
- On Windows, an alternative short instruction document for building,
testing and installing HDF5 is provided. This instruction is supposed to
be convenient for general users, please read
INSTALL_Windows_Short.txt for details.
- On Windows, h5repack,h5diff,h5ls and h5import tool tests have been added.
Library:
- Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for
SZIP compression. Now there is no restriction on the size and shape of the
chunk except that the total number of elements in the chunk cannot be
bigger than 'pixels_per_block' parameter provided by the user.
- HDF5 can now link to SZIP with or without szip's encoder.
The new API function H5Zget_filter_info can be used to check
szip's status. Attempting to assign szip to a dataset property
list or attempting to write with szip will generate an error if
szip's encoder is disabled. JL/NF - 2004/6/30
- SZIP always uses K13 compression. This flag no longer needs to
be set when calling H5Pset_szip. If the flag for CHIP
compression is set, it will be ignored (since the two are mutually
exclusive). JL/NF - 2004/6/30
- A new API function H5Fget_name was added. It returns the name
of the file by object(file, group, data set, named data type,
attribute) ID. SLU - 2004/06/29
- A new API function H5Fget_filesize was added. It returns the
actual file size of the opened file. SLU - 2004/06/24
- Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2,
will suppress all library version mismatch warning messages.
Tools:
- h5repack was added to the tools suite. h5repack regenerates an HDF5 file
from another HDF5 file, optionally applying HDF5 filters (compression)
and/or chunking to the copied file. The filters options are read from
the command line. See /doc/html/Tools.html for more details.
PVN - 2004/9/13
- h5dump includes new features:
1) Printing of dataset filters, storage layout and fill value information.
2) Print a list of the file contents.
3) Escape non printing characters.
4) Print the content of the boot block.
5) Print array indices with the data (the default).
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in the process. (More information on tech-pkg.)
Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and
installing .la files.
Bump PKGREVISION (only) of all packages depending directly on the above
via a buildlink3 include.
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All library names listed by *.la files no longer need to be listed
in the PLIST, e.g., instead of:
lib/libfoo.a
lib/libfoo.la
lib/libfoo.so
lib/libfoo.so.0
lib/libfoo.so.0.1
one simply needs:
lib/libfoo.la
and bsd.pkg.mk will automatically ensure that the additional library
names are listed in the installed package +CONTENTS file.
Also make LIBTOOLIZE_PLIST default to "yes".
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changes:
-new functions: H5Iget_ref, H5Iinc_ref and H5Idec_ref
-bugfixes
being here, move to USE_BUILDLINK3
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relative to ${WRKSRC}. Remove redundant LIBTOOL_OVERRIDE settings that
are automatically handled by the default setting in bsd.pkg.mk.
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Summary: This release has the following new features that are not
available in 1.4.* releases
1. Generic properties to give application more control on I/O pipeline
2. Time allocation and fill value properties
3. New filters: external compression filter szip
internal shuffling and checksum filters
4. Compact storage layout for datasets
5. Redesigned I/O pipeline for better performance.
For more information see
http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html
http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide.html
http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/Changes.html
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Should anybody feel like they could be the maintainer for any of thewe packages,
please adjust.
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This version fixes some serious bugs in version 1.4.5 and includes the
following relevant changes:
* Fixed error in B-tree deletion routine which could cause groups to be
corrupted when objects are removed from them.
* Fixed error in file space freeing code which could cause metadata to
fail to be written to the file.
* Fixed error in library when configured with --enable-debug=all.
* Added a -force option to h5redeploy.
* When using gcc 3.x, we use -std=gnu99 instead of -ansi for compiling.
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Changes:
* Allow scalar dataspaces to be used for parallel I/O. QAK - 2002/11/05
* Added environment variable "HDF5_DISABLE_VERSION_CHECK", which disables
the version checking between the header files and the library linked
into an application if set to '1'. This should be used with caution,
mis-matched headers and library binaries can cause _serious_ problems.
QAK - 2002/10/15
* Partially fixed space allocation inefficiencies in the file by
improving our algorithms for re-using freed space. QAK - 2002/08/27
* API tracing has been improved. Nested API calls don't screw up the
output format; function call and return event times can be logged;
total time spent in each function can be logged. The following
HDF5_DEBUG environment variable words affect tracing:
trace -- turn on/off basic tracing
ttimes -- turn on tracing and report event times and
time spent in each API function.
ttop -- turn on tracing but display only top-level
API calls.
* Several missing fortran APIs have been added to the library:
h5get_libversion_f h5tget_member_index_f h5dget_storage_size_f
h5check_version_f h5tvlen_create_f h5dvlen_get_max_len_f
h5garbage_collect_f h5dwrite_vl_f
h5dont_atexit_f h5dread_vl_f
Functions h5dvlen_get_max_len_f, h5dwrite_vl_f, and h5dread_vl_f support
VL Length C APIs functionality for integer, real and string datatypes.
See HDF5 Reference Manual and HDF5 FORTRAN90 User's Notes for more
information and for the functions description.
* H5Fopen without the H5F_ACC_CREAT flag should not succeed in creating
a new file with the 'core' VFL driver. QAK - 2003/01/24
* Corrected metadata caching bug in parallel I/O which could cause hangs
when chunked datasets were accessed with independent transfer mode.
QAK - 2003/01/23
* Allow opening objects with unknown object header messages.
QAK - 2003/01/21
* Added improved error assertion for nil VL strings. It return error
stack instead of a simple assertion. SLU - 2002/12/16
* Fixed h5dump bug(cannot dump data and datatype) for VL string.
SLU - 2002/11/18
* Fixed error condition where "none" selections were not being handled
correctly in serial & parallel. QAK - 2002/10/29
* Fixed problem where optimized hyperslab routines were incorrectly
invoked for parallel I/O operations in collective mode. QAK - 2002/07/22
* Fixed metadata corruption problem which could occur when many objects
are created in a file during parallel I/O. QAK - 2002/07/19
* Fixed minor problem with configuration when users specified /usr/include
and /usr/lib for the --with-* options that some compilers can't
handle. BW - 2003/01/23
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relevnt changes:
-Numerous performance changes were made to the HDF5 sequential and
parallel libraries
-Several corruption problems were fixed.
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buildlink2.mk files back into the main trunk.
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* Changed internal error handling macros to reduce code size of library by
about 10%.
* API changes.
* Performance improvements
* ``h5cc'' script which helps compilation of HDF5 programs
* Bug fixes.
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into the equivalent INSTALL_*. This is fallout from the change in
revision 1.915 that removed ${MAKE_ENV} from the environment for a
recursive make.
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recent bulk build.
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New Features
============
* XML output option for h5dump utility.
A new option --xml to output data in XML format has been added. The
XML output contains a complete description of the file, marked up in
XML.
The XML conforms to the HDF5 Document Type Definition (DTD), which
is available at:
http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd
The XML output is suitable for use with other tools, including the
Java Tools:
http://hdf.ncsa.uiuc.edu/java-hdf5-html
Bug Fixes since HDF5-1.4.0 Release
==================================
* h4toh5 utility: conversion of images is fixed
Earlier releases of the h4toh5 utility produced images that did not
correctly conform to the HDF5 Image and Palette Specification.
http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html
Several required HDF5 attributes are omitted, and the dataspace
is reversed (i.e., the ht. and width of the image dataset is
incorrectly described.) For more information, please see:
http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm
* Fixed bug with contiguous hyperslabs not being detected, causing
slower I/O than necessary.
* Fixed bug where non-aligned hyperslab I/O on chunked datasets was
causing errors during I/O
* The RCSID string in H5public.h was causing the C++ compiling problem
because when it was included multiple times, C++ did not like
multiple definitions of the same static variable. All occurance of
RCSID definition are removed since we have not used it consistently
before.
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+ move the patch digest/checksum values from files/patch-sum to distinfo
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problem. Also, patch configure script to not add "-ansi -pedantic" to
CFLAGS. It seems pointless to use the "-ansi" warning when so many
warnings about ANSI C not supporting "long long", etc., appear.
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${PREFIX}/share/doc/hdf5/RELEASE.txt.
New Features
============
* The Virtual File Layer, VFL, was added to replace the old file
drivers. It also provides an API for user defined file drivers.
* New features added to snapshots. Use 'snapshot help' to see a
complete list of features.
* Improved configure to detect if MPIO routines are available when
parallel mode is requested.
* Added Thread-Safe support. Phase I implemented. See:
http://hdf.ncsa.uiuc.edu/HDF5/papers/mthdf/MTHDFpaper.htm
for more details.
* Added data sieve buffering to raw data I/O path. This is enabled
for all VFL drivers except the mpio & core drivers. Setting the
sieve buffer size is controlled with the new API function,
H5Pset_sieve_buf_size(), and retrieved with H5Pget_sieve_buf_size().
* Added new Virtual File Driver, Stream VFD, to send/receive entire
HDF5 files via socket connections.
* As parts of VFL, HDF-GASS and HDF-SRB are also added to this
release. To find out details, please read INSTALL_VFL file.
* Increased maximum number of dimensions for a dataset (H5S_MAX_RANK)
from 31 to 32 to align with HDF4 & netCDF.
* Added 'query' function to VFL drivers. Also added 'type' parameter to
VFL 'read' & 'write' calls, so they are aware of the type of data
being accessed in the file. Updated the VFL document also.
* A new h4toh5 utility, to convert HDF4 files to analogous HDF5 files.
* Added a new array datatype to the datatypes which can be created.
Removed "array fields" from compound datatypes (use an array datatype
instead).
* Parallel HDF5 works correctly with mpich-1.2.1 on Solaris, SGI, Linux.
* You can now install the HDF5 documentation using the
``make install-doc'' command. The documentation is installed in the
$(prefix)/doc directory where $(prefix) is the prefix specified by
the (optional) ``--prefix'' flag during configuration.
* HDF5 can operate correctly in the OpenMP environment in a limited way.
Check doc/html/TechNotes/openmp-hdf5.html for details.
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print a one line usage statement and exit in this case.
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out of date - it was based on a.out OBJECT_FMT, and added entries in the
generated PLISTs to reflect the symlinks that ELF packages uses. It also
tried to be clever, and removed and recreated any symbolic links that were
created, which has resulted in some fun, especially with packages which
use dlopen(3) to load modules. Some recent changes to our ld.so to bring
it more into line with other Operating Systems also exposed some cracks.
+ Modify bsd.pkg.mk and its shared object handling, so that PLISTs now contain
the ELF symlinks.
+ Don't mess about with file system entries when handling shared objects in
bsd.pkg.mk, since it's likely that libtool and the BSD *.mk processing will
have got it right, and have a much better idea than we do.
+ Modify PLISTs to contain "ELF symlinks"
+ On a.out platforms, delete any "ELF symlinks" from the generated PLISTs
+ On ELF platforms, no extra processing needs to be done in bsd.pkg.mk
+ Modify print-PLIST target in bsd.pkg.mk to add dummy symlink entries on
a.out platforms
+ Update the documentation in Packages.txt
With many thanks to Thomas Klausner for keeping me honest with this.
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Hierarchical Data Format 5
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