Configuration
-------------
- Added a configuration option to change the default plugin path.
The configure option is --with-default-plugindir=location.
The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location.
HDFFV-8513. (ADB 2013/09/04)
- Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13)
- CMake can now package a compressed examples file, the default for
Windows binaries from HDF Group. (ADB - 2013/07/22)
Tools
-----
- h5repack: Added the ability to use plugin filters to read and write
files. The option uses the filter number. HDFFV-8345
(ADB - 2013/09/04).
- h5dump: Added the option -N --any_path, which searches the file for
paths that match the search path. HDFFV-7989 (ADB - 2013/08/12).
- h5dump: Added the optional arg 0 to -A, which excludes attributes
from display. HDFFV-8134 (ADB - 2013/08/01).
C++ API
-------
- Added tutorial examples to C++/examples. They can be installed by
"make install-examples" and, in the installed directory, they can be
executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28)
- A new class, H5::H5Location, is added to represent the location concept
in the C library. It is a base class to H5::H5File and H5::H5Ojbect,
whose member functions are moved into H5::H5Location. H5::H5File can
now inherent those functions. As a result, an H5::H5File object can have
an attribute. (BMR - 2013/09/27)
- Added wrappers for H5Rget_obj_type2 to retrieve the type of the object
that an object reference points to. (BMR - 2013/09/27)
H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type)
- Added wrappers for H5Aexist to check whether an attribute exists given
a name. (BMR - 2013/09/27)
bool H5::H5Location::attrExists(const char* name)
bool H5::H5Location::attrExists(const H5std_string& name)
- Added a number of overloaded functions for convenience. (BMR - 2013/09/27)
Configuration
- Libtool version number is changed to 8.0.0 because there are API
changes. See below for details.
- Mac OS X 10.7 (Lion) and 10.8 (Mountain Lion) uses clang/clang++ as the
default C and C++ compilers.
- CMake minimum is now 2.8.10.
- A new tool, cmakehdf5, which is a build command script similar to
buildhdf5 is added and is available in the bin directory.
Library
- The library can load filter libraries dynamically during runtime. Users
can set the search path through environment variable HDF5_PLUGIN_PATH
and call H5Pset_filter to enable a dynamic filter.
- Added new API functions H5Dscatter and H5Dgather to scatter data to and
and gather data from a selection within a memory buffer.
- The library now supports the data conversion from enumeration to numeric
(integer and floating-point number) datatypes. See Issue HDFFV-8221.
Tools
- h5dump: added new option -O or -ddl to output the ddl text to a file. This
is a complement to the -o or --output option, which redirects the data to
a file.
Library
-------
- The library now behaves correctly when performing large I/O operations on
Mac OS-X. Previously, single I/O operations > 2 GB would fail since the
Darwin read/write calls cannot handle the number of bytes that their
parameter types imply.
Fixes HDFFV-7975 and HDFFV-8240 (DER - 07 JAN 2013)
- Fixed a bug in the core VFD that cause failures when opening files > 2 GB.
Fixes HDFFV-8124 and HDFFV-8158 (DER - 07 JAN 2013)
Tools
-----
- The following h5stat test case failed in BG/P machines (and potentially
other machines that display extra output if an MPI task returns with a
non-zero code.)
Testing h5stat notexist.h5
The test script was fixed to ignore the extra output.
HDFFV-8233 (AKC - 2012/12/17)
- h5diff: Fixed slowness when comparing HDF5 files with many attributes.
Much slower performance was identified with later release version
(from 1.8.7 to 1.8.10) compared to 1.8.6. The issue was introduced
from fixing an attribute related bug for 1.8.7 release in the past.
HDFFV-8145 (JKM 2012/12/13)
* The following new C function has been added:
H5Pget_mpio_no_collective_cause
* The following new Fortran subroutine has been added:
h5pget_mpio_actual_io_mode_f
* The syntax of the following high-level C function has changed:
H5TBAget_fill
This function’s return type has been changed to h5tri_t. A return value of 1 indicates that a fill value is present, 0 indicates that no fill value is present, and a negative value indicates an error. (The former return type was herr_t.)
Note that H5TBAget_fill and a companion function H5TBAget_title, both in the HDF5 Table (H5TB) high-level API, are undocumented. These functions will be added to the HDF5 Reference Manual shortly after HDF5 Release 1.8.10.
Changed Command-line Tool
* h5import has been updated to accept an input file created by h5dump.
This doesn't pass self-tests, but it isn't regression,
previous package didn't pass them as well.
(While here, make both packages share the same distinfo.)
Changes in HDF5 1.8.9
HDF5 1.8.9 is a minor release, but contains several important
new features and bug fixes. Changes in this release include the
following:
* Committed datatypes can now be merged when copying objects,
using the new flag H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG.
Several new API routines have been included in support of
this feature.
* A file in memory can now be accessed in the same way as a
file on disk. New APIs were added to support this feature.
* Many changes to the tools have been made, including the following:
+ The h5repack performance has been improved dramatically
for large chunked datasets.
+ The -S (or --summary) option was added to h5stat to
display a summary of the file space usage for a file.
+ A wildcard can now be used with h5dump to specify multiple files.
* H5LTpath_valid was added to determine if a path is correct
and a link resolves to a valid object.
* The Fortran counterpart to H5Ocopy, h5ocopy_f, was added.
This release contains many other changes and bug fixes not listed here.
Please be sure to read the Release Notes for a comprehensive
list of new features and bug fixes.
Changes in HDF5 1.8.8
HDF5 1.8.8 is a minor release, but contains a few important new
features and bug fixes. Changes in this release include the
following:
* Changes to the Fortran interface:
+ Fortran wrappers for the Dimension Scales APIs were added.
For the new subroutine signatures, see:
http://www.hdfgroup.org/HDF5/doc/HL/RM_H5DS.html
+ The Fortran interface now uses the Fortran 2003 standard,
enabling a wider set of Fortran and HDF5 datatypes to be
supported, including:
o Any kind of INTEGER or REAL
o Fortran derived types
o Fortran and HDF5 enumeration
o HDF5 variable-length datatypes
o HDF5 compound datatypes of any complexity
It also contains new subroutines corresponding to those
C APIs which have callback functions as parameters.
For a general overview and information on how to enable
these new Fortran features, please see the following paper:
http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf
HDF5 examples that use Fortran 2003 (with the suffix "F03") can be found here:
http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-fortran.html
The --enable-fortran2003 configure flag was added to
enable Fortran 2003 support in the HDF5 Fortran library.
This flag should be used along with the --enable-fortran
flag and takes affect only when a Fortran compiler is
Fortran 2003 compliant.
* H5Tcreate now supports a string type (fixed-length and variable-length).
* New APIs, H5Pget_mpio_actual_chunk_opt_mode and H5Pget_mpio_actual_io_mode,
were added for querying whether/how a collective I/O operation completed.
* Numerous changes were made to the tools (h5diff, h5repack, h5jam, h5dump).
pkgsrc notion that free software should not depend on non-free
software (because that results in not having distributable binary
packages, and makes the build fail) unless skipping the dependency
renders the software non-useful.
(The hdf web page says that the default binary builds of hdf include
szip support, but then go on about how users that don't qualify for
the no-cost license have to install a different version.)
If someone who grasps hdf5 can say that hdf5 w/o szip is generally not
useful, we can turn this back on and disable by default the hdf5
option in octave.
(yes I know there is the 1.8 branch, but I don't want to experiment
right now)
changes: many fixes, some C++ API improvements
pkgsrc change: DESTDIR support
This changes the buildlink3.mk files to use an include guard for the
recursive include. The use of BUILDLINK_DEPTH, BUILDLINK_DEPENDS,
BUILDLINK_PACKAGES and BUILDLINK_ORDER is handled by a single new
variable BUILDLINK_TREE. Each buildlink3.mk file adds a pair of
enter/exit marker, which can be used to reconstruct the tree and
to determine first level includes. Avoiding := for large variables
(BUILDLINK_ORDER) speeds up parse time as += has linear complexity.
The include guard reduces system time by avoiding reading files over and
over again. For complex packages this reduces both %user and %sys time to
half of the former time.
changes:
-minor feature additions to the command line tools
-C++ API: Added support for Szip
-bugfixes
pkgsrc changes:
-fixes for the cxx option (should be a separate pkg)
-fixes for the threadsafe option -- replaced a pthread_equal() by a
simple "==" to make it usable with non-threaded apps
(not 100% portable, but should be fine for the platforms in question)
The shared libraries should not be linked against libpthread, but
that would require serious changes to the autoconf/make machinery
so I've left it alone for now.
If that is fixed, "threadsafe" could be made default.
-Don't try to strip scripts on install.
since they always need a C compiler, even when the source code is
completely in C++.
For some other packages, stated in the comment that a C compiler is
really not needed.
and add a new helper target and script, "show-buildlink3", that outputs
a listing of the buildlink3.mk files included as well as the depth at
which they are included.
For example, "make show-buildlink3" in fonts/Xft2 displays:
zlib
fontconfig
iconv
zlib
freetype2
expat
freetype2
Xrender
renderproto
RECOMMENDED is removed. It becomes ABI_DEPENDS.
BUILDLINK_RECOMMENDED.foo becomes BUILDLINK_ABI_DEPENDS.foo.
BUILDLINK_DEPENDS.foo becomes BUILDLINK_API_DEPENDS.foo.
BUILDLINK_DEPENDS does not change.
IGNORE_RECOMMENDED (which defaulted to "no") becomes USE_ABI_DEPENDS
which defaults to "yes".
Added to obsolete.mk checking for IGNORE_RECOMMENDED.
I did not manually go through and fix any aesthetic tab/spacing issues.
I have tested the above patch on DragonFly building and packaging
subversion and pkglint and their many dependencies.
I have also tested USE_ABI_DEPENDS=no on my NetBSD workstation (where I
have used IGNORE_RECOMMENDED for a long time). I have been an active user
of IGNORE_RECOMMENDED since it was available.
As suggested, I removed the documentation sentences suggesting bumping for
"security" issues.
As discussed on tech-pkg.
I will commit to revbump, pkglint, pkg_install, createbuildlink separately.
Note that if you use wip, it will fail! I will commit to pkgsrc-wip
later (within day).
developer is officially maintaining the package.
The rationale for changing this from "tech-pkg" to "pkgsrc-users" is
that it implies that any user can try to maintain the package (by
submitting patches to the mailing list). Since the folks most likely
to care about the package are the folks that want to use it or are
already using it, this would leverage the energy of users who aren't
developers.
-make NetBSD ("netbsdelf") a recognized configuration, copied from
"freebsd"; this pulls in definitions for gcc, in particular it
disables some optimization
-work around a memory corruption problem in H5FDstream which appearently
is caused by use of free()d memory
The latter 2 changes make the library survive its selftests, and help
the "pytables" pkg as well.
bump PKGREVISION, raise BUILDLINK_RECOMMENDED
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).
