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HISTORY-1_8_0-1_10_0.txt
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HDF5 HISTORY
=============
INTRODUCTION
This document describes the development history between the HDF5-1.8.0 and
HDF5 1.10.0 releases. For more information see the SVN log.
Information about supported and tested platforms is provided for historical
reasons only and may not be accurate.
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:
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.8.0
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
New Features
============
Configuration:
-------------
- Java JNI library API wrappers and supporting files added as HDF_JAVA language
option. Both configure and CMake disable this option by default.
HDFFV-9552 (ADB 2016/02.28)
- CMake minimum is now 3.1.0. (ADB 2015/11/14)
- cmakehdf5: configure options added to enable or disable the building of
different API's and testings. See "cmakehdf5 --help" for details.
(AKC - 2014/12/09 HDFFV-8932)
- Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08)
- CMake: Moved minimum CMake version to 2.8.11 which enables better library
include processing. (ADB - 2014/03/26)
- New configuration option added to change the default plugin path.
configure option is --with-default-plugin=location
cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location
HDFFV-8513. (ADB 2013/09/04)
- Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13)
- CMake minimum is now 2.8.10. (ADB 2013/01/14)
- A new tool, cmakehdf5, which is a build command script similar to
buildhdf5 is added and is available in the bin directory.
(AKC - 2012/12/12)
- Fixed AIX Fortran compiler flags to use appropriate settings for
debugging, profiling, optimization situations. HDFFV-8069. (AKC
2012/09/27)
- Updated to latest autotools and changed all hard *.sh scripts to
configure managed *.sh.in files. Removed overloading of autotools
TESTS variable by examples and tests. Renamed configure.in to
configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
- Added code to display the version information of XL fortran and C++
in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793)
- Configure now generates Makefiles that build in "silent make mode"
by default in which compile and link lines are significantly
simplified for clarity. To override this and view actual compile and
link lines during building, the --disable-silent-rules flag can be used
at configure time, or the 'make' command can be followed by V=1, to
indicate a "verbose" make. (MAM - 2011/4/14).
- Added mpicc and mpif90 as the default C and Fortran compilers for Linux
systems when --enable-parallel is specified but no $CC or $FC is defined.
(AKC - 2011/2/7)
- Added a new configure option, "--enable-unsupported", which can
be used to stop configure from preventing the use of unsupported
configure option combinations, such as c++ in parallel or parallel
HDF5 with threadsafe. Use at your own risk, as it may result in a
library that won't compile or run as expected!
(MAM - 2010/11/17 - Bug 2061)
- PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
applications startup command as defined in the MPI-2 definition, section
4.1. (AKC - 2010/6/11 - Bug 1921)
- Configure now adds appropriate defines for supporting large (64-bit)
files on all systems, where supported, by default, instead of only linux.
This largefile support is controllable with the --enable-largefile
configure option. This is replacing the linux-specific --enable-linux-lfs
option, which has been removed from configure.
(MAM - 2010/05/05 - 1772/1434)
- Upgraded versions of autotools used to generate configuration suite.
We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b.
MAM 2010/04/15.
- Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM
compilers so that the ibm compiler options can be added properly. This
allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be
recognized. AKC 2009/11/26.
- Configuration suite now uses Automake 1.11 and Autoconf 2.64.
MAM 2009/08/11.
- Changed default Gnu fortran compiler from g95 to gfortran since
gfortran is more likely installed with gcc now. -AKC 2009/07/19-
- Added libtool version numbers to generated c++, fortran, and
hl libraries. MAM 2009/04/19.
- Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
- Added a Make target of check-all-install to test the correctness of
installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
- Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1.
MAM 2008/05/05.
- The new configure option "--disable-sharedlib-rpath" disables
embedding the '-Wl,-rpath' information into executables when
shared libraries are produced, and instead solely relies on the
information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
Library:
--------
- Virtual Dataset feature was added
(NAF - 2015-10-05, VDS-193)
- H5F_ACC_DEBUG labeled "deprecated"
The symbol was originally used to emit some extra debugging
informationi in the multi VFD. The underlying functionality
was removed due to disuse in HDF5 1.8.16 though the symbol
remained defined since it was visible in H5Fpublic.h.
In this release, the symbol has been labeled deprecated and will
not be defined when H5_NO_DEPRECATED_SYMBOLS is defined.
(DER - 2015-04-30, HDFFV-1074)
- 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. (SLU - 2013/04/08)
- Added new API functions H5Dscatter and H5Dgather to scatter data to and
and gather data from a selection within a memory buffer.
(NAF - 2013/02/05)
- The library now supports the data conversion from enumeration to numeric
(integer and floating-point number) datatypes. See Issue 8221.
(SLU - 2012/10/23)
- The data sieve buffer size was for all the datasets in the file. It
could waste memory if any dataset size is smaller than the sieve buffer
size. Now the library picks the smaller one between the dataset size
and the sieve buffer size from the file access property. See Issue 7934.
(SLU - 2012/4/2)
- I added a new parameter of object access property list to the function
H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former
H5Rdereference function has been deprecated to H5Rdereference1. (SLU -
2011/7/18)
- H5Tcreate now supports string type (fixed-length and variable-length).
(SLU - 2011/05/20)
- Added ability to cache files opened through external links. Added new
public functions H5Pset_elink_file_cache_size(),
H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache().
(NAF - 2011/02/17)
- Removed all old code for Metraowerks compilers, bracketed by
__MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17)
- Added support for threadsafety on windows using the windows threads
library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a
windows platform to enable this functionality. This is supported on
Windows Vista and newer Windows operating systems. (MAM - 2010/09/10)
- When a mandatory filter failed to write data chunks, the dataset
couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure. (SLU - 2010/9/8)
- H5Tset_order and H5Tget_order now support all data types. A new byte
order H5T_ORDER_MIXED has been added specifically for compound datatype
and its derived type. Please see bug #1934. (SLU - 2010/8/23)
- Improved performance of the chunk cache by avoiding unnecessary b-tree
lookups of chunks already in cache. (NAF - 2010/06/15)
- Greatly improved performance of extending a dataset with early
allocation. (NAF - 2010/03/24 - 1637)
- Added support for filtering densely stored groups. Many of the API
functions related to filters have been extended to support dense groups
as well as datasets. Pipeline messages can now be stored in a group's
object header. (NAF/QAK - 2009/10/8)
- The embedded library information is displayed by H5check_version() if a
version mismatch is detected. Also changed H5check_version() to
suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
or higher. (Old behavior treated 3 or higher the same as 1, that is
print a warning and allows the program to continue. (AKC - 2009/9/28)
- If a user does not care for the extra library information insert
in the executables, he may turn it off by --disable-embedded-libinfo
during configure. (AKC - 2009/9/15)
- Corrected problem where library would re-write the superblock in a file
opened for R/W access, even when no changes were made to the file.
(QAK - 2009/08/20, Bz#1473)
- Separated "factory" free list class from block free lists. These free
lists are dynamically created and manage blocks of a fixed size.
H5set_free_list_limits() will use the same settings specified for block
free lists for factory free lists. (NAF - 2009/04/08)
- Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29)
- Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
user-defined callback function for external link traversal.
(NAF - 2009/01/08)
- Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
allow the user to specify the file access flags used to open the target
file of an external link. (NAF - 2009/01/08)
- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
individual rdcc configuration for each dataset. Added
H5Dget_access_plist() function to retrieve a dataset access property
list from a dataset. (NAF - 2008/11/12)
- Added H5Iis_valid() function to check if an id is valid without producing
an error message. (NAF - 2008/11/5)
- Added two new public routines: H5Pget_elink_fapl() and
H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
Parallel Library:
-----------------
- Add H5Pget_mpio_no_collective_cause() function that retrieve reasons
why the collective I/O was broken during read/write IO access.
(JKM - 2012/08/30 HDFFV-8143)
- Special Collective IO (IO when some processes do not contribute to the
IO) and Complex Derived Datatype MPI functionalities are no longer
conditionally enabled in the library by configure. They are always
enabled in order to take advantage of performance boosts from these
behaviors. Older MPI implementations that do not allow for these
functionalities can no longer by used by HDF5. (MAM - 2011/07/08).
- Modified parallel tests to run with arbitrary number of processes. The
modified tests are testphdf5 (parallel dataset access), t_chunk_alloc
(chunk allocation), and t_posix_compliant (posix compliance). The rest of
the parallel tests already use in the code the number of processes
available in the communicator. (CMC - 2009/04/28)
Fortran Library:
----------------
- Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
- Added for the C API the Fortran wrapper:
h5ocopy_f (MSB - 2012/03/22)
HDF5 Fortran library was enhanced to support Fortran 2003 standard.
The following features are available when the HDF5 library is configured
using --enable-fortran --enable-fortran2003 configure flags AND
if fortran compiler is Fortran2003 compliant:
- Subroutines overloaded with the C_PTR derived type:
h5pget_f
h5pget_fill_value_f
h5pinsert_f
h5pregister_f
h5pset_f
h5pset_fill_value_f
h5rcreate_f
h5rderefrence_f
h5rget_name_f
h5rget_obj_type_f
- Subroutines overloaded with the C_PTR derived type and simplified signatures:
h5aread_f
h5awrite_f
h5dread_f
h5dwrite_f
- New subroutines
h5dvlen_reclaim_f
h5literate_by_name_f
h5literate_f
h5ovisit_f
h5tconvert_f
- Subroutines with additional optional parameters:
h5pcreate_class_f
(EIP - 2011/10/14)
- Added for the C APIs the Fortran wrappers:
h5dget_access_plist_f
h5iis_valid_f
h5pset_chunk_cache_f
h5pget_chunk_cache_f
(MSB - 2009/04/17)
C++ Library:
------------
- New member function added
The assignment operator ArrayType::operator= is added because ArrayType
has pointer data members.
(BMR, 2016/03/07, HDFFV-9562)
- New member functions
+ Overloaded CommonFG::getObjnameByIdx to take char* for name
+ Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
(BMR - 2010/05/02)
+ DataSet::getInMemDataSize() to simplify getting the dataset's
data size in memory. (BMR - 2009/07/26)
- These member functions were added as wrapper for H5Rdereference to
replace the incorrect IdComponent::dereference().
void H5Object::dereference(H5File& h5file, void* ref)
void H5Object::dereference(H5Object& obj, void* ref)
In addition, these constructors were added to create the associated
objects by way of dereference:
Attribute(H5Object& obj, void* ref);
Attribute(H5File& file, void* ref);
DataSet(H5Object& obj, void* ref);
DataSet(H5File& file, void* ref);
DataType(H5Object& obj, void* ref);
DataType(H5File& file, void* ref);
Group(H5Object& obj, void* ref);
Group(H5File& obj, void* ref);
(BMR - 2008/08/10)
Tools:
------
- h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04).
- h5dump: Added option -N --any_path, which searches the file for paths that
match the search path. HDFFV-7989 (ADB - 2013/08/12).
- h5dump: Added optional arg 0 to -A, which excludes attributes from display.
HDFFV-8134 (ADB - 2013/08/01).
- h5dump: Fixed displaying compression ratio for unknown or user-defined
filters. HDFFV-8344 (XCAO 2013/03/19)
- h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter.
HDFFV-8346 (XCAO 2013/03/19)
- h5dump: Added capability for "-a" option to show attributes containing "/"
by using an escape character. For example, for a dataset "/dset"
containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
to show the content of the attribute. See details at HDFFV-7523
(PC -- 2012/03/12)
- h5dump: Added ability to apply command options across multiple files using a
wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5".
HDFFV-7876 (ADB - 2012/03/12).
- h5repack: Improved performance for big chunked datasets (size > 128MB)
when used with layout (-l) or compression (-f) option.
It would perform much better prior to the improvement,
especially for cases that chunk dimensions looks like
"1024x5x1" (compare to "1x5x1024"). When bigger numbers
are toward front and smaller number is toward back in chunk
dimensions. HDFFV-7862 (JKM - 2012/03/01)
- h5dump: Added new option --no-compact-subset. This option will not
interpret the '[' character as starting the compact form of
subsetting. This is useful when the "h5dump error: unable to
open dataset "datset_name"" message is output because a dataset
name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31)
- h5dump: Corrected schema location:
<hdf5:HDF5-File
xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File
http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd">
(ADB - 2011/08/10)
- h5diff: Added new level for -v (verbose) option. The new levels are
1 and 2. So -v1 and -v2 can be specified to view more
information about attributes differences.
Bug#2121 (JKM 2011/3/23)
- h5dump: Added new option --enable-error-stack. This option will display
error stack information in the output stream. This is useful
when the "h5dump: Unable to print data" message is output.
(ADB - 2011/02/24)
- h5diff: Add a new flag --exclude-path. Specified path to an object will
be excluded from comparing the two files or two groups. If group
is specified all the member objects will be excluded.
(JKM - 2010/09/16).
- h5ls: Add new flag --no-dangling-links. (refer to --help for details)
(JKM - 2010/06/15)
- h5ls: Add new flag --follow-symlinks. (refer to --help for details)
(JKM - 2010/05/25)
- h5diff: Add new flag --no-dangling-links. (refer to --help for details)
(JKM - 2010/02/10)
- h5diff: Add new flag --follow-symlinks. (refer to --help for details)
(JKM - 2010/01/25)
- h5diff: fix for displaying garbage value on LE machine for BE data.
(JKM - 2009/11/20)
- h5dump: subsetting now allows default for count. Also trailing ; in short form
can be omitted after last specified value.
(ADB - 2009/09/04)
- h5dump/h5ls: now can display data in region references
using new -R, --region flag.
(ADB - 2009/09/04)
- h5diff: new flag, -c, --compare, list objects that are not comparable.
(PVN - 2009/4/10 - 1368)
- h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10)
- h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519)
- h5repack now handles group creation order. (PVN - 2009/4/2 - 1402)
- h5dump: added a printing of the compression ratio of uncompressed and compressed
sizes for cases where compression filters are present. (PVN - 2008/05/01)
- h5dump: added an option to allow a user defined formatting string for printf
regarding floating point numbers. (PVN - 2008/05/06)
- h5dump: support for external links, display the object that the external link
points to. (PVN - 2008/05/12)
- h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26)
- h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29)
- h5ls: added capability to traverse through external links when the -r
(recursive) flag is given. (NAF - 2008/09/16)
- h5ls: added -E option to enable traversal of external links. h5ls will
not traverse external links without this flag being set.
(NAF - 2008/10/06)
- h5diff: added support for long double (PVN - 2008/10/28)
- h5dump: binary output defaults to NATIVE with -b optionally accepting
the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30)
- h5diff: return 1 for file differences when both file graphs differ by any object.
Error return code was changed to 2 from -1. (PVN - 2008/10/30)
- h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
instead (PVN - 2008/10/30)
- h5repack: When user doesn't specify a chunk size, h5repack now defines a default
chunk size as the same size of the size of the hyperslab used to read the chunks.
The size of the hyperslabs are defined as the size of each dimension or a
predefined constant, whatever is smaller. This assures that the chunk
read fits in the chunk cache. (PVN - 2008/11/21)
- h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect)
before call ABS(...) at h5diff_array.c This will make that (INF==INF) is true
(INF is treated as an number instead of NaN) (PC -- 2009/07/28)
- h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON)
Change default to use strict equality (PC -- 2009/09/12)
High-Level APIs:
---------------
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 cases:
+ 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 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 the packet table uses */
hid_t PacketTable::GetDataset()
(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.
(BMR, 2016/03/04)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks are removed from the PT library source
except the following cases:
+ VL_PacketTable::IsVariableLength() is moved to PacketTable
+ VL_PacketTable::FreeReadBuff() now became PacketTable::FreeBuff()
(BMR, 2016/03/04, HDFFV-442)
Internal header file
--------------------
- A new API function H5DOwrite_chunk. It writes a data chunk directly
into a file bypassing hyperslab selection, data conversion, and
filter pipeline. The user must be careful with the function and
clearly understand the I/O process of the library.
(SLU - 2013/2/11)
- New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks
if a path is correct and determines if a link resolves to a valid
object and checks that the link does not dangle. (MSB- 2012/3/15)
- Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797
h5dsset_scale_f
h5dsattach_scale_f
h5dsdetach_scale_f
h5dsis_attached_f
h5dsis_scale_f
h5dsset_label_f
h5dsget_label_f
h5dsget_scale_name_f
h5dsget_num_scales_f
(EIP for SB - 2011/10/13)
- Table: In version 3.0 of Table, "NROWS" (used to store number of records) was
deprecated (PVN - 2008/11/24)
Documentation
-------------
Support for new platforms, languages and compilers.
=======================================
- Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
- PathScale compilers are recognized and can build the HDF5 library
properly. AKC - 2009/7/28 -
- SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and
Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15)
Bug Fixes since HDF5-1.8.0 release
==================================
Library
-------
- Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property
The CMake command, set_property with COMPILE_DEFINITIONS property
needs a quoted semi-colon separated list of values. CMake will
transform the list to a series of -D{value} for the compile.
(ADB - 2014/12/09, HDFV-9041)
- H5Z.c: H5Zfilter_avail(H5Z_filter_t id)
Added else block if the call to the internal H5Z_filter_avail(id) does not
fail and returns FALSE. This block calls the H5PL_load(H5PL_TYPE_FILTER, (int)id)
function to attempt to dynamically load the filter plugin.
(ADB - 2014/03/03 HDFFV-8629)
- Added const qualifier to source buffer parameters in H5Dgather and
H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/02)
- Fixed an error involving failure to write fill values to the user's
buffer when reading unallocated chunks from datasets that have a
fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this
was the reporting of spurious data values in h5dump and h5diff
output.
(HDFFV-8247; JP - 2013/05/03)
- Fixed an error that could occur when calling H5Ocopy within an
H5Literate callback (and possibly other situations).
(NAF - 2012/7/25 - HDFFV-5853)
- Fixed an error that would occur when copying an object with attribute
creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762)
- Fixed a bug in H5Ocopy(): When copying an opened object, call the
object's flush class action to ensure that cached data is flushed
so that H5Ocopy will get the correct data.
(VC - 2012/3/27 - HDFFV-7853)
- When an application tries to write or read many small data chunks and
runs out of memory, the library had a seg fault. The fix is to
return the error stack with proper information. (SLU - 2012/3/23.
Issue 7785)
- H5Pset_data_transform had seg fault in some cases like x*-100. It
works correctly now and handles other cases like 100-x or 2/x.
(SLU - 2012/3/15. Issue 7922)
- Fixed rare corruption bugs that could occur when using the new object
header format. (NAF - 2012/3/15 - HDFFV-7879)
- Creating a dataset in a read-only file caused seg fault when the file
is closed. It's fixed. The attempt to create a dataset will fail
with the error stack indicating the file is read-only. (SLU -
2012/1/25. Issue 7756)
- Fixed a seg fault that could occur when shrinking a dataset with chunks
larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
- Fixed a bug that could cause file corruption when copying named
datatypes to a file using shared messages. (NAF - 2011/11/14)
- Fixed a bug that could cause H5Oget_info to return the wrong address
after copying a named datatype. (NAF - 2011/11/14)
- The library allowed the conversion of strings between ASCII and UTF8
(Issue 7582). We have corrected it to report an error under this
situation. (SLU - 2011/11/8)
- The library had seg fault when it tried to shrink the size of compound type
through H5Tset_size immediately after the type was created (Issue
7618). It's fixed now. (SLU - 2011/10/26)
- Fixed a bug that occurred when using H5Ocopy on a committed datatype
containing an attribute using that committed datatype.
(NAF - 2011/10/13 - Issue 5854)
- #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added
H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure
never set _WIN32.
- CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
discovered 3 problems in tests and tools' library (Issue 7674):
1. In dsets.c, left shifting an unsigned int for 32 bits or more
caused undefined behavior.
2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow
when the value is negative minimal and is being subtracted one.
3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits
or more caused undefined behavior.
All the problems have been corrected. (SLU - 2011/9/2)
- In v1.6 library, there was EOA for the whole MULTI file saved in the
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. We
fixed the problem by checking the EOA value to detect the file
created with v1.6 library. (SLU - 2011/6/22)
- When a dataset had filters and reading data failed, the error message
didn't say which filter isn't registered. It's fixed now.
(SLU - 2011/6/3)
- The datatype handler created with H5Tencode/decode used to have the
reference count 0 (zero). I have fixed it. It is 1 (one) now.
(SLU - 2011/2/18)
- Fixed a bug that caused big endian machines to generate corrupt files
when using the scale-offset filter with floating point data or
fill values. Note that such datasets will no longer be readable
by any machine after this patch. (NAF - 2010/02/02 - Bug 2131)
- Retrieving a link's name by index in the case where the link is
external and the file that the link refers to doesn't exist will
now fail gracefully rather than cause a segmentation fault.
(MAM - 2010/11/17)
- Modified library to always cache symbol table information. Libraries
version 1.6.3 have a bug which causes them to require this
information for some operations. (NAF - 2010/09/21 - 1864)
- Fixed a bug that could occur when getting information for a new-style
group that was previously opened through a file handle that was
later closed. (NAF - 2010/09/15)
- Added define check in H5public.h if stdint.h is supported by the C++
compiler. This define is only available on Windows with VS2010 and
using CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
- H5Eset_current_stack now also closes the error stack to be set as the
default. This is to avoid a potential problem (Bug 1799).
(SLU - 2010/9/7)
- Fixed the bug in the filter's public CAN_APPLY function. The return
value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5)
- Fixed a bug in the direct I/O driver that could render files with
certain kinds of unaligned data unreadable or corrupt them.
(NAF - 2010/07/28)
- valgrind reported an error of copying data to itself when a new attribute
is written (Bug #1956). I fixed it by taking out the memcpy step in
the attribute code. (SLU - 2010/07/28)
- Fixed a bug that could cause file corruption when using non-default
sizes of addresses and/or lengths. This bug could also cause
uncorrupted files with this property to be unreadable. This bug
was introduced in 1.8.5. (NAF - 2010/07/16 - 1951)
- Fixed a file corruption bug that could happen when shrinking a
compressed dataset. (NAF - 2010/05/20)
- Fixed some memory leaks in VL datatype conversion when strings are
used as fill values. (MAM - 2010/05/12 - BZ# 1826)
- Fixed a bug when copying objects with NULL references with the
H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815)
- Files can now be concurrently opened more than once using the core file
driver, as long as the backing store is used. (NAF - 2010/03/09)
- Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
links will now be expanded if this flag is set.
(NAF - 2010/03/05 - 1733)
- Fixed a bug where the library, when traversing an external link, would
reopen the source file if nothing else worked. (NAF - 2010/03/05)
- Fixed an intermittent bug in the b-tree code which could be triggered
by expanding and shrinking chunked datasets in certain ways.
(NAF - 2010/02/16)
- H5Tdetect_class said a VL string is a string type. But when it's
in a compound type, it said it's a VL type (Bug #1584). I fixed it
to be consistent. It always return string type. (SLU - 2009/12/10)
- Fixed a bug where writing and deleting many global heap objects (i.e.
variable length data) would render the file unreadable. Previously
created files exhibiting this problem should now be readable.
(NAF - 2009/10/27 - 1483)
- Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628)
- Fixed an assertion failure that occurred when H5Ocopy was called on a
dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597)
- Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
(NAF - 2009/09/25 - 1620)
- Fixed a bug where properties weren't being compared with the registered
compare callback. (NAF - 2009/09/25 - 1555)
- Fixed a bug where H5Pget_fitler_by_id would succeed when called for a
filter that wasn't present. (NAF - 2009/06/25 - 1250)
- Fixed an issue with committed compound datatypes containing a vlen.
Also fixed memory leaks involving committed datatypes.
(NAF - 2009/06/10 - 1593)
- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
API. (NAF - 2009/04/20 - 1533)
- Fixed a problem with using data transforms with non-native types in the
file. (NAF - 2009/04/20 - 1548)
- Added direct.h include file to windows section of H5private.h
to fix _getcwd() warning. (ADB - 2009/04/14 - 1536)
- Fixed a bug that prevented external links from working after calling
H5close(). (NAF - 2009/04/10 - 1539)
- Modified library to write cached symbol table information to the
superblock, to allow library versions 1.3.0 to 1.6.3 to read files
created by this version. (NAF - 2009/04/08 - 1423)
- Changed skip lists to use a deterministic algorithm. The library should
now never call rand() or srand(). (NAF - 2009/04/08 - 503)
- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate
groups when that property was set. (NAF - 2009/04/07 - 1526)
- Fixed a bug that caused files with a user block to grow by the size of
the user block every time they were opened.
(NAF - 2009/03/26 - 1499)
- Fixed a rare problem that could occur with files using the old (pre 1.4)
array datatype. (NAF - 2009/03/23)
- Modified library to be able to open files with corrupt root group symbol
table messages, and correct these errors if they are found. Such
files can only be successfully opened with write access.
(NAF - 2009/03/23 - 1189)
- Removed the long_long #define and replaced all instances with
"long long". This caused problems with third party products. All
currently supported compilers support the type. (ADB - 2009/03/05)
- Fixed various bugs that could prevent the fill value from being written
in certain rare cases. (NAF - 2009/02/26 - 1469)
- Fixed a bug that prevented more than one dataset chunk from being cached
at a time. (NAF - 2009/02/12 - 1015)
- Fixed an assertion failure caused by opening an attribute multiple times
through multiple file handles. (NAF - 2009/02/12 - 1420)
- Fixed a problem that could prevent the user from adding attributes (or
any object header message) in some circumstances.
(NAF - 2009/02/12 - 1427)
- Fixed a bug that could cause problems when an attribute was added to a
committed datatype using the committed datatype's datatype.
(NAF - 2009/02/12)
- Fixed a bug that could cause problems when copying an object with a
shared message in its own object header. (NAF - 2009/01/29)
- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most
datatypes. (NAF - 2009/01/27 - 1443)
- Fixed a bug where H5Tpack wouldn't remove trailing space from an
otherwise packed compound type. (NAF - 2009/01/14)
- Fixed up some old v2 btree assertions that get run in debug mode that
were previously failing on compilation, and removed some of the
more heavily outdated and non-rewritable ones. (MAM - 2008/12/15)
- Fixed a bug that could cause problems when "automatically" unmounting
multiple files. (NAF - 2008/11/17)
- H5Ovisit and H5Ovisit_by_name will now properly terminate when the
callback function returns a positive value on the starting object.
(NAF - 2008/11/03)
- Fixed an error where a null message could be created that was larger
than could be written to the file. (NAF - 2008/10/23)
- Corrected error with family/split/multi VFD not updating driver info
when "latest" version of the file format used. (QAK - 2008/10/14)
- Corrected alignment+threshold errors to work correctly when metadata
aggregation is enabled. (QAK - 2008/10/06)
- Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered
by the library for internal library use. (NAF - 2008/10/06)
- Fixed potential memory leak during compound conversion.
(NAF - 2008/10/06)
- Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also
changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and
the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26)
- Fixed an issue that could cause data to be improperly overwritten
during compound type conversion. (NAF - 2008/09/19)
- Fixed pointer alignment violations that could occur during vlen
conversion. (NAF - 2008/09/16)
- Fixed problem where library could cause a segmentation fault when
an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
- Fixed improper shutdown when objects have reference count > 1. The
library now tracks reference count due to the application separately
from that due to internal library routines. (NAF - 2008/08/19)
- Fixed assertion failure caused by incorrect array datatype version.
(NAF - 2008/08/08)
- Fixed an issue where mount point traversal would fail when using
multiple handles for the child. (NAF - 2008/08/07)
- Fixed an issue where mount points were inaccessible when using multiple
file handles for the parent. The mount table is now in the shared
file structure (the parent pointer is still in the top structure).
(NAF - 2008/08/07)
- when an attribute was opened twice and data was written with one of the handles,
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure. SLU - 2008/07/22
- Fixed issue where a group could have a file mounted on it twice.
(QAK - 2008/07/15)
- Fixed a Windows-specific issue in the ohdr test which was causing users
in some timezones to get false errors. This a deficiency in the Windows
mktime() function, and has been handled properly. SJW - 2008/06/19
- Fixed the problem with the searching of target file for H5Lcreate_external().
The searching pattern will depend on whether the target file's
pathname is an absolute or a relative path. Please see the description
in the RM for H5Lcreate_external(). (VC - 2008/04/08)
- Fixed possible file corruption bug when encoding datatype
descriptions for compound datatypes whose size was between
256 & 511 bytes and the file was opened with the "use the
latest format" property enabled (with H5Pset_libver_bounds).
(QAK - 2008/03/13)
- Fixed bug in H5Aget_num_attrs() routine to handle invalid location
ID correctly. (QAK - 2008/03/11)
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
(PVN - 2009/01/8)
- Added code to maintain a min_clean_fraction in the metadata cache when
in serial mode. (MAM - 2009/01/9)
Configuration
-------------
- CMake: When CMake commands are executed individually on the command line
and the external filters are being built, the CMAKE_BUILD_TYPE define
must be set to the same value as the configuration
(-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed
by the szip and zlib filter build commands. (ADB - HDFFV-8695)
- CMake: Remove use of XLATE_UTILITY program. (ADB - 2014/03/28 HDFFV-8640)
- CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the
MPI option. (ADB - 2014/02/27 HDFFV-8674)
- Modified H5detect.c to scan floating point types for padding bits before
analyzing the type further. This should fix problems with gcc 4.8
(NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500)
- Fixed Makefile issue in which "-Wl," was not properly specified
prior to -rpath when building parallel fortran libraries with
an Intel compiler. (MAM - 2012/03/26)
- Makefiles generated by other packages using h5cc as the compiler
no longer error when 'make' is invoked more than once in order
to 'rebuild' after changes to source. (MAM - 2012/03/26)
- Added --enable-fortran2003 flag to enable Fortran2003 support
in the HDF5 Fortran library. The flag should be used along with the
--enable-fortran flag and takes affect only when Fortran compiler
is Fortran2003 compliant. (EIP - 2011/11/14)
- In Windows platform, the default VFD, was Windows VFD, is restored back
to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740
(AKC 2011/09/26)
- Removed config/ibm-aix6.x. All IBM-AIX settings are in one file,
ibm-aix. (AKC - 2011/4/14)
- Shared C libraries are no longer disabled on Mac when Fortran
is enabled. Shared Fortran libraries are still not supported on Mac,
so configure will disable them by default, but this is overridable
with the new --enable-unsupported configure option. The configure
summary has been updated to reflect the fact that the shared-ness of
the C++/Fortran wrapper libraries may not align with the C library.
(MAM - 04/11/2011 - HDFFV-4353).
- Removed recognition of the parallel compilers of LAM(hcc) and
ChMPIon(cmpicc) since we have no access to these two MPI implementations
and cannot verify their correctness. (AKC - 2010/7/14 - Bug 1921)
- Removed the following config files, as we no longer support them:
config/dec-osf*, config/hpux11.00, config/irix5.x,
config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
MAM - 2009/10/08
- Modified configure and make process to properly preserve user's CFLAGS
(and company) environment variables. Build will now properly use
automake's AM_CFLAGS for any compiler flags set by the configure
process. Configure will no longer modify CFLAGS directly, nor will
setting CFLAGS during make completely replace what configure has set up.
MAM - 2009/10/08
- Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
machine has long retired. AKC - 2009/10/06.
- Added $(EXEEXT) extension to H5detect when it's executed in the
src/Makefile to generate H5Tinit.c so it works correctly on platforms
that require the full extension when running executables.
MAM - 2009/10/01 - BZ #1613
- Configure will now set FC and CXX to "no" when fortran and c++
are not being compiled, respectively, so configure will not run
some of the compiler tests for these languages when they are not
being used. MAM - 2009/10/01
- The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -
- The --enable-static-exec flag will now properly place the -static flag
on the link line of all installed executables. This will force the
executable to link with static libraries over shared libraries, provided
the static libraries are available. MAM - 2009/08/31 - BZ #1583
- The --includedir=DIR configuration option now works as intended, and can
be used to specify the location to install C header files. The default
location remains unchanged, residing at ${prefix}/include.
MAM - 2009/03/10 - BZ #1381
- Configure no longer removes the '-g' flag from CFLAGS when in production
mode if it has been explicitly set in the CFLAGS environment variable
prior to configuration. MAM - 2009/03/09 - BZ #1401.
- Fixed error with 'make check install' failing due to h5dump
needing other tools built first. MAM - 2008/10/24.
- Wpen using shared szip, it is no longer necessary to specify
the path to the shared szip libraries in LD_LIBRARY_PATH. MAM -
2008/10/24.
- The file libhdf5_fortran.settings is not installed since its content
is included in libhdf5.settings now. AKC - 2008/10/21
- "make DESTDIR=xxx install" failed to install some tools and files
(e.g., h5cc and fortran modules). Fixed. AKC - 2008/10/8.
- Autotools: An export of LD_LIBRARY_PATH=<szip library location> was
removed from configure and make installcheck was revised to run
scripts installed in share/hdf5_examples to use the installed h5cc, etc.
to compile and run example source files also installed there. Make
installcheck will now fail when a shared szip or other external lib file
cannot be found in the same manner that executables compiled and linked
with h5cc will fail to run when those lib files cannot be found after
install. Make installcheck should pass after setting LD_LIBRARY_PATH to the
szip location.
(LRK - 2014/04/16)
Performance
-------------
- Removed program perform/benchpar from the enable-build-all list. The
program will be retired or moved to another location. HDFFV-8156
(AKC 2012/10/01)
- Retired program perform/mpi-perf. Its purpose has been incorporated
into h5perf before. (AKC 2012/09/20)
- ifdefs added to tests around include unistd.h and function to simulate
getlogin() on Windows.
(ADB - 2011/08/15)
- perf_serial test added to Windows projects and check batch file.
(ADB - 2009/06/11)
Fortran
--------
- Fixed a typo in return value of the nh5dread_f_c function ( was 1
instead of 0 on success); fixed the return value to make it consistent
with other Fortran functions; cleaned the code from debug statements.
(EIP - 2012/06/23)
- Fixed problem writing/reading control characters to a dataset; writing
a string containing: alerts, backspace, carriage_return, form_feed,
horizontal_tab, vertical_tab, new_line is now tested and working.
(MSB - 2012/09/01)
- Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
- Corrected the number of continuation lines in the src files
to be less then 32 lines for F95 compliance. (MSB - 2012/10/01)
Tools
-----
- h5dump subsetting fixed for dims greater then two
When a dataset has more then two dimensions, subsetting would incorrectly
calculate the data that needed to be displayed.
Added in block and stride calculation that account for dimensions greater
then two. NOTE: lines that have line breaks inserted because of display
length calculations, may have index info that is incorrect until the next
dimension break. (ADB, 2016/03/04, HDFFV-9698)
- h5repack: h5repack would not attempt to remove UD filters. Added a
check to h5repack for UD filters that checks if the filter can
be dynamically loaded. This will require a change in the library to
add the H5PL_load() to the H5Zfilter_avail(). (ADB - 2014/03/03 HDFFV-8629)
- h5repack: Fixed failure for converting a layout of small chunked dataset
(size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18)
- h5diff: Fixed to return correct exit code 1 when detect unique extra
attribute. Prior to this fix, h5diff returned exit code 0 indicating
two files are identical. HDFFV-7643 (JKM 2013/02/15)
- h5diff: Improved speed when comparing HDF5 files with lots of
attributes. Much slower performance was identified with release
version from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19)
- h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
source file contains chunked dataset and a chunk dim is bigger than
the dataset dim. Another issue is that the command changed max dims
if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact
size limit) Fixed both.
HDFFV-8012 (JKM 2012/09/24)
- h5diff: Fixed not to accumulate attribute difference to dataset
difference in verbose mode (-v, -r), which caused incorrect
difference between dataset and group/datatype object if attribute
exist with any differences. This also lead to fix inconsistent
format indicating difference between dataset and group/datatype
object. HDFFV-5919 (JKM 2012/09/05)
- h5diff: Fixed the incorrect result when comparing attribute data
values and the data type has same class but different size.
HDFFV-7942 (JKM 2012/08/15)
- ph5diff: Fixed intermittent hang issue on a certain operation in
parallel mode. It was detected by daily test for comparing
non-comparable objects, but it could have occurred in other
operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01)
- h5diff: Fixed test failure for "make check" due to failure of
copying test files when performed in HDF5 source tree. Also applied
to other tools.
HDFFV-8107 (JKM 2012/08/01)
- h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of
testh5diff.sh to better report when there is an error in the file
copying. HDFFV-8105 (AKC -2012/07/22)
- h5diff: Fixed not to check and display dangling link status without
--follow-symlinks option. This also improved performance when
comparing lots of external links without the --follow-symlinks
option. HDFFV-7998 (JKM 2012/04/26)
- h5unjam: Fixed sefgault when used -V (show version) option.
HDFFV-8001 (JKM 2012/04/19)
- h5repack: Fixed a failure when change the chunk size of a specified
chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11)
- h5diff: Fixed failure for comparing same named object with different
object types in comparing groups. Prior to the fix, h5diff resulted
in error. After the fix, h5diff detects such case as non-comparable
and display messages accordingly. HDFFV-7664 (JKM 2012/03/28)
- h5diff: If unique objects exists only in one file and try to exclude
the unique objects with --exclude-path option, h5diff missed
excluding some objects.
Fixed to exclude objects correctly in such case.
HDFFV-7837 (JKM 2012/03/20)
- h5dump: Added tools library error stack to properly catch error
information generated within the library.
HDFFV-7958 (ADB 2012/03/12)
- h5dump: Dangling links no longer throw error message, change process
when open link fails.
HDFFV-7839 (ADB 2012/03/12)
- h5diff: When two symbolic dangling links are compared with
--follow-symlinks option, the result should be same. It worked for
comparing two files, but didn't work for comparing two objects.
HDFFV-7835 (JKM 2012/03/09)
- h5dump: Refactored code to remove duplicated functions. Split XML
functions from DDL functions. Corrected indentation and formatting
errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified
all tools call tools_init() in main.
HDFFV-7560 (ADB 2012/02/17)
- h5diff: fixed to prevent from displaying error stack message when
comparing the two dangling symlinks with follow-symlinks option.
HDFFV-7836 (JKM 2012/01/13)
- h5repack: fixed memory leak for handling variable length string in
attribute. HDFFV-7840 (JKM 2012/01/06)
- h5ls: fixed segfault when access region reference data in an
attribute. HDFFV-7838 (JKM 2011/12/29)
- h5diff: fixed segfault over non-comparable attribute with different
dimension or rank, along with '-c' option to display details.
HDFFV-7770 (JKM 2011/10/24)
- Fixed h5diff to display all the comparable object and attribute