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hdf5/release_docs/RELEASE.txt
Quincey Koziol bdefbb5cba [svn-r5603] Purpose: 
Bug fix

Description:
    I/O on "Regular" hyperslab selections could fail to transfer correctly
    if the number of elements in the selection's row did now fit "evenly"
    into the buffer being used for the transfer.

Solution:
    Correct the calculation of the block & count offsets within the optimized
    "regular" hyperslab routines.

Platforms tested:
    FreeBSD 4.5 (sleipnir)
2002-06-12 12:01:01 -05:00

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HDF5 version 1.5.30 currently under development
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.0 and
HDF5-1.5-snap0, and contains information on the platforms tested and
known problems in HDF5-1.5-snap0. For more details check the HISTORY.txt
file in the HDF5 source.
The HDF5 documentation can be found on the NCSA ftp server
(ftp.ncsa.uiuc.edu) in the directory:
/HDF/HDF5/docs/
For more information look at the HDF5 home page at:
http://hdf.ncsa.uiuc.edu/HDF5/
If you have any questions or comments, please send them to:
hdfhelp@ncsa.uiuc.edu
CONTENTS
- New Features
- Bug Fixes since HDF5-1.4.0
- Support for new platforms and languages
- Platforms Tested
- Known Problems
Bug Fixes since HDF5-1.4.0
==========================
Library
-------
* Fixed bug where regular hyperslab selection could get incorrectly
transferred when the number of elements in a row did not fit evenly
into the buffer provided. QAK 2002/06/12
* Fixed bug (#499) which allowed an "empty" compound or enumerated datatype
(one with no members) to be used to create a dataset or committed to a
file. QAK - 2002/06/11
* Fixed bug (#777) which allowed a compound datatype to be inserted into
itself. QAK - 2002/06/10
* Fixed bug (#789) where creating 1-D dataset region reference caused the
library to go into infinite loop. QAK - 2002/06/10
* Fixed bug (#699, fix provided by a user) where a scalar dataspace was
written to the file and then subsequently queried with the
H5Sget_simple_extent_type function, type was reported H5S_SIMPLE instead
of H5S_SCALAR. EIP - 2002/06/04
* Clear symbol table node "dirty" flag when flushing symbol tables to
disk, to reduce I/O calls made & improve performance. QAK - 2002/06/03
* Fixed bug where an object's header could get corrupted in certain obscure
situations where many objects were created in the file. QAK - 2002/05/31
* Fixed bug where read/write intent in file IDs created with H5Freopen
was not being kept the same as the original file. QAK - 2002/05/14
* Fixed bug where selection offsets were not being used when iterating
through point and hyperslab selections with H5Diterate(). QAK - 2002/04/29
* Fixed bug where the data for several level deep nested compound &
variable-length datatypes used for datasets were getting corrupted when
written to the file. QAK - 2002/04/17
* Fixed bug where selection offset was being ignored for certain hyperslab
selections when optimized I/O was being performed. QAK - 2002/04/02
* Added serial multi-gigabyte file size test. "test/big -h" shows
the help page. AKC - 2002/03/29
* Fixed bug where variable-length string type doesn't behave as
string. SLU - 2002/03/28
* Fixed bug in H5Gget_objinfo() which was not setting the 'fileno'
of the H5G_stat_t struct. QAK - 2002/03/27
* Fixed data corruption bug in hyperslab routines when contiguous
hyperslab that spans entire dimension and is larger than type
conversion buffer is attempted to be read. QAK - 2002/03/26
* Fixed bug where non-zero fill-value was not being read correctly from
certain chunked datasets when using an "all" or contiguous hyperslab
selection. QAK - 2002/02/14
* Fixed bug where a preempted chunk in the chunk data could still be
used by an internal pointer and cause an assertion failure or core
dump. QAK - 2002/02/13
* Fixed bug where raw data re-allocated from the free-list would sometimes
overlap with the metadata accumulator and get corrupted. QAK - 2002/01/23
* Fixed bug where variable-length datatypes for attributes was not working
correctly.
* Retired the DPSS virtual file driver (--with-gridstorage configure
option).
* Corrected behavior of H5Tinsert to not allow compound datatype fields to
be inserted past the end of the datatype.
* Fixed the internal macros used to encode & decode file metadata, to avoid
an unaligned access warning on IA64 machines.
* Fixed an off-by-one error in H5Sselect_valid when hyperslab selections
which would allow hyperslab selections which overlapped the edge of the
selection by one element as valid.
* Fixed a bug in internal B-tree code where a B-tree was not being copied
correctly.
* Fixed a bug in the 'big' test where quota limits weren't being detected
properly if they caused close() to fail.
* Fixed a bug where 'or'ing a hyperslab with a 'none' selection would
fail. Now adds that hyperslab as the first hyperlab in the selection.
* Fixed a bug where appending a point selection to the current selection
would not actually append the point when there were no points defined
currently.
* Fixed a bug where reading or writing chunked data which needed datatype
conversion could result in data values getting corrupted.
* Fixed a bug where reading an entire dataset wasn't being handled
optimally when the dataset had unlimited dimensions. Dataset is read
in a single low-level I/O now, instead of being broken into separate
pieces internally.
* Fixed a bug when reading chunked datasets where the edge of the dataset
would be incorrectly detected and generate an assertion failure.
* Added new parallel hdf5 tests in t_mpi. The new test checks if the
filesystem or the MPI-IO can really handle greater than 2GB files.
If it fails, it prints information message only without failing the
test.
* Fixed a bug in H5FD_mpio_flush() that might result in negative file seek
if both MPIO and Split-file drivers are used together.
* Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be
external to C++.
* Fixed a bug of H5pubconf.h causing repeated definitions if it is included
more than once. hdf5.h now includes H5public.h which includes
H5pubconf.h. Applications should #include hdf5.h which handles multiple
inclusion correctly.
* Tweaked a few API functions to use 'size_t' instead of 'unsigned' or
'hsize_t', which may cause errors in some cases.
* Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x
when --enable-hdf5v1_2 configure flag is enabled.
* Removed limitation that the data transfer buffer size needed to be
set for datasets whose dimensions were too large for the 'all' selection
code to handle. Any size dimensioned datasets should be handled
correctly now.
* The allocation by alignment (H5Pset_alignment) feature code somehow
got dropped in some 1.3.x version. Re-implemented it with "new and
improved" algorithm. It keeps track of "wasted" file-fragment in
the free-list too.
* IMPORTANT: Fixed file metadata corruption bug which could cause metadata
data loss in certain situations.
* Fixed build on Linux systems with --enable-static-exec flag. It now
works correctly.
* Fixed bug with non-zero userblock sizes causing raw data to not write
correctly.
* 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.
* Fixed bug where non-aligned hyperslab I/O on chunked datasets was
causing errors during I/O
* Fixed bug with contiguous hyperslabs not being detected, causing
slower I/O than necessary.
Configuration
-------------
* Can use just enable-threadsafe if the C compiler has builtin pthreads
support.
* Require HDF (a.k.a. hdf4) software that consists of a newer version
of zlib library which consists of the compress2() function. Versions
HDF version 4.1r3 and newer meets this requirement. The compress2
uses a newer compression algorithm used by the HDF5 library. Also,
4.1r3 has an hdp tool that can handle "loops" in Vgroups.
* Added --enable-linux-lfs flag to allow more control over whether to enable
or disable large file support on Linux.
* Basic port to Compaq (nee DEC) Alpha OSF 5.
* Changed the default value of $NPROCS from 2 to 3 since 3 processes
have a much bigger chance catching parallel errors than just 2.
Tools
-----
* Fixed limitation in h5dumper with object names which reached over 1024
characters in length. We can now handle arbitrarily larger sizes for
object names. BW - 2002/02/27
* Fixed so that the "-i" flag works correctly with the h5dumper.
* Fixed segfault when "-v" flag was used with the h5dumper.
Documentation
-------------
New Features
============
* Allow chunks in chunked datasets to be cached when file is opened for
read-only access (bug #709). QAK - 2002/06/10
* Added internal "small data" aggregation, which can reduce the number of
actual I/O calls made, improving performance. QAK - 2002/06/05
* Improved internal metadata aggregation, which can reduce the number of
actual I/O calls made, improving performance. Additionally, this can
reduce the size of files produced. QAK - 2002/06/04
* Improved internal metadata caching, which can reduce the number of actual
I/O calls made by a substantial amount, improving
performance. QAK - 2002/06/03
* Added 'closing' parameter to VFL 'flush' callback function and H5FDflush.
This allows the library to indicate that the file will be closed
immediately following the call to 'flush' and can be used to avoid actions
that are duplicated in the VFL 'close' callback function. QAK - 2002/05/20
* Added feature to parallel chunk allocation routine to not write fill
values to chunks allocated if the user has set the "fill time" to never.
This can improve parallel I/O performance for chunked
datasets. QAK - 2002/05/17
* Changed method for allocating chunked dataset blocks in parallel to only
allocate blocks that don't already exist, instead of attempting to create
all the blocks all the time. This improves parallel I/O performance for
chunked datasets. QAK - 2002/05/17
* Allowed the call to MPI_File_sync to be avoided when the file is going to
immediately be closed, improving performance. QAK - 2002/05/13
* Allow the metadata writes to be shared among all processes, easing the
burden on process 0. QAK - 2002/05/10
* New functions H5Glink2 and H5Gmove2 were added to allow link and move to
be in different locations in the same file. The old functions H5Glink
and H5Gmove remain valid. SLU - 2002/04/26
* Fill-value's behaviors for contiguous dataset have been redefined.
Basicly, dataset won't allocate space until it's necessary. Full details
are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment.
SLU - 2002/04/11
* Added new routine "H5Dfill" to fill a selection with a particular value
in memory. QAK - 2002/04/09
* A new query function H5Tget_member_index has been added for compound
and enumeration data types, to retrieve member's index by name.
SLU - 2002/04/05
* Improved performance of "regular" hyperslab I/O when using MPI-IO and the
datatype conversion is unneccessary. QAK - 2002/04/02
* Improved performance of single hyperslab I/O when datatype conversion is
unneccessary. QAK - 2002/04/02
* New API function H5Dset_extent. Modifies the dimensions of a dataset,
allows change to a lower dimension. The unused space in the file is freed.
PVN - 2002/03/31
* Added new "H5Sget_select_type" API function to determine which type of
selection is defined for a dataspace ("all", "none", "hyperslab" or
"point"). QAK - 2002/02/07
* Added support to read/write portions of chunks directly, if they are
uncompressed and too large to cache. This should speed up I/O on chunked
datasets for a few more cases. QAK - 2002/01/31
* Parallel HDF5 is now supported on HP-UX 11.00 platforms.
* Added H5Rget_obj_type() API function, which performs the same functionality
as H5Rget_object_type(), but requires the reference type as a parameter
in order to correctly handle dataset region references. Moved
H5Rget_object_type() to be only compiled into the library when v1.4
compatibility is enabled.
* Changed internal error handling macros to reduce code size of library by
about 10-20%.
* Added a new file access property, file close degree, to control file
close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI,
H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspont functions
H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two
new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist
this new feature. For full details, please refer to the reference
manual under the description of H5Fcreate, H5Fopen, H5Fclose and the
functions mentioned above.
* Removed H5P(get|set)_hyper_cache API function, since the property is no
longer used.
* Improved performance of non-contiguous hyperslabs (built up with
several hyperslab selection calls).
* Improved performance of single, contiguous hyperslabs when reading or
writing.
* As part of the transition to using generic properties everywhere, the
parameter of H5Pcreate changed from H5P_class_t to hid_t, as well
the return type of H5Pget_class changed from H5P_class_t to hid_t.
Further changes are still necessary and will be documented here as they
are made.
* Added a new test to verify the information provided by the configure
command.
* The H5Pset_fapl_split() accepts raw and meta file names similar to the
syntax of H5Pset_fapl_multi() in addition to what it used to accept.
* Added perform programs to test the HDF5 library performance. Programs
are installed in directory perform/.
* Added new checking in H5check_version() to verify the five HDF5 version
information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent.
* Added a new public macro, H5_VERS_INFO, which is a string holding
the HDF5 library version information. This string is also compiled
into all HDF5 binary code which helps to identify the version
information of the binary code. One may use the Unix strings
command on the binary file and looks for the pattern "HDF5 library
version".
* Added a parallel HDF5 example examples/ph5example.c to illustrate
the basic way of using parallel HDF5.
* Added two simple parallel performance tests as mpi-perf.c (MPI
performance) and perf.c (PHDF5 performance) in testpar.
* Improved regular hyperslab I/O by about a factor of 6 or so.
* Modified the Pablo build procedure to permit building of the instrumented
library to link either with the Trace libraries as before or with the
Pablo Performance Caputure Facility.
* Verified correct operation of library on Solaris 2.8 in both 64-bit and
32-bit compilation modes. See INSTALL document for instructions on
compiling the distribution with 64-bit support.
* Parallel HDF5 now runs on the HP V2500 and HP N4000 machines.
* H5 <-> GIF convertor has been added. This is available under
tools/gifconv. The convertor supports the ability to create animated
gifs as well.
* Added a global string variable H5_lib_vers_info_g which holds the
HDF5 library version information. This can be used to identify
an hdf5 library or hdf5 application binary.
Also added a verification of the consistency between H5_lib_vers_info_g
and other version information in the source code.
* File sizes greater than 2GB are now supported on Linux systems with
version 2.4.x or higher kernels.
* F90 APIs are available on HPUX 11.00 and IBM SP platforms.
* F90 static library is available on Windows platforms. See
INSTALL_Windows.txt for details.
* F90 API:
- Added aditional parameter "dims" to the h5dread/h5dwrite and
h5aread/h5awrite subroutines. This parameter is 1D array of size
7 and contains the sizes of the data buffer dimensions.
- F90 subroutines h5dwrite_f, h5dread_f, h5awrite_f and h5aread_f were
overloaded with "dims" argument to be assumed size array of type
INTEGER(HSIZE_T). We recommend to use the subroutines with the new
type. Module subroutines that accept "dims" as INTEGER array of size
7 will be deprecated in 1.6 release.
EIP - 2002/05/06
* C++ API:
- Added two new member functions: Exception::getFuncName() and
Exception::getCFuncName() to provide the name of the member
function, where an exception is thrown.
- IdComponent::operator= becomes a virtual function because
DataType, DataSpace, and PropList provide their own
implementation. The new operator= functions invoke H5Tcopy,
H5Scopy, and H5Pcopy to make a copy of a datatype, dataspace,
and property list, respectively.
* A helper script called ``h5cc'', which helps compilation of HDF5
programs, is now distributed with HDF5. See the reference manual
for information on how to use this feature.
Support for new platforms and languages
=======================================
* Parallel Fortran Library works now on HP-UX B.11.00 Sys V
EIP - 2002/05/06
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) mpcc_r 3.6.6
Cray T3E sn6711 2.0.5.45 Cray Standard C Version 6.4.0.0
Cray Fortran Version 3.4.0.2
Cray SV1 sn9605 10.0.0.7 Cray Standard C Version 6.4.0.0
Cray Fortran Version 3.4.0.2
FreeBSD 4.3 gcc 2.95.2
g++ 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP-UX B.11.00 HP C HP92453-01 A.11.00.13
HP C HP92453-01 A.11.01.20
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.4.0.2
mpich-1.2.1
Linux 2.4.4 gcc-2.95.3
g++ 2.95.3
Linux 2.2.16-3smp gcc-2.95.2
g++ 2.95.2
pgf90 3.1-3
OSF1 V4.0 DEC-V5.2-040
Digital Fortran 90 V4.1-270
SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.6) WorkShop Compilers 5.0 99/10/25 Fortran 90
2.0 Patch 107356-04
Workshop Compilers 5.0 98/12/15 C++ 5.0
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 99/10/25 Fortran 90
2.0 Patch 107356-04
Workshop Compilers 5.0 98/12/15 C++ 5.0
TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes
Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0
Windows 98 MSVC++ 6.0
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not tested in this release
x = not working in this release
( ) = footnote appears below second table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries
(5)
Solaris2.7 y y (1) y n y y y y
Solaris2.8 64 y n y n y y y y
Solaris2.8 32 y y (1) y n y y y y
IA-64 y n n n n n y y
IRIX6.5 y y (1) n n n y y y
IRIX64_6.5 64 y y (2) y y n y y y
IRIX64_6.5 32 y y (2) n n n y y y
HPUX10.20 y n y n n y y y
HPUX11.00 y y y n n y y y
HPUX11 SysV y y y y n y y y
DECOSF y n y n y y y y
T3E y y y y n n y y
SV1 y n y n n n y y
TFLOPS y y (1) n n n n y y (4)
AIX-4.3 SP2 y y y y n n y n
AIX-4.3 SP3 y y y y y n y n
Win2000 y n y n y (6) y y y
Win98 y n y n y (6) y y y
WinNT y n y n y (6) y y y
WinNT CW y n n n n n y y
FreeBSD y n n n y y y y
Linux 2.2 y y (1) y n y y y y
Linux 2.4 y y (1) n n y y y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.7 n x y n n y
Solaris2.8 64 n y n n n y
Solaris2.8 32 n x y n n y
IA-64 n n n n n y
IRIX6.5 n x y n n y
IRIX64_6.5 64 n x y n y y
IRIX64_6.5 32 n x y n y y
HPUX10.20 n y n n n y
HPUX11.00 n x n n n y
HPUX11 SysV n x n n n y
DECOSF n y n n n y
T3E n y n n n y
SV1 n y n n n y
TFLOPS n y n n n n
AIX-4.3 SP2 n y (3) n n n y
AIX-4.3 SP3 n y n n n y
Win2000 n y n n n n
Win98 n y n n n n
WinNT n y n n n n
WinNT CW n n n n n n
FreeBSD n y y n n y
Linux 2.2 n y y n n y
Linux 2.4 n y y n n y
Footnotes: (1) Using mpich.
(2) Using mpt and mpich.
(3) When configured with static-exec enabled, tests fail
in serial mode.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library.
(6) Exception of (5): DLL is available for C++ API on Windows
Known Problems
==============
* Datasets or attributes which have a variable-length string datatype are not
printing correctly with h5dump and h5ls.
* DLLs do not work on Windows 98
* RELEASE DLLs will fail on some tests on Windows 2000 with Microsoft visual
studio 6.0 due to memory allocation problems caused by compiler.
Users are encouraged to go to microsoft site to find and install
visual studio 6.0 service pack 5. After that, release dlls will work.
* The stream-vfd test uses ip port 10007 for testing. If another
application is already using that port address, the test will hang
indefinitely and has to be terminated by the kill command. To try the
test again, change the port address in test/stream_test.c to one not
being used in the host.
* The --enable-static-exec configure flag fails to compile for Solaris
platforms. This is due to the fact that not all of the system
libraries on Solaris are available in a static format.
The --enable-static-exec configure flag also fails to correctly compile
on IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
It is suggested that you don't use this option on these platforms
during configuration.
* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
compilation. The ANSI version of the compiler complains about not being
able to handle the `long long' datatype with the warning:
warning: ANSI C does not support `long long'
This warning is innocuous and can be safely ignored.
* SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will
fail if library is compiled using optimization of any level.
* h5toh4 converter fails two cases (tstr.h5 and tmany.h5) for release dll
version on windows 2000 and NT. The reason is possibly due to windows
NT DLL convention on freeing memory. It seems that memory cannot be
free across library or DLL. It is still under investigated.
* The Stream VFD was not tested yet under Windows. It is not supported
in the TFLOPS machine.
* Shared library option is broken for IBM SP and some Origin 2000
platforms. One needs to run ./configure with '--disable-shared'
* The ./dsets tests failed in the TFLOPS machine if the test program,
dsets.c, is compiled with the -O option. The hdf5 library still works
correctly with the -O option. The test program works fine if it is
compiled with -O1 or -O0. Only -O (same as -O2) causes the test
program to fail.
* Certain platforms give false negatives when testing h5ls:
- Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing
when displaying object references in certain files. These are
benign differences due to the difference in sizes of the objects
created on those platforms. h5ls appears to be dumping object
references correctly.
- Cray J90 (and Cray T3E?) give errors during testing when displaying
some floating-point values. These are benign differences due to
the different precision in the values displayed and h5ls appears to
be dumping floating-point numbers correctly.
* Before building HDF5 F90 Library from source on Crays (T3E and J90)
replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src
subdirectory in the top level directory with the Cray-specific files
from the site:
ftp://hdf.ncsa.uiuc.edu/pub/ougoing/hdf5/hdf5-1.4.0-beta/F90_source_for_Crays
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
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