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hdf5/release_docs/HISTORY.txt
Elena Pourmal db2631c956 [svn-r6945] 
Purpose: Maintenance for 1.6 release

Description: HISTORY.txt was not updated in 1.5 branch since 1.2.0 release.
             RELEASE.txt had a lot of redundant info that is now in HISTORY.txt
             INSTALL_Windows_withF90.txt was lost in 1.5 branch.

Solution: I updated HISTORY.txt to include release history up to 1.4.5 release.
          After that I removed all information related to the 1.4.* releases
          from RELEASE.txt file. "Platforms Tested" section was brought up
          to date based on the information provided by developers for 1.6.0 first
          round of testing. RELEASE.txt still needs a lot of work.
          INSTALL_Windows_withF90.txt  is also a first draft, more work is needed.

Platforms tested: N/A

Misc. update:
2003-06-02 15:36:31 -05:00

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HDF5 HISTORY
============
This file contains history of the HDF5 libraries releases
CONTENTS
13. Release Information for hdf5-1.4.5
12. Release Information for hdf5-1.4.4
11. Release Information for hdf5-1.4.3
10. Release Information for hdf5-1.4.2
9. Release Information for hdf5-1.4.1
8. Release Information for hdf5-1.4.0
7. Release Information for hdf5-1.2.2
6. Release Information for hdf5-1.2.1
5. Release Information for hdf5-1.2.0
4. Changes from Release 1.0.0 to Release 1.0.1
3. Changes from the Beta 1.0.0 Release to Release 1.0.0
2. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release
1. Changes from the First Alpha 1.0.0 Release to the
Second Alpha 1.0.0 Release
[Search on the string '%%%%' for per-release section breaks.]
-----------------------------------------------------------------------
%%%%1.4.5%%%% Release Information for hdf5-1.4.5 (02/February/03)
13. Release information for HDF5 version 1.4.5
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.4 and
HDF5-1.4.5, and contains information on the platforms tested and
known problems in HDF5-1.4.5. For additional information 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, see 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 HDF5-1.4.4
- Performance Improvements
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* Added "unofficial support" for building with a C++ compiler (or at least
not failing badly when building with a C++ compiler). QAK - 2003/01/09
* Added "unofficial support" for AIX 64bits. See INSTALL for configure
details. AKC - 2002/08/29
* Added "--with-dmalloc" flag, to easily enable support for the 'dmalloc'
debugging malloc implementation. QAK - 2002/07/15
o Library
=========
o General
---------
* 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.
o APIs
------
* 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.
o Parallel library
==================
* The MPI-posix virtual file driver makes gpfs_fcntl() hints to tell
the underlying GPFS file system to avoid prefetching byte range
tokens if USE_GPFS_HINTS is defined when this file is compiled.
This temporary solution is intended to be removed once the HDF5
API supports the necessary functionality that makes it possible
for this sort of thing do be done at a higher software layer.
RPM - 2002/12/03
* Added MPI-posix VFL driver. This VFL driver uses MPI functions to
coordinate actions, but performs I/O directly with POSIX sec(2)
(i.e. open/close/read/write/etc.) calls. This driver should _NOT_
be used to access files that are not on a parallel filesystem.
The following API functions were added:
herr_t H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm);
herr_t H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/);
QAK - 2002/07/15
o Support for new platforms and languages
=========================================
* C++ API now works on the Origin2000 (IRIX6.5.14.) BMR - 2002/11/14
o Misc.
=========================================
HDF5 1.4.5 works with Portland Group Compilers (pgcc, pgf90 and pgCC
version 4.0-2) on Linux 2.4
Bug Fixes since HDF5-1.4.4 Release
==================================
* 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
Documentation
=============
New PDF files are not available for this release.
Platforms Tested
================
AIX 5.1 (32 and 64-bit) C for AIX Compiler, Version 6
xlf 8.1.0.2
poe 3.2.0.11
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.1.3
Cray Fortran Version 3.6.0.0.12
Cray SV1 10.0.1. 0 Cray Standard C Version 6.6.0.1.3
Cray Fortran Version 3.6.0.0.12
Cray T90IEEE 10.0.1.01u Cray Standard C Version 6.4.0.2.3
Cray Fortran Version 3.4.0.3
FreeBSD 4.7 gcc 2.95.4
g++ 2.95.5
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
Linux 2.4.18 gcc 3.2.1
g++ 3.2.1
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
PGI compilers (pgcc, pgf90, pgCC) version 4.0-2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran X5.4A-1684
gcc version 3.0 for C++
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.3.3 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.9 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows XP .NET
Windows NT4.0 Code Warrior 6.0
MAC OS X Darwin 6.2
gcc and g++ Apple Computer, Inc. GCC
version 1161, based on gcc version 3.1
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
dna = does not apply
( ) = footnote appears below second table
Platform C C F90 F90 C++ Shared zlib
parallel parallel libraries (5)
Solaris2.6 y n y n y y y
Solaris2.7 64-bit y y (1) y y (1) y y y
Solaris2.7 32-bit y y (1) y y (1) y y y
Solaris2.8 64-bit y n y y (1) y y y
Solaris2.8 32-bit y n y y (1) y y y
IRIX6.5 y y (1) n n n y y
IRIX64_6.5 64-bit y y (2) y y y y y
IRIX64_6.5 32-bit y y (2) n n n y y
HPUX11.00 y y (1) y n n y y
OSF1 v5.1 y n y n y y y
T3E (6) y n y n n n y
SV1 y n y n n n y
T90 IEEE y n y n n n y
TFLOPS n y (1) n n n n y
AIX-5.1 32-bit y y y y y n y
AIX-5.1 64-bit y y y y y n y
WinXP (7) y n n n y y y
WinNT/2000 y n y n y y y
WinNT CW y n n n n n y
Mac OS X 10.2 y n n n y y y
FreeBSD y y (1) n n y y y
Linux 2.2 y y (1) y y (1) y y y
Linux 2.4 gcc (3) y y (1) y n y y y
Linux 2.4 Intel (3) y n y n n n y
Linux 2.4 PGI (3) y n y n y n y
Linux 2.4 IA32 y n y n n n y
Linux 2.4 IA64 y n y n n n y
Platform static- Thread- SRB GASS STREAM-
exec safe VFD
Solaris2.6 x y n n y
Solaris2.7 64-bit x y n n y
Solaris2.7 32-bit x y n n y
Solaris2.8 64-bit x n n n y
Solaris2.8 32-bit x y n n y
IRIX6.5 x n n n y
IRIX64_6.5 64-bit x y n y y
IRIX64_6.5 32-bit x y n y y
HPUX11.00 x n n n y
OSF1 v5.1 y n n n y
T3E (6) y n n n y
SV1 y n n n y
T90 IEEE y n n n y
TFLOPS y n n n n
AIX-5.1 32-bit y n n n y
AIX-5.1 64-bit y n n n y
WinXP (7) dna n n n n
WinNT/2000 dna n n n n
WinNT CW dna n n n n
Mac OS X 10.2 y n n n y
FreeBSD y y n n y
Linux 2.2 y y n n y
Linux 2.4 gcc (3) y y n n y
Linux 2.4 Intel (3) y n n n y
Linux 2.4 PGI (3) y n n n y
Linux 2.4 IA32 y n n n y
Linux 2.4 IA64 y n n n y
Notes: (1) Using mpich 1.2.4.
(2) Using mpt and mpich 1.2.4.
(3) Linux 2.4 with GNU, Intel, and PGI compilers.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library,
except on Windows where they are provided for all languages.
(6) Debug mode only.
(7) Binaries only; source code for this platform is not being
released at this time.
Known Problems
==============
* On Linux 2.4 IA64, Fortran test fails for h5dwrite_vl_f
for integer and real base datatypes.
* When fortran library is built with Intel compilers, compilation
for fflush1.f90, fflush2.f90 and fortanlib_test.f90 will fail
complaining about EXEC function. Comment the call to EXEC subroutine
in each program, or get a patch for the HDF5 Fortran source code.
* Fortran external dataset test fails on Linux 2.4 with pgf90 compiler.
* On Windows, h5dump may abort printing if a VL string is longer than 4096
bytes due to a compiler problem. It'll be fixed in v1.6 release.
* Datasets or attributes which have a variable-length string datatype are
not printing correctly with h5dump and h5ls.
* When a dataset with the variable-length datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output on some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The executables are always dynamic on Solaris 2.7 ans 2.8(64 and n32)
even if they are configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting the environment
variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* On OSF1 v5.1 and IA32 h5dumpgentst program that generates test files
for h5dump, gives segmentation fault.
* On Windows platforms, C and Fortran tests fail with the debug DLL version
of the Library if built from all_withf90.zip file.
* On Cray T3E (sn6606 2.0.6.08 unicosmk CRAY T3E) with Cray Standard C Version 6.6.0.1.3
compiler optimization causes errors in many HDF5 Library tests. Use -g -h zero flags
to build HDF5 Library.
* On Cray SV1 10.0.1. 0 datatype convertion test fails. Please check HDF FTP site
if patch is available. We will try to provide one in the nearest future.
* For configuration, building and testing with Intel and PGI compilers see
corresponding section in INSTALL file.
%%%%1.4.4%%%% Release Information for hdf5-1.4.4 (02/July/02)
12. Release information for HDF5 version 1.4.4
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.3 and
HDF5-1.4.4, and contains information on the platforms tested and
known problems in HDF5-1.4.4. 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, see 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 HDF5-1.4.3
- Performance Improvements
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* The H4 to H5 tools have been removed from the main source and placed
in a separate package. You can get these tools from the HDF ftp site
(ftp://hdf.ncsa.uiuc.edu/). The "--with-hdf4" command-line option
during configure is no longer valid. BW - 2002/06/25
o Library
=========
o General
---------
* Fill-value forward-compatibility with release 1.5 was added. SLU -
2002/04/11
* A new query function H5Tget_member_index has been added for compound
and enumeration data types. This function retrieves a member's index
by name. SLU - 2002/04/05
* Added serial multi-gigabyte file size test. "test/big -h" shows
the help page. AKC - 2002/03/29
o APIs
------
* The F90 subroutines h5dwrite_f, h5dread_f, h5awrite_f, and h5aread_f
were overloaded with a "dims" argument of type INTEGER(HSIZE_T) to
specify the size of the array. We recommend using these subroutines
with the new type; module subroutines that accept "dims" as an i
INTEGER array of size 7 will be deprecated in release 1.6.
EIP - 2002/05/06
o Performance
-------------
* 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
o Parallel library
==================
* Fixed bug in parallel I/O routines where a collective I/O which used
MPI derived types, followed by an independent I/O would cause the library
to hang. QAK 2002/06/24
* Added environment variable flag to control whether creating MPI derived
types is preferred or not. This can affect performance, depending on
which way the MPI-I/O library is optimized. The default is set to
prefer MPI derived types for collective raw data transfers; setting the
HDF5_MPI_PREFER_DERIVED_TYPES environment variable to "0" (i.e.:
"setenv HDF5_MPI_PREFER_DERIVED_TYPES 0") changes the preference to avoid
using them whenever possible. QAK - 2002/06/19
* Changed MPI I/O routines to avoid creating MPI derived types (and thus
needing to set the file view) for contiguous selections within datasets.
This should result in some performance improvement for those types of
selections. QAK - 2002/06/18
* Changed MPI type support for collective I/O to be enabled by default.
This can be disabled by setting the HDF5_MPI_OPT_TYPES environment
variable to the value "0". QAK - 2002/06/14
* Allowed chunks in chunked datasets to be cached when parallel file is
opened for read-only access (bug #709). QAK - 2002/06/10
* Changed method for allocating chunked dataset blocks to only allocate
blocks that don't already exist, instead of attempting to create all the
blocks all the time. This improves 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
* Allowed the metadata writes to be shared among all processes, easing the
burden on process 0. QAK - 2002/05/10
o Tools
=======
* h5redeploy utility was added. It updates HDF5 compiler tools
after the HDF5 software has been installed in a new location.
o Support for new platforms and languages
=========================================
* Parallel Fortran Library works now on HP-UX B.11.00 Sys V.
EIP - 2002/05/06
* Intel C++ and F90 compilers Version 6.0 are supported on Linux 2.4.
* Intel C++ compilers Version 6.0 are supported on Windows 2000.
o Misc.
=========================================
* zlib has been moved out of the Windows source release. Users should go to
the ZLIB homepage(http://www.zlib.org) to download the corresponding
zlib library.
* The Windows binary release is built with the old version of the zlib
library. We expect users to use zlib 1.1.4 to build with the source
release.
* In the Windows-specific install document, we specify how to test backward
compatibility. However, in this release, we are not testing the backward
compatibility of HDF5.
Bug Fixes since HDF5-1.4.3 Release
==================================
* Fixed bug in chunking routines where they were using internal allocation
free routines, instead of malloc/free, preventing user filters from
working correctly. Chunks are now allocated/freed with malloc/free and
so should the chunks in user filters. QAK 2002/06/18
* 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 to be 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 as 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 when 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
* 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 - 2002/03/29
* Fixed bug where variable-length string type did not behave as a
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
Performance Improvements
========================
This release of the HDF5 library has been extensively tuned to improve
performance, especially to improve parallel I/O performance.
Most of the specific information for particular performance improvements
is mentioned in the "New Features" and "Bug Fixes since HDF5-1.4.3" sections
of this document, but in general, the library should make fewer and larger
I/O requests when accessing a file. Additionally, improvements to the parallel
I/O portions of the library should have reduced the communications and barriers
used in various internal algorithms, improving the performance of the library.
However, with the extensive changes to some portions of the library that
were required for these improvements, some errors or unanticipated results may
have been introduced also. Please report any problems encountered to our
support team at hdfhelp@ncsa.uiuc.edu.
Hopefully these improvements will benefit all HDF5 applications, but if
there are particular I/O patterns that appear to be slower than necessary,
please send e-mail to hdfhelp@ncsa.uiuc.edu with a sample program showing the
problem behavior; we will look into the issue to see if it is possible to
address it.
Documentation
=============
* Documentation was updated for the hdf5-1.4.4 release.
* A new "HDF5 User's Guide" is under development. See
http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/.
* A "Parallel HDF5 Tutorial" is available at
http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/.
* The "HDF5 Tutorial" is not distributed with this release. It is
available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 5.0.2.0
mpcc_r 5.0.2.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 3.1.0.12 (includes mpi)
AIX 5.1 xlc 5.0.2.0
xlf 07.01.0000.0002
mpcc_r 5.0.2.0; mpxlf_r 07.01.0000.0002
Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
Cray SV1 10.0.1.1 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
FreeBSD 4.6 gcc 2.95.4
g++ 2.95.4
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP MPI [not a product] (03/24/2000) B6060BA
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
Linux 2.4.9-31smp gcc 2.95.3
g++ 2.95.3
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
MPICH 1.2.2
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran V5.5-1877-48BBF
gcc version 3.0 for C++
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.2.2 i386 pgcc Rel 3.1-4i with mpich-1.2.3 with
local modifications
IA-32 Linux 2.4.9 cc Intel 5.0.1
gcc 2.96
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 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)
Solaris2.6 y n y n y y y y
Solaris2.7 64 y y (1) y n y y y y
Solaris2.7 32 y y (1) y n y y y y
Solaris2.8 64 y n y n y y y y
Solaris2.8 32 y n y n y y 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 n32 y y (2) n n n y y y
HPUX10.20 y n y n n y y y
HPUX11.00 y n y n n y y y
HPUX11 SysV y y y y n y y y
OSF1 v5.1 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 n y (1) n n n n y y (4)
AIX-4.3 y y y y y n y y
AIX-5.1 y y y y n n y y
WinNT/2000 y n y n y 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
Linux 2.4 Intel(6) y n y n y n y y
Linux 2.4 IA32 y n y n n n y y
Linux 2.4 IA64 y n y n n n y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.6 y x y n n y
Solaris2.7 64 y x y n n y
Solaris2.7 32 y x y n n y
Solaris2.8 64 y y n n n y
Solaris2.8 32 y x y n n y
IRIX6.5 y x n n n y
IRIX64_6.5 64 y x y n y y
IRIX64_6.5 n32 y x y n y y
HPUX10.20 y y n n n y
HPUX11.00 y x n n n y
HPUX11 SysV y x n n n y
OSF1 v5.1 y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 y y (3) n n n y
AIX-5.1 y y n n n y
WinNT/2000 y y n n n n
WinNT CW n n n n n n
FreeBSD y y y n n y
Linux 2.2 y y y n n y
Linux 2.4 y y y n n y
Linux 2.4 Intel(6) y y n n n y
Linux 2.4 IA32 y y n n n y
Linux 2.4 IA64 y y n 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,
except on Windows where they are provided for all languages.
(6) Linux 2.4 with Intel compilers.
Known Problems
==============
* Datasets or attributes which have a variable-length string datatype are
not printing correctly with h5dump and h5ls.
* When a dataset with the variable-length datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output on some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting the environment
variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* 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,"
* To build the Fortran library using Intel compilers, one has to
x modify the source code in the fortran/src directory to remove the
!DEC and !MS compiler directives.
x The build will fail in the fortran/test directory and then in the
fortran/examples directory; to proceed, edit the work.pcl files in
those directories to contain two lines
work.pc
../src/work.pc
* To build the Fortran library on IA64 use
setenv CC "ecc -DIA64"
setenv F9X "efc -cl,work.pcl"
before running configure and see the steps described above.
%%%%1.4.3%%%% Release Information for hdf5-1.4.3 (18/Februaru/02)
11. Release information for HDF5 version 1.4.3
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.2 and
HDF5-1.4.3, and contains information on the platforms tested and
known problems in HDF5-1.4.2. 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 HDF5-1.4.2
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* Can use just enable-threadsafe if the C compiler has built-in pthreads
support.
o Library
=========
o General
---------
* Added a new test to verify the information provided by the configure
command.
* Changed internal error handling macros to reduce code size of library by
about 10%.
o APIs
------
* Changed prototype for H5Awrite from:
H5Awrite(hid_t attr_id, hid_t type_id, void *buf)
to:
H5Awrite(hid_t attr_id, hid_t type_id, const void *buf)
* 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.
C++ API:
* Added operator= to class PredType
* Add the overloaded member function Attribute::getName to return
the attribute name's length as in C API. Note that the current
Attribute::getName, that returns "string", is still available.
* Following the change in the C library, the corresponding C++ API
is changed from:
void Attribute::write( const DataType& mem_type, void *buf )
to:
void Attribute::write( const DataType& mem_type, const void *buf )
o Performance
-------------
* Added perform programs to test the HDF5 library performance. Programs
are installed in directory perform/.
* Improved performance of byte-swapping during data conversions.
* Improved performance of single, contiguous hyperslabs when reading or
writing.
* 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, 1/31/02
o Parallel Library
==================
* Parallel C HDF5 now works on HP-UX platforms, Compaq clusters,
Linux clusters, Cplants (alpha-linux clusters).
o Tools
=======
* 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.
* The H5Dumper can now dump comments associated with groups. -WCW 01-05-02
o Support for new platforms and languages
=========================================
* HDF5 C++ Library is supported on Windows platforms (shared and static)
* HDF5 F90 shared library is supported on Windows platforms.
* HDF5 C Library is supported on IA32 and IA64 platforms.
Bug Fixes since HDF5-1.4.2 Release
==================================
* Fixed a bug when reading chunked datasets where the edge of the dataset
would be incorrectly detected and generate an assertion failure.
* 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 where reading or writing chunked data which needed datatype
conversion could result in data values getting corrupted.
* 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 'or'ing a hyperslab with a 'none' selection would
fail. Now adds that hyperslab as the first hyperlab in the selection.
* Fixed a bug in the 'big' test where quota limits weren't being detected
properly if they caused close() to fail.
* Fixed a bug in internal B-tree code where a B-tree was not being copied
correctly.
* 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 the internal macros used to encode & decode file metadata, to avoid
an unaligned access warning on IA64 machines.
* Corrected behavior of H5Tinsert to not allow compound datatype fields to
be inserted past the end of the datatype.
* Retired the DPSS virtual file driver (--with-gridstorage configure
option).
* Fixed bug where variable-length datatypes for attributes was not working
correctly.
* Fixed bug where raw data re-allocated from the free-list would sometimes
overlap with the metadata accumulator and get corrupted. QAK - 1/23/02
* 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 - 2/13/02
* 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 - 2/14/02
Documentation
=============
* Documentation was updated for the hdf5-1.4.3 release.
* A new "HDF5 User's Guide" is under development. See
http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/.
* Parallel Tutorial is available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 5.0.2.0
mpcc_r 5.0.2.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 3.1.0.12 (includes mpi)
Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
FreeBSD 4.5 gcc 2.95.3
g++ 2.95.3
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP MPI [not a product] (03/24/2000) B6060BA
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.2m
Linux 2.4.4 gcc 2.95.3
g++ 2.95.3
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.3-028
Compaq Fortran V5.4-1283
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0
Workshop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.0.8 i386 pgcc Rel 3.1-4i with mpich-1.2.1 with
local modifications
IA-32 Linux 2.2.10smpx cc Intel 5.0.1
egcs-2.91.66
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Itanium(TM) Compiler
for the Itanium(TM)-based applications,
Version 6.0 Beta, Build 20010905
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 6.0
Windows 98 MSVC++ 6.0
DEC Visual Fortran 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 n 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 n 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 n 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.
* When a dataset with the variable-legth datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting environment variable
HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* On IA64 systems one has to use -DIA64 compilation flag to compile
h4toh5 and h5toh4 utilites. After configuration step manually modify
Makefile in the tools/h4toh4 and tools/h5toh4 directories to add
-DIA64 to the compilation flags.
* On IA32 ansd IA64 systems, if you use a compiler other than GCC
(such as Intel's ecc compiler), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 102
of the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change the lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
%%%%1.4.2%%%% Release Information for hdf5-1.4.2 (31/July/01)
10. Release Information for hdf5-1.4.2
=================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.1 and
HDF5-1.4.2, and contains information on the platforms tested and
known problems in HDF5-1.4.2.
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 HDF5-1.4.1
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
* File sizes greater than 2GB are now supported on Linux systems with
version 2.4.x or higher kernels.
* 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.
* Parallel HDF5 now runs on the HP V2500 and HP N4000 machines.
* F90 API:
- Added aditional parameter "dims" to the h5dread_f/h5dwrite_f and
h5aread_f/h5awrite_f subroutines. This parameter is a 1-D array
of size 7 and contains the sizes of the data buffer dimensions.
This change enables portability between Windows and UNIX platforms.
In previous versions of the F90 APIs, the data buffer parameters of
the above functions were declared as assumed-shape arrays, which
were passed to the C functions by a descriptor. There is no
portable means, however, of passing descriptors from F90 to C,
causing portability problems between Windows and UNIX and among
UNIX platforms. With this change, the data buffers are assumed-
size arrays, which can be portably passed to the C functions.
* F90 static library is available on Windows platforms.
See INSTALL_Windows_withF90.txt for details.
* F90 APIs are available on HPUX 11.00 and 10.20 and IBM SP platforms.
* H5 <-> GIF convertor has been added. This is available under
tools/gifconv. The convertor supports the ability to create animated
gifs as well.
* 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.
* Added support for the Metrowerks Code Warrior compiler for Windows.
* For H4->H5 converter utility, added a new option to choose not to convert
HDF4 specified attributes(reference number, class) into HDF5 attributes.
* Added support chunking and compression in SDS and image in H4->H5 converter.
Currently HDF5 only supports gzip compression, so by default an HDF4 file
with any other compression method will be converted into an HDF5 file in
gzip compression.
* correct the order or reading HDF4 image array in H4->H5 conversion.
* 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.
* Added a parallel HDF5 example examples/ph5example.c to illustrate
the basic way of using parallel HDF5.
* 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 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.
Bug Fixes since HDF5-1.4.1 Release
==================================
* Fixed bug with non-zero userblock sizes causing raw data to not
write correctly.
* Fixed problems with Pablo build and linking with non-standard MPI I/O.
* Fixed build on Linux systems with --enable-static-exec flag. It now
works correctly.
* IMPORTANT: Fixed file metadata corruption bug which could cause
metadata data loss in certain situations.
* 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.
* 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.
* Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x
when --enable-hdf5v1_2 configure flag is enabled.
* Added --enable-linux-lfs flag to allow more control over whether to
enable or disable large file support on Linux.
* Fixed various bugs releated to SDS dimensional scale conversions in H4->H5
converter.
* Fixed a bug to correctly convert HDF4 objects with fill value into HDF5.
* 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.
* Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be
external to C++.
* Fixed a bug in H5FD_mpio_flush() that might result in negative file seek
if both MPIO and Split-file drivers are used together.
Documentation
=============
* The H5T_conv_t and H5T_cdata_t structures are now properly defined
in the H5Tregister entry in the "H5T" section of the "HDF5 Reference
Manual" and described in detail in section 12, "Data Conversions," in
the "Datatypes" chapter of the "HDF5 User's Guide."
* The new tools h52gif and gif2h5 have been added to the "Tools" section
of the Reference Manual.
* A "Freespace Management" section has been added to the "Performance"
chapter of the User's Guide.
* Several user-reported bugs have been fixed since Release 1.4.1.
* The "HDF5 Image and Palette Specification" (in the "HDF5 Application
Developer's Guide") has been heavily revised. Based on extensive user
feedback and input from visualization software developers, Version 1.2
of the image specification is substantially different from prior
versions.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6.0
mpcc_r 3.6.6.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 2.4.0.14 (includes mpi)
Cray T3E sn6711 2.0.5.49a Cray Standard C Version 6.5.0.1
Cray SV1 10.0.0.2 Cray Standard C Version 6.5.0.1
Cray Fortran Version 3.5.0.1
FreeBSD 4.3 gcc 2.95.3
g++ 2.95.3
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.2m
Linux 2.4.4 gcc 2.95.3
g++ 2.95.3
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V4.0 DEC-V5.2-040 on Digital UNIX V4.0 (Rev 564)
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 98/10/25 FORTRAN 90
2.0 Patch 107356-04
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0
Workshop Compilers 5.0 98/10/25 FORTRAN 90
2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
2000/09/11
Sun WorkShop 6 update 1 C++ 5.2 2000/09/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
2000/09/11
Sun WorkShop 6 update 1 C++ 5.2 2000/09/11
TFLOPS r1.0.4 v4.0.7 i386 pgcc Rel 3.1-4i with mpich-1.2.1 with
local modifications
Windows 2000 (NT5.0) MSVC++ 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 6.0
Windows 98 MSVC++ 6.0
DEC Visual Fortran 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)
Solaris2.6 y n y n y y y y
Solaris2.7 y y (1) y n y y y y
Solaris2.8 64 y n n n y y y y
Solaris2.8 32 y n y n y y 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 n y n n y y y
HPUX11 SysV y n y n n y y y
DECOSF y n y n n 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 n n y n
Win2000 y n n n n y y y
Win98 y n y n n y y y
WinNT y n y n n 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
Solaris2.6 y x n n n y
Solaris2.7 y x y n n y
Solaris2.8 64 y y n n n y
Solaris2.8 32 y x n n n y
IRIX6.5 y x y n n y
IRIX64_6.5 64 y x n n n y
IRIX64_6.5 32 y x n n n y
HPUX10.20 y y n n n y
HPUX11.00 y x n n n y
HPUX11 SysV y x n n n y
DECOSF y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 SP2 y y (3) n n n y
AIX-4.3 SP3 y y n n n y
Win2000 y y n n n n
Win98 n y n n n n
WinNT y y n n n n
WinNT CW n n n n n n
FreeBSD y y n n n y
Linux 2.2 y y y n n y
Linux 2.4 y 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.
Known Problems
==============
* When a dataset with the variable-legth datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* For 24-bit image conversion from H4->H5, the current conversion is
not consistent with HDF5 image specification.
* In some cases, and SDS with an UNLIMITED dimension that has not
been written (current size = 0) is not converted correctly.
* After "make install" or "make install-doc" one may need to reload
the source from the tar file before doing another build.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting environment variable
HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
%%%%1.4.1%%%% Release Information for hdf5-1.4.1 (April/01)
9. Release Information for hdf5-1.4.1 (April/01)
=====================================================================
HDF5 Release 1.4.1
INTRODUCTION
This document describes the differences between HDF5-1.4.0 and
HDF5-1.4.1, and contains information on the platforms tested and
known problems in HDF5-1.4.1.
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
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
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.
Documentation
=============
PDF and Postscript versions of the following documents are available
for this release:
Document Filename
-------- --------
Introduction to HDF5 H5-R141-Introduction.pdf
HDF5 Reference Manual H5-R141-RefManual.pdf
C++ APIs to HDF5 documents H5-R141-Cplusplus.pdf
Fortran90 APIs to HDF5 documents H5-R141-Fortran90.pdf
PDF and Postscript files containing H5-R141-DocSet.pdf
all of the above H5-R141-DocSet.ps
These files are not included in this distribution, but are available
via the Web or FTP at the following locations:
http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/
ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/
While these documents are labeled Release 1.4.1, they describe
Release 1.4.0 as well.
Platforms Tested
================
Due to the nature of this release only C, C++ libraries and tools were tested.
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6
mpcc_r 3.6.6
Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0
Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0
FreeBSD 4.3 gcc 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.11.01.20
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
Linux 2.2.18smp gcc-2.95.2
g++ 2.95.2
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)
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) 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
========================================
* See "Supported Configuration Features Summary" section for the HDF5
1.4.0 release in the HISTORY.txt file.
Known Problems
==============
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executable are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* The shared library failed compilation on IRIX 6.5.
* After "make install" or "make install-doc" one may need to reload the source
from the tar file before doing another build.
* See "Known problems" section for the HDF5 1.4.0 release in the
HISTORY.txt file.
%%%%1.4.0%%%% Release Information for hdf5-1.4.0 (2/22/01)
8. Release Information for hdf5-1.4.0
===================================================================
HDF5 Release 1.4.0
INTRODUCTION
This document describes the differences between HDF5-1.2.0 and
HDF5-1.4.0, and contains information on the platforms tested and
known problems in HDF5-1.4.0. 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
- h4toh5 Utility
- F90 Support
- C++ Support
- Pablo Support
- Bug Fixes since HDF5-1.2.0
- Bug Fixes since HDF5-1.4.0-beta2
- Bug Fixes since HDF5-1.4.0
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
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.
h4toh5 Utility
==============
The h4toh5 utility is a new utility that converts an HDF4 file to an
HDF5 file. For details, see the document, "Mapping HDF4 Objects to
HDF5 Objects":
http://hdf.ncsa.uiuc.edu/HDF5/papers/H4-H5MappingGuidelines.pdf
Known Bugs:
The h4toh5 utility produces images that do 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.html
This bug has been fixed for the snapshot of hdf5 1.4 release. March 12th,2001
Known Limitations of the h4toh5 release
---------------------------------------------
1. Error handlings
h4toh5 utility will print out an error message when an error occurs.
2. String Datatype
HDF4 has no 'string' type. String valued data are usually defined as
an array of 'char' in HDF4. The h4toh5 utility will generally map
these to HDF5 'String' types rather than array of char, with the
following additional rules:
* For the data of an HDF4 SDS, image, and palette, if the data is
declared 'DFNT_CHAR8' it will be assumed to be integer and will
be an H5T_INTEGER type.
* For attributes of any HDF4 object, data of type 'DFNT_CHAR8'
will be converted to an HDF5 'H5T_STRING' type.
* For an HDF4 Vdata, it is difficult to determine whether data
of type 'DFNT_CHAR8' is intended to be bytes or characters. The
h4toh5 utility will consider them to be C characters, and will
convert them to an HDF5 'H5T_STRING' type.
3. Compression, Chunking and External Storage
Chunking is supported, but compression and external storage is not.
An HDF4 object that uses chunking will be converted to an HDF5 file
with analogous chunked storage.
An HDF4 object that uses compression will be converted to an
uncompressed HDF5 object.
An HDF4 object that uses external storage will be converted to an
HDF5 object without external storage.
4. Memory Use
This version of the h4toh5 utility copies data from HDF4 objects
in a single read followed by a single write to the HDF5 object. For
large objects, this requires a very large amount of memory, which may
be extremely slow or fail on some platforms.
Note that a dataset that has only been partly written will
be read completely, including uninitialized data, and all the
data will be written to the HDF5 object.
5. Platforms
The h4toh5 utility requires HDF5-1.4.0 and HDF4r1.4
h4toh5 utility has been tested on all platforms listed below (see
section "Platforms Tested") except TFLOPS.
F90 Support
===========
This is the first release of the HDF5 Library with fully integrated
F90 API support. The Fortran Library is created when the
--enable-fortran flag is specified during configuration.
Not all F90 subroutines are implemented. Please refer to the HDF5
Reference Manual for more details.
F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX,
T3E, SV1 and O2K (64 bit option only) platforms. The Parallel version of
the HDF5 F90 Library is supported on the O2K and T3E platforms.
Changes since the last prototype release (July 2000)
----------------------------------------------------
* h5open_f and h5close_f must be called instead of h5init_types and
h5close_types.
* The following subroutines are no longer available:
h5pset_xfer_f
h5pget_xfer_f
h5pset_mpi_f
h5pget_mpi_f
h5pset_stdio_f
h5pget_stdio_f
h5pset_sec2_f
h5pget_sec2_f
h5pset_core_f
h5pget_core_f
h5pset_family_f
h5pget_family_f
* The following functions have been added:
h5pset_fapl_mpio_f
h5pget_fapl_mpio_f
h5pset_dxpl_mpio_f
h5pget_dxpl_mpio_f
* In the previous HDF5 F90 releases, the implementation of object
references and dataset region references was not portable. This
release introduces a portable implementation, but it also introduces
changes to the read/write APIs that handle references. If object or
dataset region references are written or read to/from an HDF5 file,
h5dwrite_f and h5dread_f must use the extra parameter, n, for the
buffer size:
h5dwrite(read)_f(dset_id, mem_type_id, buf, n, hdferr, &
^^^
mem_space_id, file_space_id, xfer_prp)
For other datatypes the APIs were not changed.
C++ Support
===========
This is the first release of the HDF5 Library with fully integrated
C++ API support. The HDF5 C++ library is built when the --enable-cxx
flag is specified during configuration.
Check the HDF5 Reference Manual for available C++ documentation.
C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD.
Pablo Support
=============
This version does not allow proper building of the Pablo-instrumented
version of the library. A version supporting the pablo build is
available on the Pablo Website at
www-pablo.cs.uiuc.edu/pub/Pablo.Release.5/HDFLibrary/hdf5_v1.4.tar.gz
Bug Fixes since HDF5-1.2.0
==========================
Library
-------
* The function H5Pset_mpi is renamed as H5Pset_fapl_mpio.
* Corrected a floating point number conversion error for the Cray J90
platform. The error did not convert the value 0.0 correctly.
* Error was fixed which was not allowing dataset region references to
have their regions retrieved correctly.
* Corrected a bug that caused non-parallel file drivers to fail in
the parallel version.
* Added internal free-lists to reduce memory required by the library
and H5garbage_collect API function
* Fixed error in H5Giterate which was not updating the "index"
parameter correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern
* Fixed several other problems in hyperslab iteration code.
* Fixed another H5Giterate bug which was causes groups with large
numbers of objects in them to misbehave when the callback function
returned non-zero values.
* Changed return type of H5Aiterate and H5A_operator_t typedef to be
herr_t, to align them with the dataset and group iterator functions.
* Changed H5Screate_simple and H5Sset_extent_simple to not allow
dimensions of size 0 with out the same dimension being unlimited.
* QAK - 4/19/00 - Improved metadata hashing & caching algorithms to
avoid many hash flushes and also remove some redundant I/O when
moving metadata blocks in the file.
* The "struct(opt)" type conversion function which gets invoked for
certain compound datatype conversions was fixed for nested compound
types. This required a small change in the datatype conversion
function API.
* Re-wrote lots of the hyperslab code to speed it up quite a bit.
* Added bounded garbage collection for the free lists when they run
out of memory and also added H5set_free_list_limits API call to
allow users to put an upper limit on the amount of memory used for
free lists.
* Checked for non-existent or deleted objects when dereferencing one
with object or region references and disallow dereference.
* "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved
from object headers correctly, fixed now.
* Fixed H5Dread or H5Dwrite calls with H5FD_MPIO_COLLECTIVE requests
that may hang because not all processes are transfer the same amount
of data. (A.K.A. prematured collective return when zero amount data
requested.) Collective calls that may cause hanging is done via the
corresponding MPI-IO independent calls.
* If configure with --enable-debug=all, couple functions would issue
warning messages to "stderr" that the operation is expensive time-wise.
This messed up applications (like testings) that did not expect the
extra output. It is changed so that the warning will be printed only
if the corresponding Debug key is set.
Configuration
-------------
* The hdf5.h include file was fixed to allow the HDF5 Library to be
compiled with other libraries/applications that use GNU autoconf.
* Configuration for parallel HDF5 was improved. Configure now attempts
to link with libmpi.a and/or libmpio.a as the MPI libraries by
default. It also uses "mpirun" to launch MPI tests by default. It
tests to link MPIO routines during the configuration stage, rather
than failing later as before. One can just do "./configure
--enable-parallel" if the MPI library is in the system library.
* Added support for pthread library and thread-safe option.
* The libhdf5.settings file shows the correct machine byte-sex.
* Added option "--enable-stream-vfd" to configure w/o the Stream VFD.
For Solaris, added -lsocket to the LIBS list of libraries.
Tools
-----
* h5dump now accepts both short and long command-line parameters:
-h, --help Print a usage message and exit
-B, --bootblock Print the content of the boot block
-H, --header Print the header only; no data is displayed
-i, --object-ids Print the object ids
-V, --version Print version number and exit
-a P, --attribute=P Print the specified attribute
-d P, --dataset=P Print the specified dataset
-g P, --group=P Print the specified group and all members
-l P, --soft-link=P Print the value(s) of the specified soft link
-o F, --output=F Output raw data into file F
-t T, --datatype=T Print the specified named data type
-w #, --width=# Set the number of columns
P - is the full path from the root group to the object.
T - is the name of the data type.
F - is a filename.
# - is an integer greater than 1.
* A change from the old way command line parameters were interpreted
is that multiple attributes, datasets, groups, soft-links, and
object-ids cannot be specified with just one flag but you have to
use a flag with each object. I.e., instead of doing this:
h5dump -a /attr1 /attr2 foo.h5
do this:
h5dump -a /attr1 -a /attr2 foo.h5
The cases are similar for the other object types.
* h5dump correctly displays compound datatypes.
* Corrected an error in h5toh4 which did not convert the 32bits
int from HDF5 to HDF4 correctly for the T3E platform.
* h5dump correctly displays the committed copy of predefined types
correctly.
* Added an option, -V, to show the version information of h5dump.
* Fixed a core dumping bug of h5toh4 when executed on platforms like
TFLOPS.
* The test script for h5toh4 used to not able to detect the hdp
dumper command was not valid. It now detects and reports the
failure of hdp execution.
* Merged the tools with the 1.2.2 branch. Required adding new
macros, VERSION12 and VERSION13, used in conditional compilation.
Updated the Windows project files for the tools.
* h5dump displays opaque and bitfield data correctly.
* h5dump and h5ls can browse files created with the Stream VFD
(eg. "h5ls <hostname>:<port>").
* h5dump has a new feature "-o <filename>" which outputs the raw data
of the dataset into ascii text file <filename>.
* h5toh4 used to converts hdf5 strings type to hdf4 DFNT_INT8 type.
Corrected to produce hdf4 DFNT_CHAR type instead.
* h5dump and h5ls displays array data correctly.
Bug Fixes since HDF5-1.4.0-beta2
================================
* Fixed a bug in the conversion from a little endian double to a big
endian float in some special cases.
* Corrected configuration error which was not including compression
support correctly.
* Cleaned up lots of warnings.
* Changed a few h5dump command line switches and added long versions of
the switches.
* Changed parameters for H5Tconvert, H5Pset_bufer and H5Pget_buffer from
size_t to hsize_t
* Fixed fairly obscure bug in hyperslab I/O which could (in rare cases)
not copy all the data during a transfer.
* Removed ragged array code from library.
* F90 library and module files are installed properly now on all supported
platforms.
Bug Fixes since HDF5-1.4.0 Release
==================================
* 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
* Implemented XML support in h5dump.
Documentation
=============
* A new document summarizing the changes in the library leading up to
the current release has been added:
HDF5 Software Changes from Release to Release
This document is in the Application Developer's Guide and is of
particular interest to developers who must keep an application
synchronized with the library.
* The documentation for the Fortran90 and C++ APIs is linked to the
opening page of the Reference Manual. Fortran90 functions are
individually referenced from the corresponding C functions through-
out the Reference Manual.
* User's Guide and Reference Manual were updated to reflect changed
function syntax and to fix reported bugs.
* Functions that are new at this release were added to the Reference
Manual.
* Functions that have been removed from the library were removed from
the User's Guide and the Reference Manual.
* PostScript and PDF versions of the Release 1.4 document set are
not available at the time of Release 1.4.0.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6
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 4.2 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
IRIX 6.5 MIPSpro cc 7.30
mpich-1.2.1
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.4.0.2
mpich-1.2.1
Linux 2.2.16-3smp gcc-2.95.2
g++ 2.95.2
pgf90 3.1-3
mpich-1.2.1
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
mpich-1.2.1
SunOS 5.5.1 gcc-2.7.2
(Solaris 2.5.1 (x86))
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 working in this release
( ) = footnote appears below table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries
Solaris2.6 y n y n y y y y
Solaris2.7 y y (1) y n y y y y
Solarisx86 y n n n n y y y
IRIX6.5 y y (1) n n n n 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 n n n y y y
DECOSF y n y n n 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 y y n n n n y n
Win2000 y n n n n y y y
Win98 y n n n n y y y
WinNT y n n n n y y y
FreeBSD y n n n y y y y
Linux y y (1) y n y y y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.6 y n n n n y
Solaris2.7 y n y n n y
Solarisx86 y n n n n y
IRIX6.5 y n y n n y
IRIX64_6.5 64 y n n n n y
IRIX64_6.5 32 y n n n n y
HPUX10.20 y y n n n y
DECOSF y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 y y (3) n n n y
Win2000 y y n n n n
Win98 y y n n n n
WinNT y y n n n n
FreeBSD y y n n n y
Linux y n 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.
Known Problems
==============
* 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 Linux platforms using the gcc-2.95.2 compiler.
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.
The compilation fails if configured with --enable-static-exec on IRIX 6.5.
The executable files in hdf5/bin are dynamic-linked for IRIX64 6.5(64 and
n32 modes) and IRIX 6.5, even though they are compiled with static library.
It is suggested that you don't use this option on these platforms
during configuration.
* testhdf5 got bus error with configuration options --prefix and --with-hdf4
on IRIX 6.5.
* 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.
* When building hdf5 tools and applications on windows platform, a linking
warning: defaultlib "LIBC" conflicts with use of other libs will appear
on debug version when running VC++6.0. This warning doesn't affect building
and testing hdf5 applications. We will continue investigating this.
* 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 freed
across library or DLL. It is still under investigation.
* HDF-GASS testings and testhdf5 in the test directory will get bus error if
the configured with --with-gass.
* HDF-SRB testing got segmentation error on Solaris 2.7.
* 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 --enable-static'.
* 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 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 SV1)
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 ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/hdf5-1.4.0/src/crayf90/ directory.
* The h4toh5 utility produces images that do 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
%%%%1.2.2%%%% Release Information for hdf5-1.2.2 (6/23/00)
7. Release Information for hdf5-1.2.2
=================================================================
INTRODUCTION
This document describes the differences between HDF5-1.2.1 and
HDF5-1.2.2, and contains information on the platforms where HDF5-1.2.2
was tested and known problems in HDF5-1.2.2.
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
- Features Added since HDF5-1.2.1
- Bug Fixes since HDF5-1.2.1
- Known Problems
- Platforms Tested
Features Added since HDF5-1.2.1
===============================
* Added internal free-lists to reduce memory required by the library and
H5garbage_collect API function.
* h5dump displays opaque and bitfield types.
* 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.
Bug Fixes since HDF5-1.2.1
==========================
* h5dump correctly displays compound datatypes, including simple and
nested compound types.
* h5dump correctly displays the committed copy of predefined types.
* Corrected an error in h5toh4 which did not convert the 32-bit
int from HDF5 to HDF4 correctly for the T3E platform.
* Corrected a floating point number conversion error for the
Cray J90 platform. The error did not convert the value 0.0
correctly.
* Fixed error in H5Giterate which was not updating the "index" parameter
correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern.
* Fixed several other problems in hyperslab iteration code.
* Fixed another H5Giterate bug which caused groups with large numbers
of objects in them to misbehave when the callback function returned
non-zero values.
* Changed return type of H5Aiterate and H5A_operator_t typedef to be
herr_t, to align them with the dataset and group iterator functions.
* Changed H5Screate_simple and H5Sset_extent_simple to not allow dimensions
of size 0 without the same dimension being unlimited.
* Improved metadata hashing & caching algorithms to avoid
many hash flushes and also removed some redundant I/O when moving metadata
blocks in the file.
* The libhdf5.settings file shows the correct machine byte-sex.
* The "struct(opt)" type conversion function which gets invoked for
certain compound datatype conversions was fixed for nested compound
types. This required a small change in the datatype conversion
function API.
Known Problems
==============
o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will
fail if library is compiled using optimization of any level.
o TFLOPS: dsets test fails if compiled with optimization turned on.
o J90: tools fail to dispay data for the datasets with a compound datatype.
Platforms Tested
================
AIX 4.3.3 (IBM SP) 3.6.6 | binaries
mpicc using mpich 1.1.2 | are not
mpicc_r using IBM MPI-IO prototype | available
AIX 4.3.2.0 (IBM SP) xlc 5.0.1.0
Cray J90 10.0.0.7 cc 6.3.0.2
Cray T3E 2.0.5.29 cc 6.3.0.2
mpt.1.3
FreeBSD 4.0 gcc 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32
HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler
(static library only, h5toh4 tool is not available)
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.4
Linux 2.2.10 SMP gcc 2.95.1
mpicc(gcc-2.95.1)
gcc (egcs-2.91.66)
mpicc (egcs-2.91.66)
Linux 2.2.16 (RedHat 6.2) gcc 2.95.2
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 5.0 no optimization
SunOS 5.7 cc WorkShop Compilers 5.0
SolarisX86 SunOS 5.5.1 gcc version 2.7.2 with --disable-hsizet
TFLOPS 3.2.1 pgcc Rel 3.1-3i
mpich-1.1.2 with local changes
Windows NT4.0 sp5 MSVC++ 6.0
Windows 98 MSVC++ 6.0
Windows 2000 MSVC++ 6.0
%%%%1.2.1%%%% Release Information for hdf5-1.2.1
6. Release Information for hdf5-1.2.1
================================================================
Bug fixes since HDF5-1.2.0
==========================
Configuration
-------------
* The hdf5.h include file was fixed to allow the HDF5 Library to be compiled
with other libraries/applications that use GNU autoconf.
* Configuration for parallel HDF5 was improved. Configure now attempts to
link with libmpi.a and/or libmpio.a as the MPI libraries by default.
It also uses "mpirun" to launch MPI tests by default. It tests to
link MPIO routines during the configuration stage, rather than failing
later as before. One can just do "./configure --enable-parallel"
if the MPI library is in the system library.
Library
-------
* Error was fixed which was not allowing dataset region references to have
their regions retrieved correctly.
* Added internal free-lists to reduce memory required by the library and
H5garbage_collect API function
* Fixed error in H5Giterate which was not updating the "index" parameter
correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern
* Fixed several other problems in hyperslab iteration code.
Tests
------
* Added additional tests for group and attribute iteration.
* Added additional test for staggered hyperslab iteration.
* Added additional test for random 5-D hyperslab selection.
Tools
------
* Added an option, -V, to show the version information of h5dump.
* Fixed a core dumping bug of h5toh4 when executed on platforms like
TFLOPS.
* The test script for h5toh4 used to not able to detect the hdp
dumper command was not valid. It now detects and reports the
failure of hdp execution.
Documentation
-------------
* User's Guide and Reference Manual were updated.
See doc/html/PSandPDF/index.html for more details.
Platforms Tested:
================
Note: Due to the nature of bug fixes, only static versions of the library and tools were tested.
AIX 4.3.2 (IBM SP) 3.6.6
Cray T3E 2.0.4.81 cc 6.3.0.1
mpt.1.3
FreeBSD 3.3-STABLE gcc 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.3 (SGI MPI 3.2.0.0)
Linux 2.2.10 SuSE egcs-2.91.66 configured with
(i686-pc-linux-gnu) --disable-hsizet
mpich-1.2.0 egcs-2.91.66 19990314/Linux
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 4.2 no optimization
SunOS 5.7 cc WorkShop Compilers 5.0
TFLOPS 2.8 cicc (pgcc Rel 3.0-5i)
mpich-1.1.2 with local changes
Windows NT4.0 sp5 MSVC++ 6.0
Known Problems:
==============
o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will
fail if library is compiled using optimization of any level.
%%%%1.2.0%%%% Release Information for hdf5-1.2.0
5. Release Information for hdf5-1.2.0
===================================================================
A. Platforms Supported
-------------------
Operating systems listed below with compiler information and MPI library, if
applicable, are systems that HDF5 1.2.0 was tested on.
Compiler & libraries
Platform Information Comment
-------- ---------- --------
AIX 4.3.2 (IBM SP) 3.6.6
Cray J90 10.0.0.6 cc 6.3.0.0
Cray T3E 2.0.4.61 cc 6.2.1.0
mpt.1.3
FreeBSD 3.2 gcc 2.95.1
HP-UX B.10.20 HP C HP92453-01 A.10.32
gcc 2.8.1
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.3 (SGI MPI 3.2.0.0)
Linux 2.2.10 egcs-2.91.66 configured with
--disable-hsizet
lbraries: glibc2
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 4.2
no optimization
gcc 2.8.1
SunOS 5.7 cc WorkShop Compilers 5.0
gcc 2.8.1
TFLOPS 2.7.1 cicc (pgcc Rel 3.0-4i)
mpich-1.1.2 with local changes
Windows NT4.0 intel MSVC++ 5.0 and 6.0
Windows NT alpha 4.0 MSVC++ 5.0
Windows 98 MSVC++ 5.0
B. Known Problems
--------------
* NT alpha 4.0
Dumper utiliy h5dump fails if linked with DLL.
* SunOS 5.6 with C WorkShop Compilers 4.2
Hyperslab selections will fail if library is compiled using optimization
of any level.
C. Changes Since Version 1.0.1
---------------------------
1. Documentation
-------------
* More examples
* Updated user guide, reference manual, and format specification.
* Self-contained documentation for installations isolated from the
Internet.
* HDF5 Tutorial was added to the documentation
2. Configuration
-------------
* Better detection and support for MPI-IO.
* Recognition of compilers with known code generation problems.
* Support for various compilers on a single architecture (e.g., the
native compiler and the GNU compilers).
* Ability to build from read-only media and with different compilers
and/or options concurrently.
* Added a libhdf5.settings file which summarizes the configuration
information and is installed along with the library.
* Builds a shared library on most systems that support it.
* Support for Cray T3E, J90 and Windows/NT.
3. Debugging
---------
* Improved control and redirection of debugging and tracing messages.
4. Datatypes
---------
* Optimizations to compound datatype conversions and I/O operations.
* Added nearly 100 optimized conversion functions for native datatypes
including support for non-aligned data.
* Added support for bitfield, opaque, and enumeration types.
* Added distinctions between signed and unsigned char types to the
list of predefined native hdf5 datatypes.
* Added HDF5 type definitions for C9x types like int32_t.
* Application-defined type conversion functions can handle non-packed
data.
* Changed the H5Tunregister() function to use wildcards when matching
conversion functions. H5Tregister_hard() and H5Tregister_soft()
were combined into H5Tregister().
* Support for variable-length datatypes (arrays of varying length per
dataset element). Variable length strings currently supported only
as variable length arrays of 1-byte integers.
5. Dataspaces
----------
* New query functions for selections.
* I/O operations bypass the stripmining loop and go directly to
storage for certain contiguous selections in the absense of type
conversions. In other cases the stripmining buffers are used more
effectively.
* Reduced the number of I/O requests under certain circumstances,
improving performance on systems with high I/O latency.
6. Persistent Pointers
-------------------
* Object (serial and parallel) and dataset region (serial only)
references are implemented.
7. Parallel Support
----------------
* Improved parallel I/O performance.
* Supported new platforms: Cray T3E, Linux, DEC Cluster.
* Use vendor supported version of MPIO on SGI O2K and Cray platforms.
* Improved the algorithm that translates an HDF5 hyperslab selection
into an MPI type for better collective I/O performance.
8. New API functions
-----------------
a. Property List Interface:
------------------------
H5Pset_xfer - set data transfer properties
H5Pset_preserve - set dataset transfer property list status
H5Pget_preserve - get dataset transfer property list status
H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O
H5Pget_hyper_cache - returns information regarding the caching of
hyperslab blocks during I/O
H5Pget_btree_ratios - sets B-tree split ratios for a dataset
transfer property list
H5Pset_btree_ratios - gets B-tree split ratios for a dataset
transfer property list
H5Pset_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
H5Pget_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
b. Dataset Interface:
------------------
H5Diterate - iterate over all selected elements in a dataspace
H5Dget_storage_size - return the amount of storage required for a dataset
H5Dvlen_reclaim - reclaim VL datatype memory buffers
c. Dataspace Interface:
--------------------
H5Sget_select_hyper_nblocks - get number of hyperslab blocks
H5Sget_select_hyper_blocklist - get the list of hyperslab blocks
currently selected
H5Sget_select_elem_npoints - get the number of element points
in the current selection
H5Sget_select_elem_pointlist - get the list of element points
currently selected
H5Sget_select_bounds - gets the bounding box containing
the current selection
d. Datatype Interface:
-------------------
H5Tget_super - return the base datatype from which a
datatype is derived
H5Tvlen_create - creates a new variable-length dataype
H5Tenum_create - creates a new enumeration datatype
H5Tenum_insert - inserts a new enumeration datatype member
H5Tenum_nameof - returns the symbol name corresponding to a
specified member of an enumeration datatype
H5Tvalueof - return the value corresponding to a
specified member of an enumeration datatype
H5Tget_member_value - return the value of an enumeration datatype member
H5Tset_tag - tags an opaque datatype
H5Tget_tag - gets the tag associated with an opaque datatype
e. Identifier Interface:
---------------------
H5Iget_type - retrieve the type of an object
f. Reference Interface:
--------------------
H5Rcreate - creates a reference
H5Rdereference - open the HDF5 object referenced
H5Rget_region - retrieve a dataspace with the specified region selected
H5Rget_object_type - retrieve the type of object that an
object reference points to
g. Ragged Arrays (alpha) (names of those API functions were changed):
------------------------------------------------------------------
H5RAcreate - create a new ragged array (old name was H5Rcreate)
H5RAopen - open an existing array (old name was H5Ropen)
H5RAclose - close a ragged array (old name was H5Rclose)
H5RAwrite - write to an array (old name was H5Rwrite)
H5RAread - read from an array (old name was H5Rread)
9. Tools
-----
* Enhancements to the h5ls tool including the ability to list objects
from more than one file, to display raw hexadecimal data, to
show file addresses for raw data, to format output more reasonably,
to show object attributes, and to perform a recursive listing,
* Enhancements to h5dump: support new data types added since previous
versions.
* h5toh4: An hdf5 to hdf4 converter.
%%%%1.0.1%%%% Release Information for hdf5-1.0.1
4. Changes from Release 1.0.0 to Release 1.0.1
=====================================================================
* [Improvement]: configure sets up the Makefile in the parallel tests
suit (testpar/) correctly.
* [Bug-Fix]: Configure failed for all IRIX versions other than 6.3.
It now configures correctly for all IRIX 6.x version.
* Released Parallel HDF5
Supported Features:
------------------
HDF5 files are accessed according to the communicator and INFO
object defined in the property list set by H5Pset_mpi.
Independent read and write accesses to fixed and extendable dimension
datasets.
Collective read and write accesses to fixed dimension datasets.
Supported Platforms:
-------------------
Intel Red
IBM SP2
SGI Origin 2000
Changes In This Release:
-----------------------
o Support of Access to Extendable Dimension Datasets.
Extendable dimension datasets must use chunked storage methods.
A new function, H5Dextend, is created to extend the current
dimensions of a dataset. The current release requires the
MPI application must make a collective call to extend the
dimensions of an extendable dataset before writing to the
newly extended area. (The serial does not require the
call of H5Dextend. The dimensions of an extendable
dataset is increased when data is written to beyond the
current dimensions but within the maximum dimensions.)
The required collective call of H5Dextend may be relaxed
in future release.
This release only support independent read and write accesses
to extendable datasets. Collective accesses to extendable
datasets will be implemented in future releases.
o Collective access to fixed dimension datasets.
Collective access to a dataset can be specified in the transfer
property list argument in H5Dread and H5Dwrite. The current
release supports collective access to fixed dimension datasets.
Collective access to extendable datasets will be implemented in
future releases.
o HDF5 files are opened according to Communicator and INFO object.
H5Dopen now records the communicator and INFO setup by H5Pset_mmpi
and pass them to the corresponding MPIO open file calls for
processing.
o This release has been tested on IBM SP2, Intel Red and SGI Origin 2000
systems. It uses the ROMIO version of MPIO interface for parallel
I/O supports.
%%%%1.0.0%%%% Release Information for hdf5-1.0.0
3. Changes from the Beta 1.0.0 Release to Release 1.0.0
====================================================================
* Added fill values for datasets. For contiguous datasets fill value
performance may be quite poor since the fill value is written to the
entire dataset when the dataset is created. This will be remedied
in a future version. Chunked datasets using fill values do not
incur any additional overhead. See H5Pset_fill_value().
* Multiple hdf5 files can be "mounted" on one another to create a
larger virtual file. See H5Fmount().
* Object names can be removed or changed but objects are never
actually removed from the file yet. See H5Gunlink() and H5Gmove().
* Added a tuning mechanism for B-trees to insure that sequential
writes to chunked datasets use less overhead. See H5Pset_btree_ratios().
* Various optimizations and bug fixes.
%%%%1.0.0 Beta%%%% Release Information for hdf5-1.0.0 Beta
2. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release
=========================================================================
* Strided hyperslab selections in dataspaces now working.
* The compression API has been replaced with a more general filter
API. See doc/html/Filters.html for details.
* Alpha-quality 2d ragged arrays are implemented as a layer built on
top of other hdf5 objects. The API and storage format will almost
certainly change.
* More debugging support including API tracing. See Debugging.html.
* C and Fortran style 8-bit fixed-length character string types are
supported with space or null padding or null termination and
translations between them.
* Added function H5Fflush() to write all cached data immediately to
the file.
* Datasets maintain a modification time which can be retrieved with
H5Gstat().
* The h5ls tool can display much more information, including all the
values of a dataset.
%%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2
1. Changes from the First Alpha 1.0.0 Release to
the Second Alpha 1.0.0 Release
=====================================================================
* Two of the packages have been renamed. The data space API has been
renamed from `H5P' to `H5S' and the property list (template) API has
been renamed from `H5C' to `H5P'.
* The new attribute API `H5A' has been added. An attribute is a small
dataset which can be attached to some other object (for instance, a
4x4 transformation matrix attached to a 3-dimensional dataset, or an
English abstract attached to a group).
* The error handling API `H5E' has been completed. By default, when an
API function returns failure an error stack is displayed on the
standard error stream. The H5Eset_auto() controls the automatic
printing and H5E_BEGIN_TRY/H5E_END_TRY macros can temporarily
disable the automatic error printing.
* Support for large files and datasets (>2GB) has been added. There
is an html document that describes how it works. Some of the types
for function arguments have changed to support this: all arguments
pertaining to sizes of memory objects are `size_t' and all arguments
pertaining to file sizes are `hsize_t'.
* More data type conversions have been added although none of them are
fine tuned for performance. There are new converters from integer
to integer and float to float, but not between integers and floating
points. A bug has been fixed in the converter between compound
types.
* The numbered types have been removed from the API: int8, uint8,
int16, uint16, int32, uint32, int64, uint64, float32, and float64.
Use standard C types instead. Similarly, the numbered types were
removed from the H5T_NATIVE_* architecture; use unnumbered types
which correspond to the standard C types like H5T_NATIVE_INT.
* More debugging support was added. If tracing is enabled at
configuration time (the default) and the HDF5_TRACE environment
variable is set to a file descriptor then all API calls will emit
the function name, argument names and values, and return value on
that file number. There is an html document that describes this.
If appropriate debugging options are enabled at configuration time,
some packages will display performance information on stderr.
* Data types can be stored in the file as independent objects and
multiple datasets can share a data type.
* The raw data I/O stream has been implemented and the application can
control meta and raw data caches, so I/O performance should be
improved from the first alpha release.
* Group and attribute query functions have been implemented so it is
now possible to find out the contents of a file with no prior
knowledge.
* External raw data storage allows datasets to be written by other
applications or I/O libraries and described and accessed through
HDF5.
* Hard and soft (symbolic) links are implemented which allow groups to
share objects. Dangling and recursive symbolic links are supported.
* User-defined data compression is implemented although we may
generalize the interface to allow arbitrary user-defined filters
which can be used for compression, checksums, encryption,
performance monitoring, etc. The publicly-available `deflate'
method is predefined if the GNU libz.a can be found at configuration
time.
* The configuration scripts have been modified to make it easier to
build debugging vs. production versions of the library.
* The library automatically checks that the application was compiled
with the correct version of header files.
Parallel HDF5 Changes
* Parallel support for fixed dimension datasets with contiguous or
chunked storages. Also, support unlimited dimension datasets which
must use chunk storage. No parallel support for compressed datasets.
* Collective data transfer for H5Dread/H5Dwrite. Collective access
support for datasets with contiguous storage only, thus only fixed
dimension datasets for now.
* H5Pset_mpi and H5Pget_mpi no longer have the access_mode
argument. It is taken over by the data-transfer property list
of H5Dread/H5Dwrite.
* New functions H5Pset_xfer and H5Pget_xfer to handle the
specification of independent or collective data transfer_mode
in the dataset transfer properties list. The properties
list can be used to specify data transfer mode in the H5Dwrite
and H5Dread function calls.
* Added parallel support for datasets with chunked storage layout.
When a dataset is extend in a PHDF5 file, all processes that open
the file must collectively call H5Dextend with identical new dimension
sizes.
LIST OF API FUNCTIONS
The following functions are implemented. Errors are returned if an
attempt is made to use some feature which is not implemented and
printing the error stack will show `not implemented yet'.
Library
H5check - check that lib version matches header version
H5open - initialize library (happens automatically)
H5close - shut down the library (happens automatically)
H5dont_atexit - don't call H5close on exit
H5get_libversion - retrieve library version info
H5check_version - check for specific library version
Property Lists
H5Pclose - release template resources
H5Pcopy - copy a template
H5Pcreate - create a new template
H5Pget_chunk - get chunked storage properties
H5Pset_chunk - set chunked storage properties
H5Pget_class - get template class
H5Pget_istore_k - get chunked storage properties
H5Pset_istore_k - set chunked storage properties
H5Pget_layout - get raw data layout class
H5Pset_layout - set raw data layout class
H5Pget_sizes - get address and size sizes
H5Pset_sizes - set address and size sizes
H5Pget_sym_k - get symbol table storage properties
H5Pset_sym_k - set symbol table storage properties
H5Pget_userblock - get user-block size
H5Pset_userblock - set user-block size
H5Pget_version - get file version numbers
H5Pget_alignment - get data alignment properties
H5Pset_alignment - set data alignment properties
H5Pget_external_count- get count of external data files
H5Pget_external - get information about an external data file
H5Pset_external - add a new external data file to the list
H5Pget_driver - get low-level file driver class
H5Pget_stdio - get properties for stdio low-level driver
H5Pset_stdio - set properties for stdio low-level driver
H5Pget_sec2 - get properties for sec2 low-level driver
H5Pset_sec2 - set properties for sec2 low-level driver
H5Pget_core - get properties for core low-level driver
H5Pset_core - set properties for core low-level driver
H5Pget_split - get properties for split low-level driver
H5Pset_split - set properties for split low-level driver
H5P_get_family - get properties for family low-level driver
H5P_set_family - set properties for family low-level driver
H5Pget_cache - get meta- and raw-data caching properties
H5Pset_cache - set meta- and raw-data caching properties
H5Pget_buffer - get raw-data I/O pipe buffer properties
H5Pset_buffer - set raw-data I/O pipe buffer properties
H5Pget_preserve - get type conversion preservation properties
H5Pset_preserve - set type conversion preservation properties
H5Pget_nfilters - get number of raw data filters
H5Pget_filter - get raw data filter properties
H5Pset_filter - set raw data filter properties
H5Pset_deflate - set deflate compression filter properties
H5Pget_mpi - get MPI-IO properties
H5Pset_mpi - set MPI-IO properties
H5Pget_xfer - get data transfer properties
+ H5Pset_xfer - set data transfer properties
+ H5Pset_preserve - set dataset transfer property list status
+ H5Pget_preserve - get dataset transfer property list status
+ H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O
+ H5Pget_hyper_cache - returns information regarding the caching of
hyperslab blocks during I/O
+ H5Pget_btree_ratios - sets B-tree split ratios for a dataset
transfer property list
+ H5Pset_btree_ratios - gets B-tree split ratios for a dataset
transfer property list
+ H5Pset_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
+ H5Pget_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
Datasets
H5Dclose - release dataset resources
H5Dcreate - create a new dataset
H5Dget_space - get data space
H5Dget_type - get data type
H5Dget_create_plist - get dataset creation properties
H5Dopen - open an existing dataset
H5Dread - read raw data
H5Dwrite - write raw data
H5Dextend - extend a dataset
+ H5Diterate - iterate over all selected elements in a dataspace
+ H5Dget_storage_size - return the amount of storage required for a dataset
+ H5Dvlen_reclaim - reclaim VL datatype memory buffers
Attributes
H5Acreate - create a new attribute
H5Aopen_name - open an attribute by name
H5Aopen_idx - open an attribute by number
H5Awrite - write values into an attribute
H5Aread - read values from an attribute
H5Aget_space - get attribute data space
H5Aget_type - get attribute data type
H5Aget_name - get attribute name
H5Anum_attrs - return the number of attributes for an object
H5Aiterate - iterate over an object's attributes
H5Adelete - delete an attribute
H5Aclose - close an attribute
Errors
H5Eclear - clear the error stack
H5Eprint - print an error stack
H5Eget_auto - get automatic error reporting settings
H5Eset_auto - set automatic error reporting
H5Ewalk - iterate over the error stack
H5Ewalk_cb - the default error stack iterator function
H5Eget_major - get the message for the major error number
H5Eget_minor - get the message for the minor error number
Files
H5Fclose - close a file and release resources
H5Fcreate - create a new file
H5Fget_create_plist - get file creation property list
H5Fget_access_plist - get file access property list
H5Fis_hdf5 - determine if a file is an hdf5 file
H5Fopen - open an existing file
H5Freopen - reopen an HDF5 file
H5Fmount - mount a file
H5Funmount - unmount a file
H5Fflush - flush all buffers associated with a file to disk
Groups
H5Gclose - close a group and release resources
H5Gcreate - create a new group
H5Gopen - open an existing group
H5Giterate - iterate over the contents of a group
H5Gmove - change the name of some object
H5Glink - create a hard or soft link to an object
H5Gunlink - break the link between a name and an object
H5Gget_objinfo - get information about a group entry
H5Gget_linkval - get the value of a soft link
H5Gget_comment - get the comment string for an object
H5Gset_comment - set the comment string for an object
Dataspaces
H5Screate - create a new data space
H5Scopy - copy a data space
H5Sclose - release data space
H5Screate_simple - create a new simple data space
H5Sset_space - set simple data space extents
H5Sis_simple - determine if data space is simple
H5Sset_extent_simple - set simple data space dimensionality and size
H5Sget_simple_extent_npoints - get number of points in simple extent
H5Sget_simple_extent_ndims - get simple data space dimensionality
H5Sget_simple_extent_dims - get simple data space size
H5Sget_simple_extent_type - get type of simple extent
H5Sset_extent_none - reset extent to be empty
H5Sextent_copy - copy the extent from one data space to another
H5Sget_select_npoints - get number of points selected for I/O
H5Sselect_hyperslab - set hyperslab dataspace selection
H5Sselect_elements - set element sequence dataspace selection
H5Sselect_all - select entire extent for I/O
H5Sselect_none - deselect all elements of extent
H5Soffset_simple - set selection offset
H5Sselect_valid - determine if selection is valid for extent
+ H5Sget_select_hyper_nblocks - get number of hyperslab blocks
+ H5Sget_select_hyper_blocklist - get the list of hyperslab blocks
currently selected
+ H5Sget_select_elem_npoints - get the number of element points
in the current selection
+ H5Sget_select_elem_pointlist - get the list of element points
currently selected
+ H5Sget_select_bounds - gets the bounding box containing
the current selection
Datatypes
H5Tclose - release data type resources
H5Topen - open a named data type
H5Tcommit - name a data type
H5Tcommitted - determine if a type is named
H5Tcopy - copy a data type
H5Tcreate - create a new data type
H5Tequal - compare two data types
H5Tlock - lock type to prevent changes
H5Tfind - find a data type conversion function
H5Tconvert - convert data from one type to another
H5Tregister - register a conversion function
H5Tunregister - remove a conversion function
H5Tget_overflow - get function that handles overflow conv. cases
H5Tset_overflow - set function to handle overflow conversion cases
H5Tget_class - get data type class
H5Tget_cset - get character set
H5Tget_ebias - get exponent bias
H5Tget_fields - get floating point fields
H5Tget_inpad - get inter-field padding
H5Tget_member_dims - get struct member dimensions
H5Tget_member_name - get struct member name
H5Tget_member_offset - get struct member byte offset
H5Tget_member_type - get struct member type
H5Tget_nmembers - get number of struct members
H5Tget_norm - get floating point normalization
H5Tget_offset - get bit offset within type
H5Tget_order - get byte order
H5Tget_pad - get padding type
H5Tget_precision - get precision in bits
H5Tget_sign - get integer sign type
H5Tget_size - get size in bytes
H5Tget_strpad - get string padding
H5Tinsert - insert scalar struct member
H5Tinsert_array - insert array struct member
H5Tpack - pack struct members
H5Tset_cset - set character set
H5Tset_ebias - set exponent bias
H5Tset_fields - set floating point fields
H5Tset_inpad - set inter-field padding
H5Tset_norm - set floating point normalization
H5Tset_offset - set bit offset within type
H5Tset_order - set byte order
H5Tset_pad - set padding type
H5Tset_precision - set precision in bits
H5Tset_sign - set integer sign type
H5Tset_size - set size in bytes
H5Tset_strpad - set string padding
+ H5Tget_super - return the base datatype from which a
datatype is derived
+ H5Tvlen_create - creates a new variable-length dataype
+ H5Tenum_create - creates a new enumeration datatype
+ H5Tenum_insert - inserts a new enumeration datatype member
+ H5Tenum_nameof - returns the symbol name corresponding to a
specified member of an enumeration datatype
+ H5Tvalueof - return the value corresponding to a
specified member of an enumeration datatype
+ H5Tget_member_value - return the value of an enumeration datatype member
+ H5Tset_tag - tags an opaque datatype
+ H5Tget_tag - gets the tag associated with an opaque datatype
- H5Tregister_hard - register specific type conversion function
- H5Tregister_soft - register general type conversion function
Filters
H5Tregister - register a conversion function
Compression
H5Zregister - register new compression and uncompression
functions for a method specified by a method number
Identifiers
+ H5Iget_type - retrieve the type of an object
References
+ H5Rcreate - creates a reference
+ H5Rdereference - open the HDF5 object referenced
+ H5Rget_region - retrieve a dataspace with the specified region selected
+ H5Rget_object_type - retrieve the type of object that an
object reference points to
Ragged Arrays (alpha)
H5RAcreate - create a new ragged array
H5RAopen - open an existing array
H5RAclose - close a ragged array
H5RAwrite - write to an array
H5RAread - read from an array
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