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|
HDF5 version 1.7.31 currently under development
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.* and
HDF5-1.7.*, and contains information on the platforms tested and
known problems in HDF5-1.7.*. 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
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.0
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
- Fixed the long compile time of H5detect.c when v7.x Intel Compiler
is used with optimization NOT off. AKC - 2004/05/20
- Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06
- Prefix default is changed from /usr/local to `pwd`/hdf5.
AKC - 2003/07/09
Library:
--------
- A new API function H5Fget_name was added. It returns the name
of the file by object(file, group, data set, named data type,
attribute) ID. SLU - 2004/06/29
- A new API function H5Fget_filesize was added. It returns the
actual file size of the opened file. SLU - 2004/06/24
- New Feature of Data transformation is added. AKC - 2004/05/03.
- New exception handler for datatype conversion is put in to
replace the old overflow callback function. This exception
handler is set through H5Pset_type_conv_cb function.
SLU - 2004/4/27
- Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2,
will suppress all library version mismatch warning messages.
AKC - 2004/4/14
- A new type of dataspace, null dataspace(dataspace without any
element) was added. SLU - 2004/3/24
- Data type conversion(software) from integer to float was added.
SLU - 2004/3/13
- Data type conversion(software) from float to integer was added.
Conversion from integer to float will be added later.
SLU -2004/2/4
- Added new H5Premove_filter routine to remove I/O pipeline filters
from dataset creation property lists. PVN - 2004/01/26
- Added new 'compare' callback parameter to H5Pregister & H5Pinsert
routines. QAK - 2004/01/07
- Data type conversion(hardware) between integers and floats was added.
SLU 2003/11/21
- New function H5Iget_file_id() was added. It returns file ID given
an object(dataset, group, or attribute) ID. SLU 2003/10/29
- Added new fields to the H5G_stat_t for more information about an
object's object header. QAK 2003/10/06
- Added new H5Fget_freespace() routine to query the free space in a
given file. QAK 2003/10/06
- Added backward compatability with v1.6 for new Error API. SLU -
2003/09/24
- Changed 'objno' field in H5G_stat_t structure from 'unsigned long[2]'
to 'haddr_t'. QAK - 2003/08/08
- Changed 'fileno' field in H5G_stat_t structure from 'unsigned long[2]'
to 'unsigned long'. QAK - 2003/08/08
- Changed 'hobj_ref_t' type from structure with array field to 'haddr_t'.
QAK - 2003/08/08
- Object references (hobj_ref_t) can now be compared with the 'objno'
field in the H5G_stat_t struct for testing if two objects are the
same within a file. QAK - 2003/08/08
- Switched over to new error API. SLU - 2003/07/25
- Added support for user defined identifier types. NF/JL - 2004/06/29
- Added support for SZIP without encoder. Added H5Zget_filter_info
and changed H5Pget_filter and H5Pget_filter_by_id to support this
change.
Parallel Library:
-----------------
- Add options of using atomicity and file-sync to test_mpio_1wMr.
AKC - 2003/11/13
- Added parallel test, test_mpio_1wMr, which tests if the
underlaying parallel I/O system is conforming to the POSIX
write/read requirement. AKC - 2003/11/12
Fortran Library:
----------------
- added new functions h5fget_name_f and h5fget_filesize_f
EIP 2004/07/08
- h5dwrite/read_f and h5awrite/read_f functions only accept dims parameter
of the type INTEGER(HSIZE_T).
Tools:
------
- h5repack.sh did not report errors encountered during tests. It does
now. AKC - 2004/04/02
- Added the MPI-I/O and MPI-POSIX drivers to the list of VFL drivers
available for h5dump and h5ls
- Added option --vfd= to h5ls to allow a VFL driver to be selected
by a user.
- Added option -showconfig to compiler tools (h5cc,h5fc,h5c++).
AKC - 2004/01/08
- Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc"
respectively if library is built in parallel mode.
WCW - 2003/11/04
- Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03
- Changed output of "OID"s from h5dump from "<number>-<number>" to
"<number". This affects both the "regular" and XML output.
QAK - 2003/08/08
- Changed output of file IDs and "OID"s from h5ls from
"<number>:<number>:<number>:<number>" to "<number>:<number>"
QAK - 2003/08/08
Support for new platforms, languages and compilers.
=======================================
- HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran
Compiler version 8.1 Beta. Use "--disable-shared --enable-static"
configure flags along with the "--enable-fortran" flag to build
Fortran library. EIP - 2004/01/07
Bug Fixes since HDF5-1.6.0 release
==================================
Library
-------
- Fixed bug where incorrect data could be read from a chunked dataset
after it was extended. QAK - 2004/07/12
- Fixed failure to read data back from file of compound type with
variable-length string as field. SLU - 2004/06/10
- Fixed potential file corruption bug when a block of metadata could
overlap the end of the internal metadata accumulator buffer and
the buffer would be extended correctly, but would incorrectly
change it's starting address. QAK - 2004/06/09
- Opaque datatype with no tag failed for some operations. Fixed.
SLU - 2004/6/3
- Fixed potential file corruption bug where dimensions that were
too large (a value greater than could be represented in 32-bits)
could cause the incorrect amount of space to be allocated in a
file for the raw data for the dataset. QAK - 2004/06/01
- Fixed dtypes "sw long double -> double" failure in QSC class
machines. AKC - 2004/4/16
- Fixed problem with fletcher32 filter when converting data of different
endianess. PVN - 2004/03/10
- Fixed problem with H5Tget_native_type() not handling opaque fields
correctly. QAK - 2004/01/31
- Fixed several errors in B-tree deletion code which could cause a
B-tree (used with groups and chunked datasets) to become corrupt
with the right sequence of deleted objects. QAK - 2004/01/19
- Fixed small internal memory leaks of fill-value information.
QAK - 2004/01/13
- Fixed bug that caused variable-length datatypes (strings or sequences)
used for datasets in files with objects that were unlinked to
fail to be read/written to a file. QAK - 2004/01/13
- Detect situation where szip 'pixels per block' is larger than the
fastest changing dimension of a dataset's chunk size and disallow
this (due to limits in szip library). QAK - 2003/12/31
- Fixed bug with flattened hyperslab selections that would generate
incorrect hyperslab information with certain high-dimensionality
combinations of start/stride/count/block information.
QAK - 2003/12/31
- Fixed bug with variable-length datatypes used in compound datatypes.
SLU - 2003/12/29
- Fixed bug in parallel I/O routines that would cause reads from
"short datasets" (datasets which were only partially written out)
to return invalid data. QAK & AKC - 2003/12/19
- Fixed bug where scalar dataspaces for attributes were reporting as
simple dataspaces. QAK - 2003/12/13
- Fixed problem with selection offsets of hyperslab selections in
chunked datasets causing the library to go into an infinite loop.
QAK - 2003/12/13
- Fixed H5Giterate to avoid re-using index parameter after iteration
callback has been called (allows iteration callback to modify the
index parameter itself). QAK - 2003/12/06
- Fixed various floating-point conversion problems, including a
change which could corrupt data when converting from double->float.
QAK - 2003/11/24
- Changed "single process" metadata writing in library to collective
I/O by all processes, in order to guarantee correct data being
written with MPI-I/O. QAK - 2003/11/20
- Fixed problems with fill values and variable-length types and also
I/O on VL values that were set to NULL. QAK - 2003/11/08
- Fixed problems with MPI datatypes that caused ASCI Q machine to
hang. QAK - 2003/10/28
- Removed HDF5_MPI_PREFER_DERIVED_TYPES environment variable support,
since it had no benefit. QAK - 2003/10/28
- Single hyperslab selections (which were set with only one call to
H5Sselect_hyperslab) that had dimensions that could be "flattened"
but were interspersed with dimensions that could not be flattened
were not correctly handled, causing core dumps. QAK - 2003/10/25
- Fixed incorrect datatype of the third parameter to the Fortran90
h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T))
EIP - 2003/10/13
- Fixed problems with accessing variable-length data datatypes on
Crays. QAK - 2003/10/10
- Fixed potential file corruption bug when too many object header
messages (probably attributes, from a user perspective) were
inserted into an object header and certain other conditions were
met. QAK - 2003/10/08
- Changed implementation of internal ID searching algorithm to avoid
O(n) behavior for many common cases. QAK - 2003/10/06
- Allow partial parallel writing to compact datasets. QAK - 2003/10/06
- Correctly create reference to shared datatype in attribute, instead
of making a copy of the shared datatype in the attribute.
QAK - 2003/10/01
- Revert changes which caused files >2GB to fail when created with
MPI-I/O file driver on certain platforms. QAK - 2003/09/16
- Allow compound datatypes to grow in size. SLU - 2003/09/10
- Detect if a type is already packed before attempting to pack it
again or check if it is locked. SLU - 2003/09/10
- Corrected bug when opening a file twice with read-only permission
for one open and then closing the read-only access file ID would
generate an error. QAK - 2003/09/10
- Corrected bug in repeated calls to H5Pget_access_plist() which would
incorrectly manage reference counts of internal information and
eventually blow up. QAK - 2003/09/02
- Return rank of the array datatype on successful call to
H5Tget_array_dims(). QAK - 2003/08/30
- Corrected bug in H5Tdetect_class which was not correctly detecting
datatype classes of fields in nested compound datatypes in some
circumstances. QAK - 2003/08/30
- Corrected bug in sieve buffer code which could cause loss of data
when a small dataset was created and deleted in quick succession.
QAK - 2003/08/27
- Corrected bug in H5Gget_objname_by_idx which was not allowing NULL
for the name when just querying for the object name's length.
QAK - 2003/08/25
- Corrected bug in variable-length string handling which could
generate a core dump on writing variable-length strings as part
of a compound datatype on certain architectures. QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would incorrectly compute
the size of certain compound datatypes and also incorrectly
compute the offset of the last field for those compound datatypes.
QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would drop string datatype
metadata (padding, etc.) QAK - 2003/08/25
- Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and
H5Gget_objtype_by_idx to allow them to accept location IDs, not just
group IDs. QAK - 2003/08/21
- Corrected bug when using scalar dataspace for memory selection and
operating on chunked dataset. QAK - 2003/08/18
- Corrected bugs with multiple '/' characters in names for H5Glink
and H5Gunlink. QAK - 2003/08/16
- Corrected bug with user blocks that didn't allow a user block to
be inserted in front of a file after the file was created.
QAK - 2003/08/13
- Corrected errors with using point selections to access data in
chunked datasets. QAK - 2003/07/23
- Corrected error with variable-length datatypes and chunked datasets
caused H5Dwrite to fail sometimes. QAK - 2003/07/19
- Modified library and file format to support storing indexed storage
(chunked dataset) B-tree's with non-default internal 'K' values.
QAK - 2003/07/15
- Returned H5T_BKG_TEMP support to library after it was accidentally
removed. QAK - 2003/07/14
Configuration
-------------
- Parallel I/O with the MPI-I/O driver will no longer work if the
filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE"
environment variable has been removed. QAK - 2004/01/30
- Fixed the error that cause "make install" to fail because of the
macro definition syntax of "prefix?=..." AKC - 2003/07/22
Performance
-------------
- More optimizations to inner loops of datatype conversions for
integers and floats which give a 10-50% speedup. QAK - 2003/11/07
- Hoisted invariant 'if/else's out of inner datatype conversion loop for
integer and floating-point values, giving about a 20% speedup.
QAK - 2003/10/20
Tools
-----
- Fixed h5redeploy which sometimes complain too many argument for the
test command. (The complain did not hinder the h5redploy to
proceed correctly.) AKC - 2003/11/03
- Fixed a segmentation fault of h5diff when percentage option is used.
AKC - 2003/08/27
- Switched away from tools using internal "fixtype" function(s) to use
H5Tget_native_type() internally. QAK - 2003/08/25
Documentation
-------------
Platforms Tested
================
AIX 5.1 (32 and 64-bit) xlc 6.0.0.2
xlf 8.1.0.3
xlC 6.0.0.4
xlc 5.0.2.5
xlf 7.1.1.2
xlC 5.0.2.5
mpcc_r 5.0.2.5
mpxlf_r 7.1.1.2
poe 3.2.0.10
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.0.2
mpt 2.2.0.0
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2
mpt 2.2.0.0
Cray Fortran Version 3.6.0.0.2
Cray T90IEEE 10.0.1.01y Cray Standard C Version 6.4.0.2.3
Cray Fortran Version 3.4.0.3
mpt 2.1.0.0
FreeBSD 4.9 gcc 2.95.4
g++ 2.95.4
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP ANSI C++ B3910B A.03.13
MPIch 1.2.4
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)
MPIch 1.2.4
Linux 2.4.18 gcc 2.96, 3.2.2, 3.2.3
g++ 3.2.2, 3.2.3
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 4.0-2
MPIch 1.2.4
OSF1 V5.1 Compaq C V6.4-014
Compaq C V6.3-027
Compaq Fortran V5.5-1877
Compaq C++ V6.5-014
MPI_64bit_R5
g++ 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 2 C 5.3
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90
Sun WorkShop 6 update 2 C++ 5.3
SunOS 5.8/64 Sun WorkShop 6 update 2 C 5.3
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90
Sun WorkShop 6 update 2 C++ 5.3
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
Intel C and F90 compilers version 7.1
Code Warrior 8.0
Windows XP MSVC++.NET
MAC OS X Darwin 6.5
gcc and g++ Apple Computer, Inc. GCC
version 1161, based on gcc version 3.1
IBM XL Fortran compiler version 8.1 Beta
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 (4)
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 y (1) y y (1) y y y
Solaris2.8 32-bit y y 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 y y y y
OSF1 v5.1 y y y y y y y
T3E y y (5) y y (5) n n y
SV1 y y (5) y y (5) n n y
T90 IEEE y y (5) y y (5) 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 (6) y n n n y y y
WinXP Intel y n n n y y y
Win2000 y n y n y y y
Win2000 Intel 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 2.4 gcc (3) y y (1) y (PGI) n y y y
Linux 2.4 Intel (3) y n y n y n y
Linux 2.4 PGI (3) y n y n y n y
Linux 2.4 IA32 Intel y n y n y n y
Linux 2.4 IA64 Intel y n y n y n y
ASCII Table 2 -- for RELEASE.txt
Platform static- Thread- SZIP GASS STREAM- High-level H4/H5
exec safe VFD APIs tools (7)
Solaris2.7 64-bit x y y n y y n
Solaris2.7 32-bit x y y n y y y
Solaris2.8 64-bit x y y n y y n
Solaris2.8 32-bit x y y n y y y
IRIX6.5 x n y n y y y
IRIX64_6.5 64-bit x y y y y y y
IRIX64_6.5 32-bit x y y y y y y
HPUX11.00 x n y n y y y
OSF1 v5.1 y n y n y y y
T3E y n n n y y y
SV1 y n n n y y y
T90 IEEE y n n n y y n
TFLOPS y n n n n n n
AIX-5.1 32-bit y n y n y y y
AIX-5.1 64-bit y n y n y y y
WinXP (6) y n y n n y y
WinXP Intel y n y n n y y
Win2000 y n y n n y y
Win2000 Intel y n y n n y y
WinNT CW y n y n n y y
Mac OS X 10.2 y n y n y y n
FreeBSD y y y n y y y
Linux 2.4 gcc (3) y y y n y y y
Linux 2.4 Intel (3) y n y n y n n
Linux 2.4 PGI (3) y n y n y n n
Linux 2.4 IA32 Intel y n y n y y y
Linux 2.4 IA64 Intel y n y n y y 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, respectively.
(4) Shared libraries are provided only for the C library, except
on Windows where they are provided for C and C++.
(5) Using mpt.
(6) Binaries only; source code for this platform is not being
released at this time.
(7) Includes the H4toH5 Library and the h4toh5 and h5toh4
utilities.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* PGI C++ compiler fails when compiling the C++ library's tests.
Therefore, we cannot verify that the C++ library built with the PGI C++
compiler is correct.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, 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 stream-vfd test uses ip port 10007 for testing. If another
application is already using that port address, the test will hang
indefinitely and has to be terminated by the kill command. To try the
test again, change the port address in test/stream_test.c to one not
being used in the host.
* The --enable-static-exec configure flag fails to compile for Solaris
platforms. This is due to the fact that not all of the system
libraries on Solaris are available in a static format.
The --enable-static-exec configure flag also fails to correctly compile
on IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
It is suggested that you don't use this option on these platforms
during configuration.
* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
compilation. The ANSI version of the compiler complains about not being
able to handle the `long long' datatype with the warning:
warning: ANSI C does not support `long long'
This warning is innocuous and can be safely ignored.
* The Stream VFD was not tested yet under Windows. It is not supported
in the TFLOPS machine.
* 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:
- Cray J90 and Cray T90IEEE 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
replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src
subdirectory in the top level directory with the Cray-specific files
from the site:
* On some platforms that use Intel compilers to build HDF5 fortran library,
compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
complaining about exit subroutine. Comment out the line
IF (total_error .ne. 0) CALL exit (total_error)
ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
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