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HDF5 version 1.6.2-pre2 currently under development
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.1 and
HDF5-1.6.1-post*, and contains information on the platforms tested and
known problems in HDF5-1.6.1-post*. 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 HDF5-1.6.1
- Documentation
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
- Default of $prefix is changed to $PWD/hdf5 so that multiple
builds using --srcdir is possible in the same machine.
AKC - 2003/12/1
Library:
--------
- Added H5Iget_ref, H5Iinc_ref and H5Idec_ref routines to the C
library and the FORTRAN wrapper. See the reference manual for a
full description of these new routines. QAK - 2003/12/11
Parallel Library:
-----------------
- The parallel tests in testpar/ now provides different levels of
verbosity via the '-v' option. The default is less verbose
than before. AKC - 2004/01/23
- Added parallel test, test_mpio_1wMr, which tests if the
underlaying parallel I/O system is conforming to the POSIX
write/read requirement. This version includes options of using
atomicity and file-sync. AKC - 2003/11/27
Tools:
------
- 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. AKC - 2004/01/07
- Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03
C++ API:
--------
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 --disbale-shared --enable-static flags with configure when
building HDF5 Fortran Library on MAC OSX.
- C and C++ Libraries are available for Linux64 RH8
- C, C++ and Fortran sequential Libraries, and C and Fortran parallel
Libraries are available for Altix (Linux ia64)
Bug Fixes since HDF5-1.6.1 release
==================================
Library
-------
- 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
- Avoid metadata cache from preempting current dataset object header
when looking up information about the named datatype that the
dataset uses. QAK - 2003/10/20
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
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
Documentation
-------------
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 3.6.0.2
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.2
Cray T90IEEE 10.0.0md Cray Standard C Version 6.4.0.3
Cray Fortran Version 3.4.0.0
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
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
C++ MIPSpro cc 7.3.1.3m
Linux 2.4.18 gcc 2.96, 3.3.2
g++ 3.3.2
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Linux 2.4.20-8 gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Linux 2.4.21-2.9.5ws #3 gcc 3.2.3 (Red Hat Linux 3.2.3-16)
SMP x86_64 g++ 3.2.3
Linux 2.4.21-sgi SMP ia64 Intel(R) C++ Version 7.1
Intel(R) Fortran Itanium(R) Version 7.1
SGI MPI
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran V5.5-2602
Compaq Fortran V5.5-1877
Compaq C++ V6.5-033
Compaq C++ V6.5-030
MPI_64bit_R13
SunOS 5.7(32 and 64 bit) 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 and 64 bit) 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 v4.4.2 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 2.4.18 ia64 gcc version 3.0.4
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 7.2
gcc and g++ Apple Computer, Inc. GCC
version 1175, based on gcc version 3.3.2
IBM XL Fortran 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 system MPI and MPIO libraries.
(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
==============
* Fortran subroutine h5pget_driver_f doesn't return a correct driver information.
The fix willl be available in the 1.6.2 release.
* There are two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5)
failed on windows xp with .NET for debug and debug dll. Release and Release
dll work fine.
* 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
|
