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|
HDF5 version 1.6.6 released on Thu Aug 16 11:17:10 CDT 2007
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.5 and
HDF5-1.6.6 It contains information on the platforms tested and
known problems in HDF5-1.6.6. For more details, check the HISTORY.txt
file in the HDF5 source.
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ or on the THG (The HDF Group)
ftp server (ftp.hdfgroup.org) in the directory:
/HDF5/docs/
Documentation for the current release is also on the HDF web site:
http://hdfgroup.org/HDF5/doc/
For more information, see the HDF5 home page at:
http://hdfgroup.org/HDF5/
If you have any questions or comments, please send them to:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.5
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
- HDF5 now uses autoconf 2.61 to generate configure. MAM - 2007/7/25.
Source code distribution
========================
Library:
--------
- None
Parallel Library:
-----------------
- None
Tools:
------
- h52gif and gif2h5: Both these tools were revised to include High
Level Image API support. Tests were added to /hl/tools/gif2h5.
PVN - 2007/04/13
- h5dump: Added support for double long type H5T_NATIVE_LDOUBLE.
PVN - 2007/03/13
- h5dump: Added support for binary output; see usage. PVN 2007/03/13
- h5repack: Added support for reading and writing by hyperslabs for
large files. PVN - 2007/03/01
- h5repack: A new option allows the copy to use the source file type
(default) instead of the previous conversion to native type.
PVN - 2007/03/01
- h5repack: Added output of the percentage of compression achieved.
PVN - 2007/03/01
- h5diff: Added support for comparing dataset regions. PVN - 2007/02/20
- h5diff: Added support for reading and comparing by hyperslabs for
large files. PVN - 2007/02/20
- h5diff: Added printing of dataset dimensions along with dataset name.
PVN - 2007/02/19
F90 API:
--------
- None
C++ API:
--------
- Added support for Szip: DSetCreatPropList::setSzip - BMR 2007/01/24
Support for New Platforms, Languages and Compilers
==================================================
- Added support for MAC Intel (Darwin 8.8.2) (gcc 4.0.1 and g95 0.91)
EIP - 2007/02/13
- Added support for GNU C compiler version 4.2.1 for FreeBSD 6.2
(32- and 64-bit)
Bug Fixes since HDF5-1.6.5 Release
==================================
Library
-------
- Fixed several bugs with writing fill values for datasets that have
a variable-length datatype or component datatype. QAK - 2007/06/19
- STDIO driver didn't support files bigger than 2GB because the OFFSET
parameter of fseek is of type LONG INT, not big enough for big
files. Use fseeko instead for big files if it's available on the
system. SLU - 2007/4/5
- Relaxed restrictions on attribute operations to allow a file ID to
be used as the "location ID". If a file ID is used, the attribute
operation will occur on the root group of the file.
QAK - 2007/02/09
- Fixed a bug in H5Sselect_valid() that caused an incorrect value to
be returned (0) instead of FAIL on error conditions such as the
selection or extent not being defined. CMC - 2007/01/05
- Fixed potential file corruption bug which could overwrite a portion
of an object's header when an attribute was renamed. If the new
name for the attribute was longer than the old name, it was possible
that the attribute would grow enough to overwrite another message
in the object's header. QAK - 2007/01/02
- Fixed file corruption bug which could write an incorrect number of
messages to an object's header under certain circumstances.
Generally, the sequence of actions to generate this bug looks
like this:
- Create an object.
- Close the file.
- Re-open the file.
- Add 2 (or more) attributes to the object.
- Close the file.
- Re-open the file.
- Delete one of the attributes on the object.
- Add a smaller attribute to the object.
- Delete the smaller atttribute on the object.
- Add a larger attribute on the object.
After this, the number of header messages stored for the object
will be off by one. Other sequences of modifying attributes on an
object could also trigger this bug. If you are opening an
object and the bottom few messages of the HDF5 error stack
resembles the following, the object has been affected by this bug:
#007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): unable to load entry
major(08): Meta data cache layer
minor(40): Unable to load metadata into cache
#008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): corrupt object header - too few messages
major(12): Object header layer
minor(40): Unable to load metadata into cache
Specifically, "corrupt object header" is the best string to search
for in the HDF5 error stack output.
If your files have been affected by this bug, or you are concerned
that your files might have been, please contact the HDF Helpdesk
at help@hdfgroup.org for a tool to detect and repair files
affected by this problem. QAK - 2006/6/16
- Fixed various problems with retrieving names of objects, especially
with mounted files. QAK - 2005/12/25
Configuration
-------------
- Changed to default to --disable-shared if parallel is enabled.
AKC - 2007/5/12
- Corrected a coding error in configure when it tries to locate the
needed MPI and MPI-IO library for the fortran interface.
AKC - 007/5/9.
- Changed default fortran compiler to g95 when gcc is used.
AKC - 007/2/17.
- Configure can now use any tr command. No more need for
defining the variable TR, nor is it supported. AKC - 2006/05/20
Performance
-------------
- None
Tools
-----
- Fixed a bug in h5dump regarding the display of named datatypes
attributes. PVN - 2007/03/13
- Fixed a bug in h5dump regarding the display of group comments.
PVN - 2007/03/13
- Fixed a bug in h5dump regarding the display of hardlinks pointing
to the root group. PVN - 2007/03/13
- Fixed a bug in the h5diff percentage option -p. PVN - 2007/03/05
- Fixed a bug in h5dump that caused array indices greater than 2^32-1
not to be printed correctly. PVN - 2007/2/19
Documentation
-------------
- Corrected errors and extended the descriptions in Reference Manual
entries for several functions.
F90 API
-------
- None
C++ API
-------
- Changed
StrType::StrType(const size_t& size);
to
StrType::StrType(const int dummy, const size_t& size);
because the first one clashed with
StrType::StrType(const hid_t existing_id); - BMR 2007/05/03
- Wrappers of H5Rcreate had incorrect prototypes. Added these
overloaded functions:
IdComponent::reference(void* ref, const char* name, DataSpace&
dataspace, H5R_type_t ref_type = H5R_DATASET_REGION)
IdComponent::void reference(void* ref, const char* name)
IdComponent::reference(void* ref, const H5std_string& name)
and will remove these incorrect member functions:
DataSet::Reference
DataType::Reference
Group::Reference
H5File::Reference
- Added wrappers for H5Rdereference as constructors:
DataSet(IdComponent& obj, void* ref);
Group(IdComponent& obj, void* ref);
DataType(IdComponent& obj, void* ref);
Documentation
=============
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ (start with index.html) or on the
THG (The HDF Group) ftp server (ftp.hdfgroup.org) in the directory:
/HDF5/docs/
Online documentation for the current release can be found on the THG
web site:
http://hdfgroup.org/HDF5/doc/
Platforms Tested
================
AIX 5.2 (32/64 bit) xlc 6.0.0.8
(datastar) xlC 6.0.0.9
xlf 8.1.1.7
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.7
AIX 5.3 (32/64 bit) xlc 7.0.0.0
(copper) xlC 7.0.
xlf 9.1.0.3
FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6
(duty and liberty) gcc and g++ 4.2.1
HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.02
(sirius) HP F90 v3.1 (32-bit only)
HP aC++/ANSI C B3910B A.06.02
IRIX64 6.5 MIPSpro cc 7.4.4m
(ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only)
C++ MIPSpro cc 7.4.4m
Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3
i686 i386 GNU/Linux
(osage)
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
(kagiso) PGI C, Fortran, C++ 6.2-5 32-bit
icc (ICC) 9.1
Intel(R) C++ Compiler for 32-bit
applications, Version 9.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 9.1
Absoft 32-bit Fortran 95 10.0.4
MPICH mpich2-1.0.4p1 compiled with
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.91!)
Linux 2.6.16.46-0.12-debug #1
SMP ia64 GNU/Linux Intel(R) C++ Version 10.0.025
(ucar hir1) Intel(R) Fortran Itanium(R) Version 10.0.025
Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037
SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031
(smirom) PGI C, Fortran, C++ Version 6.2-5
for 64-bit target on x86-64
tested for both 32- and 64-bit binaries
Linux 2.6.5-7.283-rtgfx Altix
SMP ia64 Intel(R) C++ Version 9.0
(cobalt) Intel(R) Fortran Itanium(R) Version 9.0
SGI MPI
OSF1 V5.1 (QSC) Compaq C V6.5-011
(See "Known Problems.") HP Fortran V5.5A-3548
Compaq C++ V6.5-036
MPIX200_64_r13.4
SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3
(sol) Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8
(linew) Sun WorkShop 6 update 2 Fortran 95 8.2
Sun WorkShop 6 update 2 C++ 5.8
Patch 121019-06
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) Intel(R) C++ Version 9.0
Intel(R) Fortran Compiler Version 9.0
PGI C Version 6.0
PGI C++ Version 6.0
PGI Fortran Version 6.0
gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5)
Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) Intel(R) C++ Version 10.0
Intel(R) Fortran Compiler Version 10.0
Open MPI 1.2.2
IA-64 Linux 2.4.21.SuSE_292.til1
ia64 gcc (GCC) 3.2.2
(NCSA tg-login) Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
mpich-gm-1.2.5..10-intel-r2
Windows XP Visual Studio 6.0
Visual Studio .NET (with Intel Fortran 9.0)
Visual Studio 2005 (with Intel Fortran 9.0)
cygwin (gcc 3.4.4)
MAC OS X Intel Darwin 8.10.1
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
g95 0.91
Supported Configuration Features Summary
========================================
Key: y = Tested and supported
n = Not supported or not tested in this release
C = Cluster
W = Workstation
( ) = Footnote appears below second table
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.8 32- and 64-bit n y n y y y
Solaris2.10 32- and 64-bit n y n y y y
IRIX64_6.5 32-bit n n n n y y
IRIX64_6.5 64-bit n y n n y y
HPUX11.23-32bit n y n y y y
HPUX11.23-64bit n n n y y y
WinXP Visual Studio 6.0 n n n y y y
WinXP CYGWIN n n n y y y
WinXP 2005 n y n y y y
WinXP .Net n y n y y y
Mac OS X 10.4.10 n y n y y y
AIX-5.2 & 5.3 32- and 64-bit y y y y y y
FreeBSD 6.2 32- and 64-bit n n n y y y
RedHat Linux 2.4.21 W n n n y y y
SuSE Linux 2.6.9-42 i686 GNU (1) W y y y y y y
SuSE Linux 2.6.9-42 i686 Intel W n y n y y y
SuSE Linux 2.6.9-42 i686 PGI W n y n y y y
SuSE Linux 2.6.16 x86_64 GNU (1) W y y y y y y
SuSE Linux 2.6.16 x86_64 Intel W n y n y y y
SuSE Linux 2.6.16 x86_64 PGI W n y n y y y
RHEL 4 Linux 2.6.9 Xeon Lustre C y y y y y y
RedHat Linux 2.4 Xeon Lustre C n y n y y y
SuSE Linux 2.4 ia64 C y y y y y y
SuSe Linux 2.6.16 SGI Altix ia64 n y n y y y
SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y
OSF1 v5.1 y y y y y n
Platform Shared static- Thread- STREAM-
libraries(4) exec safe VFD
Solaris2.8 32- and 64-bit y n y y
Solaris2.10 32- and 64-bit y n y y
IRIX64_6.5 32-bit y n y y
IRIX64_6.5 64-bit y n y y
HPUX11.23-32bit y (3) n n y
HPUX11.23-64bit y (3) n n y
WinXP Visual Studio 6.0 y n n n
WinXP CYGWIN y n n n
WinXP 2005 y n n n
WinXP .Net y n n n
Mac OS X 10.4.10 y n n y
AIX-5.2 & 5.3 32- and 64-bit n n n y
FreeBSD 6.2 32- and 64-bit y n n y
RedHat Linux 2.4.21 W y n n y
SuSE Linux 2.6.9-42 i686 GNU (1) W y n y y
SuSE Linux 2.6.9-42 i686 Intel W y n n y
SuSE Linux 2.6.9-42 i686 PGI W n n n y
SuSE Linux 2.6.16 x86_64 GNU (1) W y n n y
SuSE Linux 2.6.16 x86_64 Intel W y n n y
SuSE Linux 2.6.16 x86_64 PGI W n n n y
RHEL 4 Linux 2.6.9 Xeon Lustre C y n n y
RedHat Linux 2.4 Xeon Lustre C y n n y
SuSE Linux 2.4 ia64 C y n n y
SuSe Linux 2.6.16 SGI Altix ia64 n n n y
SuSe Linux 2.6.5 SGI Altix ia64 n n n y
OSF1 v5.1 n n n y
Compiler versions for each platform are listed in the "Platforms Tested"
table found elsewhere in this file (RELEASE.txt). Unless otherwise noted,
compilers used are the system compilers.
Footnotes:
(1) Fortran compiled with g95.
(2) In most cases, shared libraries are provided only for the C library,
except on Windows where they are provided for C, C++, and Fortran.
(3) C++ works only with static libraries.
Known Problems
==============
* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It
does not include the -lmpi properly. This will be fixed in the next
release. AKC - 2007/08/07.
* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared
library, especially for h5repacktst and h52gifgentst, the following (or
similar) error message may appear:
"523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname
'libh5test.so.1' under any of the filenames .......(bunch of directories)
"
And the testing will fail.
We believe this is a libtool problem. One way to get rid of this is to
add the paths of libh5test.so.1 and libh5.so.1 to the shared library path.
For 32-bit:
You may do this, under csh:
setenv LD_LIBRARYN32_PATH .......(existing pathes):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
For 64-bit:
setenv LD_LIBRARY64_PATH ......(existing pathes):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
NOTE: This problem ONLY affects the testing of the HDF5 library when you
build from source. It won't affect any applications that would like to link
with the HDF5 shared library since the shared library path needs to be set
anyway. KY - 2007/8/2
* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
"calloc". All other tests passed. This indicates that a dataset using
chunked storage created by serial HDF5 may not work properly with parallel
HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x
calloc". AKC - 2007/7/12.
* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has
an optimization error in the datax types conversion code. Before running
configure, edit the file config/intel-flags by changing the setting of
PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10.
* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX
6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for
example 120000, in order to pass the complicated collective IO tests inside
the parallel HDF5 library. This is not a problem inside the parallel HDF5
library. You can always set a bigger number on your system. KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version of HDF5
might not be able to be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem. EIP - 2005/09/09
* The dataset created or rewritten with the v1.6.3 library or after can't
be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is
enabled. There was a bug in the calculating code of the Fletcher32
checksum in the library before v1.6.3. The checksum value wasn't consistent
between big-endian and little-endian systems. This bug was fixed in
Release 1.6.3. However, after fixing the bug, the checksum value is no
longer the same as before on little-endian system. The library release
after 1.6.4 can still read the dataset created or rewritten with the library
of v1.6.2 or before. SLU - 2005/7/8
* For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron
processor, there's a bug in the compiler for optimization(-O2). The library
failed in several tests, all related to the multi driver. The problem has
been reported to the vendor.
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but
have a "guard" statement in stdint.h that will #error and skip the rest
of the header file if the C99 option is not used explicitly. Hardsetting
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may also fail with messages like "The socket name is already
in use". HDF5 does not use sockets (except for stream-VFD). This is
due to problems of the poe command trying to set up the debug socket.
Check whether there are many old /tmp/s.pedb.* files staying around. These
are sockets used by the poe command and left behind due to failed commands.
Ask your system administrator to clean them out. Lastly, request IBM
to provide a means to run poe without the debug socket.
* 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 the IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* The Stream VFD is not supported under Windows.
* Use the --disable-shared configure flag if building with Absoft Fortran
compiler.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8.
* In LANL QSC, the new cc compiler has problems converting small values of
long long (absolute values less than 1**-308) to double. This triggers
the test/dtypes to report failure in the following test:
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to
10**-308. If -ieee is not used, the converted double values are mostly
0.0, but occasionally appear as 10**-308. This has been reported to the
system staff.
All other tests have passed.
* On at least one system, SDSC DataStar, the scheduler (in this case
LoadLeveler) sends job status updates to standard error when you run
any executable that was compiled with the parallel compilers.
This causes problems when running "make check" on parallel builds, as
many of the tool tests function by saving the output from test runs,
and comparing it to an exemplar.
The best solution is to reconfigure the target system so it no longer
inserts the extra text. However, this may not be practical.
In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
the configure and build. This will cause "make check" to continue after
detecting errors in the tool tests. However, in the case of SDSC DataStar,
it also leaves you with some 150 "failed" tests to examine by hand.
A second solution is to write a script to run serial tests and filter
out the text added by the scheduler. A sample script used on SDSC
DataStar is given below, but you will probably have to customize it
for your installation.
Observe that the basic idea is to insert the script as the first item
on the command line which executes the test. The script then
executes the test and filters out the offending text before passing
it on.
#!/bin/csh
set STDOUT_FILE=~/bin/serial_filter.stdout
set STDERR_FILE=~/bin/serial_filter.stderr
rm -f $STDOUT_FILE $STDERR_FILE
($* > $STDOUT_FILE) >& $STDERR_FILE
set RETURN_VALUE=$status
cat $STDOUT_FILE
tail +3 $STDERR_FILE
exit $RETURN_VALUE
You get the HDF5 make files and test scripts to execute your filter script
by setting the environment variable "RUNSERIAL" to the full path of the
script prior to running configure for parallel builds. Remember to
"unsetenv RUNSERIAL" before running configure for a serial build.
Note that the RUNSERIAL environment variable exists so that we can
prefix serial runs as necessary on the target system. On DataStar,
no prefix is necessary. However, on an MPICH system, the prefix might
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
get the serial tests to run at all.
In such cases, you will have to include the regular prefix in your
filter script. JM - 2004/9/15
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