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|
HDF5 version 1.6.6-pre1 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.5 and
HDF5-1.6.5-*. It contains information on the platforms tested and
known problems in HDF5-1.6.5. 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/
Documentation for the current release is also on the HDF web site:
http://hdf.ncsa.uiuc.edu/HDF5/doc/
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, Languages and Compilers
- Bug Fixes since HDF5-1.6.5
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
Source code distribution:
-------------------------
Library:
--------
Parallel Library:
-----------------
Tools:
------
- h52gif and gif2h5: Both these tools were revised to include the High
Level Image API support, and 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 using the file type (default)
instead of the previous conversion to native type. PVN - 2007/03/01
- h5repack: output the percentage of compression used. 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: printing of dataset dimensions along with dataset name. PVN -
2007/02/19
F90 API:
--------
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
Configuration
-------------
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 confitions 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's possible
that the attribute could 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 this, 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 hdfhelp@ncsa.uiuc.edu 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
- Correct an coding error in configure when it tries to locate the
needed MPI and MPI-IO library for the fortran interface. - AKC
2007/5/9.
- Changed default fortran compiler to g95 when gcc is used. - AKC
2007/2/17.
- Configure can now use any tr command. No more need for
defining variable TR nor is it supported. -AKC 2006/05/20
Performance
-------------
Tools
-----
- Fixed a bug on h5dump regarding the display of named datatypes
attributes. PVN 2007/03/13
- Fixed a bug on h5dump regarding the display of group comments. PVN
2007/03/13
- Fixed a bug on 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
-------------
F90 API
-------
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);
Platforms Tested
================
AIX 5.2 (32/64 bit) xlc 6.0.0.8
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
xlC 7.0.
xlf 9.1.0.3
Cray X1 water 3.0.35 Cray Standard C Version 5.4.0.7.4
Cray Fortran 5.4.0.7.3
Cray C++ 5.4.0.7.4
FreeBSD 6.2 gcc 3.4.6
g++ 3.4.6
HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.02
HP F90 v3.1 (32-bit only)
HP aC++/ANSI C B3910B A.06.02
IRIX64 6.5 (tesla -64) MIPSpro cc 7.4.2m
F90 MIPSpro 7.4.2m
C++ MIPSpro cc 7.4.2m
IRIX64 6.5
(ucar mop1 64 & n32)
MIPSpro cc 7.4.4m
F90 MIPSpro 7.4.4m (64 only)
C++ MIPSpro cc 7.4.4m
Linux 2.4.20-28.7 gcc 2.96
(eirene, verbena) gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC)
version 5.2-1
Absoft Fortran compiler v9.0
Intel(R) C++ 32-bit Version 8.1
Intel(R) Fortran 32-bit Version 8.1
MPIch 1.2.6
Linux 2.4.21-268-smp x86_64 gcc 3.3.1 (SuSE Linux, AMD)
(mir) PGI 5.2-1 C and F90 (with k3-32)
Intel(R) C++ 32-bit Version 8.1
Intel(R) Fortran 32-bit Version 8.1
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 2.6.5-7.283-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
HP Fortran V5.5A-3548
Compaq C++ V6.5-036
MPIX200_64_r13.4
SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
SunOS 5.10 Sun WorkShop 6 update 2 C 5.3
Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
Patch 111685-13
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
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
(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
Supported Configuration Features Summary
========================================
Key: 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 F90 F90 C++ zlib SZIP
parallel parallel
IBM BG/L (15) n n n n y y
Solaris2.8 64-bit y y y(1) y y y
Solaris2.8 32-bit y y y(1) y y y
Solaris2.9 64-bit y(1) y y(1) y y y
Solaris2.9 32-bit y(1) y y(1) y y y
Solaris2.10 64-bit y(1) y n y y y
Solaris2.10 32-bit y(1) y n y y y
IRIX64_6.5 64-bit y(2) y y y y y
IRIX64_6.5 32-bit y(2) n n n y y
HPUX11.00 y(1) y y y y y
HPUX11.23-32bit n y n y y y
HPUX11.23-64bit n n n y y y
OSF1 v5.1 y y y y y y
X1 y y y y y n
AIX-5.1, 5.2 & 5.3 32-bit y y y y y y
AIX-5.1, 5.2 & 5.3 64-bit y y y y y y
Windows XP Visual Studio 6.0 n n n y y y
Windows XP Visual Studio .NET n y(8) n y y y
Windows XP Visual Studio 2005 n y(8) n y y y
Windows XP Cygwin n n n y y y
Mac OS X 10.3 n y(9) n y y y
FreeBSD 6.2 n n n y y y
RedHat 7.3 W (3) y(1) y(10) n y y y
RedHat 7.3 W Intel (3) n y n y y y
RedHat 7.3 W PGI (3) n y n y y y
RedStorm (15) n y n y y n
SuSe x86_64 gcc (3,13) n y(11) n y y y
SuSe x86_64 icc (3,13) n y(13) n y y y
Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y y
Linux 2.4 SuSE ia64 C Intel (3,7) y y y y y y
Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y
Platform Shared static- Thread- STREAM-
libraries(4) exec safe VFD
IBM BG/L n y n n
Solaris2.8 64-bit y x y y
Solaris2.8 32-bit y x y y
Solaris2.9 64-bit y x y y
Solaris2.9 32-bit y x y y
Solaris2.10 64-bit y x y y
Solaris2.10 32-bit y x y y
IRIX64_6.5 64-bit y y y y
IRIX64_6.5 32-bit y y y y
HPUX11.00 y x n y
HPUX11.23 y y n y
OSF1 v5.1 y y n y
X1 n y n y
AIX-5.1, 5.2 & 5.3 32-bit n y n y
AIX-5.1, 5.2 & 5.3 64-bit n y n y
Windows XP Visual Studio 6.0 y y n n
Windows XP Visual Studio .Net y y n n
Windows XP Visual Studio 2005 y y n n
Windows XP Cygwin y y n n
Mac OS X 10.3 y y n y
FreeBSD 6.2 y y y y
RedHat 7.3 W (3) y y y y
RedHat 7.3 W Intel (3) n y n y
RedHat 7.3 W PGI (3) n y n y
RedStorm n y n y
SuSe x86_64 gcc (3,13) n y n y
SuSe x86_64 icc (3,13) y y(14) n y
Linux 2.4 Xeon C Lustre Intel (3,6) y y n y
Linux 2.4 SuSE ia64 C Intel (3,7) y y n n
Linux 2.4 SGI Altix ia64 Intel (3) y y 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) Using mpich 1.2.6
(2) Using mpt and mpich 1.2.6.
(3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, 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) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp-perfctr-lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.til1. Ia64 cluster with Intel compilers
(8) Requires Intel Fortran Compiler 9.0 integration
(9) IBM XLF and Absoft
(10) PGI, Absoft. No shared libraries with Absoft;
use '--disable-shared'.
(11) PGI and Intel compilers for both C and Fortran
(12) AMD Opteron x86_64
(13) ifort
(14) Yes with C and Fortran, but not with C++
(15) Only serial is ported. PFS does not work for PHDF5 yet.
FMB/EIP - 2005/11/10
Known Problems
==============
* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
"calloc". All other tests passed. This indicates 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.
* Newer versions of g95 are not compatible with v1.6.5. Last known g95
version that is still compatiable with v1.6.5 is May 17, 2006.
AKC - 2006/11/29.
* Intel Compilers for Linux x86_86 platforms (EM64T-based, v8.1) has
optimization error in the data 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 at IRIX
6.5, set enviroment variable MPI_TYPE_MAX to be a bigger number, for example
120000, in order to pass the complicated collective IO tests inside parallel
HDF5 library. This is not a problem inside parallel HDF5 library. You can
always set a bigger number in your system.
KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version may
not 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(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 but all related to 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 it
has a "guard" statement in stdint.h that will #error and skip the rest
of the header file if C99 option is not used explicitly. Hardset
$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 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 if there are many old /tmp/s.pedb.* 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 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.
* 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:
ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/
* Use --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
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to 1**-308.
If -ieee is not used, the converted double values are mostly 0.0 but
occasionally as 1**-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 HDF 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.
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