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Elena Pourmal 3605a2dc2d [svn-r15105] Maintenance: Modified version to 1.8.1-snap0, and updated HISTORY-1_8.txt and RELEASE.txt 
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HDF5 History
============
This file contains development history of HDF5 1.8 branch
2. Release Information for hdf5-1.8.1
1. Release Information for hdf5-1.8.0
[Search on the string '%%%%' for per-release section breaks.]
%%%%1.8.1%%%%
HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008
================================================================================
INTRODUCTION
============
This document describes the differences between the HDF5-1.8.1 release
and HDF5 1.8.0, and contains information on the platforms tested and known
problems in HDF5-1.8.1. For more details, see the files
HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory
of the HDF5 source.
Links to the HDF5 1.8.1 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.1 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.1 can be accessed directly at this location:
http://www.hdfgroup.org/HDF5/doc/
New features in the HDF5-1.8.x release series, including brief general
descriptions of some new and modified APIs, are described in the "What's New
in 1.8.0?" document:
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.1 (current
release) versus Release 1.8.0":
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.8.0
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- The lib/libhdf5.settings file contains much more configure
information. (AKC - 2008/05/18)
- The new configure option "--disable-sharedlib-rpath" disables
embedding the '-Wl,-rpath' information into executables when
shared libraries are produced, and instead solely relies on the
information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and
Libtool 2.2.2 (MAM - 2008/05/01)
Source code distribution
========================
Library
-------
- None
Parallel Library
----------------
- None
Tools
-----
- h5repack: Reinstated the -i and -o command line flags to specify
input and output files. h5repack now understands both the old
syntax (with -i and -o) and the new syntax introduced in Release
1.8.0. (PVN - 2008/05/23)
- h5dump: Added support for external links, displaying the object that
an external link points to. (PVN - 2008/05/12)
- h5dump: Added an option, -m, to allow user-defined formatting in the
output of floating point numbers. (PVN - 2008/05/06)
- h5dump, in output of the -p option: Added effective data compression
ratio to the dataset storage layout output when a compression filter
has been applied to a dataset. (PVN - 2008/05/01)
F90 API
------
New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were
added. See "Release 1.8.1 (current release) versus Release 1.8.0" in
the document "HDF5 Software Changes from Release to Release"
(http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the
complete list of the new APIs.
C++ API
------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- Both serial and parallel HDF5 are supported for the Red Storm machine
which is a Cray XT3 system.
- The Fortran library will work correctly if compiled with the -i8
flag. This has been tested with the g95, PGI and Intel Fortran
compilers.
Bug Fixes since HDF5-1.8.0
==========================
Configuration
-------------
- None
Source code distribution
========================
Library
-------
- Chunking: Chunks greater than 4GB are disallowed.
(QAK - 2008/05/16)
- Fixed the problem with searching for a target file when following
an external link. The search pattern will depend on whether the
target file's pathname is an absolute or a relative path.
Please see the H5Lcreate_external description in the "HDF5
Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html).
(VC - 2008/04/08)
- Fixed possible file corruption bug when encoding datatype
descriptions for compound datatypes whose size was between
256 and 511 bytes and the file was opened with the "use the
latest format" property enabled (with H5Pset_libver_bounds).
(QAK - 2008/03/13)
- Fixed bug in H5Aget_num_attrs() routine to correctly handle an
invalid location identifier. (QAK - 2008/03/11)
Parallel Library
----------------
- None
Tools
-----
- Fixed bug in h5diff that prevented datasets and attributes with
variable-length string elements from comparing correctly.
(QAK - 2008/02/28)
- Fixed bug in h5dump that caused binary output to be made only for
the first dataset, when several datasets were requested.
(PVN - 2008/04/07)
F90 API
------
- The h5tset(get)_fields subroutines were missing the parameter to
specify a sign position; fixed. (EIP - 2008/05/23)
- Many APIs were fixed to work with the 8-byte integers in Fortran vs.
4-byte integers in C. This change is trasparent to user applications.
C++ API
------
- The class hierarchy was revised to address the problem reported
in bugzilla #1068, Attribute should not be derived from base
class H5Object. Classes AbstractDS was moved out of H5Object.
Class Attribute now multiply inherits from IdComponent and
AbstractDs and class DataSet from H5Object and AbstractDs.
In addition, data member IdComponent::id was moved into subclasses:
Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
(BMR - 2008/05/20)
- IdComponent::dereference was incorrect; it was changed from:
void IdComponent::dereference(IdComponent& obj, void* ref)
to:
void H5Object::dereference(H5File& h5file, void* ref)
void H5Object::dereference(H5Object& obj, void* ref)
(BMR - 2008/05/20)
- Revised Attribute::write and Attribute::read wrappers to handle
memory allocation/deallocation properly. (bugzilla 1045)
(BMR - 2008/05/20)
Platforms Tested
================
The following platforms and compilers have been tested for this release.
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
(red storm) ftn (pgf90) 7.1-4
CC (pgCC) 7.1-4
mpicc 1.0.2
mpif90 1.0.2
FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.1 20080123
g++ 4.2.1 20080123
gfortran 4.2.1 20070620
FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.1 20080123
g++ 4.2.1 20080123
gfortran 4.2.1 20080123
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
F90 MIPSpro 7.4.4m
C++ MIPSpro cc 7.4.4m
Linux 2.6.9 (RHEL4) Intel 10.0 compilers
(abe.ncsa.uiuc.edu)
Linux 2.4.21-47 gcc 3.2.3 20030502
(osage)
Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3)
(kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, ifort, icpc)
Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
(smirom) g95 (GCC 4.0.3)
PGI 7.1-6 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, ifort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
(cobalt) SGI MPI
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 cc: Sun C 5.8
(linew) f90: Sun Fortran 95 8.2
CC: Sun C++ 5.8
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) gcc 3.2.2 20030222
Intel(R) C++ Version 9.0
Intel(R) Fortran Compiler Version 9.0
IA-64 Linux 2.4.21.SuSE_309.tg1 ia64
(NCSA tg-login) gcc 3.2.2
Intel(R) C++ Version 8.1
Intel(R) Fortran Compiler Version 8.1
mpich-gm-1.2.6..14b-intel-r2
Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) gcc 3.4.6 20060404
Intel(R) C++ Version 10.0
Intel (R) Fortran Compiler Version 10.0
mvapich2-0.9.8p2patched-intel-ofed-1.2
Windows XP Visual Studio .NET
Visual Studio 2005 w/ Intel Fortran 9.1
Cygwin(native gcc compiler and g95)
MinGW(native gcc compiler and g95)
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
Windows Vista Visual Studio 2005
MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
GNU Fortran (GCC) 4.3.0 20070810
G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
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
<blank> = testing incomplete on this feature or platform
Platform C F90 F90 C++ zlib SZIP
parallel parallel
SunOS5.10 64-bit n y n y y y
SunOS5.10 32-bit n y n y y y
IRIX64_6.5 64-bit n y y y y y
IRIX64_6.5 32-bit n n n n y y
Windows XP n y(15) n(15) y y y
Windows XP x64 n y(15) n(15) y y y
Windows Vista n n n y y y
Mac OS X 10.5 Intel n y n y y y
FreeBSD 4.11 n n n y y y
RedHat EL3 W (3) y(1) y(10) y(1) y y y
RedHat EL3 W Intel (3) n y n y y n
RedHat EL3 W PGI (3) n y n y y n
SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y
SuSe x86_64 Int (3,12) n y(13) n y y n
SuSe x86_64 PGI (3,12) n y(8) n y y y
Linux 2.4 Xeon C
Lustre Intel (3,6) n y n y y n
Linux 2.6 SuSE ia64 C
Intel (3,7) y y y y y n
Linux 2.6 SGI Altix
ia64 Intel (3) y y y y y y
Linux 2.6 RHEL C
Lustre Intel (5) y(4) y y(4) y y n
Cray XT3 2.0.41 y y y y y n
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.10 64-bit y y y y
Solaris2.10 32-bit y y y y
IRIX64_6.5 64-bit y y n y
IRIX64_6.5 32-bit y dna y y
Windows XP y y(15) y y
Windows XP x64 y y(15) y y
Windows Vista y n n y
Mac OS X 10.3 y n
FreeBSD 4.11 y n y y
RedHat EL3 W (3) y y(10) y y
RedHat EL3 W Intel (3) y y y n
RedHat EL3 W PGI (3) y y y n
SuSe x86_64 W GNU (3,12) y y y y
SuSe x86_64 W Int (3,12) y y y n
SuSe x86_64 W PGI (3,12) y y y n
Linux 2.4 Xeon C
Lustre Intel (6) y y y n
Linux 2.4 SuSE
ia64 C Intel (7) y y y n
Linux 2.4 SGI Altix
ia64 Intel y n
Linux 2.6 RHEL C
Lustre Intel (5) y y y n
Cray XT3 2.0.41 n n n n n
Notes: (1) Using mpich2 1.0.6.
(2) Using mpich2 1.0.7.
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(4) Using mvapich2 0.9.8.
(5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
(8) pgf90
(9) With Compaq Visual Fortran 6.6c compiler.
(10) With PGI and Absoft compilers.
(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) Using Visual Studio 2005 or Cygwin
(16) Not tested for this release.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
message, "yod allocation delayed for node recovery". This interferes with
test suites that do not expect seeing this message. See the section of "Red
Storm" in file INSTALL_parallel for a way to deal with this problem.
AKC - 2008/05/28
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
expected to fail and exit with a non-zero code but the yod command does
not propagate the exit code of the executables. Yod always returns 0 if it
can launch the executable. The test suite shell expects a non-zero for
this particular test, therefore it concludes the test has failed when it
receives 0 from yod. To bypass this problem for now, change the following
lines in the tools/h5ls/testh5ls.sh.
======== Original =========
# The following combination of arguments is expected to return an error message
# and return value 1
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Skip the test =========
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== end of bypass ========
AKC - 2008/05/28
* We have discovered two problems when running collective IO parallel HDF5
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
Linux cluster at NCSA.
Under some complex selection cases:
1) MPI_Get_element returns the wrong value.
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
data may be generated.
These issues arise only when turning on collective IO with chunking storage
with some complex selections. We have not found these problems on other
MPI-IO compilers. If you encounter these problems, you may use independent
IO instead.
To avoid this behavior, change the following line in your code
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
to
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
KY - 2007/08/24
* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
tests failed with MPI-IO file locking message. AKC - 2007/6/25
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
use -mp -O1 compilation flags to build the libraries. A higher level of
optimization causes failures in several HDF5 library tests.
* For LLNL, uP: both serial and parallel tests pass.
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
ubgl: Serial tests pass but parallel tests fail.
* Configuring with --enable-debug=all produces compiler errors on most
platforms: Users who want to run HDF5 in debug mode should use
--enable-debug rather than --enable-debug=all to enable debugging
information on most modules.
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
double to (unsigned) long long and from (unsigned) long long to long double.
* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
optimization flag.
* On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter
supports only the IEEE standard for floating-point data; it cannot be applied
to HDF5 data generated on VAX.
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
the testh5dumpxml.sh script) is misinterpereted by the operating system
and causes an error.
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
the application asks to do collective IO, we have found that when using 4
processors, a simple collective write will sometimes be hung. This can be
verified with t_mpi test under testpar.
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
MPI derived datatype code will work. However, the user should increase
the value of the MPI_TYPE_MAX environment variable to some appropriate value
to use collective irregular selection code. For example, the current
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
There was a bug in the calculation of the Fletcher32 checksum in the
library before v1.6.3; the checksum value was not 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 was no longer the same as
before on little-endian system. Library releases after 1.6.4 can still read
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
SLU - 2005/6/30
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
Opteron processor, there is 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.
* 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",
but HDF5 does not use sockets. This failure is due to problems with the
poe command trying to set up the debug socket. To resolve this problem,
check to see 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. First, ask your system administrator to clean them out.
Lastly, request IBM to provide a means to run poe without the debug socket.
* 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 platforms for serial mode. The parallel mode works fine with
this option.
It is suggested that you do not use this option on these platforms
during configuration.
* With the gcc 2.95.2 compiler, HDF5 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 ./dsets tests fail on 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.
* Not all platforms behave correctly with Szip's shared libraries. Szip is
disabled in these cases, and a message is relayed at configure time. Static
libraries should be working on all systems that support Szip and should be
used when shared libraries are unavailable.
There is also a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* On some platforms that use Intel and Absoft compilers to build the HDF5
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
and fflush2.f90 complaining about the exit subroutine. Comment out the line
IF (total_error .ne. 0) CALL exit (total_error).
* Information about building with PGI and Intel compilers is available in
the INSTALL file sections 4.7 and 4.8.
* 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 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 scipts 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.
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
is turn on. The value of the reference in the destination attriubte is
wrong. This H5Ocopy problem will affect the h5copy tool.
* In the C++ API, it appears that there are bugs in Attribute::write/read
and DataSet::write/read for fixed- and variable-len strings. The problems
are being worked on and a patch will be provided when the fixes are
available.
%%%%1.8.0%%%%
HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008
================================================================================
INTRODUCTION
============
This document describes the differences between the HDF5-1.6.x release series
and HDF5 1.8.0, and contains information on the platforms tested and known
problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt
file in the
release_docs/ directory of the HDF5 source.
Links to the HDF5 1.8.0 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.0 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.0 can be accessed directly at this location:
http://www.hdfgroup.org/HDF5/doc/
New features in 1.8.0, including brief general descriptions of some new
and modified APIs, are described in the "What's New in 1.8.0?" document:
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.0 (current
release) versus Release 1.6.x":
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Removed Feature
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.0
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
HDF5 Release 1.8.0 is a major release with many changes and new features.
New format and interface features discussed in the "What's New in
HDF5 1.8.0" document include the following:
Enhanced group object management
Enhanced attribute management and more efficient meta data handling
Expanded datatype features
Creation order tracking and indexing
Improved meta data caching and cache control
UTF-8 encoding
New I/O filters: n-bit and scale+offset compression
New link (H5L) and object (H5O) interfaces and features
External and user-defined links
New high-level APIs:
HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS)
C++ and Fortran interfaces for older high-level APIs:
H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB)
New and improved tools
And more...
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
New APIs associated with these features, other interface changes
(e.g., ENUM and struct definitions), and new library configuration flags
are listed in the "Release 1.8.0 (current release) versus Release 1.6.x"
section of "HDF5 Software Changes from Release to Release."
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
Compatibility
-------------
Many HDF5 users and user communities have existing applications that
they may wish to port to Release 1.8.0. Alternatively, some users may
wish to take advantage of Release 1.8.0's improved performance without
having to port such applications. To facilitate managing application
compatibility and porting applications from release to release, the HDF
Team has implemented the following features:
Individually-configurable macros that selectively map common
interface names to the old and new interfaces
Library configuration options to configure the macro mappings
Two related documents accompany this release:
"API Compatibility Macros in HDF5" discusses the specifics of the
new individually-configurable macros and library configuration
options.
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
Compatibility Issues" discusses each new feature with regard to
its impact on format compatibility.
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
Referenced documents
--------------------
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
"What's New in HDF5 1.8.0"
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
The "Release 1.8.0 (current release) versus Release 1.6.x "
section in "HDF5 Software Changes from Release to Release"
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
"API Compatibility Macros in HDF5"
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
Compatibility Issues"
Removed Feature
===============
The stream virtual file driver (H5FD_STREAM) have been removed in this
release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream
and the constant H5FD_STREAM.
This virtual file driver will be available at
http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release,
the transition is still in progress; the necessary integration tools may
not be available when HDF5 Release 1.8.0 first comes out.
Support for New Platforms, Languages, and Compilers
===================================================
- Support for Open VMS 7.3 was added.
Bug Fixes since HDF5-1.6.0
==========================
This release contains numerous bug fixes. For details, see the
"Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for
this release.
Platforms Tested
================
The following platforms and compilers have been tested for for this release.
AIX 5.2 (32/64 bit) xlc 8.0.0.11
xlC 8.0
xlf 10.01.0000.0
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.7
FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.1 20080123
g++ 4.2.1 20080123
gfortran 4.2.1 20070620
FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.1 20080123
g++ 4.2.1 20080123
gfortran 4.2.1 20080123
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
F90 MIPSpro 7.4.4m
C++ MIPSpro cc 7.4.4m
Linux 2.6.9 (RHEL4) Intel 10.0 compilers
(abe.ncsa.uiuc.edu)
Linux 2.4.21-47 gcc 3.2.3 20030502
(osage)
Linux 2.6.9-42.0.10 gcc 3.4.6 20060404
(kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, ifort, icpc)
Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
(smirom) g95 (GCC 4.0.3)
PGI 6.2-5 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, iort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
(cobalt) SGI MPI
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 cc: Sun C 5.8
(linew) f90: Sun Fortran 95 8.2
CC: Sun C++ 5.8
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) gcc 3.2.2 20030222
Intel(R) C++ Version 9.0
Intel(R) Fortran Compiler Version 9.0
IA-64 Linux 2.4.21.SuSE_292.til1 ia64
(NCSA tg-login) gcc 3.2.2
Intel(R) C++ Version 8.1
Intel(R) Fortran Compiler Version 8.1
mpich-gm-1.2.5..10-intel-r2
Windows XP Visual Studio .NET
Visual Studio 2005 w/ Intel Fortran 9.1
Cygwin(native gcc compiler and g95)
MinGW(native gcc compiler and g95)
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
Windows Vista Visual Studio 2005
MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD
HP Fortran V7.6-3276
Compaq C++ V6.5-004
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
<blank> = testing incomplete on this feature or platform
Platform C F90 F90 C++ zlib SZIP
parallel parallel
SunOS5.8 64-bit n y n y y y
SunOS5.8 32-bit n y n y y y
SunOS5.10 64-bit y(1) y n y y y
SunOS5.10 32-bit y(1) y n y y y
IRIX64_6.5 64-bit n y y y y y
IRIX64_6.5 32-bit n n n n y y
AIX-5.2 32-bit y y y y y y
AIX-5.2 64-bit y y y y y y
Windows XP n y(15) n(15) y y y
Windows XP x64 n y(15) n(15) y y y
Windows Vista n n n y y y
Mac OS X 10.4 PowerPC n n
Mac OS X 10.4 Intel n y n y y y
FreeBSD 4.11 n n n y y y
RedHat EL3 W (3) y(1a) y(10) y(1a) y y y
RedHat EL3 W Intel (3) n y n y y n
RedHat EL3 W PGI (3) n y n y y n
SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y
SuSe x86_64 Int (3,12) n y(13) n y y n
SuSe x86_64 PGI (3,12) n y(8) n y y y
Linux 2.4 Xeon C
Lustre Intel (3,6) n y n y y n
Linux 2.6 SuSE ia64 C
Intel (3,7) y y y y y n
Linux 2.6 SGI Altix
ia64 Intel (3) y y y y y y
Alpha OpenVMS 7.3.2 n y n y n n
Platform Shared Shared Shared static- Thread-
C libs F90 libs C++ libs exec safe
Solaris2.8 64-bit y y y x y
Solaris2.8 32-bit y y y x y
Solaris2.10 64-bit y x y
Solaris2.10 32-bit y x y
IRIX64_6.5 64-bit y y n y y
IRIX64_6.5 32-bit y dna y y y
AIX-5.2 & 5.3 32-bit n n n y n
AIX-5.2 & 5.3 64-bit n n n y n
Windows XP y y(15) y y y
Windows XP x64 y y(15) y y y
Windows Vista y n n y y
Mac OS X 10.3 y y n
FreeBSD 4.11 y n y y y
RedHat EL3 W (3) y y(10) y y y
RedHat EL3 W Intel (3) y y y y n
RedHat EL3 W PGI (3) y y y y n
SuSe x86_64 W GNU (3,12) y y y y y
SuSe x86_64 W Int (3,12) y y y y(14) n
SuSe x86_64 W PGI (3,12) y y y y(14) n
Linux 2.4 Xeon C
Lustre Intel (6) y y y y n
Linux 2.4 SuSE
ia64 C Intel (7) y y y y n
Linux 2.4 SGI Altix
ia64 Intel y y n
Alpha OpenVMS 7.3.2 n n n y n
Notes: (1) Using mpich 1.2.6.
(1a) Using mpich2 1.0.6.
(2) Using mpt and mpich 1.2.6.
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel
compilers
(8) pgf90
(9) With Compaq Visual Fortran 6.6c compiler.
(10) With PGI and Absoft compilers.
(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) Using Visual Studio 2005 or Cygwin
(16) Not tested for this release.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* We have discovered two problems when running collective IO parallel HDF5
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
Linux cluster at NCSA.
Under some complex selection cases:
1) MPI_Get_element returns the wrong value.
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
data may be generated.
These issues arise only when turning on collective IO with chunking storage
with some complex selections. We have not found these problems on other
MPI-IO compilers. If you encounter these problems, you may use independent
IO instead.
To avoid this behavior, change the following line in your code
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
to
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
KY - 2007/08/24
* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
tests failed with MPI-IO file locking message. AKC - 2007/6/25
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
use -mp -O1 compilation flags to build the libraries. A higher level of
optimization causes failures in several HDF5 library tests.
* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass
when run against the parallel library; the parallel tests also pass, but
with lots of non-fatal error messages.
* For LLNL, uP: both serial and parallel tests pass.
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
ubgl: Serial tests pass but parallel tests fail.
* On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with
Attributes" test.
* Configuring with --enable-debug=all produces compiler errors on most
platforms: Users who want to run HDF5 in debug mode should use
--enable-debug rather than --enable-debug=all to enable debugging
information on most modules.
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
double to (unsigned) long long and from (unsigned) long long to long double.
* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
optimization flag.
* On VAX, the Scaleoffset filter is not supported. The filter cannot be
applied to HDF5 data generated on VAX. The Scaleoffset filter only supports
the IEEE standard for floating-point data.
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
the testh5dumpxml.sh script) is misinterpereted by the operating system
and causes an error.
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
the application asks to do collective IO, we have found that when using 4
processors, a simple collective write will sometimes be hung. This can be
verified with t_mpi test under testpar.
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
MPI derived datatype code will work. However, the user should increase
the value of the MPI_TYPE_MAX environment variable to some appropriate value
to use collective irregular selection code. For example, the current
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
with the v1.6.2 library or before when the 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 was not 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 was no longer the same as
before on little-endian system. Library releases after 1.6.4 can still read
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
SLU - 2005/6/30
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
Opteron processor, there is 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.
* 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",
but HDF5 does not use sockets. This failure is due to problems with the
poe command trying to set up the debug socket. To resolve this problem,
check to see 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. First, ask your system administrator to clean them out.
Lastly, request IBM to provide a means to run poe without the debug socket.
* 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 do not use this option on these platforms
during configuration.
* With the gcc 2.95.2 compiler, HDF5 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 ./dsets tests fail on 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.
* Not all platforms behave correctly with Szip's shared libraries. Szip is
disabled in these cases, and a message is relayed at configure time. Static
libraries should be working on all systems that support Szip and should be
used when shared libraries are unavailable.
There is also a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* On some platforms that use Intel and Absoft compilers to build the HDF5
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
and fflush2.f90 complaining about the exit subroutine. Comment out the line
IF (total_error .ne. 0) CALL exit (total_error).
* Information about building with PGI and Intel compilers is available in
the INSTALL file sections 4.7 and 4.8.
* 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 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 scipts 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
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.
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
is turn on. The value of the reference in the destination attriubte is
wrong. This H5Ocopy problem will affect the h5copy tool.
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