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hdf5/release_docs/RELEASE.txt
Quincey Koziol 99e6360f4b [svn-r15491] Description: 
Update release notes for last bug fix.
2008-08-19 14:44:20 -05:00

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HDF5 version 1.9.15 currently under development
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.9.0 and
HDF5 1.9.x snapshot, and contains information on the platforms
tested and known problems in HDF5-1.9.x.
For more details check the HISTORY*.txt files in the HDF5 source.
Links to HDF5 1.9.x source code can be found on THG's development
FTP server at the following location:
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
User documentation for the snapshot can be accessed directly at this location:
http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/
For more information, see the HDF5 home page:
http://www.hdfgroup.org/HDF5/
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
- Known Problems
New Features
============
Configuration:
-------------
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and
Libtool 2.2.2 (MAM - 2008/05/05)
- 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)
Library:
--------
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
Parallel Library:
-----------------
Fortran Library:
----------------
C++ Library:
------------
- These member functions were added as wrapper for H5Rdereference to
replace the incorrect IdComponent::dereference().
void H5Object::dereference(H5File& h5file, void* ref)
void H5Object::dereference(H5Object& obj, void* ref)
In addition, these constructors were added to create the associated
objects by way of dereference:
Attribute(H5Object& obj, void* ref);
Attribute(H5File& file, void* ref);
DataSet(H5Object& obj, void* ref);
DataSet(H5File& file, void* ref);
DataType(H5Object& obj, void* ref);
DataType(H5File& file, void* ref);
Group(H5Object& obj, void* ref);
Group(H5File& obj, void* ref);
(BMR - 2008/08/10)
Tools:
------
- h5dump: added a printing of the compression ratio of uncompressed and compressed
sizes for cases where compression filters are present. (PVN - 2008/05/01)
- h5dump: added an option to allow a user defined formatting string for printf
regarding floating point numbers. (PVN - 2008/05/06)
- h5dump: support for external links, display the object that the external link
points to. (PVN - 2008/05/12)
High-Level APIs:
------
Documentation
-------------
Support for new platforms, languages and compilers.
=======================================
Bug Fixes since HDF5-1.8.0 release
==================================
Library
-------
- Fixed problem where library could cause a segmentation fault when
an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
- Fixed improper shutdown when objects have reference count > 1. The
library now tracks reference count due to the application separately
from that due to internal library routines. (NAF - 2008/08/19)
- Fixed assertion failure caused by incorrect array datatype version.
(NAF - 2008/08/08)
- Fixed an issue where mount point traversal would fail when using
multiple handles for the child. (NAF - 2008/08/07)
- Fixed an issue where mount points were inaccessible when using multiple
file handles for the parent. The mount table is now in the shared
file structure (the parent pointer is still in the top structure).
(NAF - 2008/08/07)
- when an attribute was opened twice and data was written with one of the handles,
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure. SLU - 2008/07/22
- Fixed issue where a group could have a file mounted on it twice.
(QAK - 2008/07/15)
- Fixed the problem with the searching of target file for H5Lcreate_external().
The searching pattern will depend on whether the target file's
pathname is an absolute or a relative path. Please see the description
in the RM for H5Lcreate_external(). (VC - 2008/04/08)
- Fixed possible file corruption bug when encoding datatype
descriptions for compound datatypes whose size was between
256 & 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 handle invalid location
ID correctly. (QAK - 2008/03/11)
Configuration
-------------
Performance
-------------
Tools
-----
- Fixed bug in h5ls that prevented relative group listings (like
"h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
- Fixed bug in h5diff that prevented datasets & attributes with
variable-length string elements from comparing correctly.
(QAK - 2008/02/28)
- h5import bug on Windows w/binary datasets. fread in windows needs a
binary file to be open with 'rb' instead of 'r' otherwise it
terminates execution if an end of file character is found on the
input file. Besides that the binary file generated needs to be open
with 'wb' , otherwise an end of line character is read twice.
(PVN - 2008/02/19)
- 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)
- h5dump: when doing binary output (-b), the stdout printing of attributes
was done incorrectly. Removed printing of attributes when doing binary
output. PVN - 2008/06/05
Documentation
-------------
F90 APIs
--------
C++ APIs
--------
- Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20)
- Fixed bug in PropList::getClassName to use portable HDfree instead
of free. (BMR - 2008/04/20)
- Fixed a design bug which allowed an Attribute object to create/modify
attributes (bugzilla #1068). The API class hierarchy was revised
to address the problem. Classes AbstractDS and Attribute are moved
out of H5Object. Class Attribute now multiply inherits from
IdComponent and AbstractDs and class DataSet from H5Object and
AbstractDs. In addition, the data member IdComponent::id was
moved into subclasses: Attribute, DataSet, DataSpace, DataType,
H5File, Group, and PropList. (BMR - 2008/08/10)
- IdComponent::dereference was incorrect and replaced as described
in "New Features" section.
(BMR - 2008/08/10)
Platforms Tested
================
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, g95 (GCC 4.0.3)
(smirom) PGI 6.2-5 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, iort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1
SMP ia64 Intel(R) C++ Version 9.0
(cobalt) Intel(R) Fortran Itanium(R) Version 9.0
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
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
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
W or C indicates workstation or cluster, respectively.
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 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
AIX-5.2 32-bit y y y y y y
AIX-5.2 64-bit y y y y y y
Cray XT3 (not tested
for this release) n n n n n n
Windows XP n y(3) n(3) y y y
Windows XP x64 n y(3) n(3) 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 6.2 32-bit n n n y y y
FreeBSD 6.2 64-bit
RedHat EL4 2.6.9 i686 GNU W y(2) y(4) y(2) y y y
RedHat EL4 2.6.9 i686 Intel W n y n y y n
RedHat EL4 2.6.9 i686 PGI W n y n y y n
SuSe Linux 2.6.16 x86_64 GNU (5) W y(2) y n y y y
SuSe Linux 2.6.16 x86_64 Int (5) W n y n y n n
SuSe Linux 2.6.16 x86_64 PGI (5) W n y n y n n
RHL9 Linux 2.4 Xeon Lustre Intel C n y n y y n
RHEL3 Linux 2.4 Xeon Intel W n y n n y n
RHEL4 Linux 2.6 Xeon Lustre Int C n y n y y n
SuSE Linux 2.4 ia64 Intel C y(1) y y y y y
SuSe Linux 2.6.5
SGI Altix ia64 Intel C n y n y n 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
SunOS 5.8 32-bit y y y x y
SunOS 5.8 64-bit y y y x y
SunOS 5.10 32-bit y y y x y
SunOS 5.10 64-bit y y y x y
IRIX64_6.5 32-bit y n y x y
IRIX64_6.5 64-bit y y n x y
AIX-5.2 32-bit n n n x n
AIX-5.2 64-bit n n n x n
Cray XT3 (not tested
for this release) n n n x n
Windows XP y y(3) y y y
Windows XP x64 y y(3) y y y
Windows Vista y n n y y
Mac OS X 10.4 Intel Duo y y y x n
FreeBSD 6.2 32-bit y y y x n
FreeBSD 6.2 64-bit y y y x n
RHEL4 2.6.9 i686 GNU W y y(4) y x y
RHEL4 2.6.9 i686 Intel W y y y x n
RHEL4 2.6.9 i686 PGI W y y y x n
SuSE Linux 2.6.16 x86_64 GNU (5) W y y y x y
SuSE Linux 2.6.16 x86_64 Intel(5) W y y y x n
SuSE Linux 2.6.16 x86_64 PGI(5) W y y y x n
RHL9 Linux 2.4 Xeon Lustre Intel C y y y x n
RHEL3 Linux 2.4 Xeon Intel W y n n x n
RHEL4 Linux 2.6 Xeon Lustre Intel C y y y x n
SuSE Linux 2.4 ia64 Intel C y y y x n
SuSe Linux 2.6.5
SGI Altix ia64 Intel C n n n x n
Notes: (1) Using mpich 1.2.6.
(2) Using mpich2 1.0.6.
(3) Using Visual Studio 2005 or Cygwin
(4) With PGI and Absoft compilers.
(5) AMD Opteron x86_64
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* We discovered two problems when running collective IO parallel HDF5 tests
with chunking storage on 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 wrong derived data type and corrupt data
may be generated.
This only happens when turning on collective IO with chunking storage
with some complex selections. We haven't found these problems on other
MPI-IO compilers. If you encounter these problems, you may use Independent IO
instead.
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. Higher level of optimization
causes failures in several HDF5 library tests.
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
shared libraries (tested for 1.8.0-beta2)
* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass
and the parallel tests also pass with lots of non-fatal error messages.
* For LLNL, uP: both serial and parallel pass. Zeus: serial passes but
parallel fails with a known proglem in MPI. ubgl: serial passes but
parallel fails.
* on SUN 5.10 C++ test 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, Scaleoffset filter isn't supported. The filter cannot be applied to
HDF5 data generated on VAX. Scaleoffset filter only supports 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, we found that if more than two processes
contribute no IO and the application asks to do IO with collective, we found
that when using 4 processors, a simple collective write will be hung
sometimes. This can be verified with t_mpi test under testpar.
* On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type
code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment
variable to some certian value in order to use collective irregular selection code.
For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to
200,000 to make the test pass.
* 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 - 2005/6/30
* For the version 6(6.02 and 6.04) of 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.
* 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 mean to run poe without the debug socket.
* The C++ library's tests fails when compiling with PGI C++ compiler. The
workaround until the problem is correctly handled is to use the
flag "--instantiate=local" prior to the configure and build steps, as:
setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
* 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.
* 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 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)
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
* 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 HDF 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 h5copy tool
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