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hdf5/release_docs/RELEASE.txt
Jonathan Kim a9a3f22e78 [svn-r19401] Purpose: 
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object

Description:
 Merged from hdf5 trunk (r19400).
 Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.

Tested:
 jam, amani
2010-09-16 13:09:59 -05:00

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HDF5 version 1.8.5-snap5 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.5 and
HDF5 1.8.5-*, and contains information on the platforms tested and
known problems in HDF5-1.8.5-*.
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 1.8.5 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.5 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.5 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 1.8.5 (current
release) versus Release 1.8.3":
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, Languages, and Compilers
- Bug Fixes since HDF5-1.8.5
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- Changed configure default setting to --disable-production (was
--enable-production). This affects all unoffical releases such as
snapshot releases. It will be set to --enable-production for all
official releases. (AKC - 2010/05/28)
Library
-------
- Added support for threadsafety on windows using the windows threads
library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a
windows platform to enable this functionality. This is supported on
Windows Vista and newer Windows operating systems. (MAM - 2010/09/10)
- H5Tset_order and H5Tget_order now support all data types. A new byte
order H5T_ORDER_MIXED has been added specifically for compound datatype
and its derived type. Please see bug #1934. (SLU - 2010/8/23)
- Improved performance of metadata I/O by changing the default algorithm
to perform I/O from all processes (instead of just process 0) when using
parallel I/O drivers. (QAK - 2010/07/19)
- Improved performance of I/O on datasets with the same shape, but
different rank. (QAK - 2010/07/19)
- Improved performance of the chunk cache by avoiding unnecessary b-tree
lookups of chunks already in cache. (NAF - 2010/06/15)
Parallel Library
----------------
- None
Tools
-----
- h5ls: Add new flag --no-dangling-links. (refer to --help for details)
(JKM - 2010/06/15)
- h5ls: Add new flag --follow-symlinks. (refer to --help for details)
(JKM - 2010/05/25)
High-Level APIs
---------------
- None
F90 API
-------
- None
C++ API
-------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- Sun C and C++ 5.10 and Sun Fortran 95 8.4.
Bug Fixes since HDF5-1.8.5
==========================
Configuration
-------------
- Removed recognition of the parallel compilers of LAM(hcc) and
ChMPIon(cmpicc) since we have no access to these two MPI implementations
and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921)
- PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
applications startup command as defined in the MPI-2 definition, section
4.1. (AKC - 2010/06/11 - Bug 1921)
Library
-------
- Fixed a bug that could occur when getting information for a new-style
group that was previously opened through a file handle that was later
closed. (NAF - 2010/09/15)
- Added define check in H5public.h if stdint.h is supported by the C++
compiler. This define is only available on Windows with VS2010 and using
CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
- When a mandatory filter failed to write data chunks, the dataset
couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure. (SLU - 2010/09/08)
- H5Eset_current_stack now also closes the error stack to be set as the
default. This is to avoid a potential problem (Bug 1799).
(SLU - 2010/09/07)
- Corrected situation where 1-D chunked dataset could get created by an
application without calling H5Pset_chunk(). H5Pset_chunk is now
required for creating all chunked datasets. (QAK - 2010/09/02)
- Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24)
- Fixed the bug in the filter's public CAN_APPLY function. The return
value should be htri_t not herr_t (Bug #1239). (SLU - 2010/08/05)
- Fixed a bug in the direct I/O driver that could render files with certain
kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28)
- valgrind reported an error of copying data to itself when a new attribute
is written (Bug #1956). I fixed it by taking out the memcpy step in the
attribute code. (SLU - 2010/07/28)
- Corrected various issues in the MPI datatype creation code which could
cause resource leaks or incorrect behavior (and may improve the
performance as well). (QAK - 2010/07/19)
- Fixed a bug that could cause file corruption when using non-default sizes
of addresses and/or lengths. This bug could also cause uncorrupted files
with this property to be unreadable. This bug was introduced in 1.8.5.
(NAF - 2010/07/16 - Bug 1951)
Parallel Library
----------------
- None
Tools
-----
- Fixed to compare member objects and groups recursively when two
files or groups are specified to be compared. Bug#1975
(JKM 2010/9/16)
- Make h5repack be able to convert a layout to COMPACT for small size
dataset as default. bug#1896 (JKM 2010/09/15)
- Change h5ls not to manipulate special characters in object name or
attribute name for smart display. (JKM 2010/06/28 - Bug 1784)
F90 API
------
- None
C++ API
------
- None
High-Level APIs:
------
- None
Fortran High-Level APIs:
------
- None
Platforms Tested
================
The following platforms and compilers have been tested for this release.
AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4
(LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4
xlf 9.1.0.9, 10.1.0.9, 11.1.0.7
mpcc_r 7.0.0.9
mpxlf_r 09.01.0000.0008
AIX 6.1 xlc 10.1.0.6
(NCSA BP) xlC 10.1.0.6
xlf 12.1.0.7
Cray XT3 (2.1.56) cc (pgcc) 10.0-0
(SNL red storm) ftn (pgf90) 10.0-0
CC (pgCC) 10.0-0
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.3.4 20090419
g++ 4.3.4 20090419
gfortran 4.3.4 20090419
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.1 20090421
g++ 4.4.1 20090421
gfortran 4.4.1 20090421
Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2
#1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
(jam) GNU Fortran (GCC) 4.1.2 20080704
(Red Hat 4.1.2-46)
PGI C, Fortran, C++ 7.2-1 32-bit
PGI C, Fortran, C++ 8.0-1 32-bit
Intel(R) C Compiler for 32-bit
applications, Versions 10.1, 11.0
Intel(R) C++ Compiler for 32-bit
applications, Version 10.1, 11.0
Intel(R) Fortran Compiler for 32-bit
applications, Version 10.1, 11.0
Absoft 32-bit Fortran 95 10.0.7
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
(kagiso) MPICH mpich2-1.0.8 compiled with
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704
x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
(amani) tested for both 32- and 64-bit binaries
Intel(R) C, C++, Fortran Compilers for
applications running on Intel(R) 64,
Versions 11.1.
PGI C, Fortran, C++ Version 9.0-4
for 64-bit target on x86-64
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
MPICH mpich2-1.0.8 compiled with
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
GNU Fortran (GCC) 4.1.2 20080704
(Red Hat 4.1.2-46)
Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074
SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074
(cobalt) SGI MPI 1.38
SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09
(linew) Sun WorkShop 6 update 2 Fortran 95 8.3
Patch 127000-07
Sun WorkShop 6 update 2 C++ 5.9
Patch 124863-16 2009/09/15
Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404
92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026
perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026
(abe) Open MPI 1.2.2
MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
compiled with icc v10.0.026 and ifort 10.0.026
Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
SMP x86_64 GNU/Linux applications running on Intel(R) 64,
(SNL Glory) Versions 11.1.
Windows XP Visual Studio 2008 w/ Intel Fortran 11.1
Cygwin(1.7.5 native gcc(4.3.4) compiler and gfortran)
Windows XP x64 Visual Studio 2008 w/ Intel Fortran 11.1
Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1
Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1
MAC OS 10.5.6 (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)
Intel C, C++ and Fortran compilers 10.1
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not tested in this release
C = Cluster
W = Workstation
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
Solaris2.10 32-bit n y n y y y
Solaris2.10 64-bit n y n y y y
Windows XP n y(4) n(4) y y y
Windows XP x64 n y(4) n(4) y y y
Windows Vista n y(4) n(4) y y y
Windows Vista x64 n y(4) n(4) y y y
Mac OS X 10.5 Intel n y n y y y
AIX 5.3 32- and 64-bit n y n y y n
AIX 6.1 32- and 64-bit n y n y y n
FreeBSD 6.3-STABLE 32&64 bit n y n y y y
RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y
RedHat EL5 2.6.18-128 i686 Intel W n y n y y n
RedHat EL5 2.6.18-128 i686 PGI W n y n y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
SuSe Linux 2.4.21 ia64 Intel C y y y y y n
Cray XT3 2.1.56 y y y y y n
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.10 32-bit y y y y
Solaris2.10 64-bit y y y y
Windows XP y y(4) y n
Windows XP x64 y y(4) y n
Windows Vista y y(4) y n
Windows Vista x64 y y(4) y n
Mac OS X 10.5 y n y n
AIX 5.3 32- and 64-bit n n n n
AIX 6.1 32- and 64-bit n n n n
FreeBSD 6.3-STABLE 32&64 bit y n y y
RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y
RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
RedHat EL5 2.6.18-128 i686 Intel W y y y n
RedHat EL5 2.6.18-128 i686 PGI W y y y n
SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
SuSe Linux 2.6.16 x86_64 Intel W y y y n
SuSe Linux 2.6.16 x86_64 PGI W y y y n
SuSe Linux 2.6.16 SGI Altix ia64 C y n
RedHat EL4 2.6.18 Xeon Lustre C y y y n
SuSe Linux 2.4.21 ia64 Intel C y y y n
Cray XT3 2.1.56 n n n n
(1) Fortran compiled with g95.
(2) With PGI and Absoft compilers.
(3) With PGI compiler for Fortran.
(4) Using Visual Studio 2008 (Cygwin shared libraries are not supported)
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* The library's test dt_arith.c showed a compiler's rounding problem on
Cygwin when converting from unsigned long long to long double. The
library's own conversion works fine. We defined a macro for Cygwin to
skip this test until we can solve the problem. Please see bug #1813.
SLU - 2010/5/5
* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
structure H5FD_class_t changed in 1.8. There is new parameter added to
get_eoa and set_eoa callback functions. A new callback function
get_type_map was added in. The public function H5FDrealloc was taken
out in 1.8. The problem only happens when users define their own driver
for 1.6 and try to plug in 1.8 library. Because there's only one user
complaining about it, we (Elena, Quincey, and I) decided to leave it as
it is (see bug report #1279). Quincey will make a plan for 1.10.
SLU - 2010/2/2
* MinGW has a missing libstdc++.dll.a library file and will not successfully link
C++ applications/tests. Do not use the enable-cxx configure option. Read all of
the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11
* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
The error is due to insufficient memory requested. Request a large amount
of runtime memory by setting the following environment variable for more
memory.
LDR_CNTRL=MAXDATA=0x20000000@DSA
AKC - 2009/10/31
* The PathScale MPI implementation, accessing a Panasas file system, would
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
existing. This is due to the MPI_File_open() call failing if the amode has
the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
with MPI IO. CMC - 2009/04/28
* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
AKC - 2009/04/20
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
are expected to fail and should 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. Skip all the "failing" test for now
by changing them as following.
======== Original tools/h5ls/testh5ls.sh =========
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Change to ===============================
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
==================================================
======== Original tools/h5copy/testh5copy.sh =========
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
H5LSTEST $FILEOUT
======== Change to ===============================
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
echo SKIP H5LSTEST $FILEOUT
==================================================
AKC - 2008/11/10
* 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
* 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.
* 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.
* 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
* 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 will only statically link libraries
if the static version of that library is present. If only the shared version
of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
for example, only have shared versions), the flag should still result in a
successful compilation, but note that the installed executables will not be
fully static. Thus, the only guarantee on these systems is that the
executable is statically linked with just the HDF5 library.
* There is also a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which
is the default on that system) does not work properly, and results in
failures during make check (in a static build) and make installcheck (during
a shared build). This appears to be a compiler optimization problem.
Reducing optimization by setting CFLAGS to -O1 or below resolves the issue.
Alternatively, using a newer version of the compiler (11.0) also works as
intended. MAM - 2010/06/01
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