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|
HDF5 version 1.8.12-snap19 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.11 and
HDF5-1.8.12-*, and contains information on the platforms tested and
known problems in HDF5-1.8.12-*.
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 1.8.12 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.12 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.12 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 1.8.12 (current
release) versus Release 1.8.11":
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 HDF5-1.8.11
- Supported Platforms
- Supported Configuration Features Summary
- More Tested Platforms
- Known Problems
New Features
============
Configuration
-------------
- New configuration option added to change the default plugin path.
configure option is --with-default-plugin=location
cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location
HDFFV-8513. (ADB 2013/09/04)
- Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13)
- CMake can now package a compressed examples file, the default for
Windows binaries from HDF Group. (ADB - 2013/07/22)
Library
-------
- None
Parallel Library
----------------
- None
Tools
-----
- h5dump: Added option -N --any_path, which searches the file for paths that
match the search path. HDFFV-7989 (ADB - 2013/08/12).
- h5dump: Added optional arg 0 to -A, which excludes attributes from display.
HDFFV-8134 (ADB - 2013/08/01).
High-Level APIs
---------------
- None
Fortran API
-----------
- None
C++ API
-------
- Added tutorial examples to c++/examples. They can be installed by
"make install-examples" and, in the installed directory, they can be
executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28)
- A new class, H5::H5Location, is added to represent the location concept
in the C library. It is a base class to H5::H5File and H5::H5Ojbect,
whose member functions are moved into H5::H5Location. H5::H5File can
now inherent those functions. As a result, an H5::H5File object can have
an attribute. (BMR - 2013/09/27)
- Added wrappers for H5Rget_obj_type2 to retrieve the type of the object
that an object reference points to. (BMR - 2013/09/27)
H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type)
- Added wrappers for H5Aexist to check whether an attribute exists given
a name. (BMR - 2013/09/27)
bool H5::H5Location::attrExists(const char* name)
bool H5::H5Location::attrExists(const H5std_string& name)
- Added a number of overloaded functions for convenience. (BMR - 2013/09/27)
Support for New Platforms, Languages, and Compilers
===================================================
- None
Bug Fixes since HDF5-1.8.11
===========================
Configuration
-------------
- Modified H5detect.c to scan floating point types for padding bits before
analyzing the type further. This should fix problems with gcc 4.8
(NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500)
- HDF5 rpaths are no longer encoded in the library files when configured
with --disable-sharedlib-rpath. (LRK-2013-09-23 - HDFFV-8276)
Library
-------
- Added const qualifier to source buffer parameters in H5Dgather and
H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/09)
- CMake can now creates *.so.{lt_version} files with the same version as
configure. (ADB - 2013/06/05 HDFFV-8437)
Parallel Library
----------------
- None
Performance
-------------
- None
Tools
-----
- h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04).
- h5dump: Added option -N --any_path, which searches the file for paths that
match the search path. HDFFV-7989 (ADB - 2013/08/12).
- h5dump: Added optional arg 0 to -A, which excludes attributes from display.
HDFFV-8134 (ADB - 2013/08/01).
- h5dump correctly exports subsetted data to a file, using the --output
option. (ADB - 2013/06/07 HDFFV-8447)
- h5cc and other compile scripts now default to linking shared libraries
when HDF5 is configured with the --disable-static option.
(LRK - 2013-09-23 - HDFFV-8141)
F90 API
-------
- None
C++ API
------
- None
High-Level APIs:
------
- None
Fortran High-Level APIs:
------
- None
Testing
-------
- test/big sometimes failed with the message of "file selection+offset not
within extent". This has been fixed. (AKC - 2013/09/28 HDFFV-8271).
- tools/h5diff/testh5diff.sh is run in every "make check", even after it
has passed in the previous run. It should not run again if there is no
code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392)
Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.
AIX 5.3 xlc 10.1.0.5
(NASA G-ADA) xlC 10.1.0.5
xlf90 12.1.0.6
Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP i686 i686 i386 compilers for 32-bit applications;
(jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
Version 4.8.1
PGI C, Fortran, C++ Compilers for 32-bit
applications;
Version 13.7-0
Intel(R) C, C++, Fortran Compiler for 32-bit
applications;
Version 13.1.3 (Build 20130607)
Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
(koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
Version 4.8.1
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 13.7-0
Intel(R) C, C++, Fortran Compilers for
applications running on Intel(R) 64;
Version 13.1.3 (Build 20130607)
Linux 2.6.32-358.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(platypus) Version 4.4.7 20120313
Version 4.8.1
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 13.7-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 13.1.3 (Build 20130607)
Linux 2.6.32-358.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
IBM XL C/C++ V11.1
IBM XL Fortran V13.1
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
Visual Studio 2010 w/ Intel Fortran 12 (cmake)
Visual Studio 2012 w/ Intel Fortran 13 (cmake)
Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
(cmake and autotools)
Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
Visual Studio 2010 w/ Intel Fortran 12 (cmake)
Visual Studio 2012 w/ Intel Fortran 13 (cmake)
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 13 (cmake)
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 13 (cmake)
Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
64-bit gfortran GNU Fortran (GCC) 4.6.2
(fred) Intel C (icc), Fortran (ifort), C++ (icpc)
12.1 Build 20120928
Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1
64-bit gfortran GNU Fortran (GCC) 4.6.2
(duck) Intel icc/icpc/ifort version 13.0.3
Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1
64-bit gfortran GNU Fortran (GCC) 4.6.2
(wren) Intel icc/icpc/ifort version 13.0.3
OpenVMS IA64 V8.4 HP C V7.3-018
(Boeing) HP Fortran V8.2-104939-50H96
HP C++ V7.4-004
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = 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 F2003 parallel
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 64-bit n y/y n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y n y y y
Windows 7 Cygwin n y/n n y y y
Windows 8.1 n y/y n y y y
Windows 8.1 x64 n y/y n y y y
Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y
Mac OS X Lion 10.7.3 64-bit n y/y n y y y
Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y
AIX 5.3 32- and 64-bit n y/n n y y y
CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y
CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y
CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/y n y y y
CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y
OpenVMS IA64 V8.4 n y/n n y y n
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.11 32-bit y y y y
Solaris2.11 64-bit y y y y
Windows 7 y y y y
Windows 7 x64 y y y y
Windows 7 Cygwin n n n y
Windows 8.1 y y y y
Windows 8.1 x64 y y y y
Mac OS X Snow Leopard 10.6.8 64-bit y n y n
Mac OS X Lion 10.7.3 64-bit y n y y
Mac OS X Mountain Lion 10.8.1 64-bit y n y y
AIX 5.3 32- and 64-bit y n n y
CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n
CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
Linux 2.6.32-358.2.1.el6.ppc64 y y y n
OpenVMS IA64 V8.4 n n n n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with
#1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2
(jam) g95 (GCC 4.0.3 (g95 0.94!)
Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with
#1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2
(koala) g95 (GCC 4.0.3 (g95 0.94!)
FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
(loyalty) gcc 4.6.1 20110527
g++ 4.6.1 20110527
gfortran 4.6.1 20110527
FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
(freedom) gcc 4.6.1 20110527
g++ 4.6.1 20110527
gfortran 4.6.1 20110527
Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 x86_64 GNU/Linux
gcc (Debian 4.7.2-5) 4.7.2
GNU Fortran (Debian 4.7.2-5) 4.7.2
(cmake and autotools)
Fedora19 3.11.1-200.fc19.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)
GNU Fortran (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)
(cmake and autotools)
SUSE 12.3 3.7.10-1.16-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
gcc (SUSE Linux) 4.7.2
GNU Fortran (SUSE Linux) 4.7.2
(cmake and autotools)
Ubuntu 13.04 3.8.0-30-generic #44-Ubuntu SMP x86_64 GNU/Linux
gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
GNU Fortran (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
(cmake and autotools)
Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
Known Problems
==============
* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i)
have bugs. They convert data between floating-point numbers and integers.
But the library's default is hard conversion. The user should avoid
explicitly enabling soft conversion between floating-point numbers and
integers. (Issue VMS-8; SLU - 2013/09/19)
* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works
fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5;
SLU 2013/09/19)
* When building using the Cray compilers on Cray machines, HDF5
configure mistakenly thinks the compiler is an intel compiler and
sets the -std=c99 flag which breaks configure on Cray. To build HDF5
properly on a Cray machine, please consult with the instructions in
INSTALL_parallel for building on Hopper.
(MSC - 2013/04/26 - HDFFV-8429)
* The h5dump and h5diff utilities occasionally produce different output
between Linux and Windows systems. This is caused by lower-level library
routines that fail to write fill values to the user's buffer when reading
unallocated chunks from datasets that have a fill value set to
H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of
spurious data values has only been encountered on Windows 32-bit systems.
(Issue HDFFV-8247; JP - 2013/03/27)
* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
complains with this message:
"/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
The reason is that __func__ is a predefined identifier in C99 standard. The
HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
C++ compiler doesn't support __func__, thus fails to compile the C++ test.
But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler
knows this identifier, try to compile the following simple C++ program:
#include<stdio.h>
int main(void)
{
printf("%s\n", __func__);
return 0;
}
(SLU - 2012/11/5)
* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
ports (and probably gcc releases after that).
(QAK - 2012/10/19)
* The following h5dump test case fails in BG/P machines (and potentially other
machines that use a command script to launch executables):
h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
tno-subset.h5
This is due to the embedded spaces in the dataset name being interpreted
by the command script launcher as meta-characters, thus passing three
arguments to h5dump's -d flag. The command passes if run by hand, just
not via the test script.
(AKC - 2012/05/03)
* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
to aprun -np X, because the H5lib_settings.c file was not generated
properly. Not setting those environment variables works, because
configure was able to automatically detect that it's a Cray system
and used the proper launch commands when necessary.
(MSC - 2012/04/18)
* The data conversion test dt_arith.c fails in "long double" to integer
conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal
(3.2.2 on Fedora) doesn't have the problem. Users should lower the
optimization level (-O1 or -O0) by defining CFLAGS in the command line of
"configure" like:
CFLAGS=-O1 ./configure
This will overwrite the library's default optimization level.
(SLU - 2012/02/07 - HDFFV-7829)
This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with
gcc 4.7.2.
* The STDIO VFD does not work on some architectures, possibly due to 32/64
bit or large file issues. The basic STDIO VFD test is known to fail on
64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
10.7.0. The STDIO VFD test has been disabled while we investigate and
a fix should appear in a future release.
(DER - 2011/10/14 - HDFFV-8235)
* h5diff can report inconsistent results when comparing datasets of enum type
that contain invalid values. This is due to how enum types are handled in
the library and will be addressed in a future release.
(DER - 2011/10/14 - HDFFV-7527)
* The links test can fail under the stdio VFD due to some issues with external
links. This will be investigated and fixed in a future release.
(DER - 2011/10/14 - HDFFV-7768)
* After the shared library support was fixed for some bugs, it was discovered
that "make prefix=XXX install" no longer works for shared libraries. It
still works correctly for static libraries. Therefore, if you want to
install the HDF5 shared libraries in a location such as /usr/local/hdf5,
you need to specify the location via the --prefix option during configure
time. E.g, ./configure --prefix=/usr/local/hdf5 ...
(AKC - 2011/05/07 - HDFFV-7583)
* The parallel test, t_shapesame, in testpar/, may run for a long time and may
be terminated by the alarm signal. If that happens, one can increase the
alarm seconds (default is 1200 seconds = 20 minutes) by setting the
environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
(60 minutes). Note that the t_shapesame test may fail in some systems
(see the "While working on the 1.8.6 release..." problem below). If
it does, it will waste more time if $HDF5_ALARM_SECONDS is set
to a larger value.
(AKC - 2011/05/07)
* The C++ and FORTRAN bindings are not currently working on FreeBSD.
(QAK - 2011/04/26)
* Shared Fortran libraries are not quite working on AIX. While they are
generated when --enable-shared is specified, the fortran and hl/fortran
tests fail. We are looking into the issue. HL and C++ shared libraries
should now be working as intended, however.
(MAM - 2011/04/20)
* The --with-mpe configure option does not work with Mpich2.
(AKC - 2011/03/10)
* While working on the 1.8.6 release of HDF5, a bug was discovered that can
occur when reading from a dataset in parallel shortly after it has been
written to collectively. The issue was exposed by a new test in the parallel
HDF5 test suite, but had existed before that. We believe the problem lies with
certain MPI implementations and/or file systems.
We have provided a pure MPI test program, as well as a standalone HDF5
program, that can be used to determine if this is an issue on your system.
They should be run across multiple nodes with a varying number of processes.
These programs can be found at:
http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
(NAF - 2011/01/19)
* 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 - 2010/02/02)
* 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.
(MAM - 2009/11/04)
* 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)
* On an 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.
* 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 - 2005/06/30)
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