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|
HDF5 version 1.6.8-snap0 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.8 and
HDF5-1.6.8-snap*.
It contains information on the platforms tested and known problems in
HDF5-1.6.8-snap*. For more details, check the HISTORY.txt file in
the HDF5 source.
HDF5 documentation can be found in the distributed release source code
in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Documentation for the current release in the HDF5 Release 1.6.x series is
also on the HDF web site:
http://hdfgroup.org/HDF5/doc1.6/
For more information, see the HDF5 home page:
http://hdfgroup.org/products/hdf5/
If you have any questions or comments, please see the HDF Support page
for a list of available resources:
http://hdfgroup.org/services/support.html
CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.8
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
- Add description here. Do not exceed 80 characters for a line
EIP - 2008/11/12 (year/month/day format)
Library:
--------
Parallel Library:
-----------------
Tools:
------
- h5dump: binary output defaults to NATIVE with -b optionally accepting
the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/11/14)
F90 API:
--------
C++ API:
--------
Support for New Platforms, Languages and Compilers
==================================================
Bug Fixes since HDF5-1.6.8 Release
==================================
Library
-------
Configuration
-------------
- h5perf will now get installed during 'make install'.
MAM - 2008/11/17
Performance
-------------
Tools
-----
Documentation
-------------
F90 API
-------
C++ API
-------
Documentation
=============
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ (start with index.html) or on the
THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Online documentation for the current release in the HDF5 Release 1.6.x
series can be found on the THG web site:
http://hdfgroup.org/HDF5/doc1.6/
A listing of interface changes from release to release can be found
in the document "HDF5 Software Changes from Release to Release":
http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html
Since the stream I/O driver is not included in this release, the
functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream
ENUM value H5FD_STREAM have been removed from the documentation.
Platforms Tested
================
AIX 5.3 xlc 7.0.0.8
xlf 09.01.0000.0008
xlC 7.0.0.8
mpcc_r 7.0.0.8
mpxlf_r 09.01.0000.0008
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
(duty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.5 20080702
g++ 4.2.5 20080702
gfortran 4.2.5 20080702
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.2.5 20080702
g++ 4.2.5 20080702
gfortran 4.2.5 20080702
IRIX64 6.5 MIPSpro cc 7.4.4m
(ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only)
C++ MIPSpro cc 7.4.4m
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007)
(kagiso) PGI C, Fortran, C++ 7.2-1 32-bit
Intel(R) C Compiler for 32-bit
applications, Version 10.1
Intel(R) C++ Compiler for 32-bit
applications, Version 10.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 10.1
Absoft 32-bit Fortran 95 10.0.4
MPICH mpich-1.2.7 compiled with
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
MPICH mpich2-1.0.6p1 compiled with
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025
SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025
(ucar hir1)
Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 10.1.013
SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 10.1.013
(smirom) PGI C, Fortran, C++ Version 7.2-1
for 64-bit target on x86-64
MPICH mpich-1.2.7 compiled with
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
MPICH mpich2-1.0.7 compiled with
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
tested for both 32- and 64-bit binaries
Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
(cobalt) SGI MPI 1.16
SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8
(linew) Sun WorkShop 6 update 2 Fortran 95 8.2
Sun WorkShop 6 update 2 C++ 5.8
Patch 121019-06
Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) Intel(R) C++ Version 10.0.026
Intel(R) Fortran Compiler Version 10.0.026
Open MPI 1.2.2
MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
compiled with icc v10.0.026 and ifort 10.0.026
IA-64 Linux 2.4.21-309.tg1 #1 SMP
ia64 gcc (GCC) 3.2.2
(NCSA tg-login) Intel(R) C++ Version 8.1.037
Intel(R) Fortran Compiler Version 8.1.033
mpich-gm-1.2.7p1..16-intel-8.1.037-r1
Windows XP Visual Studio 6.0
Visual Studio .NET (with Intel Fortran 9.1)
Visual Studio 2005 (with Intel Fortran 9.1)
cygwin (gcc 3.4.4)
Windows Vista Visual studio 2005
Mac OS X Intel 10.5.4 i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
g95 0.91
Supported Configuration Features Summary
========================================
Key: y = Tested and supported
n = Not supported or not tested in this release
C = Cluster
W = Workstation
( ) = Footnote appears below second table
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 n y y
IRIX64_6.5 32-bit n n n n y y
IRIX64_6.5 64-bit n y n n y y
WinXP Visual Studio 6.0 n n n y y y
WinXP CYGWIN n n n y y y
WinXP 2005 n y n y y y
WinXP .Net n y n y y y
WinVista 2005 n n n y y y
Mac OS X 10.4.10 n y n y y y
AIX 5.3 32-bit n y n y y n
FreeBSD 6.3 32- and 64-bit n n n y y y
RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
RedHat EL4 2.6.9-42 i686 Intel W n y n y y n
RedHat EL4 2.6.9-42 i686 PGI W n y n y y n
SuSE Linux 2.6.16 x86_64 GNU (1) W y y n 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 n
RedHat EL 4 2.6.9 Xeon Lustre C n y n y y y
SuSE Linux 2.4.21 ia64 C y y y y y y
SuSe Linux 2.6.16 SGI Altix ia64 C n y n y y y
Platform Shared static- Thread-
libraries(4) exec safe
Solaris2.10 32- and 64-bit y n y
IRIX64_6.5 32-bit y n y
IRIX64_6.5 64-bit y n y
WinXP Visual Studio 6.0 y n n
WinXP CYGWIN y n n
WinXP 2005 y n n
WinXP .Net y n n
WinVista 2005 y n n
Mac OS X 10.4.10 y n n
AIX 5.3 32-bit n n n
FreeBSD 6.3 32- and 64-bit y n n
RedHat EL4 2.6.9-42 i686 GNU (1) W y n y
RedHat EL4 2.6.9-42 i686 Intel W y n n
RedHat EL4 2.6.9-42 i686 PGI W n n n
SuSE Linux 2.6.16 x86_64 GNU (1) W y n y
SuSE Linux 2.6.16 x86_64 Intel W y n n
SuSE Linux 2.6.16 x86_64 PGI W n n n
RedHat EL4 2.6.9 Xeon Lustre C y n n
SuSE Linux 2.4.21 ia64 C y n n
SuSe Linux 2.6.16 SGI Altix ia64 C n n n
Compiler versions for each platform are listed in the "Platforms Tested"
table found elsewhere in this file (RELEASE.txt). Unless otherwise noted,
compilers used are the system compilers.
Footnotes:
(1) Fortran compiled with g95.
Known Problems
==============
* We discovered two problems when running collective IO parallel HDF5 tests
with chunking storage with 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.
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.
To avoid this problem, 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
* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It
does not include the -lmpi properly. This will be fixed in the next
release. AKC - 2007/08/07.
* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared
library, especially for h5repacktst and h52gifgentst, the following (or a
similar) error message may appear:
"523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname
'libh5test.so.1' under any of the filenames .......(bunch of directories)
"
And the testing will fail.
We believe this is a libtool problem. One way to get rid of this is to
add the paths of libh5test.so.1 and libh5.so.1 to the shared library path.
You may do this, under csh:
setenv LD_LIBRARYN32_PATH [full path of HDF5 directory/test/.libs]:[full
path of HDF5 directory/src/.libs]:(existing paths)...
NOTE: This problem ONLY affects the testing of the HDF5 library when you
build from source. It won't affect any applications that would like to link
with the HDF5 shared library since the shared library path needs to be set
anyway. KY - 2007/8/2
* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
"calloc". All other tests passed. This indicates that a dataset using
chunked storage created by serial HDF5 may not work properly with parallel
HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x
calloc". AKC - 2007/7/12.
* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX
6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for
example 120000, in order to pass the complicated collective IO tests inside
the parallel HDF5 library. This is not a problem inside the parallel HDF5
library. You can always set a bigger number on your system. KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version of HDF5
might not be able to be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem. EIP - 2005/09/09
* A 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 (a 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. HDF5 library releases
after 1.6.4 can still read datasets created or rewritten with an HDF5
library of v1.6.2 or before. SLU - 2005/7/8
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but
have a "guard" statement in stdint.h that will #error and skip the rest
of the header file if the C99 option is not used explicitly. Hardsetting
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may also fail with messages like "The socket name is already
in use". HDF5 does not use sockets. This is due to problems of the
poe command trying to set up the debug socket. Check 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. Ask your system
administrator to clean them out. Lastly, request IBM to provide a means
to run poe without the debug socket.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, Windows) where the error messages directed to
"stderr" do not appear in the "right order" with output from stdout.
This is not an error.
* The --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 the IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* Use the --disable-shared configure flag if building with an Absoft Fortran
compiler.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8.
* In LANL QSC, the new cc compiler has problems converting small values of
long long (absolute values less than 1**-308) to double. This triggers
the test/dtypes to report failure in the following test:
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to
10**-308. If -ieee is not used, the converted double values are mostly
0.0, but occasionally appear as 10**-308. This has been reported to the
system staff.
All other tests have passed.
|
