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|
HDF5 version 1.8.4-snap0 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.4 and
HDF5 1.8.4-*, and contains information on the platforms tested and
known problems in HDF5-1.8.4-*.
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 1.8.4 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.4 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.4 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 1.8.4 (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 HDF5-1.8.4
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- None EIP 2009/10/21
Library
-------
- None
Parallel Library
----------------
- None
Tools
-----
High-Level APIs
---------------
- None
F90 API
-------
- None
C++ API
-------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- None
Bug Fixes since HDF5-1.8.4
==========================
Configuration
-------------
- None EIP - 2009/10/21
Library
-------
- None EIP - 2009/10/21
Parallel Library
----------------
- None EIP - 2009/10/21
Tools
-----
- None EIP - 2009/10/21
F90 API
------
- None EIP - 2009/10/21
C++ API
------
- The parameters 'size' and 'bufsize' in CommonFG::getLinkval and
CommonFG::getComment, respectively, now have default values for
user's convenience. (BMR - 2009/10/23)
High-Level APIs:
------
- None EIP - 2009/10/21
Fortran High-Level APIs:
------
- None EIP - 2009/10/21
Platforms Tested
================
The following platforms and compilers have been tested for this release.
AIX 5.3 xlc 7.0.0.8
(LLNL Up) xlf 09.01.0000.0008
xlC 7.0.0.8
mpcc_r 7.0.0.8
mpxlf_r 09.01.0000.0008
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
(SNL red storm) ftn (pgf90) 7.1-4
CC (pgCC) 7.1-4
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
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
F90 MIPSpro 7.4.4m
C++ MIPSpro cc 7.4.4m
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) 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 2.6.16.60-0.37-smp #1 gcc 4.1.2
SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
(smirom) Intel(R) C, C++, Fortran Compilers for
applications running on Intel(R) 64,
Versions 10.1, 11.0.
PGI C, Fortran, C++ Version 7.2-1, 8.0-1
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!)
tested for both 32- and 64-bit binaries
Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
(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++ 5.8
Patch 124863-11
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
IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2
#1 SMP ia64 Intel(R) C++ Version 8.1.037
(NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033
mpich-gm-1.2.7p1..16-intel-8.1.037-r1
Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
.1.4.11.1smp #1 SMP applications running on Intel(R) 64,
SMP x86_64 GNU/Linux Versions 9.1.
(SNL Spirit)
Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
.1.4.11.1smp #1 SMP applications running on Intel(R) 64,
SMP x86_64 GNU/Linux Versions 10.1.
(SNL Thunderbird)
Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
SMP x86_64 GNU/Linux applications running on Intel(R) 64,
(SNL Glory) Versions 10.1.
Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
SMP x86_64 GNU/Linux applications running on Intel(R) 64,
(LLNL Zeus) Versions 9.1.
gcc/gfortran/g++ (GCC) 4.1.2.
Windows XP Visual Studio .NET
Visual Studio 2005 w/ Intel Fortran 9.1
Cygwin(native gcc compiler and g95)
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
Windows Vista Visual Studio 2005
MAC OS 10.5.6 (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
IRIX64_6.5 32-bit n n n n y y
IRIX64_6.5 64-bit n y y 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 n n 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
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 2.0.41 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
IRIX64_6.5 32-bit y dna y y
IRIX64_6.5 64-bit y y n y
Windows XP y y(4) y y
Windows XP x64 y y(4) y y
Windows Vista y n n y
Mac OS X 10.5 y n y n
AIX 5.3 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 2.0.41 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 2005 or Cygwin
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* 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
* There is a known issue in which HDF5 will change the timestamp on a file
simply by opening it with read/write permissions, even if the file is not
modified in any way. This is due to the way in which HDF5 manages the file
superblock. A fix is currently underway and should be included in the 1.8.4
release of HDF5. MAM - 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
* 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
* 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.
* 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
* 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.
* There is also a configure error on Altix machines that incorrectly reports
when a version of Szip without an encoder is being used.
* Information about building with PGI and Intel compilers is available in
the INSTALL file sections 4.7 and 4.8.
|
