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HDF5 History
============
This file contains development history of HDF5 1.8 branch
5. Release Information for hdf5-1.8.4
4. Release Information for hdf5-1.8.3
3. Release Information for hdf5-1.8.2
2. Release Information for hdf5-1.8.1
1. Release Information for hdf5-1.8.0
[Search on the string '%%%%' for per-release section breaks.]
%%%%1.8.4%%%%
HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.3 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 HDF5-1.8.3
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- Configuration suite now uses Automake 1.11 and Autoconf 2.64.
MAM 2009/08/31.
- Changed default Gnu fortran compiler from g95 to gfortran since
gfortran is more likely installed with gcc now. -AKC 2009/07/19-
Library
-------
- The embedded library information is displayed by H5check_version() if a
version mismatch is detected. Also changed H5check_version() to
suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
or higher. (Old behavior treated 3 or higher the same as 1, that is
print a warning and allows the program to continue. (AKC - 2009/9/28)
- If a user does not care for the extra library information insert
in the executables, he may turn it off by --disable-embedded-libinfo
during configure. (AKC - 2009/9/15)
Parallel Library
----------------
- None
Tools
-----
- h5diff: h5diff treats two INFINITY values different. Fixed by checking
(value==expect) before call ABS(...) at h5diff_array.c. This will make
that (INF==INF) is true (INF is treated as an number instead of NaN)
(PC -- 2009/07/28)
- h5diff: add option "--use-system-epsilon" to print difference if
(|a-b| > EPSILON).
Change default to use strict equality (PC -- 2009/09/12)
High-Level APIs
---------------
- None
F90 API
-------
- Added H5Oopen_by_addr_f MSB - 9/14/09
C++ API
-------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- PathScale compilers are recognized and can build the HDF5 library
properly. AKC - 2009/7/28 -
Bug Fixes since HDF5-1.8.3
==========================
Configuration
-------------
- Removed the following config files, as we no longer support them:
config/dec-osf*, config/hpux11.00, config/irix5.x,
config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
MAM - 2009/10/08
- Modified configure and make process to properly preserve user's CFLAGS
(and company) environment variables. Build will now properly use
automake's AM_CFLAGS for any compiler flags set by the configure
process. Configure will no longer modify CFLAGS directly, nor will
setting CFLAGS during make completely replace what configure has set up.
MAM - 2009/10/08
- Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
machine has long retired. AKC - 2009/10/06.
- Added $(EXEEXT) extension to H5detect when it's executed in the
src/Makefile to generate H5Tinit.c so it works correctly on platforms
that require the full extension when running executables.
MAM - 2009/10/01 - BZ #1613
- Configure will now set FC and CXX to "no" when fortran and c++
are not being compiled, respectively, so configure will not run
some of the compiler tests for these languages when they are not
being used. MAM - 2009/10/01
- The --enable-static-exec flag will now properly place the -static flag
on the link line of all installed executables. This will force the
executable to link with static libraries over shared libraries, provided
the static libraries are available. MAM - 2009/08/31 - BZ #1583
- The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -
Library
-------
- Fixed a bug where writing and deleting many global heap objects (i.e.
variable length data) would render the file unreadable. Previously
created files exhibiting this problem should now be readable.
NAF - 2009/10/27 - 1483
- Fixed error in library's internal caching mechanisms which could cause
an assertion failure (and attendent core dump) when encountering an
unusually formatted file. (QAK - 2009/10/13)
- Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628
- Fixed an assertion failure that occurred when H5Ocopy was called on a
dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597
- Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
NAF - 2009/09/25 - 1620
- Fixed a bug where properties weren't being compared with the registered
compare callback. NAF - 2009/09/25 - 1555
- Corrected problem where library would re-write the superblock in a file
opened for R/W access, even when no changes were made to the file.
(QAK - 2009/08/20, Bz#1473)
- Fixed a bug where H5Pget_filter_by_id would succeed when called for a
filter that wasn't present. NAF - 2009/06/25 - 1250
- Fixed an issue with committed compound datatypes containing a vlen. Also
fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593
Parallel Library
----------------
- None
Tools
-----
- h5dump/h5ls display buffer resize fixed in tools library.
ADB - 2009/7/21 - 1520
- perf_serial test added to Windows projects and check batch file.
ADB - 2009/06/11 -1504
F90 API
------
- Fixed bug in h5lget_info_by_idx_f by adding missing arguments,
consequently changing the API. New API is:
SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, &
link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id)
MSB - 2009/9/17 - 1652
- Corrected the values for the H5L_flags FORTRAN constants:
H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F
MSB - 2009-09-17 - 1653
- Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F
MSB - 2009-9-24 - 1471
C++ API
------
- None
High-Level APIs:
------
- Fixed a bug where the H5TB API would forget the order of fields when added
out of offset order. NAF - 2009/10/27 - 1582
- H5DSis_attached failed to account for different platform types. Added a
get native type call. ADB - 2009/9/29 - 1562
Fortran High-Level APIs:
------
- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions
had memory problems with the g95 fortran compiler. (PVN <20> 5/13/2009) 1522
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 4.3.5 20091004
g++ 4.3.5 20091004
gfortran 4.3.5 20091004
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
(liberty) g++ 3.4.6 [FreeBSD] 20060305
gcc 4.4.2 20091006
g++ 4.4.2 20091006
gfortran 4.4.2 20091006
Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704
#1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
(jam) GNU Fortran (GCC) 4.1.2 20080704
(Red Hat 4.1.2-46)
PGI C, Fortran, C++ 8.0-5 32-bit
PGI C, Fortran, C++ 8.0-1 32-bit
Intel(R) C Compiler for 32-bit
applications, Versions 11.0, 11.1
Intel(R) C++ Compiler for 32-bit
applications, Version 11.0, 11.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 11.0, 11.1
Absoft 32-bit Fortran 95 10.0.7
MPICH mpich2-1.0.8 compiled with
gcc (GCC) 4.1.2 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 2.6.16.60-0.42.5 #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 C 5.9 SunOS_sparc Patch 124867-11 2009/04/30
(linew) Sun Fortran 95 8.3 SunOS_sparc
Patch 127000-11 2009/10/06
Sun C++ 5.9 SunOS_sparc
Patch 124863-16 2009/09/15
Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026
92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026
perfctr #6 SMP Open MPI 1.2.2
(abe) 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 10.1.
(SNL Thunderbird)
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 10.1.
Windows XP 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 w/ Intel Fortran 9.1
Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1
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 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 EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y
RedHat EL5 2.6.18-164 i686 Intel W n y n y y n
RedHat EL5 2.6.18-164 i686 PGI W n y n y y n
RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y
RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n
RedHat EL5 2.6.18-164 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 2.0.62 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 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 y y y
RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y
RedHat EL5 2.6.18-164 i686 Intel W y y y n
RedHat EL5 2.6.18-164 i686 PGI W y y y n
RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y
RedHat EL5 2.6.18-164 x86_64 IntelW y y y n
RedHat EL5 2.6.18-164 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 2.0.62 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
==============
* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
it treats "exit(134) the same as if process 0 had received an abort signal.
This is fixed and will be available in the next release. AKC - 2009/11/3
* 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
* 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
* 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.
%%%%1.8.3%%%%
HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.2 and
HDF5 1.8.3, and contains information on the platforms tested and
known problems in HDF5-1.8.3.
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 1.8.3 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.3 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.3 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 1.8.3 (current
release) versus Release 1.8.2":
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 HDF5-1.8.2
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- Added libtool version numbers to generated c++, fortran, and
hl libraries. MAM 2009/04/19.
- Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
- Added a Make target of check-all-install to test the correctness of
installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
Library
-------
- Embed the content of libhdf5.settings into the hdf5 executables
so that an "orphaned" executables can display (via the Unix
strings command, for example) the library settings used to build
the executables. This is a prototype implementation. Improvement will
be added in next release. AKC - 2009/04/20
- Separated "factory" free list class from block free lists. These free
lists are dynamically created and manage blocks of a fixed size.
H5set_free_list_limits() will use the same settings specified for block
free lists for factory free lists. NAF - 2009/04/08
- Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29
- Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
user-defined callback function for external link traversal.
NAF - 2009/01/08
- Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
allow the user to specify the file access flags used to open the target
file of an external link. NAF - 2009/01/08
- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
individual rdcc configuration for each dataset. Added
H5Dget_access_plist() function to retrieve a dataset access property
list from a dataset. NAF - 2008/11/12
- Added H5Iis_valid() function to check if an id is valid without
producing an error message. NAF - 2008/11/5
- Added code to maintain a min_clean_fraction in the metadata cache when
in serial mode. MAM - 2009/01/9
Parallel Library
----------------
- Modified parallel tests to run with arbitrary number of processes. The
modified tests are testphdf5 (parallel dataset access), t_chunk_alloc
(chunk allocation), and t_posix_compliant (posix compliance). The rest of
the parallel tests already use in the code the number of processes
available in the communicator. (CMC - 2009/04/28)
Tools
-----
- h5diff new flag, -c, --compare, list objects that are not comparable.
PVN - 2009/4/2 - 1368
- h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
- h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519
- h5repack now handles group creation order. PVN - 2009/4/2 - 1402
- h5repack: When user doesn't specify a chunk size, h5repack now
defines a default chunk size as the same size of the size of the
hyperslab used to read the chunks. The size of the hyperslabs are
defined as the size of each dimension or a predefined constant,
whatever is smaller. This assures that the chunk read fits in the
chunk cache. PVN - 2008/11/21
High-Level APIs
---------------
- Table: In version 3.0 of Table, the writing of the "NROWS" attribute
(used to store number of records) was deprecated. PVN - 2008/11/24
F90 API
-------
- Added for the C APIs the Fortran wrappers:
h5dget_access_plist_f
h5iis_valid_f
h5pset_chunk_cache_f
h5pget_chunk_cache_f
MSB - 2009/04/17
C++ API
-------
- None
Support for New Platforms, Languages, and Compilers
===================================================
Bug Fixes since HDF5-1.8.2
==========================
Configuration
-------------
- The --includedir=DIR configuration option now works as intended, and
can be used to specify the location to install C header files. The
default location remains unchanged, residing at ${prefix}/include.
MAM - 2009/03/10 - BZ #1381
- Configure no longer removes the '-g' flag from CFLAGS when in production
mode if it has been explicitly set in the CFLAGS environment variable
prior to configuration. MAM - 2009/03/09 - BZ #1401
Library
-------
- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
API. NAF - 2009/04/20 - 1533
- Fixed a problem with using data transforms with non-native types in the
file. NAF - 2009/04/20 - 1548
- Added direct.h include file to windows section of H5private.h
to fix _getcwd() warning. ADB - 2009/04/14 - 1536
- Fixed a bug that prevented external links from working after calling
H5close(). NAF - 2009/04/10 - 1539
- Modified library to write cached symbol table information to the
superblock, to allow library versions 1.3.0 to 1.6.3 to read files created
by this version. NAF - 2009/04/08 - 1423
- Changed skip lists to use a deterministic algorithm. The library should
now never call rand() or srand(). NAF - 2009/04/08 - 503
- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups
when that property was set. NAF - 2009/04/07 - 1526
- Fixed a bug that caused files with a user block to grow by the size of the
user block every time they were opened. NAF - 2009/03/26 - 1499
- Fixed a rare problem that could occur with files using the old (pre 1.4)
array datatype. NAF - 2009/03/23
- Modified library to be able to open files with corrupt root group symbol
table messages, and correct these errors if they are found. Such files
can only be successfully opened with write access. NAF - 2009/03/23 - 1189
- Removed the long_long #define and replaced all instances with
"long long". This caused problems with third party products. All
currently supported compliers support the type. ADB - 2009/03/05
- Fixed various bugs that could prevent the fill value from being written
in certain rare cases. NAF - 2009/02/26 - 1469
- Fixed a bug that prevented more than one dataset chunk from being cached
at a time. NAF - 2009/02/12 - 1015
- Fixed an assertion failure caused by opening an attribute multiple times
through multiple file handles. NAF - 2009/02/12 - 1420
- Fixed a problem that could prevent the user from adding attributes (or any
object header message) in some circumstances. NAF - 2009/02/12 - 1427
- Fixed a bug that could cause problems when an attribute was added to a
committed datatype using the committed datatype's datatype.
NAF - 2009/02/12
- Fixed a bug that could cause problems when copying an object with a shared
message in its own object header. NAF - 2009/01/29
- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes.
NAF - 2009/01/27 - 1443
- Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise
packed compound type. NAF - 2009/01/14
- Fixed up some old v2 btree assertions that get run in debug mode that
were previously failing on compilation, and removed some of the
more heavily outdated and non-rewritable ones. MAM - 2008/12/15
- Fixed a bug that could cause problems when "automatically" unmounting
multiple files. NAF - 2008/11/17
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
PVN - 2009/01/8
Parallel Library
----------------
- None
Tools
-----
- Fixed many problems that could occur when using h5repack with named
datatypes. NAF - 2009/4/20 - 1516/1466
- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant
defined as 1024Kb, such as array types with large dimensions.
PVN - 2009/4/1 - 1501
- h5import: By selecting a compression type, a big endian byte order
was being selected. PVN - 2009/3/11 - 1462
- zip_perf.c had missing argument on one of the open() calls. Fixed.
AKC - 2008/12/9
F90 API
------
- None
C++ API
------
- None
High-Level APIs:
------
- Dimension scales: The scale index return value in H5DSiterate_scales
was not always incremented. PVN - 2009/4/8 - 1538
Fortran High-Level APIs:
------
- Lite: The h5ltget_dataset_info_f function (gets information about
a dataset) was not correctly returning the dimension array
PVN - 2009/3/23
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
==============
* 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.
%%%%1.8.2%%%%
HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2,
and contains information on the platforms tested and known problems in
HDF5-1.8.2. 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 1.8.2 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.2 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.2 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 1.8.2 (current
release) versus Release 1.8.1":
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 and languages
- Bug Fixes since HDF5-1.8.1
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15).
Library
-------
- Added two new public routines: H5Pget_elink_fapl() and
H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
Parallel Library
----------------
- None
Tools
-----
- h5repack: added new options -u and -b to add a userblock to an HDF5
file during the repack. (PVN - 2008/08/26)
- h5repack: added options -t and -a to call H5Pset_alignment while
creating a repacked file. (PVN - 2008/08/29)
- h5ls: added capability to traverse through external links when the -r
(recursive) flag is given. (NAF - 2008/09/16)
- h5ls: added -E option to enable traversal of external links.
h5ls will not traverse external links without this flag being set.
(NAF - 2008/10/06)
- h5dump: when -b flag is used without a keyword after it, binary
output defaults to NATIVE. MEMORY keyword was deprecated
and replaced by NATIVE keyword. (PVN - 2008/10/30)
- h5diff: returns 1 when file graphs differ by any object.
Error return code was changed to 2 from -1. (PVN - 2008/10/30)
- h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
instead (PVN - 2008/10/30)
F90 API
------
- Added optional parameter 'mounted' to H5Gget_info_f,
H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24)
- Added H5Tget_native_type_f (MSB - 2008/09/30)
C++ API
------
- These member functions were added as wrapper for H5Rdereference to
replace the incorrect IdComponent::dereference().
void H5Object::dereference(H5Object& obj, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
void H5Object::dereference(H5File& h5file, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
void H5Object::dereference(Attribute& obj, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
In addition, these constructors were added to create the associated
objects by way of dereference:
DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
(BMR - 2008/10/29)
Support for New Platforms, Languages, and Compilers
===================================================
- Intel 10.1 is supported on Mac OS X 10.5.4.
Note:
When Fortran is enabled, configure automatically
disables the build of shared libraries (i.e., only
static C and C++ HDF5 libraries will be built
along with the static HDF5 Fortran library).
Intel 10.1 C and C++ compilers require
"-no-multibyte-chars" compilation flag due to the known
bug in the compilers.
(EIP - 2008/10/30)
Bug Fixes since HDF5-1.8.1
==========================
Configuration
-------------
- Fixed error with 'make check install' failing due to h5dump
needing other tools built first. (MAM - 2008/10/15).
- When using shared szip, it is no longer necessary to specify
the path to the shared szip libraries in LD_LIBRARY_PATH.
(MAM - 2008/10/15).
- The file libhdf5_fortran.settings is not installed since its content
is included in libhdf5.settings now. (AKC - 2008/10/21)
- "make DESTDIR=xxx install" failed to install some tools and files
(e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8).
Library
-------
- H5Ovisit and H5Ovisit_by_name will now properly terminate when the
callback function returns a positive value on the starting object.
(NAF - 2008/11/03)
- Fixed an error where a null message could be created that was larger
than could be written to the file. (NAF - 2008/10/23)
- Corrected error with family/split/multi VFD not updating driver info
when "latest" version of the file format used. (QAK - 2008/10/14)
- Corrected alignment+threshold errors to work correctly when metadata
aggregation is enabled. (QAK - 2008/10/06)
- Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects
registered by the library for internal library use.
(NAF - 2008/10/06)
- Fixed potential memory leak during compound conversion.
(NAF - 2008/10/06)
- Changed the return value of H5Fget_obj_count from INT to SSIZE_T.
Also changed the return value of H5Fget_obj_ids from HERR_T to
SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T.
(SLU - 2008/09/26)
- Fixed an issue that could cause data to be improperly overwritten
during compound type conversion. (NAF - 2008/09/19)
- Fixed pointer alignment violations that could occur during vlen
conversion. (NAF - 2008/09/16)
- 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)
- Fixed assertion failure caused by incorrect array datatype version.
(NAF - 2008/08/04)
- Fixed issue where a group could have a file mounted on it twice.
(QAK - 2008/07/15)
- 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 - 2008/07/07)
- Fixed a Windows-specific issue in the ohdr test which was causing
users in some timezones to get false errors. This a deficiency in
the Windows mktime() function, and has been handled properly.
(SJW - 2008/06/19)
Parallel Library
----------------
- None
Tools
-----
- h5dump now checks for uniqueness of committed datatypes.
(NAF - 2008/10/15)
- Fixed unnecessary indentation of committed datatypes in h5dump.
(NAF - 2008/10/15)
- Fixed bugs in h5stat: segmemtation fault when printing groups and
print warning message when traversal of objects is unsuccessful.
(see bug #1253) (VC- 2008/10/13)
- Fixed bug in h5ls that prevented relative group listings (like
"h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
- 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)
F90 API
------
- h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND
and H5S_SELECT_PREPEND (MSB - 2008/09/30)
- h5sget_select_elem_pointlist: Fixed list of returned points by
rearranging the point list correctly by accounting for C
conventions. (MSB - 2008/09/30)
- h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension
of arrays.(MSB - 2008/9/30)
- h5sget_select_bounds_f: Swapped array bounds to account for C and
Fortran reversed array notation (MSB - 2008/9/30)
- Changed to initializing string to a blank character instead of a
null type in tH5P.f90 to fix compiling error using AIX 5.3.0
(MSB - 2008/7/29)
- Fixed missing commas in H5test_kind.f90 detected by NAG compiler
(MSB - 2008/7/29)
- Fixed passing and array to a scalar in tH5A_1_8.f90 detected by
NAG compiler (MSB - 2008/7/29)
- Added the ability of the test programs to use the status of
HDF5_NOCLEANUP to determine if the *.h5 files should be removed
or not after the tests are completed (MSB - 2008/10/1)
- In nh5tget_offset_c: (MSB 9/12/2008)
If offset was equal to 0 it returned the error code of -1,
this was changed to return an error code of -1 when the offset
value is < 0.
- Uses intrinsic Fortran function SIZEOF if available when detecting
type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3)
- Put the DOUBLE PRECISION interfaces in a separate module and
added a USE statement for the module. The interfaces are
included/excluded depending on the state of FORTRAN_DEFAULT_REAL
is DBLE_F which detects if the default REAL is DOUBLE PRECISION.
This allows the library to be compiled with -r8 Fortran flag
without the user needing to edit the source code.
(MSB - 200/8/27)
- Enable building shared library for fortran by adding the flag -fPIC
to the compile flags for versions of Intel Fortran compiler >=9
(MSB - 2008/8/26)
C++ API
------
- 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 - 2008/05/20)
- IdComponent::dereference was incorrect and replaced as described
in "New Features" section.
(BMR - 2008/10/29)
Platforms Tested
================
The following platforms and compilers have been tested for this release.
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
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
(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 4.2.5 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 (64 & n32) MIPSpro cc 7.4.4m
F90 MIPSpro 7.4.4m
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 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T
SMP x86_64 GNU/Linux Ver. 10.1.013
(smirom) Intel(R) Fortran Intel(R) EM64T
Ver. 10.1.013
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
Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) gcc 3.4.6 20060404
Intel(R) C++ Version 10.0
Intel (R) Fortran Compiler Version 10.0
mvapich2-0.9.8p2patched-intel-ofed-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 10.5.4 (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
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(15) n(15) y y y
Windows XP x64 n y(15) n(15) 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 (3) W y(1) y(10) y(1) y y y
RedHat EL4 Intel (3) W n y n y y n
RedHat EL4 PGI (3) W n y n y y n
SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y
SuSe x86_64 Int(3,12) W n y(13) n y y n
SuSe x86_64 PGI(3,12) W n y(8) n y y y
Linux 2.6 SuSE ia64 C
Intel (3,7) y y y y y n
Linux 2.6 SGI Altix
ia64 Intel (3) y y y y y y
Linux 2.6 RHEL C
Lustre Intel (5) y(4) y y(4) 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(15) y y
Windows XP x64 y y(15) 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 6.2 32&64 bit y n y y
RedHat EL4 (3) W y y(10) y y
RedHat EL4 Intel (3) W y y y n
RedHat EL4 PGI (3) W y y y n
SuSe x86_64 GNU(3,12) W y y y y
SuSe x86_64 Int(3,12) W y y y n
SuSe x86_64 PGI(3,12) W y y y n
Linux 2.4 SuSE C
ia64 C Intel (7) y y y n
Linux 2.4 SGI Altix C
ia64 Intel y n
Linux 2.6 RHEL C
Lustre Intel (5) y y y n
Cray XT3 2.0.41 n n n n
Notes: (1) Using mpich2 1.0.6.
(2) Using mpich2 1.0.7.
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(4) Using mvapich2 0.9.8.
(5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
(8) pgf90
(9) With Compaq Visual Fortran 6.6c compiler.
(10) With PGI and Absoft compilers.
(11) PGI and Intel compilers for both C and Fortran
(12) AMD Opteron x86_64
(13) ifort
(14) Yes with C and Fortran, but not with C++
(15) Using Visual Studio 2005 or Cygwin
(16) Not tested for this release.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* 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.
%%%%1.8.1%%%%
HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008
================================================================================
INTRODUCTION
============
This document describes the differences between the HDF5-1.8.1 release
and HDF5 1.8.0, and contains information on the platforms tested and known
problems in HDF5-1.8.1. 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 1.8.1 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.1 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.1 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 1.8.1 (current
release) versus Release 1.8.0":
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 and languages
- Bug Fixes since HDF5-1.8.0
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration
-------------
- The lib/libhdf5.settings file contains much more configure
information. (AKC - 2008/05/18)
- 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)
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and
Libtool 2.2.2 (MAM - 2008/05/01)
Source code distribution
========================
Library
-------
- None
Parallel Library
----------------
- None
Tools
-----
- h5repack: Reinstated the -i and -o command line flags to specify
input and output files. h5repack now understands both the old
syntax (with -i and -o) and the new syntax introduced in Release
1.8.0. (PVN - 2008/05/23)
- h5dump: Added support for external links, displaying the object that
an external link points to. (PVN - 2008/05/12)
- h5dump: Added an option, -m, to allow user-defined formatting in the
output of floating point numbers. (PVN - 2008/05/06)
- h5dump, in output of the -p option: Added effective data compression
ratio to the dataset storage layout output when a compression filter
has been applied to a dataset. (PVN - 2008/05/01)
F90 API
------
New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were
added. See "Release 1.8.1 (current release) versus Release 1.8.0" in
the document "HDF5 Software Changes from Release to Release"
(http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the
complete list of the new APIs.
C++ API
------
- None
Support for New Platforms, Languages, and Compilers
===================================================
- Both serial and parallel HDF5 are supported for the Red Storm machine
which is a Cray XT3 system.
- The Fortran library will work correctly if compiled with the -i8
flag. This has been tested with the g95, PGI and Intel Fortran
compilers.
Bug Fixes since HDF5-1.8.0
==========================
Configuration
-------------
- None
Source code distribution
========================
Library
-------
- Chunking: Chunks greater than 4GB are disallowed.
(QAK - 2008/05/16)
- Fixed the problem with searching for a target file when following
an external link. The search pattern will depend on whether the
target file's pathname is an absolute or a relative path.
Please see the H5Lcreate_external description in the "HDF5
Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html).
(VC - 2008/04/08)
- Fixed possible file corruption bug when encoding datatype
descriptions for compound datatypes whose size was between
256 and 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 correctly handle an
invalid location identifier. (QAK - 2008/03/11)
Parallel Library
----------------
- None
Tools
-----
- Fixed bug in h5diff that prevented datasets and attributes with
variable-length string elements from comparing correctly.
(QAK - 2008/02/28)
- 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)
F90 API
------
- The h5tset(get)_fields subroutines were missing the parameter to
specify a sign position; fixed. (EIP - 2008/05/23)
- Many APIs were fixed to work with the 8-byte integers in Fortran vs.
4-byte integers in C. This change is trasparent to user applications.
C++ API
------
- The class hierarchy was revised to address the problem reported
in bugzilla #1068, Attribute should not be derived from base
class H5Object. Classes AbstractDS was moved out of H5Object.
Class Attribute now multiply inherits from IdComponent and
AbstractDs and class DataSet from H5Object and AbstractDs.
In addition, data member IdComponent::id was moved into subclasses:
Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
(BMR - 2008/05/20)
- IdComponent::dereference was incorrect; it was changed from:
void IdComponent::dereference(IdComponent& obj, void* ref)
to:
void H5Object::dereference(H5File& h5file, void* ref)
void H5Object::dereference(H5Object& obj, void* ref)
(BMR - 2008/05/20)
- Revised Attribute::write and Attribute::read wrappers to handle
memory allocation/deallocation properly. (bugzilla 1045)
(BMR - 2008/05/20)
Platforms Tested
================
The following platforms and compilers have been tested for this release.
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
(red storm) ftn (pgf90) 7.1-4
CC (pgCC) 7.1-4
mpicc 1.0.2
mpif90 1.0.2
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,g++ 3.4.6 20060404, G95 (GCC 4.0.3)
(kagiso) PGI 7.1-6 (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,
(smirom) g95 (GCC 4.0.3)
PGI 7.1-6 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, ifort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
(cobalt) 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_309.tg1 ia64
(NCSA tg-login) gcc 3.2.2
Intel(R) C++ Version 8.1
Intel(R) Fortran Compiler Version 8.1
mpich-gm-1.2.6..14b-intel-r2
Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) gcc 3.4.6 20060404
Intel(R) C++ Version 10.0
Intel (R) Fortran Compiler Version 10.0
mvapich2-0.9.8p2patched-intel-ofed-1.2
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 10.5.2 (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)
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
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
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
Windows XP n y(15) n(15) y y y
Windows XP x64 n y(15) n(15) y y y
Windows Vista n n n y y y
Mac OS X 10.5 Intel n y n y y y
FreeBSD 4.11 n n n y y y
RedHat EL3 W (3) y(1) y(10) y(1) y y y
RedHat EL3 W Intel (3) n y n y y n
RedHat EL3 W PGI (3) n y n y y n
SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y
SuSe x86_64 Int (3,12) n y(13) n y y n
SuSe x86_64 PGI (3,12) n y(8) n y y y
Linux 2.4 Xeon C
Lustre Intel (3,6) n y n y y n
Linux 2.6 SuSE ia64 C
Intel (3,7) y y y y y n
Linux 2.6 SGI Altix
ia64 Intel (3) y y y y y y
Linux 2.6 RHEL C
Lustre Intel (5) y(4) y y(4) 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 64-bit y y y y
Solaris2.10 32-bit y y y y
IRIX64_6.5 64-bit y y n y
IRIX64_6.5 32-bit y dna y y
Windows XP y y(15) y y
Windows XP x64 y y(15) y y
Windows Vista y n n y
Mac OS X 10.3 y n
FreeBSD 4.11 y n y y
RedHat EL3 W (3) y y(10) y y
RedHat EL3 W Intel (3) y y y n
RedHat EL3 W PGI (3) y y y n
SuSe x86_64 W GNU (3,12) y y y y
SuSe x86_64 W Int (3,12) y y y n
SuSe x86_64 W PGI (3,12) y y y n
Linux 2.4 Xeon C
Lustre Intel (6) y y y n
Linux 2.4 SuSE
ia64 C Intel (7) y y y n
Linux 2.4 SGI Altix
ia64 Intel y n
Linux 2.6 RHEL C
Lustre Intel (5) y y y n
Cray XT3 2.0.41 n n n n n
Notes: (1) Using mpich2 1.0.6.
(2) Using mpich2 1.0.7.
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(4) Using mvapich2 0.9.8.
(5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
(8) pgf90
(9) With Compaq Visual Fortran 6.6c compiler.
(10) With PGI and Absoft compilers.
(11) PGI and Intel compilers for both C and Fortran
(12) AMD Opteron x86_64
(13) ifort
(14) Yes with C and Fortran, but not with C++
(15) Using Visual Studio 2005 or Cygwin
(16) Not tested for this release.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* 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
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
expected to fail and 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. To bypass this problem for now, change the following
lines in the tools/h5ls/testh5ls.sh.
======== Original =========
# The following combination of arguments is expected to return an error message
# and return value 1
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Skip the test =========
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== end of bypass ========
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
* 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. 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.
* 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, the Scaleoffset filter is not supported. The Scaleoffset filter
supports only the IEEE standard for floating-point data; it cannot be applied
to HDF5 data generated on VAX.
* 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, 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
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
Opteron processor, there is a bug in the compiler for optimization(-O2).
The library failed in several tests, all related to the 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",
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.
* With the gcc 2.95.2 compiler, HDF5 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 ./dsets tests fail on 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.
* 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 the HDF5
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
and fflush2.f90 complaining about the 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
the INSTALL file sections 4.7 and 4.8.
* 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 HDF5 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
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 the h5copy tool.
* In the C++ API, it appears that there are bugs in Attribute::write/read
and DataSet::write/read for fixed- and variable-len strings. The problems
are being worked on and a patch will be provided when the fixes are
available.
%%%%1.8.0%%%%
HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008
================================================================================
INTRODUCTION
============
This document describes the differences between the HDF5-1.6.x release series
and HDF5 1.8.0, and contains information on the platforms tested and known
problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt
file in the
release_docs/ directory of the HDF5 source.
Links to the HDF5 1.8.0 source code, documentation, and additional materials
can be found on the HDF5 web page at:
http://www.hdfgroup.org/products/hdf5/
The HDF5 1.8.0 release can be obtained from:
http://www.hdfgroup.org/HDF5/release/obtain5.html
User documentation for 1.8.0 can be accessed directly at this location:
http://www.hdfgroup.org/HDF5/doc/
New features in 1.8.0, 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 1.8.0 (current
release) versus Release 1.6.x":
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
- Removed Feature
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.0
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
HDF5 Release 1.8.0 is a major release with many changes and new features.
New format and interface features discussed in the "What's New in
HDF5 1.8.0" document include the following:
Enhanced group object management
Enhanced attribute management and more efficient meta data handling
Expanded datatype features
Creation order tracking and indexing
Improved meta data caching and cache control
UTF-8 encoding
New I/O filters: n-bit and scale+offset compression
New link (H5L) and object (H5O) interfaces and features
External and user-defined links
New high-level APIs:
HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS)
C++ and Fortran interfaces for older high-level APIs:
H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB)
New and improved tools
And more...
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
New APIs associated with these features, other interface changes
(e.g., ENUM and struct definitions), and new library configuration flags
are listed in the "Release 1.8.0 (current release) versus Release 1.6.x"
section of "HDF5 Software Changes from Release to Release."
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
Compatibility
-------------
Many HDF5 users and user communities have existing applications that
they may wish to port to Release 1.8.0. Alternatively, some users may
wish to take advantage of Release 1.8.0's improved performance without
having to port such applications. To facilitate managing application
compatibility and porting applications from release to release, the HDF
Team has implemented the following features:
Individually-configurable macros that selectively map common
interface names to the old and new interfaces
Library configuration options to configure the macro mappings
Two related documents accompany this release:
"API Compatibility Macros in HDF5" discusses the specifics of the
new individually-configurable macros and library configuration
options.
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
Compatibility Issues" discusses each new feature with regard to
its impact on format compatibility.
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
Referenced documents
--------------------
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
"What's New in HDF5 1.8.0"
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
The "Release 1.8.0 (current release) versus Release 1.6.x "
section in "HDF5 Software Changes from Release to Release"
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
"API Compatibility Macros in HDF5"
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
Compatibility Issues"
Removed Feature
===============
The stream virtual file driver (H5FD_STREAM) have been removed in this
release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream
and the constant H5FD_STREAM.
This virtual file driver will be available at
http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release,
the transition is still in progress; the necessary integration tools may
not be available when HDF5 Release 1.8.0 first comes out.
Support for New Platforms, Languages, and Compilers
===================================================
- Support for Open VMS 7.3 was added.
Bug Fixes since HDF5-1.6.0
==========================
This release contains numerous bug fixes. For details, see the
"Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for
this release.
Platforms Tested
================
The following platforms and compilers have been tested for for this release.
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,
(smirom) g95 (GCC 4.0.3)
PGI 6.2-5 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, iort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
(cobalt) 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 Compaq C V6.5-001-48BCD
HP Fortran V7.6-3276
Compaq C++ V6.5-004
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
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
SunOS5.8 64-bit n y n y y y
SunOS5.8 32-bit n y n y y y
SunOS5.10 64-bit y(1) y n y y y
SunOS5.10 32-bit y(1) 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
Windows XP n y(15) n(15) y y y
Windows XP x64 n y(15) n(15) 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 4.11 n n n y y y
RedHat EL3 W (3) y(1a) y(10) y(1a) y y y
RedHat EL3 W Intel (3) n y n y y n
RedHat EL3 W PGI (3) n y n y y n
SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y
SuSe x86_64 Int (3,12) n y(13) n y y n
SuSe x86_64 PGI (3,12) n y(8) n y y y
Linux 2.4 Xeon C
Lustre Intel (3,6) n y n y y n
Linux 2.6 SuSE ia64 C
Intel (3,7) y y y y y n
Linux 2.6 SGI Altix
ia64 Intel (3) y y y y y 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
Solaris2.8 64-bit y y y x y
Solaris2.8 32-bit y y y x y
Solaris2.10 64-bit y x y
Solaris2.10 32-bit y x y
IRIX64_6.5 64-bit y y n y y
IRIX64_6.5 32-bit y dna y y y
AIX-5.2 & 5.3 32-bit n n n y n
AIX-5.2 & 5.3 64-bit n n n y n
Windows XP y y(15) y y y
Windows XP x64 y y(15) y y y
Windows Vista y n n y y
Mac OS X 10.3 y y n
FreeBSD 4.11 y n y y y
RedHat EL3 W (3) y y(10) y y y
RedHat EL3 W Intel (3) y y y y n
RedHat EL3 W PGI (3) y y y y n
SuSe x86_64 W GNU (3,12) y y y y y
SuSe x86_64 W Int (3,12) y y y y(14) n
SuSe x86_64 W PGI (3,12) y y y y(14) n
Linux 2.4 Xeon C
Lustre Intel (6) y y y y n
Linux 2.4 SuSE
ia64 C Intel (7) y y y y n
Linux 2.4 SGI Altix
ia64 Intel y y n
Alpha OpenVMS 7.3.2 n n n y n
Notes: (1) Using mpich 1.2.6.
(1a) Using mpich2 1.0.6.
(2) Using mpt and mpich 1.2.6.
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel
compilers
(8) pgf90
(9) With Compaq Visual Fortran 6.6c compiler.
(10) With PGI and Absoft compilers.
(11) PGI and Intel compilers for both C and Fortran
(12) AMD Opteron x86_64
(13) ifort
(14) Yes with C and Fortran, but not with C++
(15) Using Visual Studio 2005 or Cygwin
(16) Not tested for this release.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* 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
* 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. A higher level of
optimization causes failures in several HDF5 library tests.
* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass
when run against the parallel library; the parallel tests also pass, but
with lots of non-fatal error messages.
* 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 SUN 5.10 C++, testing 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, the Scaleoffset filter is not supported. The filter cannot be
applied to HDF5 data generated on VAX. The Scaleoffset filter only supports
the 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, 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 calculating code 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
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
Opteron processor, there is a bug in the compiler for optimization(-O2).
The library failed in several tests, all related to the 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",
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 platform for the 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.
* With the gcc 2.95.2 compiler, HDF5 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 ./dsets tests fail on 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.
* 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 the HDF5
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
and fflush2.f90 complaining about the 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
the INSTALL file sections 4.7 and 4.8.
* 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 HDF5 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 the h5copy tool.
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