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HDF5 version 1.6.4-post7 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.4 and
HDF5-1.6.4-post*, and contains information on the platforms tested and
known problems in HDF5-1.6.4. For more details check the HISTORY.txt
file in the HDF5 source.
The HDF5 documentation can be found on the NCSA ftp server
(ftp.ncsa.uiuc.edu) in the directory:
/HDF/HDF5/docs/
For more information look at the HDF5 home page at:
http://hdf.ncsa.uiuc.edu/HDF5/
If you have any questions or comments, please send them to:
hdfhelp@ncsa.uiuc.edu
CONTENTS
========
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.4
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Source code distribution:
-------------------------
Library:
--------
- Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to
allow querying for objects in file that were opened with a particular
file ID, instead of all objects opened in file with any file ID.
QAK - 2005/06/01
Parallel Library:
-----------------
Tools:
------
F90 API:
--------
- Added missing h5tget_member_class_f function
EIP 2005/04/06
C++ API:
--------
- Added missing member functions
H5::CompType::getMemberArrayType
H5::CompType::getMemberVarLenType
H5::AbstractDs::getArrayType
H5::AbstractDs::getVarLenType
H5::CommonFG::openArrayType
H5::CommonFG::openVarLenType
H5::PropList::copyProp -- this will replace the current
H5::PropList::copyProp in later releases due
to incorrect prototype.
BMR - 2005/07/27
Support for new platforms, languages and compilers.
=======================================
Configuration
-------------
Bug Fixes since HDF5-1.6.4 release
==================================
Library
-------
- Corrected errors when querying information about a group opened
by dereferencing an object reference. QAK - 2005/07/30
- Fixed a bug with named datatypes where a copy of a named datatype
used to create a dataset would accidentally use the original
named datatype for the dataset's datatype. QAK - 2005/07/23
- Made H5Fget_name() be consistent and always return name of actual
file the ID is in. (Instead of the name of the top file in a
file mounting hierarchy). QAK - 2005/07/19
- Reworked internal file mounting semantics to hopefully eliminate
mounting problems. We now require that files that are mounting
together all have the same "file close degree". QAK - 2005/07/19
- More bug fixes on holding open files that are mounted and have
IDs open. QAK - 2005/07/14
- More bug fixes on holding open files that are mounted and have
IDs open. QAK - 2005/07/14
- Dataset sieve buffer cache was inadvertantly disabled - re-enable
it. QAK - 2005/07/08
- Don't unmount child files until the parent file actually closes.
(Previously, if an object is holding open a file, the child files
would get unmounted too early). QAK - 2005/07/05
- Fixed bug where unmounted files could cause the library to go into
an infinite loop when shutting down. QAK - 2005/06/30
- Fixed bug with hyperslab selections that use selection offsets and
operate on chunked datasets going into infinite loop or dumping
core. QAK - 2005/06/17
- Corrected memory leak and possible corruption when opening a group.
QAK - 2005/06/17
- Added check for opaque datatype tags being too long (check against
H5T_OPAQUE_TAG_MAX, currently set to 256). QAK - 2005/06/14
- Fixed various errors in maintaining names for open objects in the
face of unusual mount & unmount operations. QAK - 2005/06/08
- "SEMI" and "STRONG" file close degree settings now apply only to the
particular file ID being closed, instead of operating on all open
file IDs for a given file. QAK - 2005/06/01
- Fixed error in opening object in group that was opened in mounted
file which has been unmounted. QAK - 2005/03/17
Configuration
-------------
Performance
-------------
- Optimized I/O for enumerated datatypes that are a superset of source
enumerated datatype. QAK - 2005/03/19
Tools
-----
Documentation
-------------
F90 API
-------
- h5pget_driver_f was returning information that could not be
interpreted by fortran application program; fixed. EIP - 2005/04/10
C++ API
-------
- Several member functions' prototype changed due to the
"int -> unsigned" change in the main library. They are:
H5::CompType::getMemberDataType(unsigned member_num)
H5::CompType::getMemberCompType(unsigned member_num)
H5::CompType::getMemberEnumType(unsigned member_num)
H5::CompType::getMemberIntType(unsigned member_num)
H5::CompType::getMemberFloatType(unsigned member_num)
H5::CompType::getMemberStrType(unsigned member_num)
BMR - 2005/07/27
Documentation
=============
Platforms Tested
================
AIX 5.1 (32 and 64-bit) xlc 6.0.0.6
xlf 8.1.1.3
xlC 6.0.0.6
mpcc_r 6.0.0.6
mpxlf_r 8.1.1.3
xlc 5.0.2.5
xlf 7.1.1.2
xlC 5.0.2.5
mpcc_r 5.0.2.5
mpxlf_r 7.1.1.2
AIX 5.2 (32/64 bit) xlc 6.0.0.8
xlC 6.0.0.9
xlf 8.1.1.7
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.7
AIX 5.2 (32/64 bit, LLNL frost) xlc 6.0.0.8
xlC 6.0.0.8
xlf 8.1.1.7
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.7
Cray T90 sn7001 10.0.0md Cray Standard C Version 6.4.0.3
Cray Fortran Version 3.4.0.0
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.3.6
Cray Fortran Version 3.6.0.3.1
FreeBSD 4.9 gcc 2.95.4
g++ 2.95.4
gcc 3.2.3, 3.3.6, 3.4.4, 4.0.0
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP ANSI C++ B3910B A.03.13
MPIch 1.2.4
IRIX64 6.5 (tesla -64) MIPSpro cc 7.4.2m
F90 MIPSpro 7.4.2m
C++ MIPSpro cc 7.4.2m
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
C++ MIPSpro cc 7.3.1.3m
mpt 1.6
Linux 2.4.20-28.7 gcc 2.96
(eirene, verbena) gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC)
version 5.2-1
Absoft Fortran compiler v9.0
Intel(R) C++ 32-bit Version 8.1
Intel(R) Fortran 32-bit Version 8.1
MPIch 1.2.6
Linux 2.4.21-268-smp x86_64 gcc 3.3.1 (SuSE Linux, AMD)
(mir) PGI 5.2-1 C and F90 (with k3-32)
Intel(R) C++ 32-bit Version 8.1
Intel(R) Fortran 32-bit Version 8.1
Linux 2.4.21-sgi303r2 Altix
SMP ia64 Intel(R) C++ Version 8.1
(cobalt) Intel(R) Fortran Itanium(R) Version 8.1
SGI MPI
OSF1 V5.1 (QSC) Compaq C V6.5-011
HP Fortran V5.5A-3548
Compaq C++ V6.5-036
MPIX200_64_r13.4
OSF1 V5.1 (PSC) Compaq C V6.5-303
HP Fortran V5.5A-3548
Compaq C++ V6.5-040
MPIX200_64_r13.4
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90
Sun WorkShop 6 update 2 C++ 5.3
SunOS 5.9 32,64 Sun C 5.6 2004/07/15
(Solaris 2.9) Sun Fortran 95 8.0 2004/07/15
Sun C++ 5.6 2004/07/15
TFLOPS r1.0.4 v4.5.2 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
Xeon Linux 2.4.20-31.9smp_perfctr_lustre
(tungsten) Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
IA-64 Linux 2.4.21.SuSE_128.bef1 ia64
(NCSA tg-login) Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
mpich-gm-1.2.5..intel
Windows XP MSVC++.NET
MSVC++ 6.0
Compaq Visual Fortran 6.6C
Intel 8.1 C++
MAC OS X Darwin 7.5
gcc and g++ Apple Computer, Inc. GCC
version 1175, based on gcc version 3.3.2
IBM XL Fortran version 8.1
Absoft Fortran compiler v8.2
Supported Configuration Features Summary
========================================
Key: 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
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.8 64-bit y y y(1) y y y
Solaris2.8 32-bit y y y(1) y y y
Solaris2.9 64-bit y(1) y y(1) y y y
Solaris2.9 32-bit y(1) y y(1) y y y
IRIX64_6.5 64-bit y(2) y y y y y
IRIX64_6.5 32-bit y(2) n n n y y
HPUX11.00 y(1) y y y y y
OSF1 v5.1 y y y y y y
T90 IEEE n y n n y n
SV1 y(5) y y(5) n y n
TFLOPS y(1) n n n y n
AIX-5.1 & 5.2 32-bit y y y y y y
AIX-5.1 & 5.2 64-bit y y y y y y
WinXP Visual Studio 6.0 n y(9) n y y y
WinXP .Net n n n y(8) y y
Mac OS X 10.3 n y(10) n y y y
FreeBSD 4.9 y(1) n n y y y
RedHat 7.3 W (3) y(1) y(11) n y y y
RedHat 7.3 W Intel (3) n y n y y y
RedHat 7.3 W PGI (3) n y n y y y
SuSe x86_64 gcc (3,13) n y(12) n y y y
SuSe x86_64 icc (3,13) n y(14) n y y y
Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y y
Linux 2.4 SuSE ia64 C Intel (3,7) y y y y y y
Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y
Platform Shared static- Thread- STREAM-
libraries(4) exec safe VFD
Solaris2.8 64-bit y x y y
Solaris2.8 32-bit y x y y
Solaris2.9 64-bit y x y y
Solaris2.9 32-bit y x y y
IRIX64_6.5 64-bit y y y y
IRIX64_6.5 32-bit y y y y
HPUX11.00 y x n y
OSF1 v5.1 y y n y
T90 IEEE n y n y
SV1 n y n y
TFLOPS n y n n
AIX-5.1 & 5.2 32-bit n y n y
AIX-5.1 & 5.2 64-bit n y n y
WinXP Visual Studio 6.0 y y n n
WinXP .Net y y n n
Mac OS X 10.3 y y n y
FreeBSD 4.9 y y y y
RedHat 7.3 W (3) y y y y
RedHat 7.3 W Intel (3) n y n y
RedHat 7.3 W PGI (3) n y n y
SuSe x86_64 gcc (3,13) n y n y
SuSe x86_64 icc (3,13) y y(15) n y
Linux 2.4 Xeon C Lustre Intel (3,6) y y n y
Linux 2.4 SuSE ia64 C Intel (3,7) y y n n
Linux 2.4 SGI Altix ia64 Intel (3) y y n y
Compiler versions for each platform are listed in the "Platforms Tested"
table found elsewhere in this file (RELEASE.txt). Unless otherwise noted,
compilers used are the system compilers.
Footnotes: (1) Using mpich 1.2.6
(2) Using mpt and mpich 1.2.6.
(3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated.
W or C indicates workstation or cluster, respectively.
(4) Shared libraries are provided only for the C library,
except on Windows where they are provided for C and C++.
(5) Using mpt.
(6) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers
(8) Intel 8.1
(9) Compaq Visual Fortran 6.6C
(10) IBM XLF and Absoft
(11) PGI, Absoft. No shared libraries with Absoft;
use '--disable-shared'.
(12) PGI and Intel compilers for both C and Fortran
(13) AMD Opteron x86_64
(14) ifort
(15) Yes with C and Fortran, but not with C++
FMB/EIP - 2005/03/15
Known Problems
==============
* The dataset created or rewritten with the v1.6.3 library or after can't
be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is
enabled. There was a bug in the calculating code of the Fletcher32
checksum in the library before v1.6.3. The checksum value wasn't consistent
between big-endian and little-endian systems. This bug was fixed in
Release 1.6.3. However, after fixing the bug, the checksum value is no
longer the same as before on little-endian system. The library release
after 1.6.4 can still read the dataset created or rewritten with the library
of v1.6.2 or before. SLU - 2005/7/8
* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
processor, there's a bug in the compiler for optimization(-O2). The library
failed in several tests but all related to multi driver. The problem has
been reported to the vendor.
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is an bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Cray SV1 fails to correctly convert between floating-point and "long double"
for software conversion. Problem is being investigated. SLU - 2005/03/04
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but it
has a "guard" statement in stdint.h that will #error and skip the rest
of the header file if C99 option is not used explicitly. Hardset
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may fail with messages like "The socket name is already
in use". HDF5 does not use sockets (except for stream-VFD). This is
due to problems of the poe command trying to set up the debug socket.
Check if there are many old /tmp/s.pedb.* staying around. These are
sockets used by the poe command and left behind due to failed commands.
Ask your system administrator to clean them out. Lastly, request IBM
to provide a mean to run poe without the debug socket.
* There are two h5dump xml tests(h5dump --xml thlink.h5 and
h5dump --xml tmany.h5) failed on windows xp with .NET for debug and
debug dll. Release and Release dll work fine.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, Windows) where the error messages directed to
"stderr" do not appear in the "right order" with output from stdout.
This is not an error.
* The stream-vfd test uses ip port 10007 for testing. If another
application is already using that port address, the test will hang
indefinitely and has to be terminated by the kill command. To try the
test again, change the port address in test/stream_test.c to one not
being used in the host.
* 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 don't use this option on these platforms
during configuration.
* The Stream VFD was not tested yet under Windows. It is not supported
in the TFLOPS machine.
* The ./dsets tests failed in 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.
* Certain platforms give false negatives when testing h5ls:
- Cray T90IEEE give errors during testing when displaying
some floating-point values. These are benign differences due to
the different precision in the values displayed.
h5ls appears to be dumping floating-point numbers correctly.
* Before building HDF5 F90 Library from source on Crays
replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src
subdirectory in the top level directory with the Cray-specific files
from the site:
ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/
* On some platforms that use Intel and Absoft compilers to build HDF5 fortran
library, compilation may fail for fortranlib_test.f90, fflush1.f90 and
fflush2.f90 complaining about exit subroutine. Comment out the line
IF (total_error .ne. 0) CALL exit (total_error)
* Use --disable-shared configure flag if building with Absoft Fortran
compiler
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
* In LANL QSC, the new cc compiler has problems converting small values of
long long (absolute values less than 1**-308) to double. This triggers
the test/dtypes to report failure in the
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to 1**-308.
If -ieee is not used, the converted double values are mostly 0.0 but
occasionally as 1**-308. This has been reported to the system staff.
All other tests have passed.
* The C++ library's tests fails when compiling with PGI C++ compiler. The
workaround until the problem is correctly handled is to use the
flag "--instantiate=local" prior to the configure and build steps, as:
setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
setenv CXX "pgCC -tlocal" for others
* Fortran release DLL randomly failed with compaq visual fortran 6.6c on
windows.
* Fortran DLL built with Intel 8.1 in .NET environment crushed the compiler,
To build Fortran Static library with Intel 8.1 in .NET environment
needs manually setting the project file,
please contact to hdfhelp@ncsa.uiuc.edu if you need to build
fortran static library with Intel 8.1 with .NET environment.
* 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 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 HDF make files and test scripts 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.
|
