HDF5 version 1.6.4 released on Tue Mar 15 20:38:48 CST 2005
This document describes the differences between HDF5-1.6.3 and
HDF5-1.6.4, 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:
For more information look at the HDF5 home page at:
If you have any questions or comments, please send them to:
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.3
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
Source code distribution:
The High-Level (HL) C APIs were added to the source code distribution.
For HL documentation, see
The HL library, libhdf5_hl.a(so), is built and installed by default.
Use --disable-hl configure flag to disable the HL library.
- We recommend you to use SZIP v2.0 with this release.
For more information see
- The compound datatype has been enhanced with a new feature of size
adjustment. The size can be increased and decreased (without
cutting the last member). No API change is involved. SLU -
- Removed PABLO support. 2005/01/20 EIP
- Allow compressed, chunked datasets to be read in parallel.
QAK - 2004/10/04
- New tool, h5jam. See HDF5 Reference Manual. 2004/10/08
No new features in this release.
- Started using C library's reference counting in place of the class
RefCounter, which existed before the C mechanism was available.
As a result, RefCounter has been removed. 2005/03/12 BMR
Support for new platforms, languages and compilers.
- Upgraded from GNU autoconf 2.53 to autoconf 2.59. JML - 2005/01/31
Bug Fixes since HDF5-1.6.3 release
- Fixed a racing condition in MPIPOSIX virtual file drive close
function. Now all processes must completed the close before any
of them is returned. This prevents some "faster" processes start
accessing the file for another purpose (e.g., open with truncate)
while other "slower" processes have not closed the same file with
the previous purpose. AKC - 2005/03/01
- H5Tget_member_value calls for enum datatype didn't return correct
value if H5Tenum_valueof was called first. It's fixed. SLU -
- For variable-length string, H5Tget_class returned H5T_STRING as its
class. But H5Tdetect_class and H5Tget_member_class considered it
as H5T_VLEN. This is fixed to let all these 3 functions treat it
as H5T_STRING. SLU - 2005/02/08
- The byte order of all 1-byte integer types was fixed as
little-endian even on a big-endian machine. It's corrected.
SLU - 2005/02/07
- Fixed segmentation fault when calling H5Fflush with an attribute that
hasn't had a value written to it open. QAK - 2004/10/18
- Backed out support for bitfield and time types in H5Tget_native_type.
Leave it to future support. The function simply returns error
message of "not support" for bitfield and time types. SLU - 2004/10/5
- Fixed address check in Core VFL driver to avoid spurious address/size
overflows for odd valued addresses and/or sizes. QAK - 2004/09/27
- Fixed problem where chunked datasets were not able to be deleted
from a file under certain circumstances. QAK - 2004/09/27/
- IRIX64 MIPSpro compiler of 7.4.x supports C99 features. Default
to use the 'c99' compiler if available. AKC - 2004/12/13
- Intel v8.0 compiler would infinite loop when compiling some test
code with -O3 option. Changed enable-production default compiler
option to -O2. AKC - 2004/12/06
- Long double is assumed to be a supported C data type. It is a
standard C89 type. AKC - 2004/10/22
Many changes were made to the library to improve performance,
especially for the variable-length datatypes and metadata cache.
- h5fc and h5c++ work correctly when -c compiler flag
is used. EIP - 2005/03/14
- Fixed h5dump to print attributes data in ASCII if -r option is used.
AKC - 2004/11/18
- Fixed space utilization reported in h5ls to correct error
in formula used. QAK - 2004/10/22
- On windows, previously Fortran DLL built and tested failed.
Now Fortran DLL has been built and tested successfully
with Dec Fortran 6.6c or Dec Fortran 6.0.
HDF5 Library documentation
No substantive changes to the structure or types of content in the
HDF5 Library documentation.
Windows installation documentation
1. On Windows zlib has been updated to 1.2.2. You may find the binary at
either http://www.zlib.net/zlib122-dll.zip or
2. Only DLLs of external libraries (zlib and szip) are linked with the
HDF5 Library. We will no longer provide binary to link static library
with HDF5. For details, please check INSTALL_Windows in this directory.
AIX 5.1 (32 and 64-bit) xlc 220.127.116.11
AIX 5.2 (32/64 bit) xlc 18.104.22.168
AIX 5.2 (32/64 bit, LLNL frost) xlc 22.214.171.124
Cray T90 sn7001 10.0.0md Cray Standard C Version 126.96.36.199
Cray Fortran Version 188.8.131.52
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 184.108.40.206.6
Cray Fortran Version 220.127.116.11.1
FreeBSD 4.9 gcc 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
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 18.104.22.168m
F90 MIPSpro 22.214.171.124m (64 only)
C++ MIPSpro cc 126.96.36.199m
Linux 2.4.20-28.7 gcc 2.96
(eirene, verbena) gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC)
Absoft Fortran compiler v9.0
Intel(R) C++ 32-bit Version 8.1
Intel(R) Fortran 32-bit Version 8.1
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
OSF1 V5.1 (QSC) Compaq C V6.5-011
HP Fortran V5.5A-3548
Compaq C++ V6.5-036
OSF1 V5.1 (PSC) Compaq C V6.5-303
HP Fortran V5.5A-3548
Compaq C++ V6.5-040
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
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
Windows XP MSVC++.NET
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
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;
(12) PGI and Intel compilers for both C and Fortran
(13) AMD Opteron x86_64
(15) Yes with C and Fortran, but not with C++
FMB/EIP - 2005/03/15
* 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.
* Fortran subroutine h5pget_driver_f doesn't return a correct driver
* 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
* 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:
* 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
* 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
* 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 firstname.lastname@example.org 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
rm -f $STDOUT_FILE $STDERR_FILE
($* > $STDOUT_FILE) >& $STDERR_FILE
tail +3 $STDERR_FILE
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