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HDF5 HISTORY
============
This file contains history of the HDF5 libraries releases starting with
HDF5-1.0.0 and ending with HDF5-1.8.0-rc3 (the state of the code before
the HDF5 1.8.0 release).
CONTENTS
22. Changes from 1.6.0 to 1.8.0-rc3
21. Release Information for hdf5-1.6.7
20. Release Information for hdf5-1.6.6
19. Release Information for hdf5-1.6.5
18. Release Information for hdf5-1.6.4
17. Release Information for hdf5-1.6.3
16. Release Information for hdf5-1.6.2
15. Release Information for hdf5-1.6.1
14. Release Information for hdf5-1.6.0
13. Release Information for hdf5-1.4.5
12. Release Information for hdf5-1.4.4
11. Release Information for hdf5-1.4.3
10. Release Information for hdf5-1.4.2
9. Release Information for hdf5-1.4.1
8. Release Information for hdf5-1.4.0
7. Release Information for hdf5-1.2.2
6. Release Information for hdf5-1.2.1
5. Release Information for hdf5-1.2.0
4. Changes from Release 1.0.0 to Release 1.0.1
3. Changes from the Beta 1.0.0 Release to Release 1.0.0
2. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release
1. Changes from the First Alpha 1.0.0 Release to the
Second Alpha 1.0.0 Release
[Search on the string '%%%%' for per-release section breaks.]
%%%%1.8.0-rc3%%%% Changes from 1.6.0 to 1.8.0-rc3
HDF5 version 1.8.0-rc3
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.* and
Hdf5 1.8.0 release candidate "HDF5-1.8.0-rc3", and contains information
on the platforms tested and known problems in HDF5-1.8.0-rc3.
For more details check the HISTORY.txt file in the HDF5 source.
Links to HDF5 1.8.0-rc3 source code, documentation, and additional materials
can be found on THG's development server (www.hdfgroup.uiuc.edu) at the
following location:
http://www.hdfgroup.uiuc.edu/HDF5/release/beta/obtain518.html
User documentation for the beta can be accessed directly at this location:
http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/
New features of the upcoming 1.8.0 release are described in
the "What's New in 1.8.0?" document:
http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html
New and modified APIs are described briefly in
http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html
and will be listed in the "HDF5 Software Changes" document:
http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ADGuide/Changes.html
For more information, see the HDF5 home page:
http://www.hdfgroup.org/HDF5/
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 HDF5-1.6.0
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
- Removed stream-vfd from the HDF5 library. - AKC 2007/11/19.
- Updated versions of autotools. HDF5 now uses automake 1.10.0,
autoconf 2.61, and libtool 1.5.22. MAM - 2007/7/25.
- Changed default fortran compiler to g95 when gcc is used. - AKC
2007/2/17.
- 'make check-vfd' can now be run from the top level directory. Not all
tests that 'make check' invokes work with certain Virtual File Drivers,
so those tests have been skipped. - MAM 2006/7/17
- Added the variable HDF5TestExpress to control how long tests run.
Setting it to a value between 0 and 3 controls how thoroughly the
library is tested, with 0 being an "exhaustive run" and 3 being a
very quick "smoke test." 1 (a "full run") is the default.
-JML 2006/6/21
- If both shared and static libraries are installed, now both will be
tested during 'make install'. -MAM 2006/06/21
- Added support to explicitly enable stream_vfd or shared libraries
when using parallel via the '--enable-stream_vfd' and
'--enable-shared' options, respectively. If not explicitly defined,
These settings default to enabled when parallel is not used,
and disabled when parallel is used. -MAM 2006/06/17
- Remove the flexible parallel code and the --enable-fphdf5
configure option, it was never up to production standards
anyway. -QAK 2006/4/20
- Added a macro hdf5_mpi_special_collective_io_works to filter out
some mpi-io packages that don't support collective IO for no IO
contributions in some processes. -KY 2006/2/16
- Added -shlib option to link against installed shared libraries to
h5c++ and h5fc. -JML 2005/11/1
- Added --enable-build-all option to configure, which only developers
should need to use. -JML 2005/10/24
- Configure uses the 'TR' variable to let the user override the path
to the 'tr' utility. -JML 2005/10/17
- Configure can recognize -lmpich as a form of MPI library. -AKC-
2005/9/28.
- MD5 checksumming has been added to snapshot releases. Release
tarballs will be accompanied by .md5 checksum files, which can
be verified using the md5sum utility. -JML 2005/9/6
- Some configure flags are incompatible (e.g., the C++ APIs cannot
be built using the parallel version of HDF5). configure will now
output errors when some common incompatible features are used
together. -JML 2005/9/6
- A new API function, H5Tis_hard(), was added to the library. It
checks if a conversion function is a compiler (hard) conversion.
SLU - 2005/9/6
- t_mpi will run the test_mpio_derived_dtype by default unless it is
known not working (indicated by macro H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS
not defined.) -AKC- 2005/8/23.
- Test execution has changed in a number of ways:
When make is invoked in parallel (using -j), sequential tests
are now executed as parallel make targets. This should make them
finish more quickly on machines with multiple processors.
Since test output is garbled when they are executed by parallel make,
tests now dump their output to foo.log files and foo.logsh files
(for test scripts). These logs are printed to the screen only
when a test fails or when all tests in the current directory have
completed successfully.
When tests pass, they will create a foo.chkexe file.
This prevents the test from executing again until the test or
main library changes.
All files generated by tests (*.chkexe, *.log, and any *.h5 files
created) can be removed by invoking 'make check-clean'.
Sequential and parallel library tests can now be invoked separately.
'make check-s' will execute only sequential tests, and 'make check-p'
will execute only parallel tests. 'make check' will still execute
all tests.
JML - 2005/08/03
- On windows, all.zip is deprecated. users should
read INSTALL_Windows.txt to know the details.
Reasons to deprecate all.zip:
1. Avoid confliction for windows programmers
2. Decrease size of CVS tree by adding all.zip
3. Avoid using winzip as the intermediate step
--KY 2005/04/22
- When HDF5 is created as a shared library, it now uses libtool's
shared library versioning scheme. -JML 2005/04/18
- HDF5 now uses automake 1.9.5 to generate Makefiles.in.
This has a number of effects on users:
The Fortran compiler should be set using the environment
variable $FC, not $F9X. F9X still works, but is depreciated.
The output of make may be different. This should be only a
cosmetic effect.
make depend (or make dep) is no longer recognized, since automake
handles dependency tracking.
Some new configure options exist. --enable-dependency-tracking
and --disable-dependency-tracking are used to control automake's
dependency tracking. Dependencies are on by default *on most
platforms and compilers*. If --enable-dependency-tracking is
used, they will be enabled on any platform. However, this can
slow down builds or even cause build errors in some cases.
Likewise, --disable-dependency-tracking can speed up builds and
avoid some build errors.
Some make targets have alternate names. make check-install and
make installcheck do the same thing, for instance.
pmake on IRIX can be invoked from the root directory, but the
-V flag must be used to invoke it in any subdirectory or it
will give an error about undefined variables.
JML 2005/01 - 2005/03
- Hardware conversion between long double and integers is also added.
SLU 2005/02/10
- Started to support software conversion between long double and
integers. Hardware conversion will come very soon. SLU - 2005/1/6
- 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
stanadard C89 type. AKC - 2004/10/22
- The IA64 will use ecc as the C++ compiler by default.
- Added some initial support for making valgrind/Purify (or similar
memory checking products) happier by initializing buffers to zero
and disabling the internal free list code. To take advantage of
this, use the "--enable-using-memchecker" configure option when
building the library. QAK - 2004/07/23
- Fixed the long compile time of H5detect.c when v7.x Intel Compiler
is used with optimization NOT off. AKC - 2004/05/20
- Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06
- Prefix default is changed from /usr/local to `pwd`/hdf5.
AKC - 2003/07/09
Library:
--------
- Removed size restrictions on attributes, when using the "latest"
version of the file format. - QAK - 2007/02/21
- Relaxed restrictions on attribute operations to allow a file ID to
be used as the "location ID". If a file ID is used, the attribute
operation will occur on the root group of the file.
- QAK - 2007/02/09
- Enabled the CORE driver to read an existing file depending on
the setting of the backing_store for H5Pset_fapl_core and file
open flags. - SLU - 2006/11/30
- Added new H5Gget_info_by_idx() routine to query the information about
a group according to the order within an index.
- QAK - 2006/11/27
- Added new H5Gget_info() routine to query the information about a
group by name.
- QAK - 2006/11/27
- Added new H5Oget_info_by_idx() routine to query the information about
an object in a group according to the order within an index.
- QAK - 2006/11/26
- Added new H5Oget_info() routine to query the information about an
object in a group by name.
- QAK - 2006/11/26
- Added new H5Oopen_by_idx() routine to open an object in a group
according to the order within an index.
- QAK - 2006/11/20
- Added new H5Literate() routine to iterate over links in a group
according to the order within an index.
- QAK - 2006/11/20
- Added new H5Ldelete_by_idx() routine to delete a link according to
the order within an index.
- QAK - 2006/11/13
- Added new H5Lget_val_by_idx() routine to query the value of a soft link
according to the order within an index.
- QAK - 2006/11/13
- Added new H5Lget_name_by_idx() routine to query the name of a link
according to the order within an index.
- QAK - 2006/11/12
- Added new H5Rget_name() routine to determine the name of the object
that a reference points to, as long as the object is still
reachable in the group hierarchy.
- QAK - 2006/11/10
- Added new H5Lget_info_by_idx() routine to query the link information
according to the order within an index.
- QAK - 2006/11/10
- Added feature to H5Iget_name to allow retrieving the name of any
object's ID, as long as the object is still reachable in the
group hierarchy.
- LA - 2006/11/01
- Added External and User-defined links.
External links are links from one HDF5 file to another; they
require both the name of the file and a path within that file.
User-defined links allow users to supply callback functions
for link traversals, allowing links to exhibit essentially
any behavior.
External links are a kind of user-defined link, so their default
behavior can be overridden by the user.
-JML 2006/8/23
- Added H5Oopen and H5Oclose for opening objects of unknown type
(as link callback functions do).
-JML 2006/8/23
- Added H5Oopen_by_addr, H5Oincr_refcount, and H5Odecr_refcount for
opening objects by address. Be very careful with these!
-JML 2006/8/23
- Added H5Fget_intent to get the "intent" of a file (whether it
was opened with read-write access or read-only.
-JML 2006/8/23
- Added Link Access Property Lists. They currently contain two
properties, nlinks (H5Pget/set_nlinks) and elink_prefix
(H5Pget/set_elink_prefix). nlinks controls how many soft and
user-defined traversals are allowed before HDF5 assumes it has
found a cycle (previously this defaulted to 16).
The elink_prefix is a filesystem path that is prefixed to the
names of any external link files opened using this LAPL.
-JML 2006/8/23
- Add H5L link APIs. Old APIs (H5Glink, H5Gmove, etc.) are still
supported but deprecated.
New APIs are:
H5Llink - create a link to an object given its ID
H5Lmove - just like H5Gmove2
H5Lcopy - copy a link without copying the underlying object
H5Lcreate_hard - like H5Glink2 for hard links
H5Lcreate_soft - like H5Glink2 for soft links
H5Ldelete - just like H5Gunlink
H5Lget_val - just like H5Gget_linkval
H5Lget_info - gets link-specific info (like H5Gget_objinfo)
In addition, H5Gcreate_anon, H5Tcommit_anon, and H5Dcreate_anon
no longer create links to objects; objects must be manually linked
using H5Llink or they will be deleted when the ID is closed.
Link Creation Property Lists can be used to pass character
encoding (ASCII or UTF-8) for link names and to set the Intermediate
Group Creation Flag:
H5Pset_char_encoding, H5Pget_char_encoding
H5Pset_copy_object, H5Pget_copy_object
-JML 2006/7/5
- Added managements of collective IO supports for chunking storage
inside parallel HDF5
1) Implemented One IO with collective mode for all chunks in the
application by building one MPI derived datatype across all
chunks.
2) Implemented the decision-making support to do collective IO inside
MPI-IO per chunk.
3) Added the decision-making support to do one IO across all chunks
or to do multiple IOs with each IO per chunk.
4) Added the support to handle the case some processes won't do any IOs in
collectively.
5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle
collective IO correctly for the case when some processes have no
contributions to IOs, a special macro is added to change
collective IO mode to independent IO mode inside HDF5 library.
Currently we find that MPICH at Linux and vendor MPI-IO package at NCSA
Altix cannot handle this case.
"hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}"
has been added at the end of file <ia64-linux-gnui> and
<linux-gnulibc1>.
If MPI-IO packages at your Linux and Altix support this case,
please comment out the last line and report to us at
help@hdfgroup.org. We can tune in our configuration to
support this.
KY - 2006/02/16
- Added character encoding to attribute creation property lists.
JML - 2006/01/02
- Added H5Gcopy() routine to copy objects between while keeping
data in compressed form. QAK - 2005/11/06
- Added H5Sextent_equal() routine. QAK - 2005/11/06
- Added HSYS_ERROR which retrieves the system error message and pushes
it to the error stack. This gives more information of the failed
system call. AKC - 2005/08/04
- 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
- Added H5T_CSET_UTF8 character set to mark datatypes that use the
UTF-8 Unicode character encoding. Added tests to ensure that
library handles UTF-8 object names, attributes, etc. -JL 2005/05/13
- HDF5 supports collective MPI-IO for irregular selection with HDF5
dataset. Irregular selection is when users use H5Sselect_hyperslab
more than once for the same dataset.
Currently, not all MPI-IO packages support complicated MPI derived
datatype used in the implementation of irregular
selection INSIDE HDF5.
1) DEC 5.x is not supporting complicated derived datatype.
2) For AIX 5.1,
if your poe version number is 3.2.0.19 or lower,
please edit powerpc-ibm-aix5.x under hdf5/config,
Find the line with
<< hdf5_mpi_complex_derived_datatype_works>>
and UNCOMMENT this line before the configure.
check poe version with the following command:
lpp -l all | grep ppe.poe
3) For Linux cluster,
if mpich version is 1.2.5 or lower, collective irregular selection
IO is not supported, internally independent IO is used.
4) For IRIX 6.5,
if C compiler version is 7.3 or lower, collective irregular selection
IO is not supported, internally independent IO is used.
5) For platforms which internally used mpich, if the
mpich version is 1.2.5 or lower, please find the
corresponding config file and add
hdf5_mpi_complex_derived_datatype_works='no' at the
end of the configuration file. For example, at NCSA
SGI Altix, the internal mpich library is 1.2.5. So
hdf5_mpi_complex_derived_datatype_works='no' should be
added at the end of the config file ia64-linux-gnu.
KY - 2005/09/12
We also found not all MPI-IO packages support collective IO with one
or more processes to have no contributions to IO.
For mpich version 1.2.6 or lower and all IRIX machine,
if the library checks that there are no IO contributions for some
processes, collective IO request is replaced with
independent inside HDF5.
KY - 2006/05/04
- HDF5 N-bit filter
HDF5 support N-bit filter from this version,
The N-Bit filter is used effectively for compressing data of N-Bit
datatype as well as compound and array datatype with N-Bit fields.
KY - 2005/04/15
- HDF5 scaleoffset filter
HDF5 supports scaleoffset filter for users to do data
compression through HDF5 library.
Scale-Offset compression performs a scale and/or offset operation
on each data value and truncates the resulting value to a minimum
number of bits and then stores the data.
Scaleoffset filter supports floating-point and integer datatype.
Please check the HDF5 reference manual for this.
KY - 2005/06/06
- Retired SRB vfd (--with-srb). Functions H5Pset_fapl_srb and
H5Pget_fapl_srb were removed. EIP - 2005/04/07
- Retired GASS vfd (--with-gass). Functions H5Pset_fapl_gass and
H5Pget_fapl_gass are removed too. AKC - 2005/3/3
- Pablo was removed from the source code EIP - 2005/01/21
- Modified registration of SZIP to dynamically detect the presence
or absence of the encoder. Changed configure and Makefiles,
and tests to dynamically detect encoder. BEM - 2004/11/02
- Added function H5Pget_data_transform, together with the previously
added H5Pset_data_transform, to support the data transform
feature. AKC - 2004/10/26
- Compound datatype has been enhanced with a new feature of size
adjustment. The size can be increased and decreased(without
cutting the last member) as long as it doesn't go down to zero.
No API change is involved. SLU - 2004/10/1
- Put back 6 old error API functions to be backward compatible with
version 1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear,
H5Eset_auto, H5Eget_auto. Their new equivalent functions are
called H5Epush_stack, H5Eprint_stack, H5Ewalk_stack,
H5Eclear_stack, H5Eset_auto_stack, H5Eget_auto_stack. SLU -
2004/9/2
- 4 new API functions, H5Tencode, H5Tdecode, H5Sencode, H5Sdecode were
added to the library. Given object ID, these functions encode and
decode HDF5 objects(data type and space) information into and from
binary buffer. SLU - 2004/07/21
- Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for
SZIP compression. Now there is no restriction on the size and shape of the
chunk except that the total number of elements in the chunk cannot be
bigger than 'pixels_per_block' parameter provided by the user.
EIP - 2004/07/21
- Added support for SZIP without encoder. Added H5Zget_filter_info
and changed H5Pget_filter and H5Pget_filter_by_id to support this
change. JL/NF - 2004/06/30
- SZIP always uses K13 compression. This flag no longer needs to
be set when calling H5Pset_szip. If the flag for CHIP
compression is set, it will be ignored (since the two are mutually
exclusive). JL/NF - 2004/6/30
- A new API function H5Fget_name was added. It returns the name
of the file by object(file, group, data set, named data type,
attribute) ID. SLU - 2004/06/29
- Added support for user defined identifier types. NF/JL - 2004/06/29
- A new API function H5Fget_filesize was added. It returns the
actual file size of the opened file. SLU - 2004/06/24
- New Feature of Data transformation is added. AKC - 2004/05/03.
- New exception handler for datatype conversion is put in to
replace the old overflow callback function. This exception
handler is set through H5Pset_type_conv_cb function.
SLU - 2004/4/27
- Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2,
will suppress all library version mismatch warning messages.
AKC - 2004/4/14
- A new type of dataspace, null dataspace(dataspace without any
element) was added. SLU - 2004/3/24
- Data type conversion(software) from integer to float was added.
SLU - 2004/3/13
- Data type conversion(software) from float to integer was added.
Conversion from integer to float will be added later.
SLU -2004/2/4
- Added new H5Premove_filter routine to remove I/O pipeline filters
from dataset creation property lists. PVN - 2004/01/26
- Added new 'compare' callback parameter to H5Pregister & H5Pinsert
routines. QAK - 2004/01/07
- Data type conversion(hardware) between integers and floats was added.
SLU 2003/11/21
- New function H5Iget_file_id() was added. It returns file ID given
an object(dataset, group, or attribute) ID. SLU 2003/10/29
- Added new fields to the H5G_stat_t for more information about an
object's object header. QAK 2003/10/06
- Added new H5Fget_freespace() routine to query the free space in a
given file. QAK 2003/10/06
- Added backward compatibility with v1.6 for new Error API. SLU -
2003/09/24
- Changed 'objno' field in H5G_stat_t structure from 'unsigned long[2]'
to 'haddr_t'. QAK - 2003/08/08
- Changed 'fileno' field in H5G_stat_t structure from 'unsigned long[2]'
to 'unsigned long'. QAK - 2003/08/08
- Changed 'hobj_ref_t' type from structure with array field to 'haddr_t'.
QAK - 2003/08/08
- Object references (hobj_ref_t) can now be compared with the 'objno'
field in the H5G_stat_t struct for testing if two objects are the
same within a file. QAK - 2003/08/08
- Switched over to new error API. SLU - 2003/07/25
Parallel Library:
-----------------
- Added mpich2 as a testing "platform" informally. AKC - 2005/9/28.
- A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation
setting was not extendible, either explicitly by H5Dextend or
implicitly by writing to unallocated chunks. Library now allocates
more space when needed or directed if the file is opened by parallel
mode, independent of what the dataset allocation mode is.
CC/AKC - 2005/08/29.
- Allow compressed, chunked datasets to be read in parallel.
QAK - 2004/10/04
- Add options of using atomicity and file-sync to test_mpio_1wMr.
AKC - 2003/11/13
- Added parallel test, test_mpio_1wMr, which tests if the
underlying parallel I/O system is conforming to the POSIX
write/read requirement. AKC - 2003/11/12
Fortran Library:
----------------
- added support for shared Fortran libraries. -JML 2005/09/20
- added missing h5tget_member_class_f function
EIP 2005/04/06
- added new functions h5fget_name_f and h5fget_filesize_f
EIP 2004/07/08
- h5dwrite/read_f and h5awrite/read_f functions only accept dims parameter
of the type INTEGER(HSIZE_T).
- added support for native integers of 8 bytes (i.e. when special
compiler flag is specified to set native fortran integers to 8 bytes,
for example, -i8 flag for PGI and Absoft Fortran compilers,
-qintsize=8 flag for IBM xlf compiler).
EIP 2005/06/20
- added support for "big" REAL and DOUBLE PRECISION types
(usually the size is specified by compilers flags like
-r8, -r16, etc.)
Known problem: multi file test fails when REAL is 16 bytes.
EIP 2005/09/8
C++ Library:
----------------
- added support for shared C++ libraries. -JML 2005/09/20
- 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.
H5::IdComponent::getHDFObjType
BMR - 2005/08/08
Tools:
------
- h5repack and h5diff changed command line parameter syntax to be
similar to h5dump, adding also long switch names. PVN - 2008/1/16
- h5repack now supports adding multiple filters to all objects.
PVN - 2008/1/16
- h5dump lists groups and attributes in requested orders (by name and
creation order, both ascending and descending). PVN - 2007/10/5
- h5import imports string (text) data. PVN - 2007/10/5
- h52gif and gif2h5: Both these tools were revised to include the High
Level Image API support, and tests were added to /hl/tools/gif2h5.
PVN - 2007/04/13
- h5dump: added support for double long type H5T_NATIVE_LDOUBLE. PVN
2007/03/13
- h5dump: added support for binary output, see usage. PVN 2007/03/13
- h5repack: added support for the new nbit and scaleoffset filters.
PVN - 2007/05/07
- h5repack: now uses the API function H5Ocopy (of the tool h5copy) to
recreate objects if there is not a user input for changes. PVN -
2007/05/07
- h5repack: added support for reading and repacking by hyperslabs for
large files. PVN - 2007/03/01
- h5repack: a new option allows the copy using the file type (default)
instead of the previous conversion to native type. PVN - 2007/03/01
- h5repack: output the percentage of compression used. PVN - 2007/03/01
- h5diff: added support for -p option for unsigned long_long data. PVN
2007/02/26
- h5diff: added support for comparing dataset regions. PVN - 2007/02/20
- h5diff: added support for reading and comparing by hyperslabs for large files.
PVN - 2007/02/20
- h5diff: printing of dataset dimensions along with dataset name. PVN -2007/02/19
- h5dump now uses the new API function H5Rget_name to display the name
of the dataset referenced instead of its ID. PVN - 2007/02/19
- Added new tool, h5mkgrp. QAK - 2007/02/14
- Added new tool, h5copy. PVN - 2006/7/15
- Removed obsolete pdb2hdf5 tool from tools/misc -JML 2005/10/24
- Added build_h5perf_alone.sh that builds h5perf by standalone mode.
AKC - 2005/09/18.
- Sped up h5dump on files with large numbers of objects.
QAK - 2005/08/25
- Added a standalone mode for building h5perf. AKC - 2005/08/12
- new tool, h5jam. See reference manual. 2004/10/08
- h5repack.sh did not report errors encountered during tests. It does
now. AKC - 2004/04/02
- Added the MPI-I/O and MPI-POSIX drivers to the list of VFL drivers
available for h5dump and h5ls. RPM & QAK - 2004/02/01
- Added option --vfd= to h5ls to allow a VFL driver to be selected
by a user. RPM & QAK - 2004/02/01
- Added option -showconfig to compiler tools (h5cc,h5fc,h5c++).
AKC - 2004/01/08
- Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc"
respectively if library is built in parallel mode.
WCW - 2003/11/04
- Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03
- Changed output of "OID"s from h5dump from "<number>-<number>" to
"<number". This affects both the "regular" and XML output.
QAK - 2003/08/08
- Changed output of file IDs and "OID"s from h5ls from
"<number>:<number>:<number>:<number>" to "<number>:<number>"
QAK - 2003/08/08
High-Level APIs:
------
- Fortran interfaces for the Image, Table and Lite APIs. PVN - 2007/5/1
- New HDF5 Dimension Scale API (H5DS) allows dimension scales to be
created in an HDF5 file and associated with specific datasets. PVN - 2007/5/1
- There are two new functions in the Lite library, H5LTtext_to_dtype
and H5LTdtype_to_text. H5LTtext_to_dtype creates a HDF5 data type
given a text description; H5LTdtype_to_text converts a data type
to text description. Only DDL definition is supported as text
description now. SLU - 2006/05/17
- Added Packet Table API for creating tables with less overhead than
H5TB API. Added C++ wrapper for Packet Tables. See documentation.
JML - 2004/03/28
Documentation
-------------
- The documentation for this release is largely complete, but
trails the source code. A few of the newer functions are
not yet documented. FMB - 2007/04/18
- The user documents for this release can be accessed directly at
this location:
http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/
The most recent document versions (updated daily) in the
1.8 development branch can be accessed at this location:
http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/
FMB - 2007/04/18
Support for new platforms, languages and compilers.
=======================================
- Added support for Free-BSD on amd64 with GNU C and Fortran compilers
4.2.1
EIP - 2007/06/25
- Added support for sequential and parallel libraries for Intel 64 Linux
cluster (abe.ncsa.uiuc.edu). Among three MPICH packages available on
this machine, only Open MPI works. The VMI has seg fault in hyperslab.c
and bittests.c tests. The MVAPICH2 complained about mpd not running
the parallel test. (see Known Problems section for more info)
EIP - 2007/06/25
- Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++
- Added support for 64-bit Windows with Visual Studio .NET and 2005.
SJW - 2007/06/25
- Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++
shared library is not supported with +DD64 flag.
EIP - 2006/06/22
- Added support for VAX floating numbers for Alpha Open VMS 7.3.2
EIP - 2006/05/05
- Fixed broken make.com files in tools directories
EIP - 2006/05/05
- Added support for Alpha Open VMS 7.3.2 EIP - 2006/04/15
- Added support for Cray X1. JML - 2005/10/03
- PGI Fortran compiler is supported on Linux64 systems (x86_64)
EIP - 2004/08/19
- Absoft compiler f95 v9.0 supported on Linux 2.4
EIP - 2004/07/29
- HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran
compiler version 8.1. This is a default compiler.
- HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler
version 8.2; set F9X environment variable to f95, for example
setenv F9X f95
Use --disable-shared --enable-static configure flags when Absoft
compiler is used.
EIP - 2004/07/27
- HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran
Compiler version 8.1 Use "--disable-shared --enable-static"
configure flags along with the "--enable-fortran" flag to build
Fortran library. EIP - 2004/01/07
Bug Fixes since HDF5-1.6.0 release
==================================
Library
-------
- Changed library's behavior for reading files that might have
corrupted object header information from a previous (buggy)
version of the library. By default, the library now rebuilds the
correct object header information instead of issuing an error.
Previous "strict" file format interpretation can be enabled with
the "--enable-strict-format-checks" configure option.
QAK - 2008/01/13
- Fixed several bugs with writing fill values for datasets that have
a variable-length datatype or component datatype. QAK - 2007/06/19
- STDIO driver didn't support files bigger than 2GB because the OFFSET
parameter of fseek is of type LONG INT, not big enough for big files.
Use fseeko instead for big files if it's available on the system.
SLU - 2007/4/5
- Fixed a bug in H5Sselect_valid() that caused an incorrect value to
be returned (0) instead of FAIL on error conditions such as the
selection or extent not being defined. CMC - 2007/01/17
- Fixed the MULTI driver problem (Bug #731) that corruptted the data.
SLU - 2007/1/12
- Fixed file corruption bug which could write an incorrect number of
messages to an object's header under certain circumstances.
Generally, the sequence of actions to generate this bug looks
like this:
- Create an object
- Close the file
- Re-open the file
- Add 2 (or more) attributes to the object
- Close the file
- Re-open the file
- Delete one of the attributes on the object
- Add a smaller attribute to the object
- Delete the smaller attribute on the object
- Add a larger attribute on the object
After this, the number of header messages stored for the object
will be off by one. Other sequences of modifying attributes on an
object could also trigger this bug. If you are opening an
object and the bottom few messages of the HDF5 error stack
resembles this, the object has been affected by this bug:
#007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): unable to load entry
major(08): Meta data cache layer
minor(40): Unable to load metadata into cache
#008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): corrupt object header - too few messages
major(12): Object header layer
minor(40): Unable to load metadata into cache
Specifically, "corrupt object header" is the best string to search
for in the HDF5 error stack output.
If your files have been affected by this bug, or you are concerned
that your files might have been, please contact the HDF Helpdesk
at help@hdfgroup.org for a tool to detect and repair files
affected by this problem. QAK - 2006/6/16
- Fixed various problems with retrieving names of objects, especially
with mounted files. QAK - 2005/12/25
- Fixed core dump when closing root groups opened through two different
file handles that operate on the same actual file. QAK - 2005/10/02
- Corrected errors when performing various operations on 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
- 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
- The library didn't save the information of family driver in file.
The original file member size was lost after file was closed (see
bug #213). This has been fixed by saving driver name and member
file size in the superblock. SLU - 2005/6/24
- 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
- For family driver, the library didn't save member size in file.
When file is reopened, the size of 1st member file determine the
member size. Now member size is saved in file and is used to
define member file size. Wrong file access property of member size
will result in a failure. Using any other driver except family
will cause library to return error. So is multi driver. SLU -
2005/05/24
- Fixed error in opening object in group that was opened in mounted
file which has been unmounted. QAK - 2005/03/17
- 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 -
2005/02/08
- 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 1-byte integer types was fixed as little endian
even on a big-endian machine. This has been corrected. SLU -
2005/02/07
- Fix segmentation fault when calling H5Fflush with an attribute that
hasn't had a value written to it open. QAK - 2004/10/18
- Back up supporting 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 parallel bug in which some processes attempted collective
I/O while others did independent I/O. Bug appeared when some
processes used point selections, and others didn't. JRM - 2004/9/15
- Corrected error where dataset region references were written in an
incorrect way on Cray machines. PVN & QAK - 2004/09/13
- The H5Tget_native_type now determines the native type for integers
based on the precision. This is to avoid cases of wrongly converting
an int to a short in machines that have a short of 8 bytes but with
32bit precision (e.g Cray SV1). PVN - 2004/09/07
- Changed H5Dread() to not overwrite data in an application's buffer
with garbage when accessing a chunked dataset with an undefined
fill value and an unwritten chunk is uncountered. QAK - 2004/08/25
- Fixed error which could cause a core dump when a type conversion
routine was registered after a compound datatype had been
converted and then an equivalment compound datatype was converted
again. QAK - 2004/08/07
- Fixed memory overwrite when encoding "multi" file driver information
for file's superblock. QAK - 2004/08/05
- Fixed obscure bug where a filter which failed during chunk allocation
could allow library to write uncompressed data to disk but think
the data was compressed. QAK - 2004/07/29
- Fixed bug where I/O to an extendible chunked dataset with zero-sized
dimensions would cause library to fail an assertion.
QAK - 2004/07/27
- Fixed bug where chunked datasets which have filters defined,
allocation time set to "late" and whose chunks don't align with
the dataspace bounds could have incorrect data stored when
overwriting the entire dataset on the first write. QAK - 2004/07/27
- Added check to ensure that dataspaces have extents set. JML-2004/07/26
- Fixed bug on some Solaris systems where HDF5 would try to use
gettimeofday() when that function didn't work properly.
JML - 2004/07/23
- Fixed bug in H5Sset_extent_simple where setting maximum size to
non-zero, then to zero would cause an error. JML - 2004/07/20
- Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite
when not writing data ("none" selection or hyperslab or point
selection with no elements defined). QAK - 2004/07/20
- Calling H5Gcreate() on "/" or "." throws an error instead of
failing quietly. JML - 2004/07/19
- Fixed bug where setting file address size to be very small could
trigger an assert if the file grew to more than 64 KB. Now throws
an error and data can be recovered. JL/NF - 2004/07/14
- Fixed bug where "resurrecting" a dataset was failing.
QAK - 2004/07/14
- Fixed bug where incorrect data could be read from a chunked dataset
after it was extended. QAK - 2004/07/12
- Fixed failure to read data back from file of compound type with
variable-length string as field. SLU - 2004/06/10
- Fixed potential file corruption bug when a block of metadata could
overlap the end of the internal metadata accumulator buffer and
the buffer would be extended correctly, but would incorrectly
change it's starting address. QAK - 2004/06/09
- Opaque datatype with no tag failed for some operations. Fixed.
SLU - 2004/6/3
- Fixed potential file corruption bug where dimensions that were
too large (a value greater than could be represented in 32-bits)
could cause the incorrect amount of space to be allocated in a
file for the raw data for the dataset. QAK - 2004/06/01
- Fixed dtypes "sw long double -> double" failure in QSC class
machines. AKC - 2004/4/16
- Fixed problem with fletcher32 filter when converting data of different
endianness. PVN - 2004/03/10
- Fixed problem with H5Tget_native_type() not handling opaque fields
correctly. QAK - 2004/01/31
- Fixed several errors in B-tree deletion code which could cause a
B-tree (used with groups and chunked datasets) to become corrupt
with the right sequence of deleted objects. QAK - 2004/01/19
- Fixed small internal memory leaks of fill-value information.
QAK - 2004/01/13
- Fixed bug that caused variable-length datatypes (strings or sequences)
used for datasets in files with objects that were unlinked to
fail to be read/written to a file. QAK - 2004/01/13
- Detect situation where szip 'pixels per block' is larger than the
fastest changing dimension of a dataset's chunk size and disallow
this (due to limits in szip library). QAK - 2003/12/31
- Fixed bug with flattened hyperslab selections that would generate
incorrect hyperslab information with certain high-dimensionality
combinations of start/stride/count/block information.
QAK - 2003/12/31
- Fixed bug with variable-length datatypes used in compound datatypes.
SLU - 2003/12/29
- Fixed bug in parallel I/O routines that would cause reads from
"short datasets" (datasets which were only partially written out)
to return invalid data. QAK & AKC - 2003/12/19
- Fixed bug where scalar dataspaces for attributes were reporting as
simple dataspaces. QAK - 2003/12/13
- Fixed problem with selection offsets of hyperslab selections in
chunked datasets causing the library to go into an infinite loop.
QAK - 2003/12/13
- Fixed H5Giterate to avoid re-using index parameter after iteration
callback has been called (allows iteration callback to modify the
index parameter itself). QAK - 2003/12/06
- Fixed various floating-point conversion problems, including a
change which could corrupt data when converting from double->float.
QAK - 2003/11/24
- Changed "single process" metadata writing in library to collective
I/O by all processes, in order to guarantee correct data being
written with MPI-I/O. QAK - 2003/11/20
- Fixed problems with fill values and variable-length types and also
I/O on VL values that were set to NULL. QAK - 2003/11/08
- Fixed problems with MPI datatypes that caused ASCI Q machine to
hang. QAK - 2003/10/28
- Removed HDF5_MPI_PREFER_DERIVED_TYPES environment variable support,
since it had no benefit. QAK - 2003/10/28
- Single hyperslab selections (which were set with only one call to
H5Sselect_hyperslab) that had dimensions that could be "flattened"
but were interspersed with dimensions that could not be flattened
were not correctly handled, causing core dumps. QAK - 2003/10/25
- Fixed incorrect datatype of the third parameter to the Fortran90
h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T))
EIP - 2003/10/13
- Fixed problems with accessing variable-length data datatypes on
Crays. QAK - 2003/10/10
- Fixed potential file corruption bug when too many object header
messages (probably attributes, from a user perspective) were
inserted into an object header and certain other conditions were
met. QAK - 2003/10/08
- Changed implementation of internal ID searching algorithm to avoid
O(n) behavior for many common cases. QAK - 2003/10/06
- Allow partial parallel writing to compact datasets. QAK - 2003/10/06
- Correctly create reference to shared datatype in attribute, instead
of making a copy of the shared datatype in the attribute.
QAK - 2003/10/01
- Revert changes which caused files >2GB to fail when created with
MPI-I/O file driver on certain platforms. QAK - 2003/09/16
- Allow compound datatypes to grow in size. SLU - 2003/09/10
- Detect if a type is already packed before attempting to pack it
again or check if it is locked. SLU - 2003/09/10
- Corrected bug when opening a file twice with read-only permission
for one open and then closing the read-only access file ID would
generate an error. QAK - 2003/09/10
- Corrected bug in repeated calls to H5Pget_access_plist() which would
incorrectly manage reference counts of internal information and
eventually blow up. QAK - 2003/09/02
- Return rank of the array datatype on successful call to
H5Tget_array_dims(). QAK - 2003/08/30
- Corrected bug in H5Tdetect_class which was not correctly detecting
datatype classes of fields in nested compound datatypes in some
circumstances. QAK - 2003/08/30
- Corrected bug in sieve buffer code which could cause loss of data
when a small dataset was created and deleted in quick succession.
QAK - 2003/08/27
- Corrected bug in H5Gget_objname_by_idx which was not allowing NULL
for the name when just querying for the object name's length.
QAK - 2003/08/25
- Corrected bug in variable-length string handling which could
generate a core dump on writing variable-length strings as part
of a compound datatype on certain architectures. QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would incorrectly compute
the size of certain compound datatypes and also incorrectly
compute the offset of the last field for those compound datatypes.
QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would drop string datatype
metadata (padding, etc.) QAK - 2003/08/25
- Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and
H5Gget_objtype_by_idx to allow them to accept location IDs, not just
group IDs. QAK - 2003/08/21
- Corrected bug when using scalar dataspace for memory selection and
operating on chunked dataset. QAK - 2003/08/18
- Corrected bugs with multiple '/' characters in names for H5Glink
and H5Gunlink. QAK - 2003/08/16
- Corrected bug with user blocks that didn't allow a user block to
be inserted in front of a file after the file was created.
QAK - 2003/08/13
- Corrected errors with using point selections to access data in
chunked datasets. QAK - 2003/07/23
- Corrected error with variable-length datatypes and chunked datasets
caused H5Dwrite to fail sometimes. QAK - 2003/07/19
- Modified library and file format to support storing indexed storage
(chunked dataset) B-tree's with non-default internal 'K' values.
QAK - 2003/07/15
- Returned H5T_BKG_TEMP support to library after it was accidentally
removed. QAK - 2003/07/14
Configuration
-------------
- Configure can now use any tr command. No more need for
defining variable TR nor is it supported. -AKC 2006/05/19
- Parallel I/O with the MPI-I/O driver will no longer work if the
filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE"
environment variable has been removed. QAK - 2004/01/30
- Fixed the error that cause "make install" to fail because of the
macro definition syntax of "prefix?=..." AKC - 2003/07/22
Performance
-------------
- Optimized I/O for enumerated datatypes that are a superset of source
enumerated datatype. QAK - 2005/03/19
- More optimizations to inner loops of datatype conversions for
integers and floats which give a 10-50% speedup. QAK - 2003/11/07
- Hoisted invariant 'if/else's out of inner datatype conversion loop for
integer and floating-point values, giving about a 20% speedup.
QAK - 2003/10/20
Tools
-----
- Fixed h5dump regarding the display of blocks in hyperslab
selections. PVN 2008/01/16
- Fixed h5diff regarding the display of NaN (Not a Number)
values. PVN 2008/01/16
- Fixed h5dump regarding the parsing of binary output parameters.
PVN 2008/01/16
- Fixed memory problems in h52gif and gif2h5. PVN 2008/01/16
- Fixed h5repack dealing with NULL references. PVN 2008/01/16
- Fixed h5dump & h5ls to display attributes in "name" order, rather
than the order they are encountered in the object header.
QAK - 2007/10/04
- Fixed h5dump regarding the display of named datatypes
attributes. PVN 2007/03/13
- Fixed h5dump regarding the display of group comments. PVN
2007/03/13
- Fixed h5dump regarding the display of hardlinks pointing
to the root group. PVN 2007/03/13
- Fixed h5diff percentage option -p. PVN 2007/03/05
- Fixed h5dump that caused array indices greater than 2 ^32-1
not to be printed correctly - PVN 2007/2/19
- 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
- Fixed h5redeploy which sometimes complain too many argument for the
test command. (The complain did not hinder the h5redploy to
proceed correctly.) AKC - 2003/11/03
- Fixed a segmentation fault of h5diff when percentage option is used.
AKC - 2003/08/27
- Switched away from tools using internal "fixtype" function(s) to use
H5Tget_native_type() internally. QAK - 2003/08/25
Documentation
-------------
F90 APIs
--------
- h5pget_driver_f was returning information that could not be
interpreted by fortran application program; fixed. EIP - 2005/04/10
Platforms Tested
================
Platforms marked with * were not tested for hdf5-1.8.0-rc* release
(This information is somewhat out of date and may be inaccurate. It will be
updated for a later 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
* AIX 5.3 (32/64 bit) xlc 7.0.0.8
xlC 7.0.0.8
xlf 09.01.0000.0007
* Cray X1 water 3.0.35 Cray Standard C Version 5.4.0.7.4
Cray Fortran 5.4.0.7.3
Cray C++ 5.4.0.7.4
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
* HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.00
HP F90 v2.9.2
HP aC++/ANSI C B3910B A.06.00
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, g95 (GCC 4.0.3)
(smirom) PGI 6.2-5 (pgcc, pgf90, pgCC)
Intel 9.1 (icc, iort, icpc)
Linux 2.6.5-7.252.1-rtgfx #1
SMP ia64 Intel(R) C++ Version 9.0
(cobalt) Intel(R) Fortran Itanium(R) Version 9.0
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 i86pc Sun C 5.7
Sun Fortran 95 8.1
Sun C++ 5.7
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
Supported Configuration Features Summary
(This table was not modified for 1.8.0-rc* release; for information contact help@hdfgroup.org)
========================================
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
Cray XT3 (16) n n n n n n
AIX-5.2 & 5.3 32-bit y y y y y y
AIX-5.2 & 5.3 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
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
HPUX11.00 y n y x n
HPUX11.23-32bit y n n y n
HPUX11.23-64bit y dna n y n
Cray XT3 (16) n n n n n
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
Mac OS X 10.4 PowerPC
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 discovered two problems when running collective IO parallel HDF5 tests
with chunking storage on 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 wrong derived data type and corrupt data
may be generated.
This only happens when turning on collective IO with chunking storage
with some complex selections. We haven't found these problems on other
MPI-IO compilers. If you encounter these problems, you may use Independent IO
instead.
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. Higher level of optimization
causes failures in several HDF5 library tests.
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
shared libraries (tested for 1.8.0-beta2)
* For SNL, Red Storm: only parallel HDF5 is supported. The serial tests pass
and the parallel tests also pass with lots of non-fatal error messages.
* For LLNL, uP: both serial and parallel pass. Zeus: serial passes but
parallel fails with a known proglem in MPI. ubgl: serial passes but
parallel fails.
* on SUN 5.10 C++ test 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, Scaleoffset filter isn't supported. The filter cannot be applied to
HDF5 data generated on VAX. Scaleoffset filter only supports 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, we found that if more than two processes
contribute no IO and the application asks to do IO with collective, we found
that when using 4 processors, a simple collective write will be hung
sometimes. This can be verified with t_mpi test under testpar.
* On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type
code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment
variable to some certain value in order to use collective irregular selection code.
For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to
200,000 to make the test pass.
* 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 - 2005/6/30
* 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.
* 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.
* 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
* 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.
* With the gcc 2.95.2 compiler, HDF 5 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 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 J90 and 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 and 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 this site:
ftp://www.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.0-pre/PATCH/
* 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 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)
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
* 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 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.
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
is turn on. The value of the reference in the destination attribute is
wrong. This H5Ocopy problem will affect h5copy tool
%%%%1.6.7%%%% Release Information for hdf5-1.6.7 (31/January/08)
HDF5 version 1.6.7 released on Thu Jan 31 21:09:10 CST 2008
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7
It contains information on the platforms tested and known problems in
HDF5-1.6.7. For more details, check the HISTORY.txt file in the HDF5 source.
HDF5 documentation can be found in the distributed release source code
in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Documentation for the current release in the HDF5 Release 1.6.x series is
also on the HDF web site:
http://hdfgroup.org/HDF5/doc1.6/
For more information, see the HDF5 home page:
http://hdfgroup.org/products/hdf5/
If you have any questions or comments, please see the HDF Support page
for a list of available resources:
http://hdfgroup.org/services/support.html
CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.6
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
'--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid
configure options because the stream I/O driver has ben removed from
the distribution.
Source code distribution
========================
Library:
--------
The stream I/O driver is not included with the HDF5 Library in this
release. The source code files hdf5/src/H5FDstream.c and
hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been
removed.
Parallel Library:
-----------------
None
Tools:
------
None
F90 API:
--------
None
C++ API:
--------
None
Support for New Platforms, Languages and Compilers
==================================================
No new platorms, languages, or compilers are supported in this release.
Bug Fixes since HDF5-1.6.6 Release
==================================
Library
-------
- H5Iget_name could not be used with an object identifier returned
by H5Rdereference; the function would not be able to determine
a valid object name. It has been fixed. SLU - 2008/1/30
- Changed library's behavior for reading files that might have
corrupted object header information from a previous (buggy)
version of the library. By default, the library now rebuilds the
correct object header information instead of issuing an error.
Previous "strict" file format interpretation can be enabled with
the "--enable-strict-format-checks" configure option.
QAK - 2008/01/13
- Fixed bug in H5Epush() which was clearing the error stack before
pushing new error value. QAK - 2007/08/23
- Fixed bug in H5Ewalk() which was not passing back the return value
from error stack walking callback. QAK - 2007/08/23
Configuration
-------------
None
Performance
-------------
None
Tools
-----
None
Documentation
-------------
None
F90 API
-------
None
C++ API
-------
None
Documentation
=============
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ (start with index.html) or on the
THG (The HDF Group) FTP server:
ftp://ftp.hdfgroup.org/HDF5/docs/
Online documentation for the current release in the HDF5 Release 1.6.x
series can be found on the THG web site:
http://hdfgroup.org/HDF5/doc1.6/
A listing of interface changes from release to release can be found
in the document "HDF5 Software Changes from Release to Release":
http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html
Since the stream I/O driver is not included in this release, the
functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream
ENUM value H5FD_STREAM have been removed from the documentation.
Platforms Tested
================
AIX 5.2 (32/64 bit) xlc 8.0.0.11
(datastar) xlC 8.0
xlf 10.01.0000.0002
FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6
(duty and liberty) gcc and g++ 4.2.1
IRIX64 6.5 MIPSpro cc 7.4.4m
(ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only)
C++ MIPSpro cc 7.4.4m
Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3
i686 i386 GNU/Linux
(osage)
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) April 18 2007)
(kagiso) PGI C, Fortran, C++ 7.0-7 32-bit
Intel(R) C Compiler for 32-bit
applications, Version 9.1
Intel(R) C++ Compiler for 32-bit
applications, Version 9.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 9.1
Absoft 32-bit Fortran 95 10.0.4
MPICH mpich2-1.0.6p1 compiled with
gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!)
Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025
SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025
(ucar hir1)
Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037
SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031
(smirom) PGI C, Fortran, C++ Version 7.0-7
for 64-bit target on x86-64
tested for both 32- and 64-bit binaries
Linux 2.6.5-7.287.3-sn2 #1 Intel(R) C++ Version 9.0
Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
(cobalt) SGI MPI
SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3
(sol) Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
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 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) Intel(R) C++ Version 9.0
Intel(R) Fortran Compiler Version 9.0
PGI C Version 6.0-5
PGI C++ Version 6.0-5
PGI Fortran Version 6.0-5
gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5)
Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) Intel(R) C++ Version 10.0
Intel(R) Fortran Compiler Version 10.0
Open MPI 1.2.2
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
Intel(R) Fortran Compiler Version 8.1
mpich-gm-1.2.6..14-intel-r2
Windows XP Visual Studio 6.0
Visual Studio .NET (with Intel Fortran 9.1)
Visual Studio 2005 (with Intel Fortran 9.1)
cygwin (gcc 3.4.4)
Windows Vista Visual studio 2005
MAC OS X Intel Darwin 8.10.1
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
g95 0.91
Supported Configuration Features Summary
========================================
Key: y = Tested and supported
n = Not supported or not tested in this release
C = Cluster
W = Workstation
( ) = Footnote appears below second table
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.8 32-bit n y n y n y
Solaris2.8 64-bit n y n n y y
Solaris2.10 32-bit n y n y y y
Solaris2.10 64-bit n y n n y y
IRIX64_6.5 32-bit n n n n y y
IRIX64_6.5 64-bit n y n n y y
WinXP Visual Studio 6.0 n n n y y y
WinXP CYGWIN n n n y y y
WinXP 2005 n y n y y y
WinXP .Net n y n y y y
WinVista 2005 n n n y y y
Mac OS X 10.4.10 n y n y y y
AIX-5.2 & 5.3 32- and 64-bit y y y y y y
FreeBSD 6.2 32- and 64-bit n n n y y y
RedHat Linux 2.4.21 W n n n n y n
RedHat Linux 2.6.9-42 i686 GNU (1) W y y y y y y
RedHat Linux 2.6.9-42 i686 Intel W n y n y y n
RedHat Linux 2.6.9-42 i686 PGI W n y n y y n
SuSE Linux 2.6.16 x86_64 GNU (1) W y y n y y y
SuSE Linux 2.6.16 x86_64 Intel W n y n y y n
SuSE Linux 2.6.16 x86_64 PGI W n y n y y n
RHEL 4 Linux 2.6.9 Xeon Lustre C n y n y y y
RedHat Linux 2.4 Xeon Lustre C n y n y y n
SuSE Linux 2.4 ia64 C y y y y y y
SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y
Platform Shared static- Thread-
libraries(4) exec safe
Solaris2.8 32- and 64-bit y n y
Solaris2.10 32- and 64-bit y n y
IRIX64_6.5 32-bit y n y
IRIX64_6.5 64-bit y n y
WinXP Visual Studio 6.0 y n n
WinXP CYGWIN y n n
WinXP 2005 y n n
WinXP .Net y n n
WinVista 2005 y n n
Mac OS X 10.4.10 y n n
AIX-5.2 & 5.3 32- and 64-bit n n n
FreeBSD 6.2 32- and 64-bit y n n
RedHat Linux 2.4.21 W y n n
SuSE Linux 2.6.9-42 i686 GNU (1) W y n y
SuSE Linux 2.6.9-42 i686 Intel W y n n
SuSE Linux 2.6.9-42 i686 PGI W n n n
SuSE Linux 2.6.16 x86_64 GNU (1) W y n y
SuSE Linux 2.6.16 x86_64 Intel W y n n
SuSE Linux 2.6.16 x86_64 PGI W n n n
RHEL 4 Linux 2.6.9 Xeon Lustre C y n n
RedHat Linux 2.4 Xeon Lustre C y n n
SuSE Linux 2.4 ia64 C y n n
SuSe Linux 2.6.5 SGI Altix ia64 n n n
Compiler versions for each platform are listed in the "Platforms Tested"
table found elsewhere in this file (RELEASE.txt). Unless otherwise noted,
compilers used are the system compilers.
Footnotes:
(1) Fortran compiled with g95.
Known Problems
==============
* We discovered two problems when running collective IO parallel HDF5 tests
with chunking storage with the ChaMPIon MPI compiler on tungsten, a Linux
cluster at NCSA.
Under some complex selection cases,
1) MPI_Get_element returns the wrong value.
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
data may be generated.
This only happens when turning on collective IO with chunking storage
with some complex selections. We haven't found these problems on other
MPI-IO compilers. If you encounter these problems, you may use Independent
IO instead.
To avoid this problem, change the following line in your code:
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
to
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
KY - 2007/08/24
* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It
does not include the -lmpi properly. This will be fixed in the next
release. AKC - 2007/08/07.
* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared
library, especially for h5repacktst and h52gifgentst, the following (or a
similar) error message may appear:
"523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname
'libh5test.so.1' under any of the filenames .......(bunch of directories)
"
And the testing will fail.
We believe this is a libtool problem. One way to get rid of this is to
add the paths of libh5test.so.1 and libh5.so.1 to the shared library path.
For 32-bit:
You may do this, under csh:
setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
For 64-bit:
setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
NOTE: This problem ONLY affects the testing of the HDF5 library when you
build from source. It won't affect any applications that would like to link
with the HDF5 shared library since the shared library path needs to be set
anyway. KY - 2007/8/2
* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
"calloc". All other tests passed. This indicates that a dataset using
chunked storage created by serial HDF5 may not work properly with parallel
HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x
calloc". AKC - 2007/7/12.
* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has
an optimization error in the datatypes conversion code. Before running
configure, edit the file config/intel-flags by changing the setting of
PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10.
* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX
6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for
example 120000, in order to pass the complicated collective IO tests inside
the parallel HDF5 library. This is not a problem inside the parallel HDF5
library. You can always set a bigger number on your system. KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version of HDF5
might not be able to be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem. EIP - 2005/09/09
* A dataset created or rewritten with the v1.6.3 library or after can't
be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is
enabled. There was a bug in the calculating code of the Fletcher32
checksum in the library before v1.6.3. The checksum value wasn't consistent
between big-endian and little-endian systems. This bug was fixed in
Release 1.6.3. However, after fixing the bug, the checksum value is no
longer the same as before on little-endian system. HDF5 library releases
after 1.6.4 can still read datasets created or rewritten with an HDF5
library of v1.6.2 or before. SLU - 2005/7/8
* For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron
processor, there's 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.
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but
have a "guard" statement in stdint.h that will #error and skip the rest
of the header file if the C99 option is not used explicitly. Hardsetting
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may also fail with messages like "The socket name is already
in use". HDF5 does not use sockets. This is due to problems of the
poe command trying to set up the debug socket. Check whether there are
many old /tmp/s.pedb.* files staying around. These are sockets used by
the poe command and left behind due to failed commands. Ask your system
administrator to clean them out. Lastly, request IBM to provide a means
to run poe without the debug socket.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, Windows) where the error messages directed to
"stderr" do not appear in the "right order" with output from stdout.
This is not an error.
* The --enable-static-exec configure flag fails to compile for Solaris
platforms. This is due to the fact that not all of the system
libraries on Solaris are available in a static format.
The --enable-static-exec configure flag also fails to correctly compile
on the IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* Use the --disable-shared configure flag if building with an Absoft Fortran
compiler.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8.
* In LANL QSC, the new cc compiler has problems converting small values of
long long (absolute values less than 1**-308) to double. This triggers
the test/dtypes to report failure in the following test:
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to
10**-308. If -ieee is not used, the converted double values are mostly
0.0, but occasionally appear as 10**-308. This has been reported to the
system staff.
All other tests have passed.
* 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 HDF5 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
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. JM - 2004/9/15
%%%%1.6.6%%%% Release Information for hdf5-1.6.6 (16/August/08)
HDF5 version 1.6.6 released on Thu Aug 16 11:17:10 CDT 2007
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.5 and
HDF5-1.6.6 It contains information on the platforms tested and
known problems in HDF5-1.6.6. For more details, check the HISTORY.txt
file in the HDF5 source.
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ or on the THG (The HDF Group)
ftp server (ftp.hdfgroup.org) in the directory:
/HDF5/docs/
Documentation for the current release is also on the HDF web site:
http://hdfgroup.org/HDF5/doc/
For more information, see the HDF5 home page at:
http://hdfgroup.org/HDF5/
If you have any questions or comments, please send them to:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.5
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
- HDF5 now uses autoconf 2.61 to generate configure. MAM - 2007/7/25.
Source code distribution
========================
Library:
--------
- None
Parallel Library:
-----------------
- None
Tools:
------
- h52gif and gif2h5: Both these tools were revised to include High
Level Image API support. Tests were added to /hl/tools/gif2h5.
PVN - 2007/04/13
- h5dump: Added support for double long type H5T_NATIVE_LDOUBLE.
PVN - 2007/03/13
- h5dump: Added support for binary output; see usage. PVN 2007/03/13
- h5repack: Added support for reading and writing by hyperslabs for
large files. PVN - 2007/03/01
- h5repack: A new option allows the copy to use the source file type
(default) instead of the previous conversion to native type.
PVN - 2007/03/01
- h5repack: Added output of the percentage of compression achieved.
PVN - 2007/03/01
- h5diff: Added support for comparing dataset regions. PVN -
2007/02/20
- h5diff: Added support for reading and comparing by hyperslabs for
large files. PVN - 2007/02/20
- h5diff: Added printing of dataset dimensions along with dataset
name.
PVN - 2007/02/19
F90 API:
--------
- None
C++ API:
--------
- Added support for Szip: DSetCreatPropList::setSzip - BMR 2007/01/24
Support for New Platforms, Languages and Compilers
==================================================
- Added support for MAC Intel (Darwin 8.8.2) (gcc 4.0.1 and g95 0.91)
EIP - 2007/02/13
- Added support for GNU C compiler version 4.2.1 for FreeBSD 6.2
(32- and 64-bit)
Bug Fixes since HDF5-1.6.5 Release
==================================
Library
-------
- Fixed several bugs with writing fill values for datasets that have
a variable-length datatype or component datatype. QAK -
2007/06/19
- STDIO driver didn't support files bigger than 2GB because the OFFSET
parameter of fseek is of type LONG INT, not big enough for big
files. Use fseeko instead for big files if it's available on the
system. SLU - 2007/4/5
- Relaxed restrictions on attribute operations to allow a file ID to
be used as the "location ID". If a file ID is used, the attribute
operation will occur on the root group of the file.
QAK - 2007/02/09
- Fixed a bug in H5Sselect_valid() that caused an incorrect value to
be returned (0) instead of FAIL on error conditions such as the
selection or extent not being defined. CMC - 2007/01/05
- Fixed potential file corruption bug which could overwrite a portion
of an object's header when an attribute was renamed. If the new
name for the attribute was longer than the old name, it was
possible
that the attribute would grow enough to overwrite another message
in the object's header. QAK - 2007/01/02
- Fixed file corruption bug which could write an incorrect number of
messages to an object's header under certain circumstances.
Generally, the sequence of actions to generate this bug looks
like this:
- Create an object.
- Close the file.
- Re-open the file.
- Add 2 (or more) attributes to the object.
- Close the file.
- Re-open the file.
- Delete one of the attributes on the object.
- Add a smaller attribute to the object.
- Delete the smaller attribute on the object.
- Add a larger attribute on the object.
After this, the number of header messages stored for the object
will be off by one. Other sequences of modifying attributes on an
object could also trigger this bug. If you are opening an
object and the bottom few messages of the HDF5 error stack
resembles the following, the object has been affected by this bug:
#007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry():
unable to load entry
major(08): Meta data cache layer
minor(40): Unable to load metadata into cache
#008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load():
corrupt object header - too few messages
major(12): Object header layer
minor(40): Unable to load metadata into cache
Specifically, "corrupt object header" is the best string to search
for in the HDF5 error stack output.
If your files have been affected by this bug, or you are concerned
that your files might have been, please contact the HDF Helpdesk
at help@hdfgroup.org for a tool to detect and repair files
affected by this problem. QAK - 2006/6/16
- Fixed various problems with retrieving names of objects, especially
with mounted files. QAK - 2005/12/25
Configuration
-------------
- Changed to default to --disable-shared if parallel is enabled.
AKC - 2007/5/12
- Corrected a coding error in configure when it tries to locate the
needed MPI and MPI-IO library for the fortran interface.
AKC - 007/5/9.
- Changed default fortran compiler to g95 when gcc is used.
AKC - 007/2/17.
- Configure can now use any tr command. No more need for
defining the variable TR, nor is it supported. AKC - 2006/05/20
Performance
-------------
- None
Tools
-----
- Fixed a bug in h5dump regarding the display of named datatypes
attributes. PVN - 2007/03/13
- Fixed a bug in h5dump regarding the display of group comments.
PVN - 2007/03/13
- Fixed a bug in h5dump regarding the display of hardlinks pointing
to the root group. PVN - 2007/03/13
- Fixed a bug in the h5diff percentage option -p. PVN - 2007/03/05
- Fixed a bug in h5dump that caused array indices greater than 2^32-1
not to be printed correctly. PVN - 2007/2/19
Documentation
-------------
- Corrected errors and extended the descriptions in Reference Manual
entries for several functions.
F90 API
-------
- None
C++ API
-------
- Changed
StrType::StrType(const size_t& size);
to
StrType::StrType(const int dummy, const size_t& size);
because the first one clashed with
StrType::StrType(const hid_t existing_id); - BMR 2007/05/03
- Wrappers of H5Rcreate had incorrect prototypes. Added these
overloaded functions:
IdComponent::reference(void* ref, const char* name,
DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION)
IdComponent::void reference(void* ref, const char* name)
IdComponent::reference(void* ref, const H5std_string& name)
and will remove these incorrect member functions:
DataSet::Reference
DataType::Reference
Group::Reference
H5File::Reference
- Added wrappers for H5Rdereference as constructors:
DataSet(IdComponent& obj, void* ref);
Group(IdComponent& obj, void* ref);
DataType(IdComponent& obj, void* ref);
Documentation
=============
HDF5 documentation can be found in the distributed release source
code in the subdirectory doc/html/ (start with index.html) or on the
THG (The HDF Group) ftp server (ftp.hdfgroup.org) in the directory:
/HDF5/docs/
Online documentation for the current release can be found on the THG
web site:
http://hdfgroup.org/HDF5/doc/
Platforms Tested
================
AIX 5.2 (32/64 bit) xlc 6.0.0.8
(datastar) xlC 6.0.0.9
xlf 8.1.1.7
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.7
AIX 5.3 (32/64 bit) xlc 7.0.0.0
(copper) xlC 7.0.
xlf 9.1.0.3
FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6
(duty and liberty) gcc and g++ 4.2.1
HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.02
(sirius) HP F90 v3.1 (32-bit only)
HP aC++/ANSI C B3910B A.06.02
IRIX64 6.5 MIPSpro cc 7.4.4m
(ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only)
C++ MIPSpro cc 7.4.4m
Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3
i686 i386 GNU/Linux
(osage)
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
(kagiso) PGI C, Fortran, C++ 6.2-5 32-bit
icc (ICC) 9.1
Intel(R) C++ Compiler for 32-bit
applications, Version 9.1
Intel(R) Fortran Compiler for 32-bit
applications, Version 9.1
Absoft 32-bit Fortran 95 10.0.4
MPICH mpich2-1.0.4p1 compiled with
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.91!)
Linux 2.6.16.46-0.12-debug #1
SMP ia64 GNU/Linux Intel(R) C++ Version 10.0.025
(ucar hir1) Intel(R) Fortran Itanium(R) Version 10.0.025
Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037
SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031
(smirom) PGI C, Fortran, C++ Version 6.2-5
for 64-bit target on x86-64
tested for both 32- and 64-bit binaries
Linux 2.6.5-7.283-rtgfx Altix
SMP ia64 Intel(R) C++ Version 9.0
(cobalt) Intel(R) Fortran Itanium(R) Version 9.0
SGI MPI
OSF1 V5.1 (QSC) Compaq C V6.5-011
(See "Known Problems.") HP Fortran V5.5A-3548
Compaq C++ V6.5-036
MPIX200_64_r13.4
SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3
(sol) Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
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 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) Intel(R) C++ Version 9.0
Intel(R) Fortran Compiler Version 9.0
PGI C Version 6.0
PGI C++ Version 6.0
PGI Fortran Version 6.0
gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5)
Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
(abe) Intel(R) C++ Version 10.0
Intel(R) Fortran Compiler Version 10.0
Open MPI 1.2.2
IA-64 Linux 2.4.21.SuSE_292.til1
ia64 gcc (GCC) 3.2.2
(NCSA tg-login) Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
mpich-gm-1.2.5..10-intel-r2
Windows XP Visual Studio 6.0
Visual Studio .NET (with Intel Fortran 9.0)
Visual Studio 2005 (with Intel Fortran 9.0)
cygwin (gcc 3.4.4)
MAC OS X Intel Darwin 8.10.1
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
g95 0.91
Supported Configuration Features Summary
========================================
Key: y = Tested and supported
n = Not supported or not tested in this release
C = Cluster
W = Workstation
( ) = Footnote appears below second table
Platform C F90 F90 C++ zlib SZIP
parallel parallel
Solaris2.8 32- and 64-bit n y n y y y
Solaris2.10 32- and 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 n n y y
HPUX11.23-32bit n y n y y y
HPUX11.23-64bit n n n y y y
WinXP Visual Studio 6.0 n n n y y y
WinXP CYGWIN n n n y y y
WinXP 2005 n y n y y y
WinXP .Net n y n y y y
Mac OS X 10.4.10 n y n y y y
AIX-5.2 & 5.3 32- and 64-bit y y y y y y
FreeBSD 6.2 32- and 64-bit n n n y y y
RedHat Linux 2.4.21 W n n n y y y
SuSE Linux 2.6.9-42 i686 GNU (1) W y y y y y y
SuSE Linux 2.6.9-42 i686 Intel W n y n y y y
SuSE Linux 2.6.9-42 i686 PGI W n y n y y y
SuSE Linux 2.6.16 x86_64 GNU (1) W y y y y y y
SuSE Linux 2.6.16 x86_64 Intel W n y n y y y
SuSE Linux 2.6.16 x86_64 PGI W n y n y y y
RHEL 4 Linux 2.6.9 Xeon Lustre C y y y y y y
RedHat Linux 2.4 Xeon Lustre C n y n y y y
SuSE Linux 2.4 ia64 C y y y y y y
SuSe Linux 2.6.16 SGI Altix ia64 n y n y y y
SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y
OSF1 v5.1 y y y y y n
Platform Shared static- Thread- STREAM-
libraries(4) exec safe VFD
Solaris2.8 32- and 64-bit y n y y
Solaris2.10 32- and 64-bit y n y y
IRIX64_6.5 32-bit y n y y
IRIX64_6.5 64-bit y n y y
HPUX11.23-32bit y (3) n n y
HPUX11.23-64bit y (3) n n y
WinXP Visual Studio 6.0 y n n n
WinXP CYGWIN y n n n
WinXP 2005 y n n n
WinXP .Net y n n n
Mac OS X 10.4.10 y n n y
AIX-5.2 & 5.3 32- and 64-bit n n n y
FreeBSD 6.2 32- and 64-bit y n n y
RedHat Linux 2.4.21 W y n n y
SuSE Linux 2.6.9-42 i686 GNU (1) W y n y y
SuSE Linux 2.6.9-42 i686 Intel W y n n y
SuSE Linux 2.6.9-42 i686 PGI W n n n y
SuSE Linux 2.6.16 x86_64 GNU (1) W y n n y
SuSE Linux 2.6.16 x86_64 Intel W y n n y
SuSE Linux 2.6.16 x86_64 PGI W n n n y
RHEL 4 Linux 2.6.9 Xeon Lustre C y n n y
RedHat Linux 2.4 Xeon Lustre C y n n y
SuSE Linux 2.4 ia64 C y n n y
SuSe Linux 2.6.16 SGI Altix ia64 n n n y
SuSe Linux 2.6.5 SGI Altix ia64 n n n y
OSF1 v5.1 n n 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) Fortran compiled with g95.
(2) In most cases, shared libraries are provided only for the C library,
except on Windows where they are provided for C, C++, and Fortran.
(3) C++ works only with static libraries.
Known Problems
==============
* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It
does not include the -lmpi properly. This will be fixed in the next
release. AKC - 2007/08/07.
* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared
library, especially for h5repacktst and h52gifgentst, the following (or
similar) error message may appear:
"523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname
'libh5test.so.1' under any of the filenames .......(bunch of directories)
"
And the testing will fail.
We believe this is a libtool problem. One way to get rid of this is to
add the paths of libh5test.so.1 and libh5.so.1 to the shared library path.
For 32-bit:
You may do this, under csh:
setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
For 64-bit:
setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5
directory/test/.libs]:[full path of HDF5 directory/src/.libs]
NOTE: This problem ONLY affects the testing of the HDF5 library when you
build from source. It won't affect any applications that would like to link
with the HDF5 shared library since the shared library path needs to be set
anyway. KY - 2007/8/2
* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
"calloc". All other tests passed. This indicates that a dataset using
chunked storage created by serial HDF5 may not work properly with parallel
HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x
calloc". AKC - 2007/7/12.
* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has
an optimization error in the datax types conversion code. Before running
configure, edit the file config/intel-flags by changing the setting of
PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10.
* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX
6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for
example 120000, in order to pass the complicated collective IO tests inside
the parallel HDF5 library. This is not a problem inside the parallel HDF5
library. You can always set a bigger number on your system. KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version of HDF5
might not be able to be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem. EIP - 2005/09/09
* 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 (a filter) is
enabled. There was a bug in the calculating code of the Fletcher32
checksum in the library before v1.6.3. The checksum value wasn't consistent
between big-endian and little-endian systems. This bug was fixed in
Release 1.6.3. However, after fixing the bug, the checksum value is no
longer the same as before on little-endian system. 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 version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron
processor, there's 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.
* test/big fails sometimes with the message "Possible overlap with another
region." The test selects regions randomly, and this error occurs when
two regions overlap each other; it is a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but
have a "guard" statement in stdint.h that will #error and skip the rest
of the header file if the C99 option is not used explicitly. Hardsetting
$CC to c99 will resolve the problem. AKC - 2004/12/13
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
messages like "INFO: 0031-XXX ...". This is from the command poe.
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
and run the tests again.
The tests may also fail with messages like "The socket name is already
in use". HDF5 does not use sockets (except for stream-VFD). This is
due to problems of the poe command trying to set up the debug socket.
Check whether there are many old /tmp/s.pedb.* files staying around. These
are sockets used by the poe command and left behind due to failed commands.
Ask your system administrator to clean them out. Lastly, request IBM
to provide a means to run poe without the debug socket.
* The h5dump tests may fail to match the expected output on some platforms
(e.g. parallel jobs, Windows) where the error messages directed to
"stderr" do not appear in the "right order" with output from stdout.
This is not an error.
* The 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 the IBM SP2 platform for the serial mode. The parallel mode works fine
with this option.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* The Stream VFD is not supported under Windows.
* Use the --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 following test:
Testing random sw long double -> double conversions
If -ieee is used, the converted doubles spread over the range 0.0 to
10**-308. If -ieee is not used, the converted double values are mostly
0.0, but occasionally appear as 10**-308. This has been reported to the
system staff.
All other tests have passed.
* 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 HDF5 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
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. JM - 2004/9/15
%%%%1.6.5%%%% Release Information for hdf5-1.6.5 (10/November/05)
HDF5 version 1.6.5 released on Thu Nov 10 18:17:53 CST 2005
================================================================================
INTRODUCTION
============
This document describes the differences between HDF5-1.6.4 and
HDF5-1.6.5. It contains information on the platforms tested and
known problems in HDF5-1.6.5. 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/
Documentation for the current release is also on the HDF web site:
http://hdf.ncsa.uiuc.edu/HDF5/doc/
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, Languages and Compilers
- Bug Fixes since HDF5-1.6.4
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
-------------------------
- Added yodconfigure, a configure tool, that patches up the configure
file to allow configure to launch executable via the proper
launching command like "yod -sz 1". AKC - 2005/11/10
- Configure now recognizes the TR variable as the location of the
tr utility. JML 2005/10/20
Source code distribution:
-------------------------
- Added g95 as a testing "platform" informally. AKC - 2005/10/04.
- Added MD5 checksumming to snapshot releases. Releases will now
produce an .md5 file as well as a .tar archive. md5sum can be
used to verify the arvhice with the .md5 checksum. -JL 2005/09/06
Library:
--------
- Added HSYS_ERROR which retrieves the system error message and pushes
it to the error stack. This provides more information regarding the
failed system call. AKC - 2005/08/04
- Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to
allow querying for objects in a file that was opened with a particular
file ID, instead of all objects opened in the file with any file ID.
QAK - 2005/06/01
Parallel Library:
-----------------
- Added mpich2 as a testing "platform" informally. AKC - 2005/10/04.
- HDF5 supports collective MPI-IO for irregular selection with HDF5
dataset. Irregular selection is when users use API H5Sselect_hyperslab
more than once for the same dataset.
Currently, not all MPI-IO packages support the complicated
MPI derived datatypes used in the implementation of irregular
selections INSIDE HDF5.
1) DEC 5.x wdoes not support complicated derived datatypes.
2) For AIX 5.1:
If your poe version number is 3.2.0.20 or lower,
please edit powerpc-ibm-aix5.x in the directory hdf5/config/.
Find the line with
<< hdf5_mpi_complex_derived_datatype_works >>
and UNCOMMENT this line before the configure.
check poe version with the following command:
lpp -l all | grep ppe.poe
3) For Linux cluster,:
If mpich version is 1.2.5 or lower, collective irregular selection
IO is not supported; internally independent IO is used.
4) For IRIX 6.5:
if C compiler version is 7.3 or lower, collective irregular
selection IO is not supported; internally independent IO is used.
5) For platforms which internally used mpich:
If the mpich version is 1.2.5 or lower, please find the
corresponding config (in hdf5/config) file and add
hdf5_mpi_complex_derived_datatype_works='no'
at the end of the configuration file. For example, on the
NCSA SGI Altix, the internal mpich library is 1.2.5. So
hdf5_mpi_complex_derived_datatype_works='no'
should be added at the end of the config file ia64-linux-gnu.
KY - 2005/09/12
Tools:
------
- Removed obsolete pdb2hdf tool. JML - 2005/10/28
- Sped up h5dump on files with large numbers of objects.
QAK - 2005/08/25
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
==================================================
- Added support for RedStorm platform (serial only.) AKC 2005/11/10
- Added support for BG/L platform (serial only.) LA 2005/11/10
- Added support for HPUX 11.23 (IA64); only C and C++ are supported
with the +DD64 flag
EIP 2005/10/05
Configuration
-------------
- Added support for Cray X1. JML 2005/10/03
Bug Fixes since HDF5-1.6.4 Release
==================================
Library
-------
- Fixed collective IO in chunking-storage. HDF5 may have called the
wrong routine when the shape of the dataspace in the file and in
the buffered chunk were different. This bug was fixed to make sure
the correct routine is called. KY - 2005/10/19
- Fixed core dump when closing root groups opened through two different
file handles that operate on the same actual file. QAK - 2005/10/02
- The ./dsets tests used to fail in the TFLOPS machine if the
test program, dsets.c, was compiled with the -O option.
The HDF5 library still worked correctly with the -O option. Only
the ./dsets failed. It is fixed. AKC - 2005/09/14
- Corrected errors when performing various operations on 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() to 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
- Dataset sieve buffer cache was inadvertently disabled; it has been
re-enabled. QAK - 2005/07/08
- Don't unmount child files until the parent file actually closes.
(Previously, if an object was 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 a group that was opened in a mounted
file which has been unmounted. QAK - 2005/03/17
Configuration
-------------
- Configure can recognize -lmpich as a form of MPI library. -AKC-
2005/9/28.
- Changed default C++ compiler for the IA64 platform from icc to
icpc which is the preferred compiler for Intel Compiler version
8. AKC - 2005/09/02
Performance
-------------
- Optimized I/O for enumerated datatypes that are a superset of a
source enumerated datatype. QAK - 2005/03/19
Tools
-----
Documentation
-------------
F90 API
-------
- h5pget_driver_f was returning information that could not be
interpreted by a 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
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
AIX 5.3 (32/64 bit) xlc 7.0.0.0
xlC 7.0.
xlf 9.1.0.3
Cray X1 water 3.0.35 Cray Standard C Version 5.4.0.7.4
Cray Fortran 5.4.0.7.3
Cray C++ 5.4.0.7.4
FreeBSD 4.11 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
HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.00
HP F90 v2.9
HP aC++/ANSI C B3910B A.06.00
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-sgi306rp21 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
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
SunOS 5.10 Sun WorkShop 6 update 2 C 5.3
Sun WorkShop 6 update 2 Fortran 95 6.2
Sun WorkShop 6 update 2 C++ 5.3
Patch 111685-13
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
(tungsten) 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) Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
mpich-gm-1.2.5..10-intel-r2
Windows XP MSVC++.NET
MSVC++ 6.0
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
IBM BG/L (16) n n n n y y
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
Solaris2.10 64-bit y(1) y n y y y
Solaris2.10 32-bit y(1) y n 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
HPUX11.23-32bit n y n y y y
HPUX11.23-64bit n n n y y y
OSF1 v5.1 y y y y y y
X1 y y y y y n
AIX-5.1, 5.2 & 5.3 32-bit y y y y y y
AIX-5.1, 5.2 & 5.3 64-bit y y y y y y
WinXP Visual Studio 6.0 n n(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 4.11 n 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
RedStorm (16) n y n y y n
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
IBM BG/L n y n n
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
Solaris2.10 64-bit y x y y
Solaris2.10 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
HPUX11.23 y y n y
OSF1 v5.1 y y n y
X1 n y n y
AIX-5.1, 5.2 & 5.3 32-bit n y n y
AIX-5.1, 5.2 & 5.3 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 4.11 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
RedStorm 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 2.4.21-32.0.1. Xeon cluster with ELsmp-perfctr-lustre
and Intel compilers
(7) Linux 2.4.21, SuSE_292.til1. Ia64 cluster with Intel compilers
(8) Intel 8.1
(9) One test of this release failed with Compaq Visual Fortran 6.6c.
No binary fortran release will be provided. Users should build
the library by themselves and use it at their own risk.
We recommend that users use HDF5 1.7 instead
or use Compaq Visual Fortran 6.0.
(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++
(16) Only serial is ported. PFS does not work for PHDF5 yet.
FMB/EIP - 2005/11/10
Known Problems
==============
* Intel Compilers for Linux x86_86 platforms (EM64T-based, v8.1) has
optimization error in the data types conversion code. Before running
configure, edit the file config/intel-flags by changing the setting of
PROD_CFLAGS from -O3 to -O0, then run configure. AKC - 2005/11/10.
* Fortran testing and compiling failures on windows XP
1. Compaq visual fortran 6.6c with VS 6.0
The Fortran tests failed for both release, release dll, debug and debug
dll. The failure is a random one. We won't provide fortran libraries. The
same test passed with the 1.7.51 snapshot. You may find the 1.7.51
snapshot under ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots/.
2. Intel fortran 8.1 under .Net environment
The fortran library cannot even be compiled. Some users have pointed this
to intel forum.
* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 at IRIX
6.5, set environment variable MPI_TYPE_MAX to be a bigger number, for example
120000, in order to pass the complicated collective IO tests inside parallel
HDF5 library. This is not a problem inside parallel HDF5 library. You can
always set a bigger number in your system.
KY - 2005/10/6
* A contiguous or chunked dataset created by a sequential version may
not be modified with a parallel version of the library.
Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the
dataset creation property list to avoid the problem.
EIP - 2005/09/09
* 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 version 6 (6.02 and 6.04) of the 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 a bug in the test and not in
HDF5. Since the error is triggered by a random situation, it will
usually disappear if the test is re-run.
* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but 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 means to run poe without the debug socket.
* 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.
The --enable-static-exec configure flag also fails to correctly compile
on the HPUX 11.00.
It is suggested that you don't use this option on these platforms
during configuration.
* The Stream VFD was not tested yet under Windows.
* 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/
* 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.
* 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,
Building Fortran static library with Intel 8.1 in .NET environment
requires 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
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.
%%%%1.6.4%%%% Release Information for hdf5-1.6.4 (15/March/05)
HDF5 version 1.6.4 released on Tue Mar 15 20:38:48 CST 2005
================================================================================
INTRODUCTION
============
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:
/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 HDF5-1.6.3
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Source code distribution:
-------------------------
The High-Level (HL) C APIs were added to the source code distribution.
For HL documentation, see
http://hdf.ncsa.uiuc.edu/HDF5/hdf5_hl/doc/RM_hdf5hl.html.
The HL library, libhdf5_hl.a(so), is built and installed by default.
Use --disable-hl configure flag to disable the HL library.
Library:
--------
- We recommend you to use SZIP v2.0 with this release.
For more information see
http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/
- 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 -
2004/10/1
- Removed PABLO support. 2005/01/20 EIP
Parallel Library:
-----------------
- Allow compressed, chunked datasets to be read in parallel.
QAK - 2004/10/04
Tools:
------
- New tool, h5jam. See HDF5 Reference Manual. 2004/10/08
F90 API:
--------
No new features in this release.
C++ API:
--------
- 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.
=======================================
Configuration
-------------
- Upgraded from GNU autoconf 2.53 to autoconf 2.59. JML - 2005/01/31
Bug Fixes since HDF5-1.6.3 release
==================================
Library
-------
- 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 -
2005/02/08
- 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/
Configuration
-------------
- 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
Performance
-------------
Many changes were made to the library to improve performance,
especially for the variable-length datatypes and metadata cache.
Tools
-----
- 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
Documentation
-------------
F90 API
-------
- 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.
C++ API
-------
Documentation
=============
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
ftp://hdf.ncsa.uiuc.edu/lib-external/zlib/bin/windows
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.
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
==============
* 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
information.
* 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.
%%%%1.6.3%%%% Release Information for hdf5-1.6.3 (22/September/04)
HDF5 version 1.6.3 released on Wed Sep 22 11:30:11 CDT 2004
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.2 and
HDF5-1.6.3, and contains information on the platforms tested and
known problems in HDF5-1.6.3. 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 HDF5-1.6.2
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
--------------
- Added some initial support for making purify (or similar memory
checking products) happier by initializing buffers to zero and
disabling the internal free list code. To take advantage of this,
define 'H5_USING_PURIFY' in your CFLAGS when building the library.
QAK - 2004/07/23
- WINDOWS building,testing and installing improvements
- On Windows, FORTRAN,C++ and C projects are merged into one zip file,
users can choose an option to build either FORTRAN or C++ or both
with basic C library.For detailed information,
please read INSTALL_Windows.txt.
- On Windows, szip compression library with or without encoder can be easily
turned off or on when building HDF5. For detailed information,
please read INSTALL_Windows.txt, especially section V.
- On Windows, an optional procedure for building,testing and installing
HDF5 from command line is provided. This procedure is supposed to be
convenient for experienced users, please read
INSTALL_windows_From_Command_Line.txt for details.
- On Windows, an alternative short instruction document for building,
testing and installing HDF5 is provided. This instruction is supposed to
be convenient for general users, please read
INSTALL_Windows_Short.txt for details.
- On Windows, h5repack,h5diff,h5ls and h5import tool tests have been added.
KY - 2004/9/16
Library:
--------
- Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for
SZIP compression. Now there is no restriction on the size and shape of the
chunk except that the total number of elements in the chunk cannot be
bigger than 'pixels_per_block' parameter provided by the user.
EIP - 2004/07/21
- HDF5 can now link to SZIP with or without szip's encoder.
The new API function H5Zget_filter_info can be used to check
szip's status. Attempting to assign szip to a dataset property
list or attempting to write with szip will generate an error if
szip's encoder is disabled. JL/NF - 2004/6/30
- SZIP always uses K13 compression. This flag no longer needs to
be set when calling H5Pset_szip. If the flag for CHIP
compression is set, it will be ignored (since the two are mutually
exclusive). JL/NF - 2004/6/30
- A new API function H5Fget_name was added. It returns the name
of the file by object(file, group, data set, named data type,
attribute) ID. SLU - 2004/06/29
- A new API function H5Fget_filesize was added. It returns the
actual file size of the opened file. SLU - 2004/06/24
- Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2,
will suppress all library version mismatch warning messages.
AKC - 2004/4/14
Parallel Library:
-----------------
Tools:
------
- h5repack was added to the tools suite. h5repack regenerates an HDF5 file
from another HDF5 file, optionally applying HDF5 filters (compression)
and/or chunking to the copied file. The filters options are read from
the command line. See /doc/html/Tools.html for more details.
PVN - 2004/9/13
- h5dump includes new features:
1) Printing of dataset filters, storage layout and fill value information.
2) Print a list of the file contents.
3) Escape non printing characters.
4) Print the content of the boot block.
5) Print array indices with the data (the default).
These options are all switch controlled. See /doc/html/Tools.html for more details.
PVN - 2004/9/13
F90 API:
--------
- added new subroutines:
h5fget_filesize_f
h5iget_file_id_f
h5premove_filter_f
h5zget_filter_info_f
EIP 2004/9/21
- added new h5fget_name_f and h5fget_filesize_f subroutines
EIP 2004/07/08
C++ API:
--------
- Added wrappers for array and variable length datatypes APIs
- Added wrappers for newly added APIs from H5T, H5F, and H5I
- Added many wrappers that were missing from the H5P API
- Added the ability to reference HDF5 objects to these classes:
DataSet, DataType, Group, and H5File (wrappers for H5R APIs)
BMR 2004/08/04
Support for new platforms, languages and compilers.
=======================================
- Added PGI Fortran support for Linux64 (x86_64) systems
EIP - 2004/08/19
- Absoft compiler f95 v9.0 is supported on Linux 2.4 32bit
EIP - 2004/07/29
- HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran
compiler version 8.1. This is a default compiler.
- HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler
version 8.2; set F9X environment variable to f95, for example
setenv F9X f95
Use --disable-shared --enable-static configure flags when Absoft
compiler is used.
EIP - 2004/07/27
Bug Fixes since HDF5-1.6.2 release
==================================
Library
-------
- Fixed parallel bug in which some processes attempted collective
I/O while others did independent I/O. Bug appeared when some
processes used point selections, and others didn't. JRM - 2004/9/15
- Corrected error where dataset region references were written in an
incorrect way on Cray machines. PVN & QAK - 2004/09/13
- The H5Tget_native_type now determines the native type for integers
based on the precision. This is to avoid cases of wrongly converting
an int to a short in machines that have a short of 8 bytes but with
32bit precision (e.g Cray SV1). PVN - 2004/09/07
- Changed H5Dread() to not overwrite data in an application's buffer
with garbage when accessing a chunked dataset with an undefined fill
value and an unwritten chunk is uncountered. QAK - 2004/08/25
- Fixed error which could cause a core dump when a type conversion
routine was registered after a compound datatype had been
converted and then an equivalent compound datatype was converted
again. QAK - 2004/08/07
- Fixed memory overwrite when encoding "multi" file driver information
for file's superblock. QAK - 2004/08/05
- Fixed obscure bug where a filter which failed during chunk allocation
could allow library to write uncompressed data to disk but think
the data was compressed. QAK - 2004/07/29
- Fixed bug where I/O to an extendible chunked dataset with zero-sized
dimensions would cause library to fail an assertion.
QAK - 2004/07/27
- Fixed bug where chunked datasets which have filters defined,
allocation time set to "late" and whose chunks don't align with
the dataspace bounds could have incorrect data stored when
overwriting the entire dataset on the first write. QAK - 2004/07/27
- Added check to ensure that dataspaces have extents set. JML-2004/07/26
- Fixed bug on some Solaris systems where HDF5 would try to use
gettimeofday() when that function didn't work properly.
JML - 2004/07/23
- Fixed bug in H5Sset_extent_simple where setting maximum size to
non-zero, then to zero would cause an error. JML - 2004/07/20
- Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite
when not writing data ("none" selection or hyperslab or point
selection with no elements defined). QAK - 2004/07/20
- Calling H5Gcreate() on "/" or "." throws an error instead of
failing quietly. JML - 2004/07/19
- Fixed bug where setting file address size to be very small could
trigger an assert if the file grew to more than 64 KB. Now throws
an error and data can be recovered. JL/NF - 2004/07/14
- Fixed bug where "resurrecting" a dataset was failing.
QAK - 2004/07/14
- Fixed bug where incorrect data could be read from a chunked dataset
after it was extended. QAK - 2004/07/12
- After compound datatype with variable-length string in the fields
is committed to file, the size is messed up when it's read back.
Fixed. SLU - 2004/06/11
- Fixed potential file corruption bug when a block of metadata could
overlap the end of the internal metadata accumulator buffer and
the buffer would be extended correctly, but would incorrectly
change it's starting address. QAK - 2004/06/09
- Opaque datatype with no tag failed for some operations. Fixed.
SLU - 2004/6/3
- Fixed potential file corruption bug where dimensions that were
too large (a value greater than could be represented in 32-bits)
could cause the incorrect amount of space to be allocated in a
file for the raw data for the dataset. QAK - 2004/06/01
- Fixed dtypes "sw long double -> double" failure in QSC class
machines. AKC - 2004/4/16
Configuration
-------------
- Fixed the long compile time of H5detect.c when v7.x Intel Compiler
is used with optimization NOT off. AKC - 2004/05/20
Performance
-------------
Tools
-----
- On SGI h5dump displayed only part of the data due to the bug
in the system printf; fixed.
EIP - 2004/09/21
Documentation
-------------
- Several descriptive errors have been fixed throughout the
documentation, particularly in the reference manual (RM).
A selection particularly worthy of note would be these:
- The H5Pset_szip description in the RM has been expanded and
corrected to facilitate use of SZIP compression.
- A note has been added to the H5Dcreate description that an
unexplained failure is likely to be due to a property list error
that is detected only at the time of dataset creation.
FMB - 2004/09/21
F90 API
-------
- Fortran functions h5dwrite/read_f and h5awrite/read_f do not
accept dims parameter of INTEGER type anymore. Code was removed.
2004/04/15
C++ API
-------
- H5::Exception's and its subclasses' constructors that were
overloaded to take char pointers are removed and constructors
that passed in reference of 'string' are changed to pass
by value. In addition, the default value of the data member
H5::Exception::detailMessage is changed from 0/NULL to
DEFAULT_MSG ("No detailed information provided".)
- Prototype for DSetCreatPropList::setLayout is changed: 1st parameter
is removed because it was there only by mistake.
BMR 2004/08/04
Documentation
=============
HDF5 Library documentation
--------------------------
- HDF5 C++ API Reference Manual
This document has been added to the HDF5 document set.
The predecessor document, "HDF5 C++ Interfaces," has been removed.
- HDF5 C++ API Design Specification
A first draft of this document has been added to the HDF5 document
set. The draft has been posted on the HDF5 website and a link
has been added to the HDF5 documents index (index.html at the top
level of the document set).
- Parallel HDF5
In prior releases, the HDF5 document set included two parallel
HDF5 documents. Those documents have been deleted and the
HDF5 documents index (index.html) now links to a "Parallel HDF5"
page on the HDF5 website (http://hdf.ncsa.uiuc.edu/HDF5/PHDF5/).
- HDF5 High Level APIs
Links to the HDF5 High Level APIs and to the HDF5 High Level
Reference Manual have been added to the HDF5 documents index
(index.html).
- HDF5 Reference Manual
Tools: h5repack -- A description of the new h5repack tool has been
added to the Tools page.
Tools: h5dump -- Several new options have been added to h5dump.
New functions -- All new functions have been added to the RM.
API changes -- Relevant function descriptions have been updated in
instances where programming interfaces have changed.
FMB - 2004/09/21
Windows installation documentation
----------------------------------
- INSTALL_Windows.txt has been enhanced to include instructions building
HDF5 with FORTRAN and C++.
- Two optional installation documents have been added. They are
INSTALL_Windows_Short.txt and INSTALL_Windows_From_Command_Line.txt.
INSTALL_Windows_Short.txt is supposed to help general users who
only want to build,test and install HDF5 in a quick way.
INSTALL_Windows_From_Command_Line.txt is supposed to help users who
would like to compile,test and install HDF5 in command line environment.
- INSTALL_Windows_withcpp.txt and INSTALL_Windows_withF90.txt became
obsolete. Files are deleted from the release_docs directory.
KY 2004/09/16, EIP 2004/9/21
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 xlc 6.0.0.8
xlC 6.0.0.8
xlf 8.1.1.6
mpcc_r 6.0.0.8
mpxlf_r 8.1.1.6
Cray T90 sn7001 10.0.0md Cray Standard C Version 6.4.0.3
Cray Fortran Version 3.4.0.0
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.3
Cray Fortran Version 3.6.0.3
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
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 (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 2.4.18 gcc 2.96, 3.3.2
g++ 3.3.2
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Absoft Fortran compiler v9.0
Linux 2.4.20-8 gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Linux 2.4.21-2.9.5ws #3 gcc 3.2.3 (Red Hat Linux 3.2.3-16)
SMP x86_64 g++ 3.2.3
Linux 2.4.21-4.ELsmp Intel(R) C++ 32-bit Version 8.0
Intel(R) Fortran 32-bit Version 8.0
gcc 3.4.0
MPICH 1..5.2 Inmel 8.0
Linux 2.4.19-SMP x86_64 gcc (GCC) 3.2.2 (SuSE Linux)
g++ 3.2.2
Linux 2.6.4-52smp x86_64 gcc 3.3.3 (SuSE Linux 9.1 AMD64))
PGI 5.2-1 C and F90
Linux 2.4.21-sgi Altix
SMP ia64 Intel(R) C++ Version 8.0
Intel(R) Fortran Itanium(R) Version 8.0
SGI MPI
OSF1 V5.1 Compaq C V6.5-303
HP Fortran V5.5A-3548
Compaq C++ V6.5-040
MPI_64bit_R13
SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8(32 and 64 bit) 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
TFLOPS r1.0.4 v4.4.3 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.18 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
Xeon Linux 2.4.20-31.9smp_perfctr_lustre
Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
IA-64 Linux 2.4.16 ia64 gcc version 3.0.4
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
IA-64 Linux 2.4.21.SuSE_128.bef1 ia64
Intel(R) C++ Version 8.0
Intel(R) Fortran Compiler Version 8.0
mpich-gm-1.2.5..intel
Windows 2000 (NT5.0) MSVC++ 6.0
MSVC++ .NET
DEC Visual Fortran 6.0
Intel C and F90 compilers version 7.1
Code Warrior 8.0
Windows XP MSVC++.NET
MSVC++ 6.0
DEC Visual Fortran 6.0
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
Solaris2.7 64-bit y (1) y y (1) y y y
Solaris2.7 32-bit y (1) y y (1) y y y
Solaris2.8 64-bit y (1) y y (1) y y y
Solaris2.8 32-bit y 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
T3E y (5) y y (5) 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 y y
WinXP Code Warrior n n n n y y
Win2000 Visual Studio 6.0 n y (10) n y y y
Win2000 Visual Studio Intel (6) n y n y y y
Win2000 .Net n n n y y y
Mac OS X 10.3 n y (11) n y y y
FreeBSD 4.9 y (1) n n y y y
RedHat 7 W (3) y (1) y (12) 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
RedHat 8 & SuSe x86_64 gcc (3) n y (13) n y y y
Linux 2.4 Xeon C Lustre Intel (3,7) n y n y y y
Linux 2.4 SuSE ia64 C Intel (3,8) 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
Solaris2.7 64-bit y x y y
Solaris2.7 32-bit y x y y
Solaris2.8 64-bit y x y y
Solaris2.8 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
T3E 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
WinXP Code Warrior n y n n
Win2000 Visual Studio 6.0 y y n n
Win2000 Visual Studio Intel (6) y y n n
Win2000 .Net y y n n
Mac OS X 10.3 y y n y
FreeBSD 4.9 y y y y
RedHat 7 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
RedHat 8 & SuSe x86_64 gcc (3) n y n y
Linux 2.4 Xeon C Lustre Intel (3,7) y y n y
Linux 2.4 SuSE ia64 C Intel (3,8) 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 1.2.4
(2) Using mpt and mpich 1.2.4
(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) Intel 7.1 compilers in Visual Studio 6.0 environment
(7) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre
and Intel compilers
(8) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers
(9) DEC Visual Fortran 6.0 and Intel 7.1
(10) DEC Visual Fortran 6.0
(11) IBM XLF and Absoft
(12) PGI, Absoft
(13) PGI
FMB/EIP - 2004/09/21
Known Problems
==============
* h5fc and h5c++ compilation scripts have a bug: object files (*.o) cannot be
created when source code is compiled using h5fc or h5c++. We will provide
a fix. Please check ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/
for the patches.
* Fortran subroutine h5pget_driver_f doesn't return a correct driver information.
* 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 J90 and 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 and 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)
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* 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.
* 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.
%%%%1.6.2%%%% Release Information for hdf5-1.6.2 (12/February/04)
HDF5 version 1.6.2 released on Thu Feb 12 14:18:13 CST 2004
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.1 and
HDF5-1.6.2, and contains information on the platforms tested and
known problems in HDF5-1.6.2. 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 HDF5-1.6.1
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems
New Features
============
Configuration:
--------------
- Default of $prefix is changed to $PWD/hdf5 so that multiple
builds using --srcdir is possible in the same machine.
AKC - 2003/12/1
Library:
--------
- Added H5Iget_ref, H5Iinc_ref and H5Idec_ref routines to the C
library and the FORTRAN wrapper. See the reference manual for a
full description of these new routines. QAK - 2003/12/11
Parallel Library:
-----------------
- The parallel tests in testpar/ now provides different levels of
verbosity via the '-v' option. The default is less verbose
than before. AKC - 2004/01/23
- Added parallel test, test_mpio_1wMr, which tests if the
underlying parallel I/O system is conforming to the POSIX
write/read requirement. This version includes options of using
atomicity and file-sync. AKC - 2003/11/27
Tools:
------
- Added option -showconfig to compiler tools (h5cc,h5fc,h5c++).
AKC - 2004/01/08
- Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc"
respectively if library is built in parallel mode. AKC - 2004/01/07
- Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03
C++ API:
--------
Support for new platforms, languages and compilers.
=======================================
- HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran compiler
version 8.1 Beta
Use --disbale-shared --enable-static flags with configure when
building HDF5 Fortran Library on MAC OSX.
- C and C++ Libraries are available for Linux64 RH8
- C, C++ and Fortran sequential Libraries, and C and Fortran parallel
Libraries are available for Altix (Linux ia64)
Bug Fixes since HDF5-1.6.1 release
==================================
Library
-------
- Fixed problem with H5Tget_native_type() not handling opaque fields
correctly. QAK - 2004/01/31
- Fixed several errors in B-tree deletion code which could cause a
B-tree (used with groups and chunked datasets) to become corrupt
with the right sequence of deleted objects. QAK - 2004/01/19
- Fixed small internal memory leaks of fill-value information.
QAK - 2004/01/13
- Fixed bug that caused variable-length datatypes (strings or sequences)
used for datasets in files with objects that were unlinked to
fail to be read/written to a file. QAK - 2004/01/13
- Detect situation where szip 'pixels per block' is larger than the
fastest changing dimension of a dataset's chunk size and disallow
this (due to limits in szip library). QAK - 2003/12/31
- Fixed bug with flattened hyperslab selections that would generate
incorrect hyperslab information with certain high-dimensionality
combinations of start/stride/count/block information.
QAK - 2003/12/31
- Fixed bug with variable-length datatypes used in compound datatypes.
SLU - 2003/12/29
- Fixed bug in parallel I/O routines that would cause reads from
"short datasets" (datasets which were only partially written out)
to return invalid data. QAK & AKC - 2003/12/19
- Fixed bug where scalar dataspaces for attributes were reporting as
simple dataspaces. QAK - 2003/12/13
- Fixed problem with selection offsets of hyperslab selections in
chunked datasets causing the library to go into an infinite loop.
QAK - 2003/12/13
- Fixed H5Giterate to avoid re-using index parameter after iteration
callback has been called (allows iteration callback to modify the
index parameter itself). QAK - 2003/12/06
- Fixed various floating-point conversion problems, including a
change which could corrupt data when converting from double->float.
QAK - 2003/11/24
- Changed "single process" metadata writing in library to collective
I/O by all processes, in order to guarantee correct data being
written with MPI-I/O. QAK - 2003/11/20
- Fixed problems with fill values and variable-length types and also
I/O on VL values that were set to NULL. QAK - 2003/11/08
- Fixed problems with MPI datatypes that caused ASCI Q machine to
hang. QAK - 2003/10/28
- Removed HDF5_MPI_PREFER_DERIVED_TYPES environment variable support,
since it had no benefit. QAK - 2003/10/28
- Single hyperslab selections (which were set with only one call to
H5Sselect_hyperslab) that had dimensions that could be "flattened"
but were interspersed with dimensions that could not be flattened
were not correctly handled, causing core dumps. QAK - 2003/10/25
- Avoid metadata cache from preempting current dataset object header
when looking up information about the named datatype that the
dataset uses. QAK - 2003/10/20
Configuration
-------------
- Parallel I/O with the MPI-I/O driver will no longer work if the
filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE"
environment variable has been removed. QAK - 2004/01/30
Performance
-------------
- More optimizations to inner loops of datatype conversions for
integers and floats which give a 10-50% speedup. QAK - 2003/11/07
- Hoisted invariant 'if/else's out of inner datatype conversion loop for
integer and floating-point values, giving about a 20% speedup.
QAK - 2003/10/20
Tools
-----
- Fixed h5redeploy which sometimes complain too many argument for the
test command. (The complain did not hinder the h5redploy to proceed
correctly.) AKC - 2003/11/03
Documentation
-------------
Documentation
=============
Platforms Tested
================
AIX 5.1 (32 and 64-bit) xlc 6.0.0.2
xlf 8.1.0.3
xlC 6.0.0.4
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
poe 3.2.0.10
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.2
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.2
Cray T90IEEE 10.0.0md Cray Standard C Version 6.4.0.3
Cray Fortran Version 3.4.0.0
FreeBSD 4.9 gcc 2.95.4
g++ 2.95.4
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 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
C++ MIPSpro cc 7.3.1.3m
Linux 2.4.18 gcc 2.96, 3.3.2
g++ 3.3.2
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Linux 2.4.20-8 gcc 3.3.2
PGI compilers (pgcc, pgf90, pgCC) version 5.0-2
MPIch 1.2.4
Linux 2.4.21-2.9.5ws #3 gcc 3.2.3 (Red Hat Linux 3.2.3-16)
SMP x86_64 g++ 3.2.3
Linux 2.4.19-SMP x86_64 gcc (GCC) 3.2.2 (SuSE Linux)
g++ 3.2.2
Linux 2.4.21-sgi Altix
SMP ia64 Intel(R) C++ Version 7.1
Intel(R) Fortran Itanium(R) Version 7.1
SGI MPI
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran V5.5-2602
Compaq Fortran V5.5-1877
Compaq C++ V6.5-033
Compaq C++ V6.5-030
MPI_64bit_R13
SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8(32 and 64 bit) 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
TFLOPS r1.0.4 v4.4.2 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.18 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
IA-64 Linux 2.4.16 ia64 gcc version 3.0.4
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
IA-64 Linux 2.4.21.SuSE_128.bef1 ia64
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
mpich-gm-1.2.5..intel
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Intel C and F90 compilers version 7.1
Code Warrior 8.0
Windows XP MSVC++.NET
MAC OS X Darwin 7.2
gcc and g++ Apple Computer, Inc. GCC
version 1175, based on gcc version 3.3.2
IBM XL Fortran version 8.1 Beta
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 C F90 F90 C++ Shared zlib
parallel parallel libraries (4)
Solaris2.7 64-bit y y (1) y y (1) y y y
Solaris2.7 32-bit y y (1) y y (1) y y y
Solaris2.8 64-bit y y (1) y y (1) y y y
Solaris2.8 32-bit y y y y (1) y y y
IRIX64_6.5 64-bit y y (2) y y y y y
IRIX64_6.5 32-bit y y (2) n n n y y
HPUX11.00 y y (1) y y y y y
OSF1 v5.1 y y y y y y y
T3E y y (5) y y (5) n n y
SV1 y y (5) y y (5) n n y
T90 IEEE y y (5) y y (5) n n y
TFLOPS n y (1) n n n n y
AIX-5.1 32-bit y y y y y n y
AIX-5.1 64-bit y y y y y n y
WinXP Visual Studio (7) y n n n y y y
WinXP Intel y n n n y y y
WinXP CW y n n n n n y
Win2000 Visual Studio y n y n y y y
Win2000 Intel y n y n y y y
Mac OS X 10.3 y n y n y y y
FreeBSD 4.9 y y (1) n n y y y
RedHat 7, 8 & 9 ia32 y y (1) y(PGI) n y y y
W gcc (3)
RedHat 7.3 ia32 W Intel (3) y n y n y n y
RedHat 7.3 ia32 W PGI (3) y n y n y n y
RedHat 7 ia32 C Intel (3) y n y n y n y
RedHat 7.1 ia64 C Intel (3) y n y n y n y
RedHat 8 & SuSe x86_64 y n n n y n y
gcc (3)
Linux 2.4 SGI Altix ia64 y n y n y y y
Intel (3)
Platform static- Thread- SZIP GASS STREAM- High- H4/H5
exec safe VFD level tools
APIs (6)
Solaris2.7 64-bit x y y n y y n
Solaris2.7 32-bit x y y n y y y
Solaris2.8 64-bit x y y n y y n
Solaris2.8 32-bit x y y n y y y
IRIX64_6.5 64-bit x y y y y y y
IRIX64_6.5 32-bit x y y y y y y
HPUX11.00 x n y n y y y
OSF1 v5.1 y n y n y y y
T3E y n n n y y y
SV1 y n n n y y y
T90 IEEE y n n n y y n
TFLOPS y n n n n n n
AIX-5.1 32-bit y n y n y y y
AIX-5.1 64-bit y n y n y y y
WinXP Visual Studio y n y n n y y
WinXP Intel y n y n n y y
WinXP CW y n y n n y y
Win2000 Visual Studio y n y n n y y
Win2000 Intel y n y n n y y
Mac OS X 10.3 y n y n y y n
FreeBSD 4.9 y y y n y y y
RedHat 7, 8 & 9 ia32 y y y n y y y
W gcc (3)
RedHat 7.3 ia32 W Intel (3) y n y n y n n
RedHat 7.3 ia32 W PGI (3) y n y n y n n
RedHat 7 ia32 C Intel (3) y n y n y y y
RedHat 7.1 ia64 C Intel (3) y n y n y y y
RedHat 8 & SuSe x86_64 y n y n y y y
gcc (3)
Linux 2.4 SGI Altix ia64 y n y n y y y
Intel (3)
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 1.2.4.
(2) Using mpt and mpich 1.2.4.
(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) Includes the H4toH5 Library and the h4toh5 and h5toh4
utilities.
Known Problems
==============
* Fortran subroutine h5pget_driver_f doesn't return a correct driver information.
* 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 J90 and 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 and 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://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.2/F90_source_for_Crays
* On some platforms that use Intel 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)
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* 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.
* On AIX 5.1 when 64-bit parallel C Library is built with zlib configured in,
compilation fails for H5Zdeflate.c. To bypass the problem, remove "const"
definition in front of H5Z_DEFLATE in H5Zpkg.h line 29.
%%%%1.6.1%%%% Release Information for hdf5-1.6.1 (16/October/03)
15. Release information for HDF5 version 1.6.1
================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.0 and
HDF5-1.6.1, and contains information on the platforms tested and
known problems in HDF5-1.6.1. 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 HDF5-1.6.0
- Documentation
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
Library:
--------
- Added new fields to the H5G_stat_t for more information about an
object's object header. QAK 2003/10/06
- Added new H5Fget_freespace() routine to query the free space in a
given file. QAK 2003/10/06
Parallel Library:
-----------------
Tools:
------
C++ API:
--------
- Added overloaded functions read and write to H5::Attribute.
BMR - 2003/04/21
- Added an overloaded constructor H5::StrType so the need to separately
set the length of the string type can be eliminated. BMR - 2003/04/21
- Added overloaded functions read and write to H5::DataSet.
BMR - 2003/04/27
The following items were added but not documented in previous releases:
- On windows, any application, that uses the C++ API dll, must
include the name HDF5CPP_USEDLL in its project setting. (Feb 17, 2002)
BMR - 2003/10/10
- Added missing default constructor H5::H5File. (Apr 26, 2002)
BMR - 2003/10/10
- Added new member function H5::DataSet::fillMemBuf per the new C
API H5Dfill, which fills the elements in a selection for a memory
buffer with a fill value. (May 16, 2002) BMR - 2003/10/10
- Added the new member function getMemberIndex to H5::EnumType
and H5::CompType to match the new C API H5Tget_member_index. Given
the name of a member of an enumeration or compound datatype, this
new function queries the index of the member. (May 16, 2002)
BMR - 2003/10/10
- Added these member functions to H5::Group per the new C functions
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx:
+ getNumObjs: Returns the number of objects in the group.
+ getObjnameByIdx: Retrieves the name of an object in a group,
given an index
+ getObjTypeByIdx: Returns the type of an object in a group,
given an index
(Jan 20, 2003) BMR - 2003/10/10
Support for new platforms, languages and compilers.
=======================================
- gcc 3.3.1 is supported on Linux.
Bug Fixes since HDF5-1.6.0 release
==================================
Library
-------
- Fixed incorrect datatype of the third parameter to the Fortran90
h5pset(get)_cache_f functions (INTEGER to INTEGER(SIZE_T)) EIP - 2003/10/13
- Fixed problems with accessing variable-length data datatypes on
Crays. QAK - 2003/10/10
- Fixed potential file corruption bug when too many object header
messages (probably attributes, from a user perspective) were
inserted into an object header and certain other conditions were
met. QAK - 2003/10/08
- Changed implementation of internal ID searching algorithm to avoid
O(n) behavior for many common cases. QAK - 2003/10/06
- Allow partial parallel writing to compact datasets. QAK - 2003/10/06
- Correctly create reference to shared datatype in attribute, instead
of making a copy of the shared datatype in the attribute.
QAK - 2003/10/01
- Revert changes which caused files >2GB to fail when created with
MPI-I/O file driver on certain platforms. QAK - 2003/09/16
- Allow compound datatypes to grow in size. SLU - 2003/09/10
- Detect if a type is already packed before attempting to pack it
again or check if it is locked. SLU - 2003/09/10
- Corrected bug when opening a file twice with read-only permission
for one open and then closing the read-only access file ID would
generate an error. QAK - 2003/09/10
- Corrected bug in repeated calls to H5Pget_access_plist() which would
incorrectly manage reference counts of internal information and
eventually blow up. QAK - 2003/09/02
- Return rank of the array datatype on successful call to
H5Tget_array_dims(). QAK - 2003/08/30
- Corrected bug in H5Tdetect_class which was not correctly detecting
datatype classes of fields in nested compound datatypes in some
circumstances. QAK - 2003/08/30
- Corrected bug in sieve buffer code which could cause loss of data
when a small dataset was created and deleted in quick succession.
QAK - 2003/08/27
- Corrected bug in H5Gget_objname_by_idx which was not allowing NULL
for the name when just querying for the object name's length.
QAK - 2003/08/25
- Corrected bug in variable-length string handling which could
generate a core dump on writing variable-length strings as part
of a compound datatype on certain architectures. QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would incorrectly compute
the size of certain compound datatypes and also incorrectly
compute the offset of the last field for those compound datatypes.
QAK - 2003/08/25
- Corrected bug in H5Tget_native_type which would drop string datatype
metadata (padding, etc.) QAK - 2003/08/25
- Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and
H5Gget_objtype_by_idx to allow them to accept location IDs, not just
group IDs. QAK - 2003/08/21
- Corrected bug when using scalar dataspace for memory selection and
operating on chunked dataset. QAK - 2003/08/18
- Corrected bugs with multiple '/' characters in names for H5Glink
and H5Gunlink. QAK - 2003/08/16
- Corrected bug with user blocks that didn't allow a user block to
be inserted in front of a file after the file was created.
QAK - 2003/08/13
- Corrected errors with using point selections to access data in
chunked datasets. QAK - 2003/07/23
- Corrected error with variable-length datatypes and chunked datasets
which caused H5Dwrite to fail sometimes. QAK - 2003/07/19
- Modified library and file format to support storing indexed storage
(chunked dataset) B-tree's with non-default internal 'K' values.
QAK - 2003/07/15
- Returned H5T_BKG_TEMP support to library after it was accidentally
removed. QAK - 2003/07/14
Configuration
-------------
- Fixed the error that caused "make install" to fail because of the
macro definition syntax of "prefix?=..." AKC - 2003/07/22
Performance
-------------
Tools
-----
- Fixed a segmentation fault of h5diff when percentage option is used.
AKC - 2003/08/27
- Switched away from tools using internal "fixtype" function(s) to use
H5Tget_native_type() internally. QAK - 2003/08/25
Documentation
-------------
- Added two missing Fortran APIs (h5pget_fapl_mpiposix_f and
h5pset_fapl_mpiposix_f) to the reference manual.
FMB - 2003/10/15
- Corrected the reference manual descriptions of H5open/h5open_f and
H5close/h5close_f to indicate that these calls are required in
Fortran90 applications. FMB - 2003/10/15
Documentation
=============
Fortran90 APIs are being integrated into the main body of the
HDF5 Reference Manual (RM). This process is complete in all RM sections
except H5P.
A PDF version of the RM will be posted on the HDF5 website
(at http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/) approximately one week
after the release.
Platforms Tested
================
AIX 5.1 (32 and 64-bit) xlc 6.0.0.2
xlf 8.1.0.3
xlC 6.0.0.4
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
poe 3.2.0.10
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.2
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.2
Cray T90IEEE 10.0.1.01y Cray Standard C Version 6.4.0.2.3
Cray Fortran Version 3.4.0.3
FreeBSD 4.9 gcc 2.95.4
g++ 2.95.4
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP ANSI C++ B3910B A.03.13
HP MPI 01.07.00.00
IRIX 6.5 MIPSpro cc 7.3.1.2m
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
MPIch 1.2.4
Linux 2.4.18 gcc 2.96, 3.2.2, 3.3.1
g++ 3.2.2, 3.2.3
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 4.0-2
MPIch 1.2.4
Linux 2.4.20-8 gcc 3.2.2
OSF1 V5.1 Compaq C V6.4-014
Compaq C V6.3-027
Compaq Fortran V5.5-2602
Compaq C++ V6.5-030
MPI_64bit_R5
g++ version 3.0 for C++
SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8(32 and 64 bit) 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
TFLOPS r1.0.4 v4.4.0 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.9 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Intel C and F90 compilers version 7.1
Code Warrior 8.0
Windows XP MSVC++.NET
MAC OS X Darwin 6.8
gcc and g++ Apple Computer, Inc. GCC
version 1175, based on gcc version 3.1
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
Platform C C F90 F90 C++ Shared zlib
parallel parallel libraries (4)
Solaris2.7 64-bit y y (1) y y (1) y y y
Solaris2.7 32-bit y y (1) y y (1) y y y
Solaris2.8 64-bit y y (1) y y (1) y y y
Solaris2.8 32-bit y y y y (1) y y y
IRIX6.5 y y (1) n n n y y
IRIX64_6.5 64-bit y y (2) y y y y y
IRIX64_6.5 32-bit y y (2) n n n y y
HPUX11.00 y y (1) y y y y y
OSF1 v5.1 y y y y y y y
T3E y y (5) y y (5) n n y
SV1 y y (5) y y (5) n n y
T90 IEEE y y (5) y y (5) n n y
TFLOPS n y (1) n n n n y
AIX-5.1 32-bit y y y y y n y
AIX-5.1 64-bit y y y y y n y
WinXP (6) y n n n y y y
WinXP Intel y n n n y y y
Win2000 y n y n y y y
Win2000 Intel y n y n y y y
WinNT CW y n n n n n y
Mac OS X 10.2 y n n n y y y
FreeBSD y y (1) n n y y y
Linux 2.4 gcc (3) y y (1) y (PGI) n y y y
Linux 2.4 Intel (3) y n y n y n y
Linux 2.4 PGI (3) y n y n y n y
Linux 2.4 IA32 Intel y n y n y n y
Linux 2.4 IA64 Intel y n y n y n y
ASCII Table 2 -- for RELEASE.txt
Platform static- Thread- SZIP GASS STREAM- High-level H4/H5
exec safe VFD APIs tools (7)
Solaris2.7 64-bit x y y n y y n
Solaris2.7 32-bit x y y n y y y
Solaris2.8 64-bit x y y n y y n
Solaris2.8 32-bit x y y n y y y
IRIX6.5 x n y n y y y
IRIX64_6.5 64-bit x y y y y y y
IRIX64_6.5 32-bit x y y y y y y
HPUX11.00 x n y n y y y
OSF1 v5.1 y n y n y y y
T3E y n n n y y y
SV1 y n n n y y y
T90 IEEE y n n n y y n
TFLOPS y n n n n n n
AIX-5.1 32-bit y n y n y y y
AIX-5.1 64-bit y n y n y y y
WinXP (6) y n y n n y y
WinXP Intel y n y n n y y
Win2000 y n y n n y y
Win2000 Intel y n y n n y y
WinNT CW y n y n n y y
Mac OS X 10.2 y n y n y y n
FreeBSD y y y n y y y
Linux 2.4 gcc (3) y y y n y y y
Linux 2.4 Intel (3) y n y n y n n
Linux 2.4 PGI (3) y n y n y n n
Linux 2.4 IA32 Intel y n y n y y y
Linux 2.4 IA64 Intel y n y n y y y
Notes: (1) Using mpich 1.2.4.
(2) Using mpt and mpich 1.2.4.
(3) Linux 2.4 with GNU, Intel, and PGI compilers, 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) Binaries only; source code for this platform is not being
released at this time.
(7) Includes the H4toH5 Library and the h4toh5 and h5toh4
utilities.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* Fortran subroutine h5pget_driver_f doesn't return a correct driver information.
The fix will be available in the 1.6.2 release.
* 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.
* With the gcc 2.95.2 compiler, HDF 5 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 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 J90 and 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 and 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 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)
ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
%%%%1.6.0%%%% Release Information for hdf5-1.6.0 (03/July/03)
14. Release information for HDF5 version 1.6.0
================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.* and
HDF5-1.6.0, and contains information on the platforms tested and
known problems in HDF5-1.6.0. 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 HDF5-1.4.0
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
The following flags have been added to the configuration script:
--enable-hdf5v1_4 Compile the HDF5 v1.4 compatibility interface
--enable-filters=all Turn on all internal I/O filters. One may also
specify a comma-separated list of filters or the
word no. The default is all internal I/O filters.
--with-mpe=DIR Use MPE instrumentation [default=no]
--with-szlib=DIR Use szlib library for external szlib I/O filter
[default=no]
Library:
--------
Summary: This release has the following new features that are not
available in 1.4.* releases
1. Generic properties to give application more control on I/O pipeline
2. Time allocation and fill value properties
3. New filters: external compression filter szip
internal shuffling and checksum filters
4. Compact storage layout for datasets
5. Redesigned I/O pipeline for better performance.
For more information see
http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html
http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide.html
http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/Changes.html
Complete list of changes:
* Changed dataset modification time to _not_ be updated when raw data is
written to a dataset. The modification time is only updated when the
dataset's metadata is modified. QAK - 2003/06/10
* Changed H5Sget_select_bounds to use 'hssize_t *' for start and end
parameters, instead of 'hsize_t *', to better match other parts of the
dataspace API. QAK - 2003/06/04
* Changed raw data I/O to only access each chunk once, improving performance
in many situations with hyperslabs and large chunks or chunks with
filters. These improvements are currently limited to serial I/O, with
similar parallel I/O improvements forthcoming sometime in the future.
QAK - 2003/05/07
* Added parameter to the MPI/POSIX driver. If GPFS is enabled (by
modifying the H5FDmpiposix.c file to uncomment the USE_GPFS_HINTS
macro), then this extra parameter will turn GPFS hints on and off
during runtime. BW - 2003/05/05
* Added option to print 1-byte integer datasets as ASCII to h5dump. BW -
2003/04/30
* Added a new utility "h5fc". It can be used to compile easily Fortran
programs which use HDF5. It automatically uses the compiler the HDF5
library was built with and links in any libraries HDF5 requires.
BW - 2003/04/10
* Added new dataset creation property list functions for working with
I/O filters: H5Pmodify_filter, H5Pget_filter_by_id and
H5Pall_filters_avail. Also changed H5Zregister to use new method
of registering filters with library. QAK - 2003/04/08
* The first version of szip compression support were implemented.
User should have static szlib library installed. Using function
H5Pset_szip to pass the szip parameters to the HDF5 library.
More detailed description of the process will be followed.
KY-2003/04/01
* Added Fletcher32 checksum as a filter in pipeline. It only works in
chunked dataset. SLU - 2003/2/11
* MPICH/MPE instrumentation feature added. Use --with-mpe[=DIR] to configure
it. AKC - 2003/1/3
* New functions H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx
are added to the library. SLU - 2002/11/25
* H5Dget_offset is added to return the offset of a dataset's data relative
to the beginning of the file. SLU - 2002/11/7
* Functions H5Tget_native_type and H5Tis_variable_str are added. The first
one reconstructs a datatype based on native memory datatype. The second
one checks if a datatype is variable string. SLU - 2002/11/6
* Added environment variable "HDF5_DISABLE_VERSION_CHECK", which disables
the version checking between the header files and the library linked into
an application if set to '1'. This should be used with caution, mis-
matched headers and library binaries can cause _serious_ problems.
QAK - 2002/10/15
* Added new API function to get the name of an object in a file, using
an open ID (hid_t). QAK - 2002/10/14
* Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
SLU - 2002/09/30
* Changed "H5P[set|get]_space_time" functions to "H5P[set|get]_alloc_time"
Unify all symbolic names for these functions to use "alloc time" instead
of other names. QAK - 2002/09/13
* Added "H5D_SPACE_ALLOC_INCR" setting to H5D_SPACE_ALLOC_EARLY and
H5D_SPACE_ALLOC_LATE for H5Dset_space_time(). This allows chunked
datasets to be incrementally allocated as in the 1.4.x branch.
QAK - 2002/08/27
* Compact dataset is added to the library. The data will be stored in
the header message of dataset layout. Space allocation time has to be
EARLY. No hyperslab is supported for parallel collective write. There
is no API changes except activating H5Pset_layout and H5Pget_layout for
compact dataset. -SLU, 2002/8/20
* Added 'closing' parameter to VFL 'flush' callback function and H5FDflush.
This allows the library to indicate that the file will be closed
immediately following the call to 'flush' and can be used to avoid actions
that are duplicated in the VFL 'close' callback function. QAK - 2002/05/20
* Added feature to parallel chunk allocation routine to not write fill
values to chunks allocated if the user has set the "fill time" to never.
This can improve parallel I/O performance for chunked
datasets. QAK - 2002/05/17
* New functions H5Glink2 and H5Gmove2 were added to allow link and move to
be in different locations in the same file. The old functions H5Glink
and H5Gmove remain valid. SLU - 2002/04/26
* Fill-value's behaviors for contiguous dataset have been redefined.
Basically, dataset won't allocate space until it's necessary. Full details
are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment.
SLU - 2002/04/11
* Added new routine "H5Dfill" to fill a selection with a particular value
in memory. QAK - 2002/04/09
* Improved performance of "regular" hyperslab I/O when using MPI-IO and the
datatype conversion is unnecessary. QAK - 2002/04/02
* Improved performance of single hyperslab I/O when datatype conversion is
unnecessary. QAK - 2002/04/02
* Added new "H5Sget_select_type" API function to determine which type of
selection is defined for a dataspace ("all", "none", "hyperslab" or
"point"). QAK - 2002/02/07
* Added support to read/write portions of chunks directly, if they are
uncompressed and too large to cache. This should speed up I/O on chunked
datasets for a few more cases. QAK - 2002/01/31
* Added H5Rget_obj_type() API function, which performs the same functionality
as H5Rget_object_type(), but requires the reference type as a parameter
in order to correctly handle dataset region references. Moved
H5Rget_object_type() to be only compiled into the library when v1.4
compatibility is enabled.
* Added a new file access property, file close degree, to control file
close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI,
H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspond functions
H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two
new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist
this new feature. For full details, please refer to the reference
manual under the description of H5Fcreate, H5Fopen, H5Fclose and the
functions mentioned above.
* Removed H5P(get|set)_hyper_cache API function, since the property is no
longer used.
* Improved performance of non-contiguous hyperslabs (built up with
several hyperslab selection calls).
* Improved performance of single, contiguous hyperslabs when reading or
writing.
* As part of the transition to using generic properties everywhere, the
parameter of H5Pcreate changed from H5P_class_t to hid_t, as well
the return type of H5Pget_class changed from H5P_class_t to hid_t.
Further changes are still necessary and will be documented here as they
are made.
* Improved regular hyperslab I/O by about a factor of 6 or so.
* Modified the Pablo build procedure to permit building of the instrumented
library to link either with the Trace libraries as before or with the
Pablo Performance Capture Facility.
* Added new F90 APIs for generic properties, new filters, and
time/space allocation properties.
* C++ API:
- Added two new member functions: Exception::getFuncName() and
Exception::getCFuncName() to provide the name of the member
function, where an exception is thrown.
- IdComponent::operator= becomes a virtual function because
DataType, DataSpace, and PropList provide their own
implementation. The new operator= functions invoke H5Tcopy,
H5Scopy, and H5Pcopy to make a copy of a datatype, dataspace,
and property list, respectively.
Parallel Library:
-----------------
Tools:
------
* When the "-S" option for "simple" output is chosen, h5ls now displays
modification times of datasets in UTC instead of local time.
QAK - 2003/06/06
* h5diff to compare two HDF5 files was added
* h5import to import ascii and binary data to an HDF5 file was added.
Old h5import tool in the tools/misc directory was renamed to
h5createU8 to reflect its purpose. h5createU8 will be deleted in
1.6.1 release.
* Two new scripts h5fc and h5c++ were added to compile F90 and C++
HDF5 applications.
Support for new platforms, languages and compilers.
=======================================
* Added C++ API support on HPUX11.00. BMR - 2003/03/19
* Absoft compiler is supported for Fortran HDF5 Library.
When building with Absoft compiler, add -DH5_ABSOFT to
C compilation flags to get correct names of C functions
called by Fortran APIs.
Bug Fixes since HDF5-1.4.0 release
==================================
Library
-------
* Don't attempt to perform collective I/O on chunked datasets with
parallel I/O. QAK - 2003/06/05
* The library now correctly reuses space when objects are deleted in the
file. This should be handled correctly for every situation, except
datasets with variable-length datatypes are not returning the space they
use in the global heap currently. QAK - 2003/04/13
* Fixed error in B-tree deletion routine which could cause groups to be
corrupted when objects are removed from them.
QAK - 2003/04/11
* Fixed error in file space freeing code which could cause metadata to
fail to be written to the file.
QAK - 2003/04/11
* -O caused errors in AIX 5.x platforms. Removed it from
--enable-production mode. AKC - 2003/03/31
* Corrected memory/resource leaks in per-thread key information when
thread-safe operation was enabled. QAK - 2003/02/07
* Improved error assertion for nil VL strings, making it fails with error
stack instead of just assertion failure. SLU - 2002/12/16
* Added two new API functions: H5Zunregister & H5Zfilter_avail.
QAK - 2002/11/16
* Add data shuffle filter(source code H5Zshuffle.c), the combination of the
shuffling and compression can make data compression better without suffering
much encoding and decoding CPU time for many application datasets(especially
for floating point data). This adds a new API function: H5Pset_shuffle.
KY - 2002/11/13
* Allow scalar dataspaces to be used for parallel I/O. QAK - 2002/11/05
* New functions H5Gget_comment(modification), H5Aget_storage_size,
H5Arename. SLU - 2002/10/29
* Fixed an assertion of H5S_select_iterate that did not account for scalar
type that has no dimension sizes. AKC - 2002/10/15
* Partially fixed space allocation inefficiencies in the file by
improving our algorithms for re-using freed space. QAK - 2002/08/27
* Fixed data corruption problem which could occur when fill values were
written to a contiguously stored dataset in parallel. QAK - 2002/08/27
* Fixed VL memory leak when data is overwritten. The heap objects holding
old data are freed. If the fill value writing time is set to
H5D_FILL_TIME_NEVER, the library prohibits user to create VL type dataset.
The library free all the heap objects storing VL type if there is nested
VL type(a VL type contains another VL type). SLU - 2002/07/10
* Tweaked a few API functions to use 'size_t' instead of 'unsigned' or
'hsize_t', which may cause errors in some cases.
Configuration
-------------
* Included the both the examples of fortran and c++ "make check-install"
testing. This tests the correctness of the h5fc command. AKC - 2003/04/22
* When using gcc 3.x, we use -std=c99 instead of -ansi for compiling.
QAK - 2003/04/11
* IA64 platform has its own configure setting and use Intel Compilers as
the default compilers (were gcc and pgf90 before.) This also eliminated
the segmentation fault in the fortran test. The missing reference of
"exit" is fixed too. AKC - 2003/04/02
Performance
-------------
* Improved dataset creation time by about 30% (relative to the 1.4.x
branch).
Tools
-----
* Added a -force option to h5redeploy. AKC - 2003/03/04
* The VL string bug(data and datatype cannot be shown) in h5dump is fixed.
-SLU - 2002/11/18
* Fixed segfault if h5dump was invoked with some options but no file
(e.g., h5dump -H). -AKC, 2002/10/15
* Fixed so that the "-i" flag works correctly with the h5dumper.
* Fixed segfault when "-v" flag was used with the h5dumper.
Documentation
-------------
Platforms Tested
================
AIX 5.1 (32 and 64-bit) xlc 6.0.0.2
xlf 8.1.0.3
xlC 6.0.0.4
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
poe 3.2.0.10
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2
Cray Fortran Version 3.6.0.0.2
mpt 2.2.0.0
Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2
mpt 2.2.0.0
Cray Fortran Version 3.6.0.0.2
Cray T90IEEE 10.0.1.01y Cray Standard C Version 6.4.0.2.3
Cray Fortran Version 3.4.0.3
mpt 2.1.0.0
FreeBSD 4.7 gcc 2.95.4
g++ 2.95.5
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
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
MPIch 1.2.4
Linux 2.4.18 gcc 2.96, 3.2.2, 3.2.3
g++ 3.2.2, 3.2.3
Intel(R) C++ Version 7.1
Intel(R) Fortran Compiler Version 7.1
PGI compilers (pgcc, pgf90, pgCC) version 4.0-2
MPIch 1.2.4
OSF1 V5.1 Compaq C V6.4-014
Compaq C V6.3-027
Compaq Fortran V5.5-1877
Compaq C++ V6.5-014
MPI_64bit_R5
g++ version 3.0 for C++
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 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 5.8/64 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
TFLOPS r1.0.4 v4.3.3 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.9 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Intel C and F90 compilers version 7.1
Code Warrior 8.0
Windows XP MSVC++.NET
MAC OS X Darwin 6.5
gcc and g++ Apple Computer, Inc. GCC
version 1161, based on gcc version 3.1
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
Platform C C F90 F90 C++ Shared zlib
parallel parallel libraries (4)
Solaris2.7 64-bit y y (1) y y (1) y y y
Solaris2.7 32-bit y y (1) y y (1) y y y
Solaris2.8 64-bit y y (1) y y (1) y y y
Solaris2.8 32-bit y y y y (1) y y y
IRIX6.5 y y (1) n n n y y
IRIX64_6.5 64-bit y y (2) y y y y y
IRIX64_6.5 32-bit y y (2) n n n y y
HPUX11.00 y y (1) y y y y y
OSF1 v5.1 y y y y y y y
T3E y y (5) y y (5) n n y
SV1 y y (5) y y (5) n n y
T90 IEEE y y (5) y y (5) n n y
TFLOPS n y (1) n n n n y
AIX-5.1 32-bit y y y y y n y
AIX-5.1 64-bit y y y y y n y
WinXP (6) y n n n y y y
WinXP Intel y n n n y y y
Win2000 y n y n y y y
Win2000 Intel y n y n y y y
WinNT CW y n n n n n y
Mac OS X 10.2 y n n n y y y
FreeBSD y y (1) n n y y y
Linux 2.4 gcc (3) y y (1) y (PGI) n y y y
Linux 2.4 Intel (3) y n y n y n y
Linux 2.4 PGI (3) y n y n y n y
Linux 2.4 IA32 Intel y n y n y n y
Linux 2.4 IA64 Intel y n y n y n y
ASCII Table 2 -- for RELEASE.txt
Platform static- Thread- SZIP GASS STREAM- High-level H4/H5
exec safe VFD APIs tools (7)
Solaris2.7 64-bit x y y n y y n
Solaris2.7 32-bit x y y n y y y
Solaris2.8 64-bit x y y n y y n
Solaris2.8 32-bit x y y n y y y
IRIX6.5 x n y n y y y
IRIX64_6.5 64-bit x y y y y y y
IRIX64_6.5 32-bit x y y y y y y
HPUX11.00 x n y n y y y
OSF1 v5.1 y n y n y y y
T3E y n n n y y y
SV1 y n n n y y y
T90 IEEE y n n n y y n
TFLOPS y n n n n n n
AIX-5.1 32-bit y n y n y y y
AIX-5.1 64-bit y n y n y y y
WinXP (6) y n y n n y y
WinXP Intel y n y n n y y
Win2000 y n y n n y y
Win2000 Intel y n y n n y y
WinNT CW y n y n n y y
Mac OS X 10.2 y n y n y y n
FreeBSD y y y n y y y
Linux 2.4 gcc (3) y y y n y y y
Linux 2.4 Intel (3) y n y n y n n
Linux 2.4 PGI (3) y n y n y n n
Linux 2.4 IA32 Intel y n y n y y y
Linux 2.4 IA64 Intel y n y n y y y
Notes: (1) Using mpich 1.2.4.
(2) Using mpt and mpich 1.2.4.
(3) Linux 2.4 with GNU, Intel, and PGI compilers, 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) Binaries only; source code for this platform is not being
released at this time.
(7) Includes the H4toH5 Library and the h4toh5 and h5toh4
utilities.
Compiler versions for each platform are listed in the preceding
"Platforms Tested" table.
Known Problems
==============
* PGI C++ compiler fails when compiling the C++ library's tests.
Therefore, we cannot verify that the C++ library built with the PGI C++
compiler is correct.
* 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.
* With the gcc 2.95.2 compiler, HDF 5 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 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 J90 and 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 and 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 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)
ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104 of
the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
UPDATE: This is now done automatically by the configure script. However, if
you still experience a problem, you may want to check this line in the
libtool file and make sure that it has the correct value.
* Information about building with PGI and Intel compilers is available in
INSTALL file sections 5.7 and 5.8
-----------------------------------------------------------------------
%%%%1.4.5%%%% Release Information for hdf5-1.4.5 (02/February/03)
13. Release information for HDF5 version 1.4.5
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.4 and
HDF5-1.4.5, and contains information on the platforms tested and
known problems in HDF5-1.4.5. For additional information 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, see 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
- Bug Fixes since HDF5-1.4.4
- Performance Improvements
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* Added "unofficial support" for building with a C++ compiler (or at least
not failing badly when building with a C++ compiler). QAK - 2003/01/09
* Added "unofficial support" for AIX 64bits. See INSTALL for configure
details. AKC - 2002/08/29
* Added "--with-dmalloc" flag, to easily enable support for the 'dmalloc'
debugging malloc implementation. QAK - 2002/07/15
o Library
=========
o General
---------
* Allow scalar dataspaces to be used for parallel I/O. QAK - 2002/11/05
* Added environment variable "HDF5_DISABLE_VERSION_CHECK", which disables
the version checking between the header files and the library linked
into an application if set to '1'. This should be used with caution,
mis-matched headers and library binaries can cause _serious_ problems.
QAK - 2002/10/15
* Partially fixed space allocation inefficiencies in the file by
improving our algorithms for re-using freed space. QAK - 2002/08/27
* API tracing has been improved. Nested API calls don't screw up the
output format; function call and return event times can be logged;
total time spent in each function can be logged. The following
HDF5_DEBUG environment variable words affect tracing:
trace -- turn on/off basic tracing
ttimes -- turn on tracing and report event times and
time spent in each API function.
ttop -- turn on tracing but display only top-level
API calls.
o APIs
------
* Several missing fortran APIs have been added to the library:
h5get_libversion_f h5tget_member_index_f h5dget_storage_size_f
h5check_version_f h5tvlen_create_f h5dvlen_get_max_len_f
h5garbage_collect_f h5dwrite_vl_f
h5dont_atexit_f h5dread_vl_f
Functions h5dvlen_get_max_len_f, h5dwrite_vl_f, and h5dread_vl_f support
VL Length C APIs functionality for integer, real and string datatypes.
See HDF5 Reference Manual and HDF5 FORTRAN90 User's Notes for more
information and for the functions description.
o Parallel library
==================
* The MPI-posix virtual file driver makes gpfs_fcntl() hints to tell
the underlying GPFS file system to avoid prefetching byte range
tokens if USE_GPFS_HINTS is defined when this file is compiled.
This temporary solution is intended to be removed once the HDF5
API supports the necessary functionality that makes it possible
for this sort of thing do be done at a higher software layer.
RPM - 2002/12/03
* Added MPI-posix VFL driver. This VFL driver uses MPI functions to
coordinate actions, but performs I/O directly with POSIX sec(2)
(i.e. open/close/read/write/etc.) calls. This driver should _NOT_
be used to access files that are not on a parallel filesystem.
The following API functions were added:
herr_t H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm);
herr_t H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/);
QAK - 2002/07/15
o Support for new platforms and languages
=========================================
* C++ API now works on the Origin2000 (IRIX6.5.14.) BMR - 2002/11/14
o Misc.
=========================================
HDF5 1.4.5 works with Portland Group Compilers (pgcc, pgf90 and pgCC
version 4.0-2) on Linux 2.4
Bug Fixes since HDF5-1.4.4 Release
==================================
* H5Fopen without the H5F_ACC_CREAT flag should not succeed in creating
a new file with the 'core' VFL driver. QAK - 2003/01/24
* Corrected metadata caching bug in parallel I/O which could cause hangs
when chunked datasets were accessed with independent transfer mode.
QAK - 2003/01/23
* Allow opening objects with unknown object header messages.
QAK - 2003/01/21
* Added improved error assertion for nil VL strings. It return error
stack instead of a simple assertion. SLU - 2002/12/16
* Fixed h5dump bug(cannot dump data and datatype) for VL string.
SLU - 2002/11/18
* Fixed error condition where "none" selections were not being handled
correctly in serial & parallel. QAK - 2002/10/29
* Fixed problem where optimized hyperslab routines were incorrectly
invoked for parallel I/O operations in collective mode. QAK - 2002/07/22
* Fixed metadata corruption problem which could occur when many objects
are created in a file during parallel I/O. QAK - 2002/07/19
* Fixed minor problem with configuration when users specified /usr/include
and /usr/lib for the --with-* options that some compilers can't
handle. BW - 2003/01/23
Documentation
=============
New PDF files are not available for this release.
Platforms Tested
================
AIX 5.1 (32 and 64-bit) C for AIX Compiler, Version 6
xlf 8.1.0.2
poe 3.2.0.11
Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.1.3
Cray Fortran Version 3.6.0.0.12
Cray SV1 10.0.1. 0 Cray Standard C Version 6.6.0.1.3
Cray Fortran Version 3.6.0.0.12
Cray T90IEEE 10.0.1.01u Cray Standard C Version 6.4.0.2.3
Cray Fortran Version 3.4.0.3
FreeBSD 4.7 gcc 2.95.4
g++ 2.95.5
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
Linux 2.4.18 gcc 3.2.1
g++ 3.2.1
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
PGI compilers (pgcc, pgf90, pgCC) version 4.0-2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran X5.4A-1684
gcc version 3.0 for C++
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.3.3 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with
local modifications
IA-32 Linux 2.4.9 gcc 2.96
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 7.0
Intel(R) Fortran Compiler Version 7.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows XP .NET
Windows NT4.0 Code Warrior 6.0
MAC OS X Darwin 6.2
gcc and g++ Apple Computer, Inc. GCC
version 1161, based on gcc version 3.1
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
Platform C C F90 F90 C++ Shared zlib
parallel parallel libraries (5)
Solaris2.6 y n y n y y y
Solaris2.7 64-bit y y (1) y y (1) y y y
Solaris2.7 32-bit y y (1) y y (1) y y y
Solaris2.8 64-bit y n y y (1) y y y
Solaris2.8 32-bit y n y y (1) y y y
IRIX6.5 y y (1) n n n y y
IRIX64_6.5 64-bit y y (2) y y y y y
IRIX64_6.5 32-bit y y (2) n n n y y
HPUX11.00 y y (1) y n n y y
OSF1 v5.1 y n y n y y y
T3E (6) y n y n n n y
SV1 y n y n n n y
T90 IEEE y n y n n n y
TFLOPS n y (1) n n n n y
AIX-5.1 32-bit y y y y y n y
AIX-5.1 64-bit y y y y y n y
WinXP (7) y n n n y y y
WinNT/2000 y n y n y y y
WinNT CW y n n n n n y
Mac OS X 10.2 y n n n y y y
FreeBSD y y (1) n n y y y
Linux 2.2 y y (1) y y (1) y y y
Linux 2.4 gcc (3) y y (1) y n y y y
Linux 2.4 Intel (3) y n y n n n y
Linux 2.4 PGI (3) y n y n y n y
Linux 2.4 IA32 y n y n n n y
Linux 2.4 IA64 y n y n n n y
Platform static- Thread- SRB GASS STREAM-
exec safe VFD
Solaris2.6 x y n n y
Solaris2.7 64-bit x y n n y
Solaris2.7 32-bit x y n n y
Solaris2.8 64-bit x n n n y
Solaris2.8 32-bit x y n n y
IRIX6.5 x n n n y
IRIX64_6.5 64-bit x y n y y
IRIX64_6.5 32-bit x y n y y
HPUX11.00 x n n n y
OSF1 v5.1 y n n n y
T3E (6) y n n n y
SV1 y n n n y
T90 IEEE y n n n y
TFLOPS y n n n n
AIX-5.1 32-bit y n n n y
AIX-5.1 64-bit y n n n y
WinXP (7) dna n n n n
WinNT/2000 dna n n n n
WinNT CW dna n n n n
Mac OS X 10.2 y n n n y
FreeBSD y y n n y
Linux 2.2 y y n n y
Linux 2.4 gcc (3) y y n n y
Linux 2.4 Intel (3) y n n n y
Linux 2.4 PGI (3) y n n n y
Linux 2.4 IA32 y n n n y
Linux 2.4 IA64 y n n n y
Notes: (1) Using mpich 1.2.4.
(2) Using mpt and mpich 1.2.4.
(3) Linux 2.4 with GNU, Intel, and PGI compilers.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library,
except on Windows where they are provided for all languages.
(6) Debug mode only.
(7) Binaries only; source code for this platform is not being
released at this time.
Known Problems
==============
* On Linux 2.4 IA64, Fortran test fails for h5dwrite_vl_f
for integer and real base datatypes.
* When fortran library is built with Intel compilers, compilation
for fflush1.f90, fflush2.f90 and fortanlib_test.f90 will fail
complaining about EXEC function. Comment the call to EXEC subroutine
in each program, or get a patch for the HDF5 Fortran source code.
* Fortran external dataset test fails on Linux 2.4 with pgf90 compiler.
* On Windows, h5dump may abort printing if a VL string is longer than 4096
bytes due to a compiler problem. It'll be fixed in v1.6 release.
* Datasets or attributes which have a variable-length string datatype are
not printing correctly with h5dump and h5ls.
* When a dataset with the variable-length datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output on some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The executables are always dynamic on Solaris 2.7 and 2.8(64 and n32)
even if they are configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting the environment
variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* On OSF1 v5.1 and IA32 h5dumpgentst program that generates test files
for h5dump, gives segmentation fault.
* On Windows platforms, C and Fortran tests fail with the debug DLL version
of the Library if built from all_withf90.zip file.
* On Cray T3E (sn6606 2.0.6.08 unicosmk CRAY T3E) with Cray Standard C Version 6.6.0.1.3
compiler optimization causes errors in many HDF5 Library tests. Use -g -h zero flags
to build HDF5 Library.
* On Cray SV1 10.0.1. 0 datatype conversion test fails. Please check HDF FTP site
if patch is available. We will try to provide one in the nearest future.
* For configuration, building and testing with Intel and PGI compilers see
corresponding section in INSTALL file.
%%%%1.4.4%%%% Release Information for hdf5-1.4.4 (02/July/02)
12. Release information for HDF5 version 1.4.4
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.3 and
HDF5-1.4.4, and contains information on the platforms tested and
known problems in HDF5-1.4.4. 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, see 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
- Bug Fixes since HDF5-1.4.3
- Performance Improvements
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* The H4 to H5 tools have been removed from the main source and placed
in a separate package. You can get these tools from the HDF ftp site
(ftp://hdf.ncsa.uiuc.edu/). The "--with-hdf4" command-line option
during configure is no longer valid. BW - 2002/06/25
o Library
=========
o General
---------
* Fill-value forward-compatibility with release 1.5 was added. SLU -
2002/04/11
* A new query function H5Tget_member_index has been added for compound
and enumeration data types. This function retrieves a member's index
by name. SLU - 2002/04/05
* Added serial multi-gigabyte file size test. "test/big -h" shows
the help page. AKC - 2002/03/29
o APIs
------
* The F90 subroutines h5dwrite_f, h5dread_f, h5awrite_f, and h5aread_f
were overloaded with a "dims" argument of type INTEGER(HSIZE_T) to
specify the size of the array. We recommend using these subroutines
with the new type; module subroutines that accept "dims" as an i
INTEGER array of size 7 will be deprecated in release 1.6.
EIP - 2002/05/06
o Performance
-------------
* Added internal "small data" aggregation, which can reduce the number of
actual I/O calls made, improving performance. QAK - 2002/06/05
* Improved internal metadata aggregation, which can reduce the number of
actual I/O calls made, improving performance. Additionally, this can
reduce the size of files produced. QAK - 2002/06/04
* Improved internal metadata caching, which can reduce the number of
actual I/O calls made by a substantial amount, improving
performance. QAK - 2002/06/03
o Parallel library
==================
* Fixed bug in parallel I/O routines where a collective I/O which used
MPI derived types, followed by an independent I/O would cause the library
to hang. QAK 2002/06/24
* Added environment variable flag to control whether creating MPI derived
types is preferred or not. This can affect performance, depending on
which way the MPI-I/O library is optimized. The default is set to
prefer MPI derived types for collective raw data transfers; setting the
HDF5_MPI_PREFER_DERIVED_TYPES environment variable to "0" (i.e.:
"setenv HDF5_MPI_PREFER_DERIVED_TYPES 0") changes the preference to avoid
using them whenever possible. QAK - 2002/06/19
* Changed MPI I/O routines to avoid creating MPI derived types (and thus
needing to set the file view) for contiguous selections within datasets.
This should result in some performance improvement for those types of
selections. QAK - 2002/06/18
* Changed MPI type support for collective I/O to be enabled by default.
This can be disabled by setting the HDF5_MPI_OPT_TYPES environment
variable to the value "0". QAK - 2002/06/14
* Allowed chunks in chunked datasets to be cached when parallel file is
opened for read-only access (bug #709). QAK - 2002/06/10
* Changed method for allocating chunked dataset blocks to only allocate
blocks that don't already exist, instead of attempting to create all the
blocks all the time. This improves performance for chunked
datasets. QAK - 2002/05/17
* Allowed the call to MPI_File_sync to be avoided when the file is going to
immediately be closed, improving performance. QAK - 2002/05/13
* Allowed the metadata writes to be shared among all processes, easing the
burden on process 0. QAK - 2002/05/10
o Tools
=======
* h5redeploy utility was added. It updates HDF5 compiler tools
after the HDF5 software has been installed in a new location.
o Support for new platforms and languages
=========================================
* Parallel Fortran Library works now on HP-UX B.11.00 Sys V.
EIP - 2002/05/06
* Intel C++ and F90 compilers Version 6.0 are supported on Linux 2.4.
* Intel C++ compilers Version 6.0 are supported on Windows 2000.
o Misc.
=========================================
* zlib has been moved out of the Windows source release. Users should go to
the ZLIB homepage(http://www.zlib.org) to download the corresponding
zlib library.
* The Windows binary release is built with the old version of the zlib
library. We expect users to use zlib 1.1.4 to build with the source
release.
* In the Windows-specific install document, we specify how to test backward
compatibility. However, in this release, we are not testing the backward
compatibility of HDF5.
Bug Fixes since HDF5-1.4.3 Release
==================================
* Fixed bug in chunking routines where they were using internal allocation
free routines, instead of malloc/free, preventing user filters from
working correctly. Chunks are now allocated/freed with malloc/free and
so should the chunks in user filters. QAK 2002/06/18
* Fixed bug where regular hyperslab selection could get incorrectly
transferred when the number of elements in a row did not fit evenly
into the buffer provided. QAK 2002/06/12
* Fixed bug (#499) which allowed an "empty" compound or enumerated datatype
(one with no members) to be used to create a dataset or to be committed
to a file. QAK - 2002/06/11
* Fixed bug (#777) which allowed a compound datatype to be inserted into
itself. QAK - 2002/06/10
* Fixed bug (#789) where creating 1-D dataset region reference caused the
library to go into infinite loop. QAK - 2002/06/10
* Fixed bug (#699, fix provided by a user) where a scalar dataspace was
written to the file and then subsequently queried with the
H5Sget_simple_extent_type function; type was reported as H5S_SIMPLE
instead of H5S_SCALAR. EIP - 2002/06/04
* Clear symbol table node "dirty" flag when flushing symbol tables to
disk, to reduce I/O calls made & improve performance. QAK - 2002/06/03
* Fixed bug where an object's header could get corrupted in certain
obscure situations when many objects were created in the
file. QAK - 2002/05/31
* Fixed bug where read/write intent in file IDs created with H5Freopen
was not being kept the same as the original file. QAK - 2002/05/14
* Fixed bug where selection offsets were not being used when iterating
through point and hyperslab selections with
H5Diterate(). QAK - 2002/04/29
* Fixed bug where the data for several level deep nested compound &
variable-length datatypes used for datasets were getting corrupted when
written to the file. QAK - 2002/04/17
* Fixed bug where selection offset was being ignored for certain hyperslab
selections when optimized I/O was being performed. QAK - 2002/04/02
* Fixed limitation in h5dumper with object names which reached over 1024
characters in length. We can now handle arbitrarily larger sizes for
object names. BW - 2002/03/29
* Fixed bug where variable-length string type did not behave as a
string. SLU - 2002/03/28
* Fixed bug in H5Gget_objinfo() which was not setting the 'fileno'
of the H5G_stat_t struct. QAK - 2002/03/27
* Fixed data corruption bug in hyperslab routines when contiguous
hyperslab that spans entire dimension and is larger than type
conversion buffer is attempted to be read. QAK - 2002/03/26
Performance Improvements
========================
This release of the HDF5 library has been extensively tuned to improve
performance, especially to improve parallel I/O performance.
Most of the specific information for particular performance improvements
is mentioned in the "New Features" and "Bug Fixes since HDF5-1.4.3" sections
of this document, but in general, the library should make fewer and larger
I/O requests when accessing a file. Additionally, improvements to the parallel
I/O portions of the library should have reduced the communications and barriers
used in various internal algorithms, improving the performance of the library.
However, with the extensive changes to some portions of the library that
were required for these improvements, some errors or unanticipated results may
have been introduced also. Please report any problems encountered to our
support team at hdfhelp@ncsa.uiuc.edu.
Hopefully these improvements will benefit all HDF5 applications, but if
there are particular I/O patterns that appear to be slower than necessary,
please send e-mail to hdfhelp@ncsa.uiuc.edu with a sample program showing the
problem behavior; we will look into the issue to see if it is possible to
address it.
Documentation
=============
* Documentation was updated for the hdf5-1.4.4 release.
* A new "HDF5 User's Guide" is under development. See
http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/.
* A "Parallel HDF5 Tutorial" is available at
http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/.
* The "HDF5 Tutorial" is not distributed with this release. It is
available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 5.0.2.0
mpcc_r 5.0.2.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 3.1.0.12 (includes mpi)
AIX 5.1 xlc 5.0.2.0
xlf 07.01.0000.0002
mpcc_r 5.0.2.0; mpxlf_r 07.01.0000.0002
Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
Cray SV1 10.0.1.1 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
FreeBSD 4.6 gcc 2.95.4
g++ 2.95.4
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP MPI [not a product] (03/24/2000) B6060BA
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m
F90 MIPSpro 7.3.1.3m (64 only)
Linux 2.4.9-31smp gcc 2.95.3
g++ 2.95.3
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
MPICH 1.2.2
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.4-014
Compaq Fortran V5.5-1877-48BBF
gcc version 3.0 for C++
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0
WorkShop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.2.2 i386 pgcc Rel 3.1-4i with mpich-1.2.3 with
local modifications
IA-32 Linux 2.4.9 cc Intel 5.0.1
gcc 2.96
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Version 6.0
Intel(R) Fortran Compiler Version 6.0
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 6.0
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
( ) = footnote appears below second table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries(5)
Solaris2.6 y n y n y y y y
Solaris2.7 64 y y (1) y n y y y y
Solaris2.7 32 y y (1) y n y y y y
Solaris2.8 64 y n y n y y y y
Solaris2.8 32 y n y n y y y y
IRIX6.5 y y (1) n n n y y y
IRIX64_6.5 64 y y (2) y y n y y y
IRIX64_6.5 n32 y y (2) n n n y y y
HPUX10.20 y n y n n y y y
HPUX11.00 y n y n n y y y
HPUX11 SysV y y y y n y y y
OSF1 v5.1 y n y n y y y y
T3E y y y y n n y y
SV1 y n y n n n y y
TFLOPS n y (1) n n n n y y (4)
AIX-4.3 y y y y y n y y
AIX-5.1 y y y y n n y y
WinNT/2000 y n y n y y y y
WinNT CW y n n n n n y y
FreeBSD y n n n y y y y
Linux 2.2 y y (1) y n y y y y
Linux 2.4 y y (1) n n y y y y
Linux 2.4 Intel(6) y n y n y n y y
Linux 2.4 IA32 y n y n n n y y
Linux 2.4 IA64 y n y n n n y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.6 y x y n n y
Solaris2.7 64 y x y n n y
Solaris2.7 32 y x y n n y
Solaris2.8 64 y y n n n y
Solaris2.8 32 y x y n n y
IRIX6.5 y x n n n y
IRIX64_6.5 64 y x y n y y
IRIX64_6.5 n32 y x y n y y
HPUX10.20 y y n n n y
HPUX11.00 y x n n n y
HPUX11 SysV y x n n n y
OSF1 v5.1 y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 y y (3) n n n y
AIX-5.1 y y n n n y
WinNT/2000 y y n n n n
WinNT CW n n n n n n
FreeBSD y y y n n y
Linux 2.2 y y y n n y
Linux 2.4 y y y n n y
Linux 2.4 Intel(6) y y n n n y
Linux 2.4 IA32 y y n n n y
Linux 2.4 IA64 y y n n n y
Footnotes: (1) Using mpich.
(2) Using mpt and mpich.
(3) When configured with static-exec enabled, tests fail in
serial mode.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library,
except on Windows where they are provided for all languages.
(6) Linux 2.4 with Intel compilers.
Known Problems
==============
* Datasets or attributes which have a variable-length string datatype are
not printing correctly with h5dump and h5ls.
* When a dataset with the variable-length datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output on some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting the environment
variable HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* On IA32 and IA64 systems, if you use a compiler other than GCC (such as
Intel's ecc or icc compilers), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 104
of the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
Change these lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
* To build the Fortran library using Intel compilers, one has to
x modify the source code in the fortran/src directory to remove the
!DEC and !MS compiler directives.
x The build will fail in the fortran/test directory and then in the
fortran/examples directory; to proceed, edit the work.pcl files in
those directories to contain two lines
work.pc
../src/work.pc
* To build the Fortran library on IA64 use
setenv CC "ecc -DIA64"
setenv F9X "efc -cl,work.pcl"
before running configure and see the steps described above.
%%%%1.4.3%%%% Release Information for hdf5-1.4.3 (18/Februaru/02)
11. Release information for HDF5 version 1.4.3
==============================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.2 and
HDF5-1.4.3, and contains information on the platforms tested and
known problems in HDF5-1.4.2. 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
- Bug Fixes since HDF5-1.4.2
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
o Configuration
================
* Can use just enable-threadsafe if the C compiler has built-in pthreads
support.
o Library
=========
o General
---------
* Added a new test to verify the information provided by the configure
command.
* Changed internal error handling macros to reduce code size of library by
about 10%.
o APIs
------
* Changed prototype for H5Awrite from:
H5Awrite(hid_t attr_id, hid_t type_id, void *buf)
to:
H5Awrite(hid_t attr_id, hid_t type_id, const void *buf)
* The H5Pset_fapl_split() accepts raw and meta file names similar to the
syntax of H5Pset_fapl_multi() in addition to what it used to accept.
C++ API:
* Added operator= to class PredType
* Add the overloaded member function Attribute::getName to return
the attribute name's length as in C API. Note that the current
Attribute::getName, that returns "string", is still available.
* Following the change in the C library, the corresponding C++ API
is changed from:
void Attribute::write( const DataType& mem_type, void *buf )
to:
void Attribute::write( const DataType& mem_type, const void *buf )
o Performance
-------------
* Added perform programs to test the HDF5 library performance. Programs
are installed in directory perform/.
* Improved performance of byte-swapping during data conversions.
* Improved performance of single, contiguous hyperslabs when reading or
writing.
* Added support to read/write portions of chunks directly, if they are
uncompressed and too large to cache. This should speed up I/O on chunked
datasets for a few more cases. -QAK, 1/31/02
o Parallel Library
==================
* Parallel C HDF5 now works on HP-UX platforms, Compaq clusters,
Linux clusters, Cplants (alpha-linux clusters).
o Tools
=======
* A helper script called ``h5cc'', which helps compilation of HDF5
programs, is now distributed with HDF5. See the reference manual
for information on how to use this feature.
* The H5Dumper can now dump comments associated with groups. -WCW 01-05-02
o Support for new platforms and languages
=========================================
* HDF5 C++ Library is supported on Windows platforms (shared and static)
* HDF5 F90 shared library is supported on Windows platforms.
* HDF5 C Library is supported on IA32 and IA64 platforms.
Bug Fixes since HDF5-1.4.2 Release
==================================
* Fixed a bug when reading chunked datasets where the edge of the dataset
would be incorrectly detected and generate an assertion failure.
* Fixed a bug where reading an entire dataset wasn't being handled
optimally when the dataset had unlimited dimensions. Dataset is read
in a single low-level I/O now, instead of being broken into separate
pieces internally.
* Fixed a bug where reading or writing chunked data which needed datatype
conversion could result in data values getting corrupted.
* Fixed a bug where appending a point selection to the current selection
would not actually append the point when there were no points defined
currently.
* Fixed a bug where 'or'ing a hyperslab with a 'none' selection would
fail. Now adds that hyperslab as the first hyperlab in the selection.
* Fixed a bug in the 'big' test where quota limits weren't being detected
properly if they caused close() to fail.
* Fixed a bug in internal B-tree code where a B-tree was not being copied
correctly.
* Fixed an off-by-one error in H5Sselect_valid when hyperslab selections
which would allow hyperslab selections which overlapped the edge of the
selection by one element as valid.
* Fixed the internal macros used to encode & decode file metadata, to avoid
an unaligned access warning on IA64 machines.
* Corrected behavior of H5Tinsert to not allow compound datatype fields to
be inserted past the end of the datatype.
* Retired the DPSS virtual file driver (--with-gridstorage configure
option).
* Fixed bug where variable-length datatypes for attributes was not working
correctly.
* Fixed bug where raw data re-allocated from the free-list would sometimes
overlap with the metadata accumulator and get corrupted. QAK - 1/23/02
* Fixed bug where a preempted chunk in the chunk data could still be
used by an internal pointer and cause an assertion failure or core
dump. QAK - 2/13/02
* Fixed bug where non-zero fill-value was not being read correctly from
certain chunked datasets when using an "all" or contiguous hyperslab
selection. QAK - 2/14/02
Documentation
=============
* Documentation was updated for the hdf5-1.4.3 release.
* A new "HDF5 User's Guide" is under development. See
http://hdf.ncsa.uiuc.edu/HDF5/doc_dev_snapshot/H5_NewUG/current/.
* Parallel Tutorial is available at http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 5.0.2.0
mpcc_r 5.0.2.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 3.1.0.12 (includes mpi)
Cray T3E sn6711 2.0.5.57 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.3
Cray Fortran Version 3.5.0.4
FreeBSD 4.5 gcc 2.95.3
g++ 2.95.3
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP MPI [not a product] (03/24/2000) B6060BA
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.2m
Linux 2.4.4 gcc 2.95.3
g++ 2.95.3
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V5.1 Compaq C V6.3-028
Compaq Fortran V5.4-1283
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0
Workshop Compilers 5.0 98/10/25
FORTRAN 90 2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
Patch 109503-07 2001/08/11
Sun WorkShop 6 update 1 C++ 5.2 Patch
109508-04 2001/07/11
TFLOPS r1.0.4 v4.0.8 i386 pgcc Rel 3.1-4i with mpich-1.2.1 with
local modifications
IA-32 Linux 2.2.10smpx cc Intel 5.0.1
egcs-2.91.66
IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731
Intel(R) C++ Itanium(TM) Compiler
for the Itanium(TM)-based applications,
Version 6.0 Beta, Build 20010905
Windows 2000 (NT5.0) MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 6.0
Windows 98 MSVC++ 6.0
DEC Visual Fortran 6.0
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
( ) = footnote appears below second table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries
(5)
Solaris2.7 y y (1) y n y y y y
Solaris2.8 64 y n y n y y y y
Solaris2.8 32 y n y n y y y y
IA-64 y n n n n n y y
IRIX6.5 y y (1) n n n y y y
IRIX64_6.5 64 y y (2) y y n y y y
IRIX64_6.5 32 y y (2) n n n y y y
HPUX10.20 y n y n n y y y
HPUX11.00 y y y n n y y y
HPUX11 SysV y y y n n y y y
DECOSF y n y n y y y y
T3E y y y y n n y y
SV1 y n y n n n y y
TFLOPS y y (1) n n n n y y (4)
AIX-4.3 SP2 y y y y n n y n
AIX-4.3 SP3 y y y y y n y n
Win2000 y n y n y (6) y y y
Win98 y n y n y (6) y y y
WinNT y n y n y (6) y y y
WinNT CW y n n n n n y y
FreeBSD y n n n y y y y
Linux 2.2 y y (1) y n y y y y
Linux 2.4 y y (1) n n y y y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.7 n x y n n y
Solaris2.8 64 n y n n n y
Solaris2.8 32 n x n n n y
IA-64 n n n n n y
IRIX6.5 n x y n n y
IRIX64_6.5 64 n x y n y y
IRIX64_6.5 32 n x y n y y
HPUX10.20 n y n n n y
HPUX11.00 n x n n n y
HPUX11 SysV n x n n n y
DECOSF n y n n n y
T3E n y n n n y
SV1 n y n n n y
TFLOPS n y n n n n
AIX-4.3 SP2 n y (3) n n n y
AIX-4.3 SP3 n y n n n y
Win2000 n y n n n n
Win98 n y n n n n
WinNT n y n n n n
WinNT CW n n n n n n
FreeBSD n y y n n y
Linux 2.2 n y y n n y
Linux 2.4 n y y n n y
Footnotes: (1) Using mpich.
(2) Using mpt and mpich.
(3) When configured with static-exec enabled, tests fail
in serial mode.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library.
(6) Exception of (5): DLL is available for C++ API on Windows
Known Problems
==============
* Datasets or attributes which have a variable-length string datatype are
not printing correctly with h5dump and h5ls.
* When a dataset with the variable-legth datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting environment variable
HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
* On IA64 systems one has to use -DIA64 compilation flag to compile
h4toh5 and h5toh4 utilities. After configuration step manually modify
Makefile in the tools/h4toh4 and tools/h5toh4 directories to add
-DIA64 to the compilation flags.
* On IA32 ansd IA64 systems, if you use a compiler other than GCC
(such as Intel's ecc compiler), you will need to modify the generated
"libtool" program after configuration is finished. On or around line 102
of the libtool file, there are lines which look like:
# How to pass a linker flag through the compiler.
wl=""
change the lines to this:
# How to pass a linker flag through the compiler.
wl="-Wl,"
%%%%1.4.2%%%% Release Information for hdf5-1.4.2 (31/July/01)
10. Release Information for hdf5-1.4.2
=================================================================
INTRODUCTION
This document describes the differences between HDF5-1.4.1 and
HDF5-1.4.2, and contains information on the platforms tested and
known problems in HDF5-1.4.2.
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
- Bug Fixes since HDF5-1.4.1
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
* File sizes greater than 2GB are now supported on Linux systems with
version 2.4.x or higher kernels.
* Added a global string variable H5_lib_vers_info_g which holds the
HDF5 library version information. This can be used to identify
an hdf5 library or hdf5 application binary.
Also added a verification of the consistency between H5_lib_vers_info_g
and other version information in the source code.
* Parallel HDF5 now runs on the HP V2500 and HP N4000 machines.
* F90 API:
- Added additional parameter "dims" to the h5dread_f/h5dwrite_f and
h5aread_f/h5awrite_f subroutines. This parameter is a 1-D array
of size 7 and contains the sizes of the data buffer dimensions.
This change enables portability between Windows and UNIX platforms.
In previous versions of the F90 APIs, the data buffer parameters of
the above functions were declared as assumed-shape arrays, which
were passed to the C functions by a descriptor. There is no
portable means, however, of passing descriptors from F90 to C,
causing portability problems between Windows and UNIX and among
UNIX platforms. With this change, the data buffers are assumed-
size arrays, which can be portably passed to the C functions.
* F90 static library is available on Windows platforms.
See INSTALL_Windows_withF90.txt for details.
* F90 APIs are available on HPUX 11.00 and 10.20 and IBM SP platforms.
* H5 <-> GIF converter has been added. This is available under
tools/gifconv. The converter supports the ability to create animated
gifs as well.
* Verified correct operation of library on Solaris 2.8 in both 64-bit and
32-bit compilation modes. See INSTALL document for instructions on
compiling the distribution with 64-bit support.
* Added support for the Metrowerks Code Warrior compiler for Windows.
* For H4->H5 converter utility, added a new option to choose not to convert
HDF4 specified attributes(reference number, class) into HDF5 attributes.
* Added support chunking and compression in SDS and image in H4->H5 converter.
Currently HDF5 only supports gzip compression, so by default an HDF4 file
with any other compression method will be converted into an HDF5 file in
gzip compression.
* correct the order or reading HDF4 image array in H4->H5 conversion.
* Added new parallel hdf5 tests in t_mpi. The new test checks if the
filesystem or the MPI-IO can really handle greater than 2GB files.
If it fails, it prints information message only without failing the
test.
* Added a parallel HDF5 example examples/ph5example.c to illustrate
the basic way of using parallel HDF5.
* Added a new public macro, H5_VERS_INFO, which is a string holding
the HDF5 library version information. This string is also compiled
into all HDF5 binary code which helps to identify the version information
of the binary code. One may use the Unix strings command on the binary
file and looks for the pattern "HDF5 library version".
* Added new checking in H5check_version() to verify the five HDF5 version
information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent.
Bug Fixes since HDF5-1.4.1 Release
==================================
* Fixed bug with non-zero userblock sizes causing raw data to not
write correctly.
* Fixed problems with Pablo build and linking with non-standard MPI I/O.
* Fixed build on Linux systems with --enable-static-exec flag. It now
works correctly.
* IMPORTANT: Fixed file metadata corruption bug which could cause
metadata data loss in certain situations.
* The allocation by alignment (H5Pset_alignment) feature code somehow
got dropped in some 1.3.x version. Re-implemented it with "new and
improved" algorithm. It keeps track of "wasted" file-fragment in
the free-list too.
* Removed limitation that the data transfer buffer size needed to be
set for datasets whose dimensions were too large for the 'all'
selection code to handle. Any size dimensioned datasets should be
handled correctly now.
* Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x
when --enable-hdf5v1_2 configure flag is enabled.
* Added --enable-linux-lfs flag to allow more control over whether to
enable or disable large file support on Linux.
* Fixed various bugs related to SDS dimensional scale conversions in H4->H5
converter.
* Fixed a bug to correctly convert HDF4 objects with fill value into HDF5.
* Fixed a bug of H5pubconf.h causing repeated definitions if it is included
more than once. hdf5.h now includes H5public.h which includes
H5pubconf.h. Applications should #include hdf5.h which handles multiple
inclusion correctly.
* Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be
external to C++.
* Fixed a bug in H5FD_mpio_flush() that might result in negative file seek
if both MPIO and Split-file drivers are used together.
Documentation
=============
* The H5T_conv_t and H5T_cdata_t structures are now properly defined
in the H5Tregister entry in the "H5T" section of the "HDF5 Reference
Manual" and described in detail in section 12, "Data Conversions," in
the "Datatypes" chapter of the "HDF5 User's Guide."
* The new tools h52gif and gif2h5 have been added to the "Tools" section
of the Reference Manual.
* A "Freespace Management" section has been added to the "Performance"
chapter of the User's Guide.
* Several user-reported bugs have been fixed since Release 1.4.1.
* The "HDF5 Image and Palette Specification" (in the "HDF5 Application
Developer's Guide") has been heavily revised. Based on extensive user
feedback and input from visualization software developers, Version 1.2
of the image specification is substantially different from prior
versions.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6.0
mpcc_r 3.6.6.0
xlf 07.01.0000.0002
mpxlf 07.01.0000.0002
AIX 4.3 (IBM SP RS6000) C for AIX Compiler, Version 5.0.2.0
xlf 7.1.0.2
poe 2.4.0.14 (includes mpi)
Cray T3E sn6711 2.0.5.49a Cray Standard C Version 6.5.0.1
Cray SV1 10.0.0.2 Cray Standard C Version 6.5.0.1
Cray Fortran Version 3.5.0.1
FreeBSD 4.3 gcc 2.95.3
g++ 2.95.3
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP F90 v2.3
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
HP F90 v2.4
HP-UX B.11.00 SysV HP C HP92453-01 A.11.01.20
HP F90 v2.4
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.2m
Linux 2.4.4 gcc 2.95.3
g++ 2.95.3
Linux 2.2.18smp gcc 2.95.2
gcc 2.95.2 with mpich 1.2.1
g++ 2.95.2
pgf90 3.2-4
OSF1 V4.0 DEC-V5.2-040 on Digital UNIX V4.0 (Rev 564)
Digital Fortran 90 V4.1-270
SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.6) WorkShop Compilers 5.0 98/10/25 FORTRAN 90
2.0 Patch 107356-04
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0
Workshop Compilers 5.0 98/10/25 FORTRAN 90
2.0 Patch 107356-04
SunOS 5.8/32 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
2000/09/11
Sun WorkShop 6 update 1 C++ 5.2 2000/09/11
SunOS 5.8/64 Sun WorkShop 6 update 1 C 5.2 2000/09/11
(Solaris 2.8) Sun WorkShop 6 update 1 Fortran 95 6.1
2000/09/11
Sun WorkShop 6 update 1 C++ 5.2 2000/09/11
TFLOPS r1.0.4 v4.0.7 i386 pgcc Rel 3.1-4i with mpich-1.2.1 with
local modifications
Windows 2000 (NT5.0) MSVC++ 6.0
Windows NT4.0 MSVC++ 6.0
DEC Visual Fortran 6.0
Windows NT4.0 Code Warrior 6.0
Windows 98 MSVC++ 6.0
DEC Visual Fortran 6.0
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
( ) = footnote appears below second table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries
(5)
Solaris2.6 y n y n y y y y
Solaris2.7 y y (1) y n y y y y
Solaris2.8 64 y n n n y y y y
Solaris2.8 32 y n y n y y y y
IRIX6.5 y y (1) n n n y y y
IRIX64_6.5 64 y y (2) y y n y y y
IRIX64_6.5 32 y y (2) n n n y y y
HPUX10.20 y n y n n y y y
HPUX11.00 y n y n n y y y
HPUX11 SysV y n y n n y y y
DECOSF y n y n n y y y
T3E y y y y n n y y
SV1 y n y n n n y y
TFLOPS y y (1) n n n n y y (4)
AIX-4.3 SP2 y y y y n n y n
AIX-4.3 SP3 y y y y n n y n
Win2000 y n n n n y y y
Win98 y n y n n y y y
WinNT y n y n n y y y
WinNT CW y n n n n n y y
FreeBSD y n n n y y y y
Linux 2.2 y y (1) y n y y y y
Linux 2.4 y y (1) n n y y y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.6 y x n n n y
Solaris2.7 y x y n n y
Solaris2.8 64 y y n n n y
Solaris2.8 32 y x n n n y
IRIX6.5 y x y n n y
IRIX64_6.5 64 y x n n n y
IRIX64_6.5 32 y x n n n y
HPUX10.20 y y n n n y
HPUX11.00 y x n n n y
HPUX11 SysV y x n n n y
DECOSF y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 SP2 y y (3) n n n y
AIX-4.3 SP3 y y n n n y
Win2000 y y n n n n
Win98 n y n n n n
WinNT y y n n n n
WinNT CW n n n n n n
FreeBSD y y n n n y
Linux 2.2 y y y n n y
Linux 2.4 y y y n n y
Footnotes: (1) Using mpich.
(2) Using mpt and mpich.
(3) When configured with static-exec enabled, tests fail
in serial mode.
(4) No HDF4-related tools.
(5) Shared libraries are provided only for the C library.
Known Problems
==============
* When a dataset with the variable-legth datatype is overwritten,
the library can develop memory leaks that cause the file to become
unnecessarily large. This is planned to be fixed in the next release.
* On the SV1, the h5ls test fails due to a difference between the
SV1 printf precision and the printf precision on other platforms.
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executables are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* IRIX 6.5 fails to compile if configured with --enable-static-exec.
* For 24-bit image conversion from H4->H5, the current conversion is
not consistent with HDF5 image specification.
* In some cases, and SDS with an UNLIMITED dimension that has not
been written (current size = 0) is not converted correctly.
* After "make install" or "make install-doc" one may need to reload
the source from the tar file before doing another build.
* The HDF5_MPI_OPT_TYPES optimization code in the parallel HDF5 will cause
a hang in some cases when chunked storage is used. This is now set to
be off by default. One may turn it on by setting environment variable
HDF5_MPI_OPT_TYPES to a non-zero value such as 1.
%%%%1.4.1%%%% Release Information for hdf5-1.4.1 (April/01)
9. Release Information for hdf5-1.4.1 (April/01)
=====================================================================
HDF5 Release 1.4.1
INTRODUCTION
This document describes the differences between HDF5-1.4.0 and
HDF5-1.4.1, and contains information on the platforms tested and
known problems in HDF5-1.4.1.
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
- Bug Fixes since HDF5-1.4.0
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
* XML output option for h5dump utility.
A new option --xml to output data in XML format has been added. The
XML output contains a complete description of the file, marked up in
XML.
The XML conforms to the HDF5 Document Type Definition (DTD), which
is available at:
http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd
The XML output is suitable for use with other tools, including the
Java Tools:
http://hdf.ncsa.uiuc.edu/java-hdf5-html
Bug Fixes since HDF5-1.4.0 Release
==================================
* h4toh5 utility: conversion of images is fixed
Earlier releases of the h4toh5 utility produced images that did not
correctly conform to the HDF5 Image and Palette Specification.
http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html
Several required HDF5 attributes are omitted, and the dataspace
is reversed (i.e., the ht. and width of the image dataset is
incorrectly described.) For more information, please see:
http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm
* Fixed bug with contiguous hyperslabs not being detected, causing
slower I/O than necessary.
* Fixed bug where non-aligned hyperslab I/O on chunked datasets was
causing errors during I/O
* The RCSID string in H5public.h was causing the C++ compiling problem
because when it was included multiple times, C++ did not like
multiple definitions of the same static variable. All occurrence of
RCSID definition are removed since we have not used it consistently
before.
Documentation
=============
PDF and Postscript versions of the following documents are available
for this release:
Document Filename
-------- --------
Introduction to HDF5 H5-R141-Introduction.pdf
HDF5 Reference Manual H5-R141-RefManual.pdf
C++ APIs to HDF5 documents H5-R141-Cplusplus.pdf
Fortran90 APIs to HDF5 documents H5-R141-Fortran90.pdf
PDF and Postscript files containing H5-R141-DocSet.pdf
all of the above H5-R141-DocSet.ps
These files are not included in this distribution, but are available
via the Web or FTP at the following locations:
http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/
ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/
While these documents are labeled Release 1.4.1, they describe
Release 1.4.0 as well.
Platforms Tested
================
Due to the nature of this release only C, C++ libraries and tools were tested.
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6
mpcc_r 3.6.6
Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0
Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0
FreeBSD 4.3 gcc 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP-UX B.11.00 HP C HP92453-01 A.11.01.20
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
Linux 2.2.18smp gcc-2.95.2
g++ 2.95.2
OSF1 V4.0 DEC-V5.2-040
Digital Fortran 90 V4.1-270
SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.6)
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0
TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes
Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0
Windows 98 MSVC++ 6.0
Supported Configuration Features Summary
========================================
* See "Supported Configuration Features Summary" section for the HDF5
1.4.0 release in the HISTORY.txt file.
Known Problems
==============
* The h5dump tests may fail to match the expected output in some
platforms (e.g. SP2 parallel, Windows) where the error messages
directed to "stderr" do not appear in the "right order" with output
from stdout. This is not an error.
* The --enable-static-exec configure flag fails to compile for HP-UX
11.00 platforms.
* The executable are always dynamic on IRIX64 6.5(64 and n32) and
IRIX 6.5 even if they are configured with --enable-static-exec.
* The shared library failed compilation on IRIX 6.5.
* After "make install" or "make install-doc" one may need to reload the source
from the tar file before doing another build.
* See "Known problems" section for the HDF5 1.4.0 release in the
HISTORY.txt file.
%%%%1.4.0%%%% Release Information for hdf5-1.4.0 (2/22/01)
8. Release Information for hdf5-1.4.0
===================================================================
HDF5 Release 1.4.0
INTRODUCTION
This document describes the differences between HDF5-1.2.0 and
HDF5-1.4.0, and contains information on the platforms tested and
known problems in HDF5-1.4.0. 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
- h4toh5 Utility
- F90 Support
- C++ Support
- Pablo Support
- Bug Fixes since HDF5-1.2.0
- Bug Fixes since HDF5-1.4.0-beta2
- Bug Fixes since HDF5-1.4.0
- Documentation
- Platforms Tested
- Supported Configuration Features
- Known Problems
New Features
============
* The Virtual File Layer, VFL, was added to replace the old file
drivers. It also provides an API for user defined file drivers.
* New features added to snapshots. Use 'snapshot help' to see a
complete list of features.
* Improved configure to detect if MPIO routines are available when
parallel mode is requested.
* Added Thread-Safe support. Phase I implemented. See:
http://hdf.ncsa.uiuc.edu/HDF5/papers/mthdf/MTHDFpaper.htm
for more details.
* Added data sieve buffering to raw data I/O path. This is enabled
for all VFL drivers except the mpio & core drivers. Setting the
sieve buffer size is controlled with the new API function,
H5Pset_sieve_buf_size(), and retrieved with H5Pget_sieve_buf_size().
* Added new Virtual File Driver, Stream VFD, to send/receive entire
HDF5 files via socket connections.
* As parts of VFL, HDF-GASS and HDF-SRB are also added to this
release. To find out details, please read INSTALL_VFL file.
* Increased maximum number of dimensions for a dataset (H5S_MAX_RANK)
from 31 to 32 to align with HDF4 & netCDF.
* Added 'query' function to VFL drivers. Also added 'type' parameter to
VFL 'read' & 'write' calls, so they are aware of the type of data
being accessed in the file. Updated the VFL document also.
* A new h4toh5 utility, to convert HDF4 files to analogous HDF5 files.
* Added a new array datatype to the datatypes which can be created.
Removed "array fields" from compound datatypes (use an array datatype
instead).
* Parallel HDF5 works correctly with mpich-1.2.1 on Solaris, SGI, Linux.
* You can now install the HDF5 documentation using the
``make install-doc'' command. The documentation is installed in the
$(prefix)/doc directory where $(prefix) is the prefix specified by
the (optional) ``--prefix'' flag during configuration.
* HDF5 can operate correctly in the OpenMP environment in a limited way.
Check doc/html/TechNotes/openmp-hdf5.html for details.
h4toh5 Utility
==============
The h4toh5 utility is a new utility that converts an HDF4 file to an
HDF5 file. For details, see the document, "Mapping HDF4 Objects to
HDF5 Objects":
http://hdf.ncsa.uiuc.edu/HDF5/papers/H4-H5MappingGuidelines.pdf
Known Bugs:
The h4toh5 utility produces images that do not correctly conform
to the HDF5 Image and Palette Specification.
http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html
Several required HDF5 attributes are omitted, and the dataspace
is reversed (i.e., the ht. and width of the image dataset is
incorrectly described.) For more information, please see:
http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.html
This bug has been fixed for the snapshot of hdf5 1.4 release. March 12th,2001
Known Limitations of the h4toh5 release
---------------------------------------------
1. Error handlings
h4toh5 utility will print out an error message when an error occurs.
2. String Datatype
HDF4 has no 'string' type. String valued data are usually defined as
an array of 'char' in HDF4. The h4toh5 utility will generally map
these to HDF5 'String' types rather than array of char, with the
following additional rules:
* For the data of an HDF4 SDS, image, and palette, if the data is
declared 'DFNT_CHAR8' it will be assumed to be integer and will
be an H5T_INTEGER type.
* For attributes of any HDF4 object, data of type 'DFNT_CHAR8'
will be converted to an HDF5 'H5T_STRING' type.
* For an HDF4 Vdata, it is difficult to determine whether data
of type 'DFNT_CHAR8' is intended to be bytes or characters. The
h4toh5 utility will consider them to be C characters, and will
convert them to an HDF5 'H5T_STRING' type.
3. Compression, Chunking and External Storage
Chunking is supported, but compression and external storage is not.
An HDF4 object that uses chunking will be converted to an HDF5 file
with analogous chunked storage.
An HDF4 object that uses compression will be converted to an
uncompressed HDF5 object.
An HDF4 object that uses external storage will be converted to an
HDF5 object without external storage.
4. Memory Use
This version of the h4toh5 utility copies data from HDF4 objects
in a single read followed by a single write to the HDF5 object. For
large objects, this requires a very large amount of memory, which may
be extremely slow or fail on some platforms.
Note that a dataset that has only been partly written will
be read completely, including uninitialized data, and all the
data will be written to the HDF5 object.
5. Platforms
The h4toh5 utility requires HDF5-1.4.0 and HDF4r1.4
h4toh5 utility has been tested on all platforms listed below (see
section "Platforms Tested") except TFLOPS.
F90 Support
===========
This is the first release of the HDF5 Library with fully integrated
F90 API support. The Fortran Library is created when the
--enable-fortran flag is specified during configuration.
Not all F90 subroutines are implemented. Please refer to the HDF5
Reference Manual for more details.
F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX,
T3E, SV1 and O2K (64 bit option only) platforms. The Parallel version of
the HDF5 F90 Library is supported on the O2K and T3E platforms.
Changes since the last prototype release (July 2000)
----------------------------------------------------
* h5open_f and h5close_f must be called instead of h5init_types and
h5close_types.
* The following subroutines are no longer available:
h5pset_xfer_f
h5pget_xfer_f
h5pset_mpi_f
h5pget_mpi_f
h5pset_stdio_f
h5pget_stdio_f
h5pset_sec2_f
h5pget_sec2_f
h5pset_core_f
h5pget_core_f
h5pset_family_f
h5pget_family_f
* The following functions have been added:
h5pset_fapl_mpio_f
h5pget_fapl_mpio_f
h5pset_dxpl_mpio_f
h5pget_dxpl_mpio_f
* In the previous HDF5 F90 releases, the implementation of object
references and dataset region references was not portable. This
release introduces a portable implementation, but it also introduces
changes to the read/write APIs that handle references. If object or
dataset region references are written or read to/from an HDF5 file,
h5dwrite_f and h5dread_f must use the extra parameter, n, for the
buffer size:
h5dwrite(read)_f(dset_id, mem_type_id, buf, n, hdferr, &
^^^
mem_space_id, file_space_id, xfer_prp)
For other datatypes the APIs were not changed.
C++ Support
===========
This is the first release of the HDF5 Library with fully integrated
C++ API support. The HDF5 C++ library is built when the --enable-cxx
flag is specified during configuration.
Check the HDF5 Reference Manual for available C++ documentation.
C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD.
Pablo Support
=============
This version does not allow proper building of the Pablo-instrumented
version of the library. A version supporting the pablo build is
available on the Pablo Website at
www-pablo.cs.uiuc.edu/pub/Pablo.Release.5/HDFLibrary/hdf5_v1.4.tar.gz
Bug Fixes since HDF5-1.2.0
==========================
Library
-------
* The function H5Pset_mpi is renamed as H5Pset_fapl_mpio.
* Corrected a floating point number conversion error for the Cray J90
platform. The error did not convert the value 0.0 correctly.
* Error was fixed which was not allowing dataset region references to
have their regions retrieved correctly.
* Corrected a bug that caused non-parallel file drivers to fail in
the parallel version.
* Added internal free-lists to reduce memory required by the library
and H5garbage_collect API function
* Fixed error in H5Giterate which was not updating the "index"
parameter correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern
* Fixed several other problems in hyperslab iteration code.
* Fixed another H5Giterate bug which was causes groups with large
numbers of objects in them to misbehave when the callback function
returned non-zero values.
* Changed return type of H5Aiterate and H5A_operator_t typedef to be
herr_t, to align them with the dataset and group iterator functions.
* Changed H5Screate_simple and H5Sset_extent_simple to not allow
dimensions of size 0 with out the same dimension being unlimited.
* QAK - 4/19/00 - Improved metadata hashing & caching algorithms to
avoid many hash flushes and also remove some redundant I/O when
moving metadata blocks in the file.
* The "struct(opt)" type conversion function which gets invoked for
certain compound datatype conversions was fixed for nested compound
types. This required a small change in the datatype conversion
function API.
* Re-wrote lots of the hyperslab code to speed it up quite a bit.
* Added bounded garbage collection for the free lists when they run
out of memory and also added H5set_free_list_limits API call to
allow users to put an upper limit on the amount of memory used for
free lists.
* Checked for non-existent or deleted objects when dereferencing one
with object or region references and disallow dereference.
* "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved
from object headers correctly, fixed now.
* Fixed H5Dread or H5Dwrite calls with H5FD_MPIO_COLLECTIVE requests
that may hang because not all processes are transfer the same amount
of data. (A.K.A. prematured collective return when zero amount data
requested.) Collective calls that may cause hanging is done via the
corresponding MPI-IO independent calls.
* If configure with --enable-debug=all, couple functions would issue
warning messages to "stderr" that the operation is expensive time-wise.
This messed up applications (like testings) that did not expect the
extra output. It is changed so that the warning will be printed only
if the corresponding Debug key is set.
Configuration
-------------
* The hdf5.h include file was fixed to allow the HDF5 Library to be
compiled with other libraries/applications that use GNU autoconf.
* Configuration for parallel HDF5 was improved. Configure now attempts
to link with libmpi.a and/or libmpio.a as the MPI libraries by
default. It also uses "mpirun" to launch MPI tests by default. It
tests to link MPIO routines during the configuration stage, rather
than failing later as before. One can just do "./configure
--enable-parallel" if the MPI library is in the system library.
* Added support for pthread library and thread-safe option.
* The libhdf5.settings file shows the correct machine byte-sex.
* Added option "--enable-stream-vfd" to configure w/o the Stream VFD.
For Solaris, added -lsocket to the LIBS list of libraries.
Tools
-----
* h5dump now accepts both short and long command-line parameters:
-h, --help Print a usage message and exit
-B, --bootblock Print the content of the boot block
-H, --header Print the header only; no data is displayed
-i, --object-ids Print the object ids
-V, --version Print version number and exit
-a P, --attribute=P Print the specified attribute
-d P, --dataset=P Print the specified dataset
-g P, --group=P Print the specified group and all members
-l P, --soft-link=P Print the value(s) of the specified soft link
-o F, --output=F Output raw data into file F
-t T, --datatype=T Print the specified named data type
-w #, --width=# Set the number of columns
P - is the full path from the root group to the object.
T - is the name of the data type.
F - is a filename.
# - is an integer greater than 1.
* A change from the old way command line parameters were interpreted
is that multiple attributes, datasets, groups, soft-links, and
object-ids cannot be specified with just one flag but you have to
use a flag with each object. I.e., instead of doing this:
h5dump -a /attr1 /attr2 foo.h5
do this:
h5dump -a /attr1 -a /attr2 foo.h5
The cases are similar for the other object types.
* h5dump correctly displays compound datatypes.
* Corrected an error in h5toh4 which did not convert the 32bits
int from HDF5 to HDF4 correctly for the T3E platform.
* h5dump correctly displays the committed copy of predefined types
correctly.
* Added an option, -V, to show the version information of h5dump.
* Fixed a core dumping bug of h5toh4 when executed on platforms like
TFLOPS.
* The test script for h5toh4 used to not able to detect the hdp
dumper command was not valid. It now detects and reports the
failure of hdp execution.
* Merged the tools with the 1.2.2 branch. Required adding new
macros, VERSION12 and VERSION13, used in conditional compilation.
Updated the Windows project files for the tools.
* h5dump displays opaque and bitfield data correctly.
* h5dump and h5ls can browse files created with the Stream VFD
(eg. "h5ls <hostname>:<port>").
* h5dump has a new feature "-o <filename>" which outputs the raw data
of the dataset into ascii text file <filename>.
* h5toh4 used to converts hdf5 strings type to hdf4 DFNT_INT8 type.
Corrected to produce hdf4 DFNT_CHAR type instead.
* h5dump and h5ls displays array data correctly.
Bug Fixes since HDF5-1.4.0-beta2
================================
* Fixed a bug in the conversion from a little endian double to a big
endian float in some special cases.
* Corrected configuration error which was not including compression
support correctly.
* Cleaned up lots of warnings.
* Changed a few h5dump command line switches and added long versions of
the switches.
* Changed parameters for H5Tconvert, H5Pset_bufer and H5Pget_buffer from
size_t to hsize_t
* Fixed fairly obscure bug in hyperslab I/O which could (in rare cases)
not copy all the data during a transfer.
* Removed ragged array code from library.
* F90 library and module files are installed properly now on all supported
platforms.
Bug Fixes since HDF5-1.4.0 Release
==================================
* Fixed bug with contiguous hyperslabs not being detected, causing
slower I/O than necessary.
* Fixed bug where non-aligned hyperslab I/O on chunked datasets was
causing errors during I/O
* Implemented XML support in h5dump.
Documentation
=============
* A new document summarizing the changes in the library leading up to
the current release has been added:
HDF5 Software Changes from Release to Release
This document is in the Application Developer's Guide and is of
particular interest to developers who must keep an application
synchronized with the library.
* The documentation for the Fortran90 and C++ APIs is linked to the
opening page of the Reference Manual. Fortran90 functions are
individually referenced from the corresponding C functions through-
out the Reference Manual.
* User's Guide and Reference Manual were updated to reflect changed
function syntax and to fix reported bugs.
* Functions that are new at this release were added to the Reference
Manual.
* Functions that have been removed from the library were removed from
the User's Guide and the Reference Manual.
* PostScript and PDF versions of the Release 1.4 document set are
not available at the time of Release 1.4.0.
Platforms Tested
================
AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6
mpcc_r 3.6.6
Cray T3E sn6711 2.0.5.45 Cray Standard C Version 6.4.0.0
Cray Fortran Version 3.4.0.2
Cray SV1 sn9605 10.0.0.7 Cray Standard C Version 6.4.0.0
Cray Fortran Version 3.4.0.2
FreeBSD 4.2 gcc 2.95.2
g++ 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32.30
HP-UX B.11.00 HP C HP92453-01 A.11.00.13
IRIX 6.5 MIPSpro cc 7.30
mpich-1.2.1
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.4.0.2
mpich-1.2.1
Linux 2.2.16-3smp gcc-2.95.2
g++ 2.95.2
pgf90 3.1-3
mpich-1.2.1
OSF1 V4.0 DEC-V5.2-040
Digital Fortran 90 V4.1-270
SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.6) WorkShop Compilers 5.0 99/10/25 Fortran 90
2.0 Patch 107356-04
Workshop Compilers 5.0 98/12/15 C++ 5.0
SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
(Solaris 2.7) WorkShop Compilers 5.0 99/10/25 Fortran 90
2.0 Patch 107356-04
Workshop Compilers 5.0 98/12/15 C++ 5.0
mpich-1.2.1
SunOS 5.5.1 gcc-2.7.2
(Solaris 2.5.1 (x86))
TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes
Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0
Windows 98 MSVC++ 6.0
Supported Configuration Features Summary
========================================
In the tables below
y = tested and supported
n = not supported or not working in this release
( ) = footnote appears below table
Platform C C F90 F90 C++ Shared zlib Tools
parallel parallel libraries
Solaris2.6 y n y n y y y y
Solaris2.7 y y (1) y n y y y y
Solarisx86 y n n n n y y y
IRIX6.5 y y (1) n n n n y y
IRIX64_6.5 64 y y (2) y y n y y y
IRIX64_6.5 32 y y (2) n n n y y y
HPUX10.20 y n n n n y y y
DECOSF y n y n n y y y
T3E y y y y n n y y
SV1 y n y n n n y y
TFLOPS y y (1) n n n n y y (4)
AIX-4.3 y y n n n n y n
Win2000 y n n n n y y y
Win98 y n n n n y y y
WinNT y n n n n y y y
FreeBSD y n n n y y y y
Linux y y (1) y n y y y y
Platform 1.2 static- Thread- SRB GASS STREAM-
compatibility exec safe VFD
Solaris2.6 y n n n n y
Solaris2.7 y n y n n y
Solarisx86 y n n n n y
IRIX6.5 y n y n n y
IRIX64_6.5 64 y n n n n y
IRIX64_6.5 32 y n n n n y
HPUX10.20 y y n n n y
DECOSF y y n n n y
T3E y y n n n y
SV1 y y n n n y
TFLOPS y y n n n n
AIX-4.3 y y (3) n n n y
Win2000 y y n n n n
Win98 y y n n n n
WinNT y y n n n n
FreeBSD y y n n n y
Linux y n y n n y
Footnotes: (1) Using mpich.
(2) Using mpt and mpich.
(3) When configured with static-exec enabled, tests fail
in serial mode.
(4) No HDF4-related tools.
Known Problems
==============
* 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 Linux platforms using the gcc-2.95.2 compiler.
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.
The compilation fails if configured with --enable-static-exec on IRIX 6.5.
The executable files in hdf5/bin are dynamic-linked for IRIX64 6.5(64 and
n32 modes) and IRIX 6.5, even though they are compiled with static library.
It is suggested that you don't use this option on these platforms
during configuration.
* testhdf5 got bus error with configuration options --prefix and --with-hdf4
on IRIX 6.5.
* With the gcc 2.95.2 compiler, HDF 5 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.
* SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will
fail if library is compiled using optimization of any level.
* When building hdf5 tools and applications on windows platform, a linking
warning: defaultlib "LIBC" conflicts with use of other libs will appear
on debug version when running VC++6.0. This warning doesn't affect building
and testing hdf5 applications. We will continue investigating this.
* h5toh4 converter fails two cases(tstr.h5 and tmany.h5) for release dll
version on windows 2000 and NT. The reason is possibly due to Windows NT
DLL convention on freeing memory. It seems that memory cannot be freed
across library or DLL. It is still under investigation.
* HDF-GASS testings and testhdf5 in the test directory will get bus error if
the configured with --with-gass.
* HDF-SRB testing got segmentation error on Solaris 2.7.
* The Stream VFD was not tested yet under Windows.
It is not supported in the TFLOPS machine.
* Shared library option is broken for IBM SP and some Origin 2000 platforms.
One needs to run ./configure with '--disable-shared --enable-static'.
* 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:
- Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing
when displaying object references in certain files. These are benign
differences due to the difference in sizes of the objects created on
those platforms. h5ls appears to be dumping object references
correctly.
- Cray J90 give errors during testing when displaying
some floating-point values. These are benign differences due to the
different precision in the values displayed and h5ls appears to be
dumping floating-point numbers correctly.
* Before building HDF5 F90 Library from source on Crays (T3E and SV1)
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 ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/hdf5-1.4.0/src/crayf90/ directory.
* The h4toh5 utility produces images that do not correctly conform
to the HDF5 Image and Palette Specification.
http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html
Several required HDF5 attributes are omitted, and the dataspace
is reversed (i.e., the ht. and width of the image dataset is
incorrectly described.) For more information, please see:
http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm
%%%%1.2.2%%%% Release Information for hdf5-1.2.2 (6/23/00)
7. Release Information for hdf5-1.2.2
=================================================================
INTRODUCTION
This document describes the differences between HDF5-1.2.1 and
HDF5-1.2.2, and contains information on the platforms where HDF5-1.2.2
was tested and known problems in HDF5-1.2.2.
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
- Features Added since HDF5-1.2.1
- Bug Fixes since HDF5-1.2.1
- Known Problems
- Platforms Tested
Features Added since HDF5-1.2.1
===============================
* Added internal free-lists to reduce memory required by the library and
H5garbage_collect API function.
* h5dump displays opaque and bitfield types.
* New features added to snapshots. Use 'snapshot help' to see a
complete list of features.
* Improved configure to detect if MPIO routines are available when
parallel mode is requested.
Bug Fixes since HDF5-1.2.1
==========================
* h5dump correctly displays compound datatypes, including simple and
nested compound types.
* h5dump correctly displays the committed copy of predefined types.
* Corrected an error in h5toh4 which did not convert the 32-bit
int from HDF5 to HDF4 correctly for the T3E platform.
* Corrected a floating point number conversion error for the
Cray J90 platform. The error did not convert the value 0.0
correctly.
* Fixed error in H5Giterate which was not updating the "index" parameter
correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern.
* Fixed several other problems in hyperslab iteration code.
* Fixed another H5Giterate bug which caused groups with large numbers
of objects in them to misbehave when the callback function returned
non-zero values.
* Changed return type of H5Aiterate and H5A_operator_t typedef to be
herr_t, to align them with the dataset and group iterator functions.
* Changed H5Screate_simple and H5Sset_extent_simple to not allow dimensions
of size 0 without the same dimension being unlimited.
* Improved metadata hashing & caching algorithms to avoid
many hash flushes and also removed some redundant I/O when moving metadata
blocks in the file.
* The libhdf5.settings file shows the correct machine byte-sex.
* The "struct(opt)" type conversion function which gets invoked for
certain compound datatype conversions was fixed for nested compound
types. This required a small change in the datatype conversion
function API.
Known Problems
==============
o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will
fail if library is compiled using optimization of any level.
o TFLOPS: dsets test fails if compiled with optimization turned on.
o J90: tools fail to display data for the datasets with a compound datatype.
Platforms Tested
================
AIX 4.3.3 (IBM SP) 3.6.6 | binaries
mpicc using mpich 1.1.2 | are not
mpicc_r using IBM MPI-IO prototype | available
AIX 4.3.2.0 (IBM SP) xlc 5.0.1.0
Cray J90 10.0.0.7 cc 6.3.0.2
Cray T3E 2.0.5.29 cc 6.3.0.2
mpt.1.3
FreeBSD 4.0 gcc 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32
HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler
(static library only, h5toh4 tool is not available)
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.4
Linux 2.2.10 SMP gcc 2.95.1
mpicc(gcc-2.95.1)
gcc (egcs-2.91.66)
mpicc (egcs-2.91.66)
Linux 2.2.16 (RedHat 6.2) gcc 2.95.2
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 5.0 no optimization
SunOS 5.7 cc WorkShop Compilers 5.0
SolarisX86 SunOS 5.5.1 gcc version 2.7.2 with --disable-hsizet
TFLOPS 3.2.1 pgcc Rel 3.1-3i
mpich-1.1.2 with local changes
Windows NT4.0 sp5 MSVC++ 6.0
Windows 98 MSVC++ 6.0
Windows 2000 MSVC++ 6.0
%%%%1.2.1%%%% Release Information for hdf5-1.2.1
6. Release Information for hdf5-1.2.1
================================================================
Bug fixes since HDF5-1.2.0
==========================
Configuration
-------------
* The hdf5.h include file was fixed to allow the HDF5 Library to be compiled
with other libraries/applications that use GNU autoconf.
* Configuration for parallel HDF5 was improved. Configure now attempts to
link with libmpi.a and/or libmpio.a as the MPI libraries by default.
It also uses "mpirun" to launch MPI tests by default. It tests to
link MPIO routines during the configuration stage, rather than failing
later as before. One can just do "./configure --enable-parallel"
if the MPI library is in the system library.
Library
-------
* Error was fixed which was not allowing dataset region references to have
their regions retrieved correctly.
* Added internal free-lists to reduce memory required by the library and
H5garbage_collect API function
* Fixed error in H5Giterate which was not updating the "index" parameter
correctly.
* Fixed error in hyperslab iteration which was not walking through the
correct sequence of array elements if hyperslabs were staggered in a
certain pattern
* Fixed several other problems in hyperslab iteration code.
Tests
------
* Added additional tests for group and attribute iteration.
* Added additional test for staggered hyperslab iteration.
* Added additional test for random 5-D hyperslab selection.
Tools
------
* Added an option, -V, to show the version information of h5dump.
* Fixed a core dumping bug of h5toh4 when executed on platforms like
TFLOPS.
* The test script for h5toh4 used to not able to detect the hdp
dumper command was not valid. It now detects and reports the
failure of hdp execution.
Documentation
-------------
* User's Guide and Reference Manual were updated.
See doc/html/PSandPDF/index.html for more details.
Platforms Tested:
================
Note: Due to the nature of bug fixes, only static versions of the library and tools were tested.
AIX 4.3.2 (IBM SP) 3.6.6
Cray T3E 2.0.4.81 cc 6.3.0.1
mpt.1.3
FreeBSD 3.3-STABLE gcc 2.95.2
HP-UX B.10.20 HP C HP92453-01 A.10.32
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.3 (SGI MPI 3.2.0.0)
Linux 2.2.10 SuSE egcs-2.91.66 configured with
(i686-pc-linux-gnu) --disable-hsizet
mpich-1.2.0 egcs-2.91.66 19990314/Linux
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 4.2 no optimization
SunOS 5.7 cc WorkShop Compilers 5.0
TFLOPS 2.8 cicc (pgcc Rel 3.0-5i)
mpich-1.1.2 with local changes
Windows NT4.0 sp5 MSVC++ 6.0
Known Problems:
==============
o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will
fail if library is compiled using optimization of any level.
%%%%1.2.0%%%% Release Information for hdf5-1.2.0
5. Release Information for hdf5-1.2.0
===================================================================
A. Platforms Supported
-------------------
Operating systems listed below with compiler information and MPI library, if
applicable, are systems that HDF5 1.2.0 was tested on.
Compiler & libraries
Platform Information Comment
-------- ---------- --------
AIX 4.3.2 (IBM SP) 3.6.6
Cray J90 10.0.0.6 cc 6.3.0.0
Cray T3E 2.0.4.61 cc 6.2.1.0
mpt.1.3
FreeBSD 3.2 gcc 2.95.1
HP-UX B.10.20 HP C HP92453-01 A.10.32
gcc 2.8.1
IRIX 6.5 MIPSpro cc 7.30
IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
mpt.1.3 (SGI MPI 3.2.0.0)
Linux 2.2.10 egcs-2.91.66 configured with
--disable-hsizet
lbraries: glibc2
OSF1 V4.0 DEC-V5.2-040
SunOS 5.6 cc WorkShop Compilers 4.2
no optimization
gcc 2.8.1
SunOS 5.7 cc WorkShop Compilers 5.0
gcc 2.8.1
TFLOPS 2.7.1 cicc (pgcc Rel 3.0-4i)
mpich-1.1.2 with local changes
Windows NT4.0 intel MSVC++ 5.0 and 6.0
Windows NT alpha 4.0 MSVC++ 5.0
Windows 98 MSVC++ 5.0
B. Known Problems
--------------
* NT alpha 4.0
Dumper utiliy h5dump fails if linked with DLL.
* SunOS 5.6 with C WorkShop Compilers 4.2
Hyperslab selections will fail if library is compiled using optimization
of any level.
C. Changes Since Version 1.0.1
---------------------------
1. Documentation
-------------
* More examples
* Updated user guide, reference manual, and format specification.
* Self-contained documentation for installations isolated from the
Internet.
* HDF5 Tutorial was added to the documentation
2. Configuration
-------------
* Better detection and support for MPI-IO.
* Recognition of compilers with known code generation problems.
* Support for various compilers on a single architecture (e.g., the
native compiler and the GNU compilers).
* Ability to build from read-only media and with different compilers
and/or options concurrently.
* Added a libhdf5.settings file which summarizes the configuration
information and is installed along with the library.
* Builds a shared library on most systems that support it.
* Support for Cray T3E, J90 and Windows/NT.
3. Debugging
---------
* Improved control and redirection of debugging and tracing messages.
4. Datatypes
---------
* Optimizations to compound datatype conversions and I/O operations.
* Added nearly 100 optimized conversion functions for native datatypes
including support for non-aligned data.
* Added support for bitfield, opaque, and enumeration types.
* Added distinctions between signed and unsigned char types to the
list of predefined native hdf5 datatypes.
* Added HDF5 type definitions for C9x types like int32_t.
* Application-defined type conversion functions can handle non-packed
data.
* Changed the H5Tunregister() function to use wildcards when matching
conversion functions. H5Tregister_hard() and H5Tregister_soft()
were combined into H5Tregister().
* Support for variable-length datatypes (arrays of varying length per
dataset element). Variable length strings currently supported only
as variable length arrays of 1-byte integers.
5. Dataspaces
----------
* New query functions for selections.
* I/O operations bypass the stripmining loop and go directly to
storage for certain contiguous selections in the absence of type
conversions. In other cases the stripmining buffers are used more
effectively.
* Reduced the number of I/O requests under certain circumstances,
improving performance on systems with high I/O latency.
6. Persistent Pointers
-------------------
* Object (serial and parallel) and dataset region (serial only)
references are implemented.
7. Parallel Support
----------------
* Improved parallel I/O performance.
* Supported new platforms: Cray T3E, Linux, DEC Cluster.
* Use vendor supported version of MPIO on SGI O2K and Cray platforms.
* Improved the algorithm that translates an HDF5 hyperslab selection
into an MPI type for better collective I/O performance.
8. New API functions
-----------------
a. Property List Interface:
------------------------
H5Pset_xfer - set data transfer properties
H5Pset_preserve - set dataset transfer property list status
H5Pget_preserve - get dataset transfer property list status
H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O
H5Pget_hyper_cache - returns information regarding the caching of
hyperslab blocks during I/O
H5Pget_btree_ratios - sets B-tree split ratios for a dataset
transfer property list
H5Pset_btree_ratios - gets B-tree split ratios for a dataset
transfer property list
H5Pset_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
H5Pget_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
b. Dataset Interface:
------------------
H5Diterate - iterate over all selected elements in a dataspace
H5Dget_storage_size - return the amount of storage required for a dataset
H5Dvlen_reclaim - reclaim VL datatype memory buffers
c. Dataspace Interface:
--------------------
H5Sget_select_hyper_nblocks - get number of hyperslab blocks
H5Sget_select_hyper_blocklist - get the list of hyperslab blocks
currently selected
H5Sget_select_elem_npoints - get the number of element points
in the current selection
H5Sget_select_elem_pointlist - get the list of element points
currently selected
H5Sget_select_bounds - gets the bounding box containing
the current selection
d. Datatype Interface:
-------------------
H5Tget_super - return the base datatype from which a
datatype is derived
H5Tvlen_create - creates a new variable-length datatype
H5Tenum_create - creates a new enumeration datatype
H5Tenum_insert - inserts a new enumeration datatype member
H5Tenum_nameof - returns the symbol name corresponding to a
specified member of an enumeration datatype
H5Tvalueof - return the value corresponding to a
specified member of an enumeration datatype
H5Tget_member_value - return the value of an enumeration datatype member
H5Tset_tag - tags an opaque datatype
H5Tget_tag - gets the tag associated with an opaque datatype
e. Identifier Interface:
---------------------
H5Iget_type - retrieve the type of an object
f. Reference Interface:
--------------------
H5Rcreate - creates a reference
H5Rdereference - open the HDF5 object referenced
H5Rget_region - retrieve a dataspace with the specified region selected
H5Rget_object_type - retrieve the type of object that an
object reference points to
g. Ragged Arrays (alpha) (names of those API functions were changed):
------------------------------------------------------------------
H5RAcreate - create a new ragged array (old name was H5Rcreate)
H5RAopen - open an existing array (old name was H5Ropen)
H5RAclose - close a ragged array (old name was H5Rclose)
H5RAwrite - write to an array (old name was H5Rwrite)
H5RAread - read from an array (old name was H5Rread)
9. Tools
-----
* Enhancements to the h5ls tool including the ability to list objects
from more than one file, to display raw hexadecimal data, to
show file addresses for raw data, to format output more reasonably,
to show object attributes, and to perform a recursive listing,
* Enhancements to h5dump: support new data types added since previous
versions.
* h5toh4: An hdf5 to hdf4 converter.
%%%%1.0.1%%%% Release Information for hdf5-1.0.1
4. Changes from Release 1.0.0 to Release 1.0.1
=====================================================================
* [Improvement]: configure sets up the Makefile in the parallel tests
suit (testpar/) correctly.
* [Bug-Fix]: Configure failed for all IRIX versions other than 6.3.
It now configures correctly for all IRIX 6.x version.
* Released Parallel HDF5
Supported Features:
------------------
HDF5 files are accessed according to the communicator and INFO
object defined in the property list set by H5Pset_mpi.
Independent read and write accesses to fixed and extendable dimension
datasets.
Collective read and write accesses to fixed dimension datasets.
Supported Platforms:
-------------------
Intel Red
IBM SP2
SGI Origin 2000
Changes In This Release:
-----------------------
o Support of Access to Extendable Dimension Datasets.
Extendable dimension datasets must use chunked storage methods.
A new function, H5Dextend, is created to extend the current
dimensions of a dataset. The current release requires the
MPI application must make a collective call to extend the
dimensions of an extendable dataset before writing to the
newly extended area. (The serial does not require the
call of H5Dextend. The dimensions of an extendable
dataset is increased when data is written to beyond the
current dimensions but within the maximum dimensions.)
The required collective call of H5Dextend may be relaxed
in future release.
This release only support independent read and write accesses
to extendable datasets. Collective accesses to extendable
datasets will be implemented in future releases.
o Collective access to fixed dimension datasets.
Collective access to a dataset can be specified in the transfer
property list argument in H5Dread and H5Dwrite. The current
release supports collective access to fixed dimension datasets.
Collective access to extendable datasets will be implemented in
future releases.
o HDF5 files are opened according to Communicator and INFO object.
H5Dopen now records the communicator and INFO setup by H5Pset_mmpi
and pass them to the corresponding MPIO open file calls for
processing.
o This release has been tested on IBM SP2, Intel Red and SGI Origin 2000
systems. It uses the ROMIO version of MPIO interface for parallel
I/O supports.
%%%%1.0.0%%%% Release Information for hdf5-1.0.0
3. Changes from the Beta 1.0.0 Release to Release 1.0.0
====================================================================
* Added fill values for datasets. For contiguous datasets fill value
performance may be quite poor since the fill value is written to the
entire dataset when the dataset is created. This will be remedied
in a future version. Chunked datasets using fill values do not
incur any additional overhead. See H5Pset_fill_value().
* Multiple hdf5 files can be "mounted" on one another to create a
larger virtual file. See H5Fmount().
* Object names can be removed or changed but objects are never
actually removed from the file yet. See H5Gunlink() and H5Gmove().
* Added a tuning mechanism for B-trees to insure that sequential
writes to chunked datasets use less overhead. See H5Pset_btree_ratios().
* Various optimizations and bug fixes.
%%%%1.0.0 Beta%%%% Release Information for hdf5-1.0.0 Beta
2. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release
=========================================================================
* Strided hyperslab selections in dataspaces now working.
* The compression API has been replaced with a more general filter
API. See doc/html/Filters.html for details.
* Alpha-quality 2d ragged arrays are implemented as a layer built on
top of other hdf5 objects. The API and storage format will almost
certainly change.
* More debugging support including API tracing. See Debugging.html.
* C and Fortran style 8-bit fixed-length character string types are
supported with space or null padding or null termination and
translations between them.
* Added function H5Fflush() to write all cached data immediately to
the file.
* Datasets maintain a modification time which can be retrieved with
H5Gstat().
* The h5ls tool can display much more information, including all the
values of a dataset.
%%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2
1. Changes from the First Alpha 1.0.0 Release to
the Second Alpha 1.0.0 Release
=====================================================================
* Two of the packages have been renamed. The data space API has been
renamed from `H5P' to `H5S' and the property list (template) API has
been renamed from `H5C' to `H5P'.
* The new attribute API `H5A' has been added. An attribute is a small
dataset which can be attached to some other object (for instance, a
4x4 transformation matrix attached to a 3-dimensional dataset, or an
English abstract attached to a group).
* The error handling API `H5E' has been completed. By default, when an
API function returns failure an error stack is displayed on the
standard error stream. The H5Eset_auto() controls the automatic
printing and H5E_BEGIN_TRY/H5E_END_TRY macros can temporarily
disable the automatic error printing.
* Support for large files and datasets (>2GB) has been added. There
is an html document that describes how it works. Some of the types
for function arguments have changed to support this: all arguments
pertaining to sizes of memory objects are `size_t' and all arguments
pertaining to file sizes are `hsize_t'.
* More data type conversions have been added although none of them are
fine tuned for performance. There are new converters from integer
to integer and float to float, but not between integers and floating
points. A bug has been fixed in the converter between compound
types.
* The numbered types have been removed from the API: int8, uint8,
int16, uint16, int32, uint32, int64, uint64, float32, and float64.
Use standard C types instead. Similarly, the numbered types were
removed from the H5T_NATIVE_* architecture; use unnumbered types
which correspond to the standard C types like H5T_NATIVE_INT.
* More debugging support was added. If tracing is enabled at
configuration time (the default) and the HDF5_TRACE environment
variable is set to a file descriptor then all API calls will emit
the function name, argument names and values, and return value on
that file number. There is an html document that describes this.
If appropriate debugging options are enabled at configuration time,
some packages will display performance information on stderr.
* Data types can be stored in the file as independent objects and
multiple datasets can share a data type.
* The raw data I/O stream has been implemented and the application can
control meta and raw data caches, so I/O performance should be
improved from the first alpha release.
* Group and attribute query functions have been implemented so it is
now possible to find out the contents of a file with no prior
knowledge.
* External raw data storage allows datasets to be written by other
applications or I/O libraries and described and accessed through
HDF5.
* Hard and soft (symbolic) links are implemented which allow groups to
share objects. Dangling and recursive symbolic links are supported.
* User-defined data compression is implemented although we may
generalize the interface to allow arbitrary user-defined filters
which can be used for compression, checksums, encryption,
performance monitoring, etc. The publicly-available `deflate'
method is predefined if the GNU libz.a can be found at configuration
time.
* The configuration scripts have been modified to make it easier to
build debugging vs. production versions of the library.
* The library automatically checks that the application was compiled
with the correct version of header files.
Parallel HDF5 Changes
* Parallel support for fixed dimension datasets with contiguous or
chunked storages. Also, support unlimited dimension datasets which
must use chunk storage. No parallel support for compressed datasets.
* Collective data transfer for H5Dread/H5Dwrite. Collective access
support for datasets with contiguous storage only, thus only fixed
dimension datasets for now.
* H5Pset_mpi and H5Pget_mpi no longer have the access_mode
argument. It is taken over by the data-transfer property list
of H5Dread/H5Dwrite.
* New functions H5Pset_xfer and H5Pget_xfer to handle the
specification of independent or collective data transfer_mode
in the dataset transfer properties list. The properties
list can be used to specify data transfer mode in the H5Dwrite
and H5Dread function calls.
* Added parallel support for datasets with chunked storage layout.
When a dataset is extend in a PHDF5 file, all processes that open
the file must collectively call H5Dextend with identical new dimension
sizes.
LIST OF API FUNCTIONS
The following functions are implemented. Errors are returned if an
attempt is made to use some feature which is not implemented and
printing the error stack will show `not implemented yet'.
Library
H5check - check that lib version matches header version
H5open - initialize library (happens automatically)
H5close - shut down the library (happens automatically)
H5dont_atexit - don't call H5close on exit
H5get_libversion - retrieve library version info
H5check_version - check for specific library version
Property Lists
H5Pclose - release template resources
H5Pcopy - copy a template
H5Pcreate - create a new template
H5Pget_chunk - get chunked storage properties
H5Pset_chunk - set chunked storage properties
H5Pget_class - get template class
H5Pget_istore_k - get chunked storage properties
H5Pset_istore_k - set chunked storage properties
H5Pget_layout - get raw data layout class
H5Pset_layout - set raw data layout class
H5Pget_sizes - get address and size sizes
H5Pset_sizes - set address and size sizes
H5Pget_sym_k - get symbol table storage properties
H5Pset_sym_k - set symbol table storage properties
H5Pget_userblock - get user-block size
H5Pset_userblock - set user-block size
H5Pget_version - get file version numbers
H5Pget_alignment - get data alignment properties
H5Pset_alignment - set data alignment properties
H5Pget_external_count- get count of external data files
H5Pget_external - get information about an external data file
H5Pset_external - add a new external data file to the list
H5Pget_driver - get low-level file driver class
H5Pget_stdio - get properties for stdio low-level driver
H5Pset_stdio - set properties for stdio low-level driver
H5Pget_sec2 - get properties for sec2 low-level driver
H5Pset_sec2 - set properties for sec2 low-level driver
H5Pget_core - get properties for core low-level driver
H5Pset_core - set properties for core low-level driver
H5Pget_split - get properties for split low-level driver
H5Pset_split - set properties for split low-level driver
H5P_get_family - get properties for family low-level driver
H5P_set_family - set properties for family low-level driver
H5Pget_cache - get meta- and raw-data caching properties
H5Pset_cache - set meta- and raw-data caching properties
H5Pget_buffer - get raw-data I/O pipe buffer properties
H5Pset_buffer - set raw-data I/O pipe buffer properties
H5Pget_preserve - get type conversion preservation properties
H5Pset_preserve - set type conversion preservation properties
H5Pget_nfilters - get number of raw data filters
H5Pget_filter - get raw data filter properties
H5Pset_filter - set raw data filter properties
H5Pset_deflate - set deflate compression filter properties
H5Pget_mpi - get MPI-IO properties
H5Pset_mpi - set MPI-IO properties
H5Pget_xfer - get data transfer properties
+ H5Pset_xfer - set data transfer properties
+ H5Pset_preserve - set dataset transfer property list status
+ H5Pget_preserve - get dataset transfer property list status
+ H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O
+ H5Pget_hyper_cache - returns information regarding the caching of
hyperslab blocks during I/O
+ H5Pget_btree_ratios - sets B-tree split ratios for a dataset
transfer property list
+ H5Pset_btree_ratios - gets B-tree split ratios for a dataset
transfer property list
+ H5Pset_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
+ H5Pget_vlen_mem_manager - sets the memory manager for variable-length
datatype allocation
Datasets
H5Dclose - release dataset resources
H5Dcreate - create a new dataset
H5Dget_space - get data space
H5Dget_type - get data type
H5Dget_create_plist - get dataset creation properties
H5Dopen - open an existing dataset
H5Dread - read raw data
H5Dwrite - write raw data
H5Dextend - extend a dataset
+ H5Diterate - iterate over all selected elements in a dataspace
+ H5Dget_storage_size - return the amount of storage required for a dataset
+ H5Dvlen_reclaim - reclaim VL datatype memory buffers
Attributes
H5Acreate - create a new attribute
H5Aopen_name - open an attribute by name
H5Aopen_idx - open an attribute by number
H5Awrite - write values into an attribute
H5Aread - read values from an attribute
H5Aget_space - get attribute data space
H5Aget_type - get attribute data type
H5Aget_name - get attribute name
H5Anum_attrs - return the number of attributes for an object
H5Aiterate - iterate over an object's attributes
H5Adelete - delete an attribute
H5Aclose - close an attribute
Errors
H5Eclear - clear the error stack
H5Eprint - print an error stack
H5Eget_auto - get automatic error reporting settings
H5Eset_auto - set automatic error reporting
H5Ewalk - iterate over the error stack
H5Ewalk_cb - the default error stack iterator function
H5Eget_major - get the message for the major error number
H5Eget_minor - get the message for the minor error number
Files
H5Fclose - close a file and release resources
H5Fcreate - create a new file
H5Fget_create_plist - get file creation property list
H5Fget_access_plist - get file access property list
H5Fis_hdf5 - determine if a file is an hdf5 file
H5Fopen - open an existing file
H5Freopen - reopen an HDF5 file
H5Fmount - mount a file
H5Funmount - unmount a file
H5Fflush - flush all buffers associated with a file to disk
Groups
H5Gclose - close a group and release resources
H5Gcreate - create a new group
H5Gopen - open an existing group
H5Giterate - iterate over the contents of a group
H5Gmove - change the name of some object
H5Glink - create a hard or soft link to an object
H5Gunlink - break the link between a name and an object
H5Gget_objinfo - get information about a group entry
H5Gget_linkval - get the value of a soft link
H5Gget_comment - get the comment string for an object
H5Gset_comment - set the comment string for an object
Dataspaces
H5Screate - create a new data space
H5Scopy - copy a data space
H5Sclose - release data space
H5Screate_simple - create a new simple data space
H5Sset_space - set simple data space extents
H5Sis_simple - determine if data space is simple
H5Sset_extent_simple - set simple data space dimensionality and size
H5Sget_simple_extent_npoints - get number of points in simple extent
H5Sget_simple_extent_ndims - get simple data space dimensionality
H5Sget_simple_extent_dims - get simple data space size
H5Sget_simple_extent_type - get type of simple extent
H5Sset_extent_none - reset extent to be empty
H5Sextent_copy - copy the extent from one data space to another
H5Sget_select_npoints - get number of points selected for I/O
H5Sselect_hyperslab - set hyperslab dataspace selection
H5Sselect_elements - set element sequence dataspace selection
H5Sselect_all - select entire extent for I/O
H5Sselect_none - deselect all elements of extent
H5Soffset_simple - set selection offset
H5Sselect_valid - determine if selection is valid for extent
+ H5Sget_select_hyper_nblocks - get number of hyperslab blocks
+ H5Sget_select_hyper_blocklist - get the list of hyperslab blocks
currently selected
+ H5Sget_select_elem_npoints - get the number of element points
in the current selection
+ H5Sget_select_elem_pointlist - get the list of element points
currently selected
+ H5Sget_select_bounds - gets the bounding box containing
the current selection
Datatypes
H5Tclose - release data type resources
H5Topen - open a named data type
H5Tcommit - name a data type
H5Tcommitted - determine if a type is named
H5Tcopy - copy a data type
H5Tcreate - create a new data type
H5Tequal - compare two data types
H5Tlock - lock type to prevent changes
H5Tfind - find a data type conversion function
H5Tconvert - convert data from one type to another
H5Tregister - register a conversion function
H5Tunregister - remove a conversion function
H5Tget_overflow - get function that handles overflow conv. cases
H5Tset_overflow - set function to handle overflow conversion cases
H5Tget_class - get data type class
H5Tget_cset - get character set
H5Tget_ebias - get exponent bias
H5Tget_fields - get floating point fields
H5Tget_inpad - get inter-field padding
H5Tget_member_dims - get struct member dimensions
H5Tget_member_name - get struct member name
H5Tget_member_offset - get struct member byte offset
H5Tget_member_type - get struct member type
H5Tget_nmembers - get number of struct members
H5Tget_norm - get floating point normalization
H5Tget_offset - get bit offset within type
H5Tget_order - get byte order
H5Tget_pad - get padding type
H5Tget_precision - get precision in bits
H5Tget_sign - get integer sign type
H5Tget_size - get size in bytes
H5Tget_strpad - get string padding
H5Tinsert - insert scalar struct member
H5Tinsert_array - insert array struct member
H5Tpack - pack struct members
H5Tset_cset - set character set
H5Tset_ebias - set exponent bias
H5Tset_fields - set floating point fields
H5Tset_inpad - set inter-field padding
H5Tset_norm - set floating point normalization
H5Tset_offset - set bit offset within type
H5Tset_order - set byte order
H5Tset_pad - set padding type
H5Tset_precision - set precision in bits
H5Tset_sign - set integer sign type
H5Tset_size - set size in bytes
H5Tset_strpad - set string padding
+ H5Tget_super - return the base datatype from which a
datatype is derived
+ H5Tvlen_create - creates a new variable-length datatype
+ H5Tenum_create - creates a new enumeration datatype
+ H5Tenum_insert - inserts a new enumeration datatype member
+ H5Tenum_nameof - returns the symbol name corresponding to a
specified member of an enumeration datatype
+ H5Tvalueof - return the value corresponding to a
specified member of an enumeration datatype
+ H5Tget_member_value - return the value of an enumeration datatype member
+ H5Tset_tag - tags an opaque datatype
+ H5Tget_tag - gets the tag associated with an opaque datatype
- H5Tregister_hard - register specific type conversion function
- H5Tregister_soft - register general type conversion function
Filters
H5Tregister - register a conversion function
Compression
H5Zregister - register new compression and uncompression
functions for a method specified by a method number
Identifiers
+ H5Iget_type - retrieve the type of an object
References
+ H5Rcreate - creates a reference
+ H5Rdereference - open the HDF5 object referenced
+ H5Rget_region - retrieve a dataspace with the specified region selected
+ H5Rget_object_type - retrieve the type of object that an
object reference points to
Ragged Arrays (alpha)
H5RAcreate - create a new ragged array
H5RAopen - open an existing array
H5RAclose - close a ragged array
H5RAwrite - write to an array
H5RAread - read from an array
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