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hdf5/release_docs/RELEASE.txt
HDF Admin c619cf0f51 [svn-r12083] Snapshot version 1.7 release 58
2006-03-13 13:38:16 -05:00

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HDF5 version 1.7.59 currently under development
================================================================================
===========================================================================
WARNING!! WARNING!! WARNING!! WARNING!! WARNING!! WARNING!! WARNING!!
______
.-" "-.
/ \
_ | | _
( \ |, .-. .-. ,| / )
> "=._ | )(__/ \__)( | _.=" <
(_/"=._"=._ |/ /\ \| _.="_.="\_)
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_ _.="_.="\ /"=._"=._ _
( \_.="_.=" `--------` "=._"=._/ )
> _.=" "=._ <
(_/ jgs \_)
This code is currently using interim file format changes that will
certainly change before the final 1.8.0 release. Please feel free to test
everything out (in fact, we'd welcome that!), but do _NOT_ keep any of the
files produced as they will not be readable by later versions of the HDF5
software. - QAK
WARNING!! WARNING!! WARNING!! WARNING!! WARNING!! WARNING!! WARNING!!
===========================================================================
INTRODUCTION
This document describes the differences between HDF5-1.6.* and
HDF5-1.7.*, and contains information on the platforms tested and
known problems in HDF5-1.7.*. 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
- Platforms Tested
- Known Problems
New Features
============
Configuration:
--------------
- 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 depened (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 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
- 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:
--------
- 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 accross 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 accross 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 vender 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
hdfhelp@ncsa.uiuc.edu. 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
- 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 compatability 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
underlaying 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:
------
- 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:
------
- 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
Support for new platforms, languages and compilers.
=======================================
- 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 varibale 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
-------
- 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
endianess. 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
-------------
- 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 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
================
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 4.9 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
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 5.0-2
MPIch 1.2.4
Absoft Fortran v9.0
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 32,46 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 v4.3.3 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 XP MSVC++ 6.0
MSVC++ .NET 2003,
Intel C++ Version 8.1
DEC Visual Fortran 6.6c
MAC OS X Darwin 6.5
gcc and g++ Apple Computer, Inc. GCC
version 1161, based on gcc version 3.1
IBM XL Fortran compiler version 8.1
Absoft Fortran v8.2
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
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
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
==============
* 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 certian 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 windows XP, Fortran DLLs are not working with DEC Fortran 6.6c and Intel
8.1.
* 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
setenv CXX "pgCC -tlocal" for others
* 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:
ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.2/F90_source_for_Crays
* 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 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 scipts to execute your filter script
by setting the environment variable "RUNSERIAL" to the full path of the
script prior to running configure for parallel builds. Remember to
"unsetenv RUNSERIAL" before running configure for a serial build.
Note that the RUNSERIAL environment variable exists so that we can
can prefix serial runs as necessary on the target system. On DataStar,
no prefix is necessary. However on an MPICH system, the prefix might
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
get the serial tests to run at all.
In such cases, you will have to include the regular prefix in your
filter script.
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