Purpose:
move zlib out of hdf5/src from development branch
update H5pubconf.h
Description:
The decision has been made to move zlib out of hdf5 source distribution, make it real in development branch.
In dev. branch, H5_HAVE_COMPRESSION replaces H5_HAVE_COMPRESS2, H5_HAVE_ZLIB_H and H5_HAVE_LIBZ etc.
Make windows consistent.
Solution:
Platforms tested:
windows 2000
Purpose:
move zlib out of hdf5/src from development branch
update H5pubconf.h
Description:
The decision has been made to move zlib out of hdf5 source distribution, make it real in development branch.
In dev. branch, H5_HAVE_COMPRESSION replaces H5_HAVE_COMPRESS2, H5_HAVE_ZLIB_H and H5_HAVE_LIBZ etc.
Make windows consistent.
Solution:
Platforms tested:
windows 2000
Large code cleanup/re-write
Description:
This is phase 1 of the data I/O re-architecture, with the following changes:
- Changed the selection drivers to not actually do any I/O, they
only generate the sequences of offset/length pairs needed for
the I/O (or memory access, in the case of iterating or filling
a selection in a memory buffer)
- Wrote more abstract I/O routines which get the sequence of offset/
length pairs for each selection and access perform the I/O or
memory access.
Benefits of this change include:
- Removed ~3400 lines of quite redundant code, with corresponding
reduction in the size of library binary.
- Any selection can now directly access memory when performing I/O,
if no type conversions are required, instead of just "regular"
hyperslab and 'all' selections, which speeds up I/O.
- Sped up I/O for hyperslab selections which have contiguous lower
dimensions by "flattening" them out into lesser dimensional objects
for the I/O.
No file format or API changes were necessary for this change.
The next phase will be to create a "selection driver" for each type of
selection, allowing each type of selection to directly call certain
methods that only apply to that type of selection, instead of passing
through dozens of functions which have switch statements to call the
appropriate method for each selection type. This will also reduce
the amount of code in the library and speed things up a bit more.
Phase 3 will involve generating an MPI datatype for all types of selections,
instead of only "regular" hyperslab and 'all' selections. This will
allow collective parallel I/O for all I/O operations which don't
require type conversions. It will also open up the door for allowing
collective I/O on datasets which require type conversion.
Phase 4 will involve changing the access pattern to deal with chunked
datasets in a more optimal way (in serial).
Phase 5 will deal with accessing chunked datasets more optimally for
collective parallel I/O operations.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/ parallel & C++ and IRIX64 6.5 (modi4) w/parallel
Purpose:
correct a typo in the H5FD_sec2_flush.
Description:
fd is not defined. It should be file->fd
Solution:
Platforms tested:
windows 2000, linux 2.2.18smp
Bug Fix
Description:
Dynamically allocated H5S_t structure was not being freed under certain
error conditions.
Solution:
Free it.
Platforms tested:
FreeBSD 4.6 (sleipnir)
Bug Fix
Description:
non-parallel case for new metadata cache flushing property wasn't set up
correctly.
Solution:
Initialize variables correctly.
Platforms tested:
FreeBSD 4.6 (sleipnir)
Bug fix
Description:
t_mpi test program was not being run with the RUNPARALLEL command
Solution:
Put the t_mpi program into the TEST_PROGS_PARA macro instead of the
TEST_PROGS macro
Hopefully this'll fix the daily test problems on arabica, but I can't test
it because I can't get mpirun to work correctly for me.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
Bug Fix
Description:
It was possible to create corrupted metadata information (either in memory
or in the file or both) with a parallel I/O program because of the way
metadata writes were being handled for writes out of the metadata cache.
Solution:
Added a dataset transfer property called "block before metadata write"
which is used by the MPI-I/O and MPI-posix drivers to sync up all the
processes before attempting a metadata write. This property is currently
only for metadata writes from the metadata cache.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
Fix
Description:
Better check for versions of Linux. We didn't support kernels with
major version numbers >2 and minor version numbers <4...
Solution:
Fixed to check just that.
Platforms tested:
Linux 2.2 && 2.4
Bug fix
Description:
Deleting objects from a global heap was incorrectly setting the free space
in the heap chunk.
Solution:
Encode correct amount of free space.
Platforms tested:
IRIX64 6.5 (modi4)
Update, Bug Fix, and Feature Add
Description:
- Updated how AC_{ENABLE,WITH} help messages were being generated.
Autoconf now gives you an AC_HELP_STRING macro to use to create
them.
- Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't
finding getdents64(), so we can't rely on that being present
anymore...
- Added GPFS detection and setting.
- Updated how compression is specified. It's no longer necessary to
test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro
{H5_}HAVE_COMPRESSION takes care of all of these.
Solution:
Changed the check for Linux LFS from looking for getdents() to
looking at the version number of the kernel (using the uname -r
command). You can still override with the --enable-linux-lfs switch
if you really believe that your <2.4 kernel has LFS support.
Platforms tested:
Linux (2.2 and 2.4)
New feature.
Description:
Added MPI-posix VFL driver. This driver uses MPI to coordinate actions, but
performs I/O directly with posix sec(2) I/O functions. This driver should
_NOT_ be used if the file accessed is not on a parallel filesystem.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel & IRIX64 6.5 (modi4) w/parallel
New feature
Description:
Changed parallel I/O tests to use test script instead of just running
testphdf5 executable. This allows the MPI-posix driver to be tested easily.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel and IRIX64 6.5 (modi4) w/parallel
Code cleanup
Description:
Changed a few direct calls to posix functions to use proper wrapper macros.
Also, changed method of extending file to use ftruncate().
Platforms tested:
FreeBSD 4.6 (sleipnir) && IRIX64 6.5 (modi4)
Bug fix.
Description:
"strong" file closing feature was re-using free'd memory for objects which
were still open in the file.
Solution:
Used the "dmalloc" tools to determine where the memory was being
re-used and re-arranged the code to avoid these cases.
Platforms tested:
FreeBSD 4.6 (sleipnir)
New feature
Description:
Add support in for "dmalloc" debugging malloc library to configure script
and library headers.
Platforms tested:
IRIX64 6.5 (modi4) and FreeBSD 4.6 (sleipnir)
Purpose:
Bug fix.
Description:
For nested VL datatype, the heap object of VL elements lower than top level
weren't freed.
Solution:
Read in the content of heap object for VL elements and free them in
function H5T_conv_vlen.
Platforms tested:
eirene
Purpose:
Add copyright and change "HDF5 Tutorial" link.
Description:
Added copyright statement and link.
Changed the "Tutorial" link to point to the copy on the HDF5 website.
Since the Tutorial is not maintained in CVS, the distributed
version of the Tutorial is being unlinked and removed from the
set of distributed files. It is hoped that we can begin
maintaining the Tutorial under CVS prior to Release 1.6 and
resume its distribution.
Platforms tested:
IE 5
Purpose:
Bugfix
Description:
Corrected H5Zregister description, syntax, and parameter descriptions.
There is one 'function' parameter, rather than the separate
'compression-function' and 'uncompression-function' parameters that
were previously listed.
Platforms tested:
IE 5
Purpose:
Clarification regarding sizes of some super block elements.
Description:
Added note to "HDF5 Super Block Layout" table that the last 5 items
are of the size specified in 'Size of Offsets'.
Platforms tested:
IE 5
Purpose:
Two new functions and a few copy-edits.
Description:
Added H5Pset/get_small_data_block_size.
Copy edits -- several typographic (spelling) corrections.
Platforms tested:
IE 5
Purpose:
New Test VL memory leak.
Description:
Test to see if VL type memory leaks when data is overwritten.
Platforms tested:
Linux 2.2(eirene), IRIX 6.5(paz).
Purpose:
Bug Fix.
Description:
VL type memory leak when data is overwritten.
Solution:
Free heap objects holding old data.
Platforms tested:
Linux 2.2(eirene), IRIX 6.5(paz).
Bug fix.
Description:
Correct the previous code for detecting 1-D contiguous hyperslabs to detect
an extra case that the development branch has, but the release branch
doesn't have.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
