Purpose:
Rename variables.
Description:
In this file, dataset address offset is misnamed as file offset. Changed
them back to dset_offset_XXX or dset_offset.
Platforms tested:
eirene
Purpose:
Bug fix.
Description:
In H5D_init_storage, contiguous dataset is not initialized properly when
fill value is library default.
Platforms tested:
eirene
bug fix
Description:
Last change of FUNC_ENTER to FUNC_ENTER_NOAPI did not include
definition of variable ret_value and label done.
Solution:
Added the missing ret_value and label done.
Not sure if the logic is correct since the function will abort
if some assert fails. This fix only takes care of the syntax
error.
Platforms tested:
eirene(pp). Did not test on other machine since the syntax fix
is pretty simple.
Purpose:
Design for compact dataset
Description:
Compact dataset is stored in the header message for dataset layout.
Platforms tested:
arabica, eirene.
Additional regression tests & bug fixes
Description:
There was no testing for the H5Dget_storage_size function and it seemed to
be having problems with compressed, chunked datasets, so write some tests
to verify that its working correctly.
Also, fix case for allocating storage early for chunked datasets
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel
Code cleanup
Description:
Move get/set routines for each type of property list (file creation,
dataset creation, file access and dataset transfer) into their own source
code module.
Platforms tested:
FreeBSD 4.6 (sleipnir)
Code cleanup
Description:
Combined H5P_isa_class and H5I_object functionality into a new internal
H5P API function: H5P_object_verify, which checks that a property list is
the appropriate class and then returns the property list object associated
with the property list ID.
This reduces the source code by about 200 LOC and trims the library binary
some more.
Platforms tested:
FreeBSD 4.6 (sleipnir)
Code cleanup
Description:
Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO*
macros, which reduces the size of the library binary in certain
configurations by another 10%
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial &
parallel
Bug fix
Description:
hsize_t comparisons for selection boundaries (in H5Sget_select_bounds)
were failing on Linux with --disable-hsizet.
Solution:
Changed comparisons to use use unsigned values instead of signed ones.
Platforms tested:
Linux 2.2.x (eirene)
Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
Code cleanup
Description:
Clean up a few warnings which were showing up with --enable-production
turned on.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel
Code cleanup
Description:
Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with
HRETURN macros to HGOTO_DONE macros. This unifies the error return path
from functions and reduces the size of the library by up to 10% on some
platforms.
Additionally, I improved a lot of the error cleanup code in many routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial &
parallel.
Code cleanup
Description:
Created a new H5I function which combined the some of the functionality of
H5I_get_type and H5I_object: H5I_object_verify.
Using this new function in the library trims another ~200 lines of code off
the library and makes the resulting binaries smaller and faster also.
Platforms tested:
FreeBSD 4.6 (sleipnir)
Code cleanup
Description:
Move operations on each type of selection into the source code file for
each selection type (all->H5Sall.c, hyperslab->H5Shyper.c, etc.)
Remove central H5S_select_<foo> operations, instead calling the operations
through function pointers in each selection (a much more object-oriented
approach).
Platforms tested:
FreeBSD 4.6 (sleipnir)
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:
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
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
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:
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
Bug fix.
Description:
1-D non-contiguous hyperslabs were erroneously being detected as contiguous
and were causing incorrect behavior for parallel I/O benchmark (and
parallel programs in general).
Solution:
Modified algorithm to handle 1-D case correctly.
Platforms tested:
IRIX64 6.5 (modi4)
Purpose:
Fix bug
Description:
In function H5HG_remove, heap object header wasn't included for size.
Solution:
Added heap object header in.
Platforms tested:
Linux 2.2(eirene).
Bug Fix.
Description:
Contiguous types created for "all" and contiguous hyperslab selections was
not being committed before using them.
Solution:
Commit them. :-) This fixes the problems on the LLNL Blue Pacific machine.
Platforms tested:
LLNL Blue Pacific w/parallel.
