Bug fix
Description:
Allow buffer parameter to H5Dread & H5Dwrite to be NULL if there are no
elements to transfer.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code cleanup & reorganization
Description:
Move further in the testing framework cleanup, eliminating all the
global variables (moving them into testframe.c as static variables) from the
testing framework code and moving it into the libh5test.a.
Platforms tested:
FreeBSD 4.9 (sleipnir) w & w/o thread-safety, c++ & parallel
h5committested
Bug fix.
Description:
Using a selection offset with hyperslab selections in chunked datasets
was getting into an infinite loop and hanging the application.
Solution:
Apply the selection offset to the hyperslab selection properly.
Platforms tested:
FreeBSD 4.9 (sleipnir) w & w/o parallel
h5committest
Bug fix
Description:
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.
Solution:
Re-work "flattening" code to handle this case properly.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
Bug fix
Description:
I/O on chunked datasets with a scalar dataspace for the memory dataspace
was not working correctly.
Solution:
Translate the scalar dataspace into a n-dimensional (where n is the number
of dimensions of the file's dataspace) dataspace of dimensions 1x1x1...
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest (modulo modi4 which is not working correctly)
Bug fix
Description:
I/O on chunked datasets with point selections was not working correctly.
Solution:
Re-wrote some parts of raw data I/O routines that build the selections for
each chunk to correctly handle point selections.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Bug fix
Description:
An earlier checkin changed some of the assumptions about single block
hyperslabs, causing them to fail in odd ways.
Solution:
Fix errors with single block hyperslabs by keying off of count==1 instead
of stride==1.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
Code cleanup & performance improvements
Description:
Optimize hyperslabs that are built to detect situations where "regular"
hyperslabs can be recovered from span tree descriptions.
Also, improve "same shape" routine to correctly work with all the different
combinations of selections.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
Code cleanup
Description:
Clean up older settings for strides of hyperslabs
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
Description: H5Sselect_hyperslab and H5Sselect_elements didn't check scalar
dataspaces.
Solution: put error detection in those functions.
Platforms tested: eirene(simple change).
New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
Update
Description:
Updated the Copyright statement
Platforms tested:
Linux (This change is only in the comments, so I just check that the
modules still compile)
Misc. update:
New feature
Description:
Add support for scalar dataspaces in parallel I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Also, FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Update release_docs/RELEASE for bug fixes, new features, etc.
Bug fix
Description:
I/O on "Regular" hyperslab selections could fail to transfer correctly
if the number of elements in the selection's row did now fit "evenly"
into the buffer being used for the transfer.
Solution:
Correct the calculation of the block & count offsets within the optimized
"regular" hyperslab routines.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix
Description:
Corrected int vs. unsigned short error that only showed up on big-endian
machines.
Also, add more testing to verify that the coordinates reported for each
element iterated through with H5Diterate are correct.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix
Description:
Selection offsets were not being used correctly when iterating through
all hyperslabs selections and point selections.
Solution:
Use the selection offset appropriately.
Platforms tested:
FreeBSD 4.5 (sleipnir)
New Feature
Description:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms tested:
FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few
minutes]
Bug Fix & Feature
Description:
The selection offset was being ignored for optimized hyperslab selection
I/O operations.
Additionally, I've found that the restrictions on optimized selection
I/O operations were too strict and found a way to allow more hyperslabs
to use the optimized I/O routines.
Solution:
Incorporate the selection offset into the selection location when performing
optimized I/O operations.
Allow optimized I/O on any single hyperslab selection and also allow
hyperslab operations on chunked datasets.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix
Description:
Regression test for following bug:
When reading a contiguous hyperslab that spanned the entire dataset and
was larger that the type conversion buffer, the hyperslab routines need
to fill the type conversion buffer and then return to the I/O routines.
When the I/O routines resume the hyperslab operation, it was possible to
have a combination of coordinates which caused the hyperslab iterator
to incorrectly advance in the file, causing some data to be re-read or
re-written.
Platforms tested:
Linux (eirene)
Bug fix & feature add
Description:
Added new API function H5Sget_select_type to determine type of selection in
a dataspace. Return values are defined by the H5S_sel_type enumerated type
in H5Spublic.h
Also, hyperslab operations involving a "all" or "none" selection are not
generating the correct resulting selections.
Solution:
Added regression tests to verify correction operation of hyperslab
operations against "all" and "none" selections. New tests also verify
H5Sget_select_type() API call.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix
Description:
The code in H5Sselect_hyperslab_valid contained an fencepost error and is
allowing selections which overlap the extent by exactly one element in any
dimension to pass as valid instead of flagging the selection as invalid.
This bug only affects hyperslabs which have been OR'ed together, not the
selection from a single H5Sselect_hyperslab.
This fixes bug #550.
Solution:
Changed an '>' to an '>=' and added new regression test to check for error.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Code cleanup
Description:
Property that H5P(g|s)et_hyper_cache uses is no longer in use inside the
library.
Solution:
Removed H5P(g|s)et_hyper_cache API functions, except when backward
compatibility is turned on. When backward compatibility is turned on,
the property is defined by the library, but unused internally.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Backward Compatibility Fix
Description:
One of H5P[gs]et_cache's parameters changed between v1.4 and the development
branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_cache implementation and testing
to allow v1.4.x users to continue to use their source code without
modification.
These changes are for everything except the FORTRAN wrappers - I spoke with
Elena and she will make the FORTRAN wrapper changes.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Code cleanup
Description:
Purify detected an uninitialized memory read in test data.
Solution:
Corrected parameters for initializing data array so entire array is
initialized.
Platforms tested:
Solaris 2.7 (arabica)
Kludge
Description:
Since we're only about halfway through converting the internal use of
property lists from the "old way" to the generic property lists, we turned
off snapshots to avoid exposing lots of API changes to users, until the
APIs settled down.
Getting the snapshots rolling again seems to have become a priority, so
some changes are going to have to be made now that were going to be
postponed until we were completely finished with the conversion. This
requires that the old API functions be able to deal with both the old
and new property lists smoothly.
Solution:
Kludge together the property list code so that they can transparently handle
dealing with both the old and new property lists
Platforms tested:
FreeBSD 4.4 (hawkwind)
Code cleanup (sorta)
Description:
When the first versions of the HDF5 library were designed, I remembered
vividly the difficulties of porting code from a 32-bit platform to a 16-bit
platform and asked that people use intn & uintn instead of int & unsigned
int, respectively. However, in hindsight, this was overkill and
unnecessary since we weren't going to be porting the HDF5 library to
16-bit architectures.
Currently, the extra uintn & intn typedefs are causing problems for users
who'd like to include both the HDF5 and HDF4 header files in one source
module (like Kent's h4toh5 library).
Solution:
Changed the uintn & intn's to unsigned and int's respectively.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Code cleanups, mostly..
Description:
Work on pacifying the SGI compiler to get the generic properties working
correctly with --enable-parallel and --enable-fortran. It's not quite
fixed yet, but I need to head home and these patches help... :-/
Platforms tested:
IRIX64 6.5 (modi4)
New Features!
Description:
Start migrating the internal use of property lists in the library from the
older implementation to the new generic property lists.
Currently, only the dataset transfer property lists are migrated to the
new architecture, all the rest of the property list types are still using
the older architecture.
Also, the backward compatibility features are not implemented yet, so
applications which use dataset transfer properties may need to make the
following changes:
H5Pcreate(H5P_DATASET_XFER) -> H5Pcreate_list(H5P_DATASET_XFER_NEW)
and
H5Pclose(<a dataset transfer property list>) -> H5Pclose_list(id)
This still may have some bugs in it, especially with Fortran, but I should
be wrapping up those later today.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Bug Fix, Code Cleanup, Code Optimization, etc.
Description:
Fold in the hyperslab speedups, clean up compile warnings and change a
few things from using 'unsigned' or 'hsize_t' to use 'size_t' instead.
Platforms tested:
FreeBSD 4.3 (hawkwind), Solaris 2.7 (arabica), Irix64 6.5 (modi4)
Regression check added
Description:
Added regression check to verify that the array reading code is now working
correctly for small data transfer buffers.
Platforms tested:
FreeBSD 4.3 (hawkwind)
Update
Description:
Changed includes of the form:
#include <hdf5_file.h>
to
#include "hdf5_file.h"
so that gcc can pick them up easier without including the system
header files since we don't care about them.
Platforms tested:
Linux
Bug fix (sort of)
Description:
The RCSID string in H5public.h was causing the C++ code problem as it
was included multiple times and C++ did not like multiple definitions
of the same static variable.
Solution:
Since we don't really make use of the RCSID strings as we have not
installed it in all source files, we decided to remove it.
Platforms tested:
eirene (linux), modi4 (IRIX64-64) both serial and parallel modes.
Bug Fixes
Description:
Wrote test to exercise hyperslab I/O on chunked datasets where the
hyperslabs aren't aligned on exact dimension boundaries.
Platforms tested:
FreeBSD 4.2. (hawkwind)
Additional testing
Description:
Added another random hyperslab test with smaller strip-mine buffers to
force more errors conditions (if they exist).
Platforms tested:
FreeBSD 4.2 (hawkwind)
Code cleanup.
Description:
Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the
extra warnings. Including a few show-stoppers for compression on IRIX
machines.
Solution:
Changed lots of variables' types to more sensible and consistent types,
more range-checking, more variable typecasts, etc.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
Backward compatibility code
Description:
Add in code to allow the library to emulate the v1.2 API and behavior.
Platforms tested:
FreeBSD 4.2 (hawkwind)
