| Commit message (Collapse) | Author | Age | Files | Lines |
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Code optimization
Description:
Instead of re-initializing the default stride & block arrays to have values
of '1' in each position each time we perform a hyperslab selection, create
static constant arrays with '1's in them.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code optimization
Description:
Don't copy hyperslab span information as much.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code optimization
Description:
Remove a memcpy() from a commonly called routine and replace a multiplication
with a series of additions.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code optimization
Description:
Avoid another extraneous dataspace copy.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
too minor to require h5committest
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Code optimization
Description:
Change algorithm to directly use coordinates describing a chunk's position
in a dataspace instead of creating a dataspace with the chunk's position
selected. This reduces the number of copies of dataspaces we need to keep
around.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
too minor to require h5committest
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Correct typo in comment
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Code optimization
Description:
Eliminate unnecessary allocation and point at existing data structure
instead.
Platforms tested:
Solaris 2.7 (arabica)
too minor to require h5committest
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Code optimization
Description:
Fix H5S_select_hyperslab to use arrays on the stack instead of dynamically
allocating them each time.
Platforms tested:
Solaris 2.7 (arabica)
too small to require h5committest
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Code optimization
Description:
Minor tweaks on the optimized offset/length sequence generator to improve
performance by reducing the number of 64-bit multiplies and calls to memcpy().
Platforms tested:
Solaris 2.7 (arabica)
too minor to require h5committest
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Bug fix
Description:
Fixed bug in hyperslab iteration where certain combinations of flattened
and non-flattened dimensions would cause incorrect locations to be iterated
over.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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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
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Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
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Code cleanup
Description:
Cleanup compiler warning by breaking apart the cast checking.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to need h5committest
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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
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Code cleanup
Description:
Re-wrote duff's device with some macro substitution to make algorithm more
obvious.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
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Update code
Description:
Move "PABLO_MASK" definition above header file inclusion to avoid problems
with inline functions in header files.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Correct a couple of mistakes in error macros.
Platforms tested:
FreeBSD 4.8 (sleipnir)
triple check not necesssary.
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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
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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
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Performance improment
Description:
Speed up chunked dataset I/O. This breaks down into several areas:
- Compute chunk selections in the file by using hyperslab operations
instead of iterating over each element in the selection.
- If the file and memory selections are the same shape, use the file
chunk selections to compute the memory chunk selections.
This required several additional dataspace, dataspace selection and
hyperslab routines.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
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Bug fix
Description:
(void *)~((size_t)NULL) on the Cray is a different value than
(foo *)~((size_t)NULL) and causes some of the hyperslab algorithms to
fail.
Solution:
Change all the 'void *' forms to 'foo *' forms.
Platforms tested:
Cray SV1
h5committest not needed.
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Description: H5Sselect_hyperslab and H5Sselect_elements didn't check scalar
dataspaces.
Solution: put error detection in those functions.
Platforms tested: eirene(simple change).
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Code cleanup.
Description:
Move many package or internal function prototypes and macro definitions
into tighter scope according to their current use.
Added more comments where appropriate.
Eliminate ancient, unused functions.
Added a couple "accessor" functions to get parts of data structures which
were moved out of scope.
Platforms tested:
h5committested
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Bug fix
Description:
Dataspace selections created for individual chunks during chunk dataset
I/O were leaking memory.
Solution:
Properly set reference count on selection, so they get free'd when the
dataspace is closed.
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed.
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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)
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Update
Description:
Updated copyright statement in files which hadn't been updated yet.
Platforms tested:
Linux (Only comment change)
Misc. update:
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Code cleanup & bug fix
Description:
Cleanup another set of warnings on Windows and also fix mis-placed assertion
that caused the daily tests to fail.
Platforms tested:
IRIX64 6.5 (modi4) w/-n32
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Code cleanup
Description:
Reduce warnings on Windows
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Bug fix & code cleanup
Description:
Hyperslab code for collapsing dimensions was incorrectly collapsing
selections inappropriately when the fastest changing dimension couldn't
be collapsed.
Also add some more assertions which will make similar bugs easier to find.
Solution:
Break out of loop earlier.
Platforms tested:
modi4 (parallel), too small to triple check.
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Code cleanup
Description:
Two of the parameters to H5S_select_hyperslab are defined as
"const hsize_t foo[]", and then "foo" is assigned another value, which is
technically against the C standard and is now causing problems for a user
with a more strict compiler.
Solution:
Changed "const hsize_t foo[]" to "const hsize_t *foo".
Platforms tested:
FreeBSD 4.6 (sleipnir) - not a significant enough change to worry about
multi-platform testing.
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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
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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)
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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.
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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)
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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)
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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
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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
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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)
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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)
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Bug Fix for bug #789
Description:
Creating a 1-D dataset region reference caused the library to hang (go into
an infinite loop).
Solution:
Corrected algorithm for serializing hyperslab regions.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
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Code cleanup.
Description:
Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros
equivalents in the SAF library and adapted them to our library. I added
an additional macro which is equivalent to FUNC_ENTER:
FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but
none of the library or interface initialization code. This is to
be used _only_ for static functions and those which explicitly
cannot have the library or interface initialization code enabled
(like the API termination routines, etc.).
This allowed many more of the functions in the library [but not all yet :-(]
to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs.
It also reduced the size of the library and executables (by cutting out a
bunch of code which was never executed), I'll e-mail the exact results when
I've finished editing it.
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
Change variable casts to use H5_ASSIGN_OVERFLOW, or check for overflow
before the cast with H5_CHECK_OVERFLOW.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Purpose:
eliminate warnings on win32
Description:
some conversion warnings were being issued
Solution:
added some type casts
Platforms tested:
w2000, linux
changed the HDmemset to include a cast in win32; this was just to eliminate a compiler
warning. probably the macro can also be used in unix
#ifdef WIN32
#define HDmemset(X,C,Z) memset((void*)(X),C,Z)
#else /* WIN32 */
#define HDmemset(X,C,Z) memset(X,C,Z)
#endif /* WIN32 */
the list of previous warnings was
D:\disk_w\hdf5\src\H5FDstdio.c(659) : warning C4244: 'initializing' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(435) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(497) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(915) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(982) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(912) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(995) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(1936) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2019) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2862) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2864) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2948) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3690) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3692) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3776) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(5167) : warning C4244: '+=' : conversion from '__int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Tvlen.c(371) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
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Code cleanup
Description:
Remove an extraneous data structure for tracking the location of a
hyperslab iterator when walking through regular hyperslab selections.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Bug Fix
Description:
Correct coordinates were not computed for iteration through irregular
hyperslab selection (although the points in the buffer that were selected
were correct).
Solution:
Add another array to track selection offset adjusted coordinates in the
selection.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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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)
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