| Commit message (Collapse) | Author | Age | Files | Lines |
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Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Clean up warnings assigned to me from today's meeting - still need
to tackle the datatype conversion ones...
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
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Refactor generic property list initialization code to put property list
specific routines in property list modules, instead of scattered to the four
winds. Also, introduce property list class initialization objects, to make
adding new property list classes in the library easier.
Fix daily test failure by using H5Pget_elink_prefix() API routine instead
of looking at the "raw" generic property list information.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & 1.6 compat
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Fix off-by-one memory error when retrieving I/O pipeline filter's name.
Tested on:
Linux/64 2.4 (mir)
FreeBSD/32 4.11 (sleipnir)
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Finish new version of the I/O pipeline message, which is much smaller than
the previous version. This version is used with the "use the latest version
of the format" flag.
Closed several memory leaks/overruns (found with valgrind).
Also, lots of compiler & formatting cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Clean up some of the warnings on 64-bit Linux...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Too minor to require h5committest
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Configure feature
Description:
Added 'make trace' target.
Solution:
Added tracing to 1.7. This was done automatically in 1.6, but left out
of 1.7 until now (oops!).
Tracing in 1.7 only happens manually, when the user types 'make trace.'
Tracing automatically requires more framework than it's worth.
I also fixed a couple of tracing bugs and ran trace.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
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Description: H5T_register() replaces any existing data conversion path
with a new path.
Solution: Added a parameter to H5T_register() and H5T_path_find() to
signal the library whether the new conversion path is from API function
H5Tregister() or from private function like H5T_init_interface(). If it
is from H5Tregister(), replace existing path. If it's from H5T_init_interface()
and the library is trying to register default hard conversion functions,
don't replace existing path because the path is registered by the library.
For example, the library registered H5T_conv_int_float() and is trying to
register H5T_conv_long_float(). The size of long is equal to int. There's
no need to replace the path H5T_conv_int_float().
Platforms tested: h5committest and fuss.
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Code cleanup
Description:
Changed some scale+offset filter symbols from H5_SO_... -> H5Z_SO_...
to indicate that they are in the H5Z package.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Update scaleoffset filter.
Description:
1. Using enum type to describe scale offset type(int, Dscale or Escale)
2. Changing some macro names
3. Fixing some minor bugs
Solution:
Platforms tested:
sol 2.8, linux 2.4, aix 5.1(32-bit and 64-bit)
Misc. update:
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Add some comments for H5Pset_scaleoffset.
Description:
Solution:
Platforms tested:
No need to test.
Misc. update:
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New feature.
Description:
The H5Pset_scaleoffset is changed for the scaleoffset filter
to handle both integer and floating-point data. Currently,
the D-scaling method from GRIB has been implemented for
compressing floating-point data.
Solution:
One more parameter is added to the H5Pset_scaleoffset interface
to let user specify what type of data is used and what method
to use as well as corresponding parameters.
Platforms tested:
heping
Misc. update:
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Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Minor modification.
Description:
Remove some redundant codes.
Solution:
Platforms tested:
heping
Misc. update:
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New feature.
Description:
Add H5Zset_scaleoffset function for setting up the scaleoffset filter.
Solution:
Platforms tested:
heping, copper, arabica
Misc. update:
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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Adding framework of N-bit filter
Description:
N-bit filter is required for NetCDF project.
To add N-bit filter, configure.in configure, Makefile.in under src and other
filter-related source code needs to be updated.
Currently, N-bit tests are turned off from the library. So the change will affect daily test.
Solution:
Platforms tested:
sol 2.7, linux 2.4, aix 5.1
Misc. update:
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Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
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Code optimization
Description:
Change how default allocation time is handled internally to the library,
to avoid some performance issues with property lists.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require h5committest
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performance.
Description:
Replaced the old metadata cache with a cache with a modified LRU
replacement policy. This should improve the hit rate.
Solution:
Since we want to flush cache entries in increasing address order, I
used the threaded binary B-tree code to store the cache entries.
There is a fair bit of overhead here, so we may want to consider
other options.
While the code is designed to allow the support of other replacement
algorithms, at present, only a modified version of LRU is supported.
The modified LRU algorithm requires that a user selectable portion
of the cache entries be clean. The clean entries are evicted first
when writes are not permitted. If the pool of clean entries is used
up, the cache grows beyond its user specified maximum size. The
cache can also exceed its maximum size if the combined size of the
protected (or locked) entries exceeds the maximum size of the cache.
Platforms tested:
eirene (serial, parallel, fp), h5committested
Misc. update:
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Code cleanup
Description:
Clean up almost all warnings from Windows builds.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
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Code cleanup & small bug fix
Description:
Regenerate dependency files
Add htri_t as separate type from hbool_t for code tracing purposes.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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Code optimization
Description:
Use 'size_t' instead of 'hsize_t' to track the number of elements in
memory buffers, especially for type conversion.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Don't recompute the internal index value for looking up the chunk in the
hash table, just use the value already computed from iterating through the
chunks.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
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Code optimization & bug fix
Description:
When dimension information is being stored in the storage layout message
on disk, it is stored as 32-bit quantities, possibly truncating the dimension
information, if a dimension is greater than 32-bits in size.
Solution:
Fix the storage layout message problem by revising file format to not store
dimension information, since it is already available in the dataspace.
Also revise the storage layout data structures to be more compartmentalized
for the information for contiguous, chunked and compact storage.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
Solaris 2.7 (arabica)
h5committest
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Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
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Code cleanup/optimization
Description:
Query property list values once, at the beginning of the I/O routines,
instead of querying the property list values multiple (lots!) of times in
lower level routines.
Solution:
Create "property list caches" for internal library queries of the property
list values.
Platforms tested:
IBM p690 (copper) w/parallel & fphdf5
h5committest
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Purpose:
replaced name of delete filter with remove filter for the new function H5Premove_filter
Description:
Solution:
Platforms tested:
linux
Misc. update:
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Code cleanup
Description:
Add C++ and FORTRAN wrappers for new H5Pdelete_filter routine, along with
documentation and a note in the release notes.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Linux 2.4 (verbena) w/ C++ and FORTRAN
Too minor for full h5committest
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new library function H5Pdelete_filter
deletes one or all filters from a dataset creation property list
this was done for the NONE option of h5repack, added tests for this feature
added a test for the new function in /test/dsets.c
Description:
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
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Bug fix
Description:
Correct two problems with variable-length datatypes in datasets:
- When overwriting an entire dataset, writing the fill value to the
file would be skipped, causing problems for VL datatypes when
objects in the file had been unlinked (and thus the space in the
file was not all zeros)
- When an application has set a fill-value for a dataset and the
dataset's datatype contained a VL datatype, the library was filling
space on disk with the memory form of the VL information, instead
of the disk form.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug fix
Description:
When two property lists are compared, the H5Pequal routine was just
comparing the raw information for the property values. This causes problems
when the raw information contains pointers to other information.
Solution:
Allow a 'compare' callback to be registered for properties, so that a user
application get perform the comparison itself, allowing for "deep" compares of
the property value.
This was exported to the H5Pregister & H5Pinsert routines in the development
branch, but not the release branch.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Checkpoint file format spec.
Description:
Clarifications and cleanups related to file format review.
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Code cleanup
Description:
Add in rest of szip "options mask" macros that were missing. Also made
"raw" options mask set by the library, instead of requiring users to always set
it.
Platforms tested:
FreeBSD 4.8 (sleipnir)
Minor tweaks too small fo h5committest
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New feature/Bug fix
Description:
Add new fill time value - H5D_FILL_TIME_IFSET which writes the fill value
to a dataset if the user has defined one, otherwise not writing the fill value
to the dataset.
Platforms tested:
FreeBSD 4.8 (sleipnir) serial & parallel
h5committest
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Code cleanup
Description:
Improve error reporting for pixels per scanline check.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not needed.
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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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Code cleanup & new features
Description:
Added three new API functions for working on I/O filters: H5Pmodify_filter,
H5Pget_filter_by_id and H5Pall_filters_avail. Documentation on these will be
added for the 1.6.0 release, until then, we'll have to use the source code.
Also, simplified the H5Pset_szip and H5Pset_shuffle API interfaces, since
those filters are using the new "set local" callback facility to set dataset-
specific parameters.
Probably, some of the changes to internal H5Z routines are captured in
these changes also.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir) w/szip
Linux 2.4 (sleipnir) w/szip
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel
Misc. update:
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Code cleanup (sorta)
Description:
The H5Pset_szip API call was forcing users to pass in their parameters
in the same way as the internal representation of the filter parameters used
by the library (as an array of unsigned values).
Solution:
Changed to pass in separate parameters in a more user-friendly format.
Platforms tested:
FreeBSD 4.8 (sleipnir)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
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To support szip compression in HDF5
Description:
szip compression support is required by NASA ESDIS. The compression algorithm
is good for scientific data. In HDF5, we add another filter
function to make szip as a default compression package as we did for gzip(or zlib).
In this check-in, a new function called H5Pset_szip was added into H5Pdcpl.c, this
function is very similar to H5Pset_deflate. The only difference is SZIP needs
four parameters from the user to get the compression done while gzip needs only one.
So we pass a pointer to this function instead of an integer number.
The description of the four parameters of szip should be in different
documents.
H5Z.c and other header files were simply modified to have HDF5 know szip.
Solution:
See the decription
Platforms tested:
Since there are changes of configure.in and configure,I didn't use h5committest.
I tested with four platforms.
1) Linux 2.4 (eirene)
2) Solaris 2.7(arabica)
3) windows 2000(VS 6.0)
4) SGI IRIX6.5-64(modi4)
For test 1)-3), only basic C tests were done
For modi4 test, I tested 64-bit C,parallel and fortran.
All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems.
Misc. update:
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Code cleanup
Description:
Changed hard-coded magic number (32) for the maximum number of filters
in a filter pipeline to use a symbolic constant (H5Z_MAX_NFILTERS)
instead. This limit could (and probably should) be removed to allow an
unlimited number of filters in a pipeline.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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Purpose:
Change feature
Description:
Switch to Fletcher32 from Adler32 checksum
Platforms tested:
arabica, eirene, modi4
Misc. update:
MANIFEST and RELEASE.txt updated.
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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