| Commit message (Collapse) | Author | Age | Files | Lines |
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revised cache.
Note that this conversion is not as efficient as it should be. Specifically,
it does it more memcpy's between the metadata cache's on disk image of the
direct block and the fractal heap's on disk image of the direct block than
is absolutely essential. Eventually, we will want to fix this -- probably
by allowing the metadata cache and the fractal heap direct block to share
a common on disk image of the direct block. However, this will require
extensions to the client / metadata cache interface, and some reworking of
the fractal heap as well.
This checkin also includes Mike M's fix to the Linew specific bug mentioned
in my checkin of 22 Aug 2008.
Tested on Phoenix (serial debug and production),
Kagiso (parallel), and
Linew (serial)
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Merge revisions 15130:15210 from trunk into metadata journaling branch
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Bring revisions 14800:14900 from trunk into metadata journaling branch
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.5.2 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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While this code doesn't break any of the existing tests, it HAS NOT
been tested beyond that.
Also mods needed to integrate the journaling code with Quincey's latest
mods, and to adapt existing test code to slight changes caused by the
addition of journaling.
Finally, fixed an undefined variable bug in the HL code exposed by the
journaling mods.
Tested serial under Linux (Phoenix) and parallel under Linux (Kagiso).
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Add "_META" suffix to FUNC_ENTER/FUNC_LEAVE API routines that can modify
metadata in the file. This will give us a single place to change to recording
the beginning & ending of transactions.
Tested on:
FreeBSD/32 6.2 (duty)
Too simple to require h5committest
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Switch v1 B-tree nodes from using previous cache to use the new journaling
cache code. This is a major switch for the cache callbacks.
Switched the metadata caching code from having a pointer to the file it's
in to receiving a pointer to the file, when needed. This was necessary in
order to avoid crashing when two files IDs were open on the same underlying
file and one of those files was closed with cache entries using the file
pointers. Also took out the check in the caching code for reading off the
end of the file, which didn't play nicely with the multi-file VFD.
Switching the cache from having a pointer internally to requiring one
externally meant tweaking almost all the test code. :-/
Added correct exit codes to cache2 tests that didn't have them already,
so the 'make check' will stop when they fail.
Use the path to the h5diff in this build in the tools/h5recover testing
script, since we can't guarantee a user has HDF5 already installed.
Assorted minor tweaks to get everything to compile more cleanly and pass
all the tests (on my Mac :-).
Tested on:
Mac OS X (10.5.2) w/C++
(more testing coming up shortly, I just didn't have my "rsync testbed" set
up for this branch when I started making changes to the code)
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Make H5Tarray_create() and H5Tget_array_dims() versioned, and drop the
"perm" parameter from the '2' versions.
Shift internal library usage to '2' versions.
Add simple regression tests for '1' versions.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Make H5Pget_filter_by_id() API versioned and switch internal usage
to H5Pget_filter_by_id2().
Add simple regression test for H5Pget_filter_by_id1().
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Fix problem with datatype messages where the version of the format
for a datatype message could depend on the "use the latest format" flag from
the file after it was initially created.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Mac OS X/32 10.4.10 (amazon)
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company. The I/O is optimized when the source and destination
members are a subset of each other one way or another, and
the order is the same, and no conversion is needed. For example:
struct source { struct destination {
TYPE1 A; --> TYPE1 A;
TYPE2 B; --> TYPE2 B;
TYPE3 C; --> TYPE3 C;
}; TYPE4 D;
TYPE5 E;
};
or
struct destination { struct source {
TYPE1 A; --> TYPE1 A;
TYPE2 B; --> TYPE2 B;
TYPE3 C; --> TYPE3 C;
}; TYPE4 D;
TYPE5 E;
};
The optimization is simply moving data from the source to the
appropriate places in the buffer and bypass the reading of
the background data and data conversion.
Tested on smirom, liberty, sol, and copper.
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Add a little more information to the debugging routine, for VL datatypes.
Minor code cleanups
Tested on:
Mac OS X/32 10.4.9 (duty)
Too minor to require h5committest
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Check in "unique, but sharable" optimization to ISOHM code, which
allows object header messages that are only used in one object to remain in
the sole user's header, but migrates messages that are used in more than one
header into the ISOHM heap.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Clean up code and reduce compiler warnings...
Tested on:
Mac OS X/32 10.4.9 (amazon)
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running on kagiso.
The static szip libraries are working as intended, but when shared szip
libraries are present and intended for use they cannot be opened. A check
has been implemented to test if shared szip libraries are functional on
current platform. If they are not, and the user is trying to use them,
szip is now disbaled and the user is informed.
This issue occurs on kagiso, and the resolution was tested on kagiso.
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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Add API routines for tracking & indexing the creation order on
attributes.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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More cleanups on the object header message handling code, to make it
easier to work with and move forward on the creation order coding.
Various other minor cleanups & warning fixes.
Tested on:
FreeBSD/32 6.2 (duty)
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Remove the "scaffolding" for shared message method invocation and
simplify the way shared messages are dealt with in general.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Move datatype messages into new shared message method interface
Clean up various formatting & compiler warnings
Minor optimizations
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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haven't
been run in a while, so many of the source files were updated with
tracing macros, etc. No code changes by me.
Tested on kagiso and smirom.
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checking in
code to copy shared messages. Should be fewer memory leaks and fewer
"uninitialized memory reads."
Tested on kagiso, smirom, and Windows.
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Finish moving object header message routines into their own source code
module, along with renaming them to have "H5O_msg_" prefix...
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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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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Finish implementation of H5Literate() [still needs real tests]
Clean up datatype macro warnings a bit more.
Unify iterator callback macros and put up in public header file, with the
iterator directions.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and 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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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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Code cleanup to improve formatting & reduce compiler warnings.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Add "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
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Add the "use the latest version of the format" support to datatype
messages. And a regression test to check that it's working.
Also, found that we have been over-allocating space for compound datatype
messages (when they have array datatypes or can use the latest version of the
format) and trimmed the size back.
Clean up datatype & dataspace encode/decode routines by having them
allocate & release "fake" file structures, which gets them out of needing to
"know" about the internals of file structures.
Other minor whitespace/formatting cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
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Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
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Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
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Description: Mac OS 10.4 on PowerPC chip has some errors to convert (unsigned)
long long to long double. When the bit sequences are 0x003ff..., 0x007fff...,
0x00ffff..., 0x01ffff..., 0x7fffff..., the converted values are twice as big
as they should be.
Solution: Detect the error in configure and disable the compiler conversion
and test case.
Platforms tested: h5committest, Mac OS 10.4, and fuss.
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New/expanded features
Description:
Check in Peter's changed for the object copy code:
- Allow/fix copying datasets using named variable-length datatypes
- Start adding framework for property list to control how object
copying occurs.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Solution: Support VAX float and double types with new byte order. There're some
details not yet included,
1. the alignment detection for VAX order in H5detect.c.
2. support for special values in library conversion functions.
3. the infinity for VAX in H5T_init_inf.
4. support for VAX types in printing hexadecimal format.
Platforms tested: h5committest and fuss.
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Bug fix
Description:
Retrieving an object's name could fail (in various ways) under certain
circumstances (mostly having to do with mounted files).
Solution:
Re-write & simplify "get object name" code to fix error in a better way
than adding yet another hack to the previous pile of hacks... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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New feature
Description:
Add in a combination of Peter's & my code to support copying
variable-length data from one file to another, although currently only
supported with contiguous data storage.
Platforms tested:
FreeBSD 4.11 (sleipnir)
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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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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New feature
Description:
Add in baseline "object copy" code from Peter [in the form of a new API
routine: H5Gcopy()]. There's still some work to do (like handling variable-
length datatypes and possibly support for references) and it hasn't been tested
on mounted files yet, but the core functionality is there and working
correctly.
I've also got a set of patches to update the 1.6 branch with tweaks to
keep the branches mostly in sync, but Elena will kill me if I import them
before the 1.6.5 release is out... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committested
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Bug fix
Description:
Fix "double root open" bug and apply same fix to datasets & named datatypes.
Also fix bug in symbol table entry lookup code that would "transfer" an
object from one file handle to another file handle when the two file handles
were opened on the same actual file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Code cleanup/bug fix
Description:
Hoist function call out of inner loop of type conversion by retrieving
source & destination precisions once, outside the loop.
There's still some overhead because this information is stored in
variables set at run-time, when it's really constant for the particular
machine. Further work to set compiler macros would allow this code to be
optimized better by the compiler with dead code removal. We'll continue
to work on this area...
Also, made new internal H5T_compiler_conv routine static instead of of
private, until we need to reference it from another source code module.
Platforms tested:
h5committest
FreeBSD 4.11 (sleipnir)
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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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Description: The API function H5Tis_hard() which was recently checked
in has been renamed to H5Tcompiler_conv() to be more descriptive. No
other changes.
Platforms tested: fuss - simple change.
Misc. update: config/lt_vers.am to update libtool version.
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Code cleanup/reorganization
Description:
Merge back some more changes extracted from the "compact group" set.
This bunch cleans up and prepares the H5G_* routines for eventual import of
new features.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X.4
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Code cleanup
Description:
Merge back changes from "compact group" work that improve the
infrastructure of the library and may impact others. In this round of
merging, that includes:
- Move datatype allocation into single internal routine, instead of
duplicated code that was spread out in a dozen or so places.
- Clean up guts of object header routines (H5O_*) to allow for some of
the fancieroperations that need to be performed on groups, along with
some general improvements.
- Added a new error code
- Some minor cleanups in other code....
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X
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Description: Put in a new API funciton, H5Tis_hard. It checks whether
the conversion function from a native type to another native type is a
compiler (hard) conversion. Also checked a test in test/dt_arith.c.
Platforms tested: h5committest and fuss.
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Description: Changed the names of macros defined in H5Tpkg.h from
H5T_CONV_INTERIM_XXX_XXX to H5T_CONV_INTERNAL_XXX_XXX to be more
descriptive.
Platforms tested: fuss - simple change
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